Category Archives: Mind & Brain

Sharks have rhythm, too

Sharks are not known for being good at running in running wheels. Or hopping from one perch to the other in a birdcage. Which is why, unlike hamsters or sparrows, sharks were never a very popular laboratory model for circadian research.

The study of fish came late into the field of chronobiology due to technical difficulties of monitoring rhythms, at the time when comparative tradition was starting to make way to the more focused approach on choice model organisms – in this case, the zebrafish.

But the comparative tradition was always very strong in the field. Reading the old papers (especially review papers and loooong theoretical papers) by the pioneers like Jurgen Asschoff and Colin Pittendrigh, it seems like researchers at the time were just going around and saying “let me try this species…and this one…and this one…”. And there were good reasons for this early approach. At the time, it was not yet known how widespread circadian rhythms were – it is this early research that showed they are ubiqutous in all organisms that live at or close to the surface of the earth or ocean.

Another reason for such broad approach to testing many species was to find generalities – the empirical generalizations (e.g,. the Aschoff’s Rules) that allowed the field to get established, and that provided a template for the entire research program, including refining the proper experimental designs.

Finally, this was also a fishing expedition (no pun intended…oh, well, OK, intended) for the best model organisms on which to focus more energies – organisms that can be studied in great detail in both field and lab, that are easy to find, breed, care for, house and handle, and organisms in which circadian rhythms are clear, robust, and are easy to monitor with relatively cheap and simple equipment. Thus hamsters, cockroaches, and sparrows, green anoles and Japanese quail. Later, with molecular discoveries, organisms with better tools for genetic manipulation, even though perhaps not as good as circadian models, took precedence – the fruit fly, mouse, zebrafish and the like.

But it’s not that sharks were never looked at before. They may not run in wheels, but researchers can be creative and monitor the rhythms nonetheless.

Horn Shark and Swell Shark

The Nelson and Johnson 1970 paper appears to be the very first systematic study of daily rhythms in sharks. They cite a number of previous non-systematic observations in the field, all suggesting that many shark species are nocturnal (night-active). They combined field and lab studies in two species (horn shark Heterodontus francisci and the swell shark Cephaloscyllium ventriosum).

Pattern of activity of bottom-dwelling sharks in the field. From Nelson and Johnson 1970.

In the field, they dove at different times of day and night, counted and observed the sharks, and rated their activity levels. Both species were exclusively nocturnal, barely making any movements at all throughout the day, while actively swimming at night.

In the lab, they placed sharks in small pools, each pool in a light-tight enclosure. They controlled lighting regimes (e.g., constant dark, constant light, or various light-dark cycles) and they monitored the activity with a nifty sensor – a set of six steel rods in each pool, each rod hanging from above all the way to the bottom of the water. Whenever a fish pushed one of the rods (and they did not observe any avoidance), the rod would move and momentarily close an electrical circuit. This would be recorded as a dash line on long paper rolls by an Esterline-Angus recorder.

Afterward, they would take those paper rolls out, cut them (by hand) into strips, glue the strips (by hand) onto large pieces of cardboard, do the measurements and calculations (by hand, using rulers and compasses), and photograph the best records for publication. Yes, very manual work! In this day of computers, it’s pretty easy to just click. Our PI used to sometimes take us grad students to a back room to show us the old equipment and to describe the process, just so we would appreciate how easy we have it now.

Actograph of the Swell shark in different light conditions. From Nelson and Johnson 1970.

What they found is that the two species are quite different. The Horn shark readily entrained to the light-dark cycles (both 24-hour and 25-hour cycles), starting activity as soon as the lights go off, and ceasing activity the moment the light come back on. They kept swimming all the time both in constant darkness and in constant light. This suggests that their behavior is triggered directly by environmental light and not driven by an internal clock.

On the other hand, the Swell sharks showed circadian rhythms – they alternated between active and inactive periods in constant light and in constant darkness. In light-dark cycles of both durations, they showed a little bit of anticipation, starting their activity a few minutes before lights-off. This suggests that the daily alteration of behavior is driven by an internal circadian clock.

In a later study (Finstad and Nelson 1975), they changed the intensity of light of the experiment, and this time Horn sharks also exhibited internally generated circadian rhythms.

Dogfish Shark

Daily rhythm in the dogfish shark. From Casterlin and Reynolds 1979.

In 1979, Casterlin and Reynolds tried a different experimental setup and a different species – smooth dogfish shark, Mustelus canis. In their setup, as sharks swim through a series of chambers they break photocell-monitored light beams. Instead of simple light-dark cycles, they used light-dusk-dark-dawn cycles in which dawn and dusk light was dim, while daytime light was bright. Again, most of the activity was observed during the night:

Lemon Shark

In 1988, Nixon and Gruber took a bunch of Lemon sharks (Negaprion brevirostris) and placed them in a complex setup in order to simultaneously monitor both locomotor activity (that is: swimming around and around in circles) and the metabolic rate (oxygen consumption):

The lemon shark setup. From Nixon and Gruber 1988.

Daily rhythms of activity (top) and metabolic rate (bottom) in the Lemon shark. From Nixon and Gruber 1988.

The sharks were only tested in light-dark cycles, which is not a proper test for the existence of the circadian clock, but the data were strikingly “clean”. While behavior can be strongly affected by direct influence from the environment (e.g., sudden lights-on), it is harder to explain changes in metabolic rate purely behaviorally, suggesting that an internal clock is likely driving the day-night differences in metabolism.

Megamouth Shark

Megamouth shark daily dives. From Nelson et al. 1997.

This big guy is hard to find. The subject of this paper was only the sixth individual known to science. It was caught, they scrambled for about a day to get all the gear in place, attached satellite telemetry radiotransmitters, and let the animal lose to swim. What they saw was a distinct pattern of diving deeper before the sunrise, and rising up closer to the surface before sundown. While nothing can be said about circadian regulation, as the pattern could just be the animal following light clues or vertical migration of its plankton food, it is nonetheless a very cool study.

Hammerhead Shark

It is interesting that a number of senior researchers, as they come close to retirement and are not in the rat-race for grant funding any more, abandon the standard lab models and go back to the old comparative tradition, picking unlikely species (from chipmunks to Monarch butterflies) and moving out of the lab back into the field. It’s definitely more fun to do!

One of them decided to shift his focus to juvenile hammerhead sharks. Unfortunately, Milton H. Stetson suddenly died in 2002, and I could only find one publication from that work (Okimoto and Stetson 1995), which I cannot read as it was published in a conference proceedings (if anyone can scan a copy and send me, I’ll be grateful):

Nonetheless, this paper was cited in several other places, and if they cited it correctly, what Okimoto and Stetson found was that the pineal glands of these sharks (and later the same also found in dogfish shark Squalus acanthias) does not show cycles of melatonin synthesis and release in constant light conditions (it does in light-dark cycles). This does not necessarily mean that there is no clock in the pineal, or that there is not rhythmic production of melatonin, as later work in our lab showed that culture medium can have a dramatic effect.

Whale Shark

Combined 206 daily records of a whale shark dives. Graham, Roberts and Smith 2006

Combined 206 daily records of a whale shark dives. From Graham, Roberts and Smith 2006

In Graham, Roberts and Smith 2006, nine whale sharks were tagged with archival satellite tags which provided data on water temperature, illumination and depth. What they found are three distinct types of rhythms: ultradian (short), circadian (about a day) and infradian (long) cycles.

The short cycle was about 45 minutes long, essentially the sharks swimming up an down underneath the surface, not really diving very deep.

One day record of a whale shark diving activity. From Graham, Roberts and Smith 2006

One day record of a whale shark diving activity. From Graham, Roberts and Smith 2006

The long cycle was a 29-day cycle, likely not generated from within the nervous system of the shark, but rather the animals following the snapper spawning events which are modulated by the moon phases.

The daily cycle was that of deep dives. The sharks made very deep dives – sometimes over a kilometer down – only during the day. Again, nothing in this experimental protocol can distinguish between internally generated rhythms and behaviors directly induced by the environment, e.g., light intensity, vertical migrations of prey, etc.

And yes, this is it, that’s all. Not much work on sharks done, for obvious reasons – they don’t do well in running wheels.


Casterlin, Martha E., and William W. Reynolds. Diel activity patterns of the smooth dogfish shark, Mustelus canis. Bulletin of Marine Science 29.3 (1979): 440-442.

Finstad WO, Nelson DR. Circadian activity rhythm in the horn shark, Heterodontus francisci: effect of light intensity. Bull. S. Calif. Acad. Sci, 1975

Graham, Rachel T., Callum M. Roberts, and James CR Smart. Diving behaviour of whale sharks in relation to a predictable food pulse. Journal of the Royal Society Interface 3.6 (2006): 109-116.

Nelson, Donald R., and Richard H. Johnson. Diel activity rhythms in the nocturnal, bottom-dwelling sharks, Heterodontus francisci and Cephaloscyllium ventriosum. Copeia (1970): 732-739.

Nelson, Donald R., et al. An acoustic tracking of a megamouth shark, Megachasma pelagios: a crepuscular vertical migrator. Environmental Biology of Fishes 49.4 (1997): 389-399.

Nixon, Asa J., and Samuel H. Gruber. Diel metabolic and activity patterns of the lemon shark (Negaprion brevirostris). Journal of experimental Zoology 248.1 (1988): 1-6.

Okimoto, D. K., and M. H. Stetson. Effect of light on melatonin secretion in vitro from the pineal of the hammerhead shark, Sphyrna lewini. Proceedings of the Fifth International Symposium on Reproductive Physiology of Fish, The University of Texas at Austin. 1995.

Images: Shark in the running wheel: shark from ClipArt Supply, wheel from Shaping Youth, photoshop by Tobias Gilk. Shark clock – ToadAndLily on Etsy (where you can actually buy the clock). Other images are figures from papers, according to the Fair Use principle.

Good Night, Moon! Now go away so I can sleep.

Mars has two moons - Phobos and Deimos. Here we see Phobos passing in front of the sun, as seen from the surface of Mars. How would having two moons with different phases affect behavior of Martians?

Mars has two moons - Phobos and Deimos. Here we see Phobos passing in front of the sun, as seen from the surface of Mars. How would having two moons with different phases affect behavior of Martians?

Scientific papers usually don’t faithfully convey exactly how the researchers came up with the idea, or the chronological order in which the investigation proceeded. And there is a good reason for that – papers need to be standardized so other scientists can easily read them, understand them, replicate them and use them to perform further research.

But sometimes, a paper is honest about the process. It is wonderful – and shows that scientists are human, with a great sense of humor – when #OverlyHonestMethods sneak into the text of a scientific paper, surprising and rewarding the careful reader with an ‘easter egg’.

One such paper – on the effects of moon phase of sleep quality – just came out in Current Biology.

The first thing I noticed was that the data were collected in 2000-2003. Why did it take a decade to publish? Was it just sitting on a back burner of a PI for years after the student left the lab? Did it have to go through many rounds of peer review in several journals until it finally managed to get published? None of those reasons, actually! See for yourself:

We just thought of it after a drink in a local bar one evening at full moon, years after the study was completed.

And that is where we encounter yet another effect of the full moon (in synergy with ethanol) on human behavior, at least on WEIRD populations, such as scientists!

But jokes aside, this is also a great example of a paper that usefully re-visits and re-analyzes old data sets. Of course, the authors emphasize the positives of this post hoc approach – nobody at the time of the study could possibly know that the data would be analyzed in this way, so there were no possible subconscious psychological effects – it was a truly triple-blind study:

Thus, the aim of exploring the influence of different lunar phases on sleep regulation was never a priori hypothesized, nor was it mentioned to the participants, technicians, and other people involved in the study.

On the other hand, a study specifically designed to test for moon-phase effects on sleep quality would have been designed differently to ensure it has just the right controls and that maximum information can be derived from the data.

Research in chronobiology is frustratingly slow. In circadian research, each day is just one data point, so each study has to keep subjects in isolation for many days. In the study of lunar rhythms, each month is a data point and the subjects need to be kept in isolation for many months.

To determine if a rhythm is generated by an internal timer (daily or monthly) as opposed to being a direct behavioral response to environmental cycles requires a whole battery of tests, which are hard and time-consuming enough in circadian research, and twenty eight times more so in circalunar rhythm research

Back in the 1960s, it was possible to keep (well compensated) human subjects in isolation rooms for long periods of time (see pioneering research by Wever and Aschoff in the underground bunker in Andechs, Germany). Likewise, animal subjects can be kept and monitored in isolation chambers for long periods of time.

As lunar rhythms are more “messy” than daily rhythms, more data over more time are necessary for the robust statistical analysis. And, due to ethics creep, it is not certain that either animal or human studies of such scope can be approved and performed any more. So, one has to be creative and get quality information out of imperfect experimental protocols (just like we cannot wait to observe multiple cycles of 17-year cicadas, but have to invent creative, short-term approaches instead).

But this time, the researchers were just lucky! Their data-set came from an old experiment which was designed well enough for this new purpose. The key is they had LOTS of data. Their subjects came in to the sleep lab many times and a number of different parameters were measured. Ideally, each subject would stay in the lab for a few months instead of just four days at a time. But having such a huge data set allowed them to weave together a patchwork of fragmented data into a large, trustworthy whole. Each first night of the test was eliminated from the data due to potential influence of the previous day (and the so-called “weekend effect”, as people tend to change sleep times on their days off). Each phase of the moon was covered by multiple subjects multiple times. So they could employ powerful statistics to tease out the effects of the moon phase on various parameters of sleep quality.

And they found some interesting stuff! My colleague Dina Fine Maron has covered the paper in greater detail here. In short, human subjects with no access to information about moon phase, or any ability to perceive the moon itself or its light intensity, nonetheless slept about 20 minutes shorter on the nights of full moon, mostly due to taking roughly 5 minutes longer to fall asleep in the evening than on a night of the new moon. Levels of melatonin, hormone released by the pineal gland during the night, were lower during full moon nights as well. Some of the age and sex differences cannot be explained at this time due to imperfect experimental design – and that is OK. I’d rather see new interesting information coming out of an old data set, than never seeing it at all just because it cannot be “just perfect”.

There are many claims around about lunar periodicities in all sorts of human behavior. For some of those, there is no evidence the claims are true. For others, there is strong evidence the claims are not true. But a few subtle effects have been documented. This paper adds another set with persuasive statistics.

Is this a demonstration that there is a working circalunar clock in humans, operating endogenously, and independently from the actual moon? It’s not possible to tell yet. Those kinds of demonstrations (just like for circadian clocks) require a battery of tests, starting with documenting multiple cycles (I’d say at least three complete monthly cycles) in complete isolation, ability of artificial moonlight to phase-shift the phase of the rhythm in a predictable manner (consistent with a Phase-Response Curve), and hopefully identification of body structures or cellular components which are devoted to generation of the rhythms, with at least some hint of the mechanism how they do it.

We are far from it yet even in animals we can manipulate in lab and field studies. Much work has been done over the decades in the study of lunar and circalunar rhythms in various animals, mostly aquatic and intertidal ones. There are documented lunar cycles (but not necessarily internal lunar clocks) in a variety of organisms, including sponges, cnidaria, polychaetes, aquatic insects, and many different crustaceans including crayfish.

In the terrestrial realm, antlions possess internal lunar clocks, but many other species show modifications of behavior during different phases of the moon, including honeybees, rattlesnakes, ratsnakes, some rodents, some lizards, and lions.

The gravitational force of the moon is so weak that it can affect only very large bodies of water on the Earth’s surface. It cannot even affect smaller lakes and rivers. There is no theoretical mechanism by which any molecule or cellular structure in a human body can be so sensitive as to detect the gravity of the moon. So that hypothesis is out.

In field studies, animals can see and synchronize to the changing night-time intensity as the moon goes through its phases. But in the lab, as in the case of this study, there are no visual clues to the moon phase for the subjects, and, since they had no idea the data would be analyzed for moon phases, they probably did not pay attention to that before they entered the light-isolation lab.

With both gravity and light eliminated as potential clues, the internal clock remains the strongest hypothesis. But it’s still a hypothesis that needs to be tested before one can state with any certainty that it is the case.

As for evolutionary explanations for the existence of a putative lunar rhythm of humans? I would be very careful about this. Demonstrating that any trait is actually an adaptation (and not an exaptation or side-effect of development, or something else) is an incredibly difficult task. Just because something seems “obviously useful” does not make it an adaptation. It is an error of hyperadaptationism to pronounce a trait an adaptation just because it exists, and then to tack on a semi-plausible scenario as to how it may have been selected for. Evolutionary biology is much more rigorous than that kind of lazy armchair speculation.

Sure, if our ancestors actually had lunar clocks as adaptations, it is possible that the mechanism for it may still remain, even if in a weak state, in at least some of today’s humans. But maybe not. And like a rudimentary organ, it does not seem to have any obviously useful function for humans living in the modern society. Twenty minutes of less sleep, that’s all. But it’s good to know. So we can find good use to those extra twenty minutes, perhaps come up with new scientific hypotheses over a pint with colleagues at a local pub.

Reference: Cajochen et al., Evidence that the Lunar Cycle Influences Human Sleep, Current Biology 23, 1–4, August 5, 2013,

Images: top: by NASA, bottom: from the paper.

Let’s Not Spring Forward.

Cross-posted from Zocalo Public Square.

Even cows don’t like Daylight Saving Time. Come Sunday morning, when the milking machines get attached to their udders a whole hour too early, the otherwise placid bovines on dairy farms around the United States will snort in surprise and dismay. They may give less milk than usual. They could take days or weeks to get used to the new milking schedules.

We are no different. While most of us won’t be hooking ourselves up to udder pumps, our bodies next week will experience a disturbance very much like the cows’ – one that can affect our mental and physical health. The reason lies in the clash between sensitive, eons-old biology deep within our cells, and human-imposed time-keeping traditions that are barely a century old. Twice every year, when we “spring forward” and “fall back,” our bodies must do battle between “sun time” and “social time.”

Before the mid-19th century, time was more flexible. Each town and village maintained the local church clock more-or-less in sync with the natural light-dark cycles of the sun. The spread of railroads changed all that. The need to keep trains moving in and out of stations at predictable times forced the adoption of a standardized time. That, in turn, led to the formation of time zones.

Daylight Saving Time (DST)—the resetting of all clocks twice a year—was first proposed by New Zealand entomologist George Vernon Hudson in 1895, for quite selfish purposes. He was studying daily cycles in insects and wanted to be able to do more of it during daylight hours. But his idea of maximizing daylight soon spread. The first country to adopt DST was Germany in 1912. Most other countries soon followed, including the United States, which instituted DST in 1918.

The leading argument in favor of DST has always been that it saves energy. Back in the early 20th century, most energy was used for lighting. So, the argument went, placing work and school schedules within daylight hours would save electricity. People wouldn’t need to use light bulbs to navigate around their homes, offices, factories, and fields in the dark, and they would have more time in the evening to indulge in commerce and entertainment.

Today, the situation is very different. The proportion of total energy that is used for lighting is miniscule compared to other, time-independent uses like factories, computers, nuclear plants, airport radars, and other facilities that run 24/7. Energy companies themselves have measured the effect, and have concluded that DST does not save energy.

With this knowledge, some nations have started re-thinking the concept. Russia, for example, abandoned the clock change in 2011, keeping one time all year round. Iceland and Belarus did the same. On the other hand, in 2007, U.S. Congress, clinging to the notion that DST saves energy, moved the onset of DST three weeks earlier than before. That change, I think, makes a difficult transition even more stressful.

Although Congress can impose these changes, it’s a bit unclear who exactly has the right to determine whether DST is implemented. Until very recently, a large number of individual counties in the state of Indiana refused to go through the clock-changing ritual. Arizona doesn’t change its clocks at all—the only state in the union (apart from Hawaii) to defy DST altogether. This lack of clarity about who is in charge may be one of the reasons why a more sustained effort to abolish DST has been unsuccessful nationwide.

Whether or not DST saves energy is the least of the reasons why it’s a bad idea. Much more important are the health effects of sudden, hour-long shifts on our bodies and minds. Chronobiologists who study circadian rhythms know that for several days after the spring-forward clock resetting – and especially that first Monday – traffic accidents increase, workplace injuries go up and, perhaps most telling, incidences of heart attacks rise sharply. Cases of depression also go up. As the faint light of dawn starts preparing our bodies for waking up (mainly through the rise of cortisol secretion), our various organs, including the heart, also start preparing for increased function. If the alarm clock suddenly rings an hour earlier than usual, a weak heart can suffer an infarct.

The reason for negative health effects of DST is that, in essence, the entire world is jet-lagged for a few days. Unlike some animals, like honeybees and reindeer, humans have a very robust circadian clock system that resists abrupt shifts.

Every cell in our bodies contains a biological clock which coordinates the events in those cells—for example, when gene transcription turns on and off, or when specific proteins are made. When we are exposed to a light-dark cycle that is different from what we experienced the previous days, some types of cells synchronize to the new environmental cycle faster than the others. Cells in our eyes, for example, may adjust in about a day, while cells in our brains take a couple of days. Cells in the digestive system and liver may take weeks. So, for weeks after the DST clock change, our bodies are like a clock shop in which each timepiece cuckoos at a different time of day—a cacophony of confusing signals.

Our bodies are constantly being pulled apart by conflicting demands of the natural ‘sun time‘ and culturally imposed ‘social time‘. People living in urban areas may be better shielded from the sun time than their rural counterparts, because of artificial lighting and the skyglow it produces, but nobody is completely isolated from its influence. Twelve noon according to the clock is not twelve noon according to the planet. Citizens of Barcelona and Bucarest are almost two hours apart in their perception of sun time, yet live in the same social time—the same time zone that encompasses most of Europe.

Even those of us who are lucky enough to work from home and can generally set our own work schedules are not completely immune to the effects of DST. I still have to drive my daughter to school at the time prescribed by the local clock, not by local sunlight. My colleagues have expectations about when I will pick up the phone for a teleconference or respond to their emails. I am supposed to show up for my dental appointment at 7am, not “two hours after dawn”.

But if I ever buy a cow—and that is not as crazy as it sounds since I live next door to a dairy farm—I have a plan. Of course I’ll ignore the bi-annual clock changes, which I hear many smart dairy farmers already do. But I’ll go a step further and ignore social time altogether, milking her at the sun time her nervous system can understand, probably the crack of dawn. Whatever I do, I will never make her suffer through the sudden shift of DST. And none of us human animals should suffer it, either.

Image: Dirk Hanson

No rats in Ryder Alley

Last week, in the wake of superstorm Sandy, I saw a number of people asking questions on social media (and some traditional media picking up on it) about a potential for ratpocalypse, i.e,. the possibility that hordes of rats will come out of the sewers and subway tunnels and flood the streets of New York City in a Pied Piper style. So I wrote a blog post debunking this and explaining why this will not happen, which made me a temporary expert on behavior of rats in storms, so I got interviewed in various places, etc.

As I noted at the very end of the post, my main source of information, at least initially, was a book, Rats: Observations on the History and Habitat of the City’s Most Unwanted Inhabitants by Robert Sullivan. I read it several years ago, when it first came out, and loved it. Reading it provoked me to read more on the topic, so when these questions came up, I already knew most of the answers, and knew where to look for additional information.

The book describes a year in Sullivan’s life, spent observing rats by night, and researching them by day. He went every night downtown to Fullton Street, and just stood there in the middle of two L-shaped alleys: Edens Alley and Ryder Alley. He watched rats come out at night, eat the food discarded by the two restuarants edging the alleys one on each side, fight, hide, and whatever else rats do when they are up on the surface.

The first opportunity I had to go up to New York City after reading the book was in 2007. I just could not resist! The book has no photos of the alleys, so I just HAD to go and see them myself.

My wife and I hailed a cab. Told the driver: Edens Alley. Driver: Hmmm, this is my first day on the job, do you know how to get there?

This was before I had iPhone, GPS, Google Maps…. I pulled out an old-style map, printed on paper, and gave the driver turn-by-turn directions. Once we got there (after making several circles around the area), the driver refused to take any money. I forced him to take double the amount of the fare. He did well for the first day as a NYC taxi driver. This place was hard to find. And off the mid/up-town grid.

Of course, this was in the middle of the day. I did not expect to see any rats there at that time. If I did, that would be an indication that the underground population is astoundingly large, forcing some of the sub-dominant individuals to forage during the day. But I was looking for traces of rats, and for holes and crevices from which they emerge at night, for bags of garbage full of Chinese food, and I took the pictures. I had the pictures stashed away in my Dropbox for more than five years. This is the first time they see the light of day. See for yourselves:

Did NYC rats survive hurricane Sandy?

Floodwaters enter Hugh L. Carey Tunnel. MTA photo

Floodwaters enter Hugh L. Carey Tunnel. MTA photo

How many of the NYC rats survived hurricane Sandy? This question has been asked in the wake of Sandy’s flooding of lower and east Manhattan. See, for example, articles in Huffington Post Green, Forbes, National Geographic, Business Insider, Mother Nature Network and NYMag.

The short answer is: some rats drowned, some survived.

The complicated question, how many drowned and how many survived, is probably impossible to answer. But we can speculate using the information and knowledge we have in our possession. But things we really need to know, we don’t – information is just not available (and some of it never will be).

How many rats are in NYC?

Nobody knows. Nobody seems to even be attempting to estimate.

Beware of the myth that there is one rat per person. That is a very old myth. It started in 1909 when W.R.Boelter published a study of rats in England. He asked farmers (but never bothered to look in the cities) to estimate how many rats they have in their fields. From that informal survey, Boelter came up with an average of one rat per acre (yes, of agricultural land). At that time, there were 40 million cultivated acres in England. From that, he estimated the total population of rats on agricultural land to be about 40 million. Completely coincidentally, England in 1909 also had a population of 40 million people. So, the 1:1 ratio stuck. And it has been repeated for more than a century, by media, by scientists, by United Nations, by pest control companies, by health departments, and apparently everyone else.

In 1949, Dave Davis did a systematic study of rats, by trapping and capturing them, and estimated that rat population in New York City was only about 250,000. Not even close to 8 million.

An aside – I have an indirect personal connection to Davis. For a while he was a professor in the Department of Zoology at NCSU, that is, in my own department. At the time he was ready to retire, in the 1970s, he was actively working on daily and seasonal rhythms in various animals. He used to work with Curt Richter before, at Johns Hopkins, and Curt is one of the pioneers of chronobiology. David sent some woodchucks on a ship from Philadelphia to Australia. While on the ship, rats kept EST time, but quickly re-entrained to the Australian local time once they arrived there and were exposed to ambient light. Although the field was still very young, Davis’ work made the rest of the department aware of it (they did not think it was Biorrhythms silliness, as many assumed at the time), so they were interested in hiring a replacement who was doing something similar. So they hired this bright, young lad from Texas in his spot – two Science papers already published and he took only 3.5 years to get both MS and PhD. The new faculty’s name was Herbert Underwood. Two decades later I joined the Underwood lab. The rest is history.

Anyway, back to rat population. Estimates vary wildly, to as high as 32 million. Nobody really knows.

New York City is old. It was built and rebuilt. New buildings were built on top of the old ones. There are old, buried tunnels, rooms, chambers, now not accessible to humans but perfectly accessible to rats. Gradually, the city dug out more and more sewers, more and more various pipes, more subways and other tunnels. Thus more places for rats to nest. We gradually built comfortable homes for more and more rats.

The rat population is not evenly distributed either. They tend to be where poor people live, and where the restaurants are. That’s where there is food.

And not all rats go to the surface. Rats are pretty loyal to the place of birth, and rarely venture more than about 60 feet from it, throughout their lives. If displaced, they can find their way home from as far as 4 miles, but for a foot-long animal, that is an extremely long distance.

If they can get food down under, e.g., from subway passengers throwing out uneaten food onto the tracks (which they do), rats never need to go up to the surface. They never get captured and counted in surface surveys.

Can rats swim?

Yes, rats are strong swimmers. They can even dive for a little while – see this video: if a domesticated rat can be trained to dive (and enjoy it), I assume that a wild rat can do it when its life is threatened:

The thing is, swimming in a water maze in the lab, or on the surface of a body of water is one thing. Swimming upward, against the powerful stream of water streaming downward is a completely different thing. They may be strong swimmers, but they are not Johnny Weissmullers.

Photo: Hiroko Masuike, NYTimes

MTA workers pumping out water from subway tracks at South Ferry subway station in New York, Tuesday, October 30, 2012. Photo: Hiroko Masuike, NYTimes

There are many ways up to the surface, but they all go up. And if the water was mainly gushing into the tunnels from above, from the streets as Sandy was flooding, they would have had to swim or dive up narrow pipes, essentially vertically up against the water. No way. Those guys drowned.

To go up to the surface, rats need to know the way to the surface. Rats know their own territory very well. But rats that never go to the surface do not know how to get there. They may still want to instinctually go up, but they don’t know the way so would have to get lucky to actually find the stairs and then fight their way up against the gushing water.

Rats already on the surface would probably be fine. The water and wind from Battery would carry them north until they reach the dry ground. They can certainly stay on the surface. Salty water is denser than fresh water, so they would find it even easier to stay on the surface, though their eyes may not like all of the salt.

What was flooded, when and how?

Right now, we do not know exactly where, when and how the water entered the subway tunnels, sewers, etc. MTA site does not provide much information. New York Times does not either – they are concerned with information useful to people, e.g., when will the subway open again, not where, when and how the subway initially flooded. Most likely the water came from above, from the flooded streets after sea water rose high at the Battery and the East side. This is important. It is easier for rats to float on the surface of water rising from below, than to fight against the water falling from above.

Also, most of Manhattan (and rest of NYC) did not flood at all. Most of the rats probably survived just fine where they were.

Who lived, who died?

NYC subways system flooding. New York Times (see link in the main text). So, from above, we can speculate that many rats survived. Some were never affected by flooding. Some were on the surface already and managed to run or swim to the higher ground. Some knew their way out to the surface and made it there. Rats are smart and crafty – if they can find a way to hide or go out, they will.

But some rats certainly drowned. Those are the rats that live deep inside holes we never know about, let alone visit. Rats that never go up to the surface. Rats that had the misfortune to have to try to escape essentially vertically up against strong gushing water.

There is a rule of thumb – if you see a rat on the surface during the daylight time, this means that the underground population is enormous. And I see them every month I go up to New York. When the rats are crowded, dominant rats take the best spots. If the population forages on the surface, dominant rats forage during the night. Subdominant (or submissive) rats are temporally displaced to the daytime shift.

This is important. If Sandy started to flood the tunnels during the day (and nobody knows, or makes public, this information as the subway was already closed to people by then), it will be the non-dominant rats who are on the surface, and thus more likely to survive. If the flooding started at night, it will be dominant rats on the surface, floating away into safety. Dominant rats are more likely to be able to relocate and survive in other places where they have to compete with locals. Non-dominant rats would have a much harder time finding a new home.

So, my guess is that most of the rats survived. But quite a large number of rats drowned – depending on exact location, depth, how much they know how to get to the surface at all, their exact route to the surface, and their status in the social hierarchy.

You can learn much more about New York City rats from Rats: Observations on the History and Habitat of the City’s Most Unwanted Inhabitants by Robert Sullivan, one of the most wonderful popular science books I have read over the past decade.

I will also be doing a HuffPoLive segment about this at 1pm EDT, will post the link in the comments once I have it.

Update: More from The Urban Scientist, Jezebel, Tha Daily Beast, Live Science, Forbes.

Charlotte’s Web: what was she smoking?

“Don’t touch those webs!”

Me and an enormous spider, at the Natural History Museum in Berlin, 2008.

A couple of decades ago, my wife and I worked on a horse farm where everyone was explicitly instructed not to ever clean the cobwebs inside the barn. Sure, the owners themselves would occasionally, very carefully, almost surgically, remove a few targeted old cobwebs here and there, but the majority of the webs remained up at all times. Explanation? Spiders don’t bother anyone, while flies and mosquitoes bother both horses and humans.

On the other hand, for balance, there is an old Serbian proverb that goes like this: “If there were no wind, spiderwebs would cover the sky”

I assume this is said every time someone complains about the strong eastern wind, Koshava, that sweeps through the country in autumn.

And this situation – spiderwebs covering the sky – is something that happens in Mark Twain’s story Some Learned Fables, For Good Old Boys And Girls, featuring Herr Spider as one of its key characters. I read Twain’s short stories over and over again as a kid. Still love them.

Why are we so enchanted by spiders, in real life, in mythology, and in popular culture? I certainly am, always was.

There were Little Miss Moffet, and Itsy Bitsy Spider.

As a little kid, I watched, and was greatly impressed by the old film Tarantula. Later I could not help myself – just had to watch Eight Legged Freaks and Arachnophobia. And yes, Spiderman, despite its scientific…er, bloopers.

Of course I knew about Arachne and the beautiful myth of the origins of the callipygous Shenora Spider (does such a species even exist in reality?).

And then there are spiders in literature. I was scared by the Spider-Man in John Wyndham’s The Chrysalids. I fought the giant spiders of Mirkwood when I played The Hobbit computer game on Sinclair ZX Spectrum back in 1981 or so, after I have already read the book both in Serbian language and the original English. There was Shelob in Lord of the Rings, and Aragog in Harry Potter.

And of course, the best spider in all of history – Charlotte!

Charlotte. She could write.

Today is the 60th anniversary of the first publication of Charlotte’s Web, the beautiful, haunting story of a talking pig and a writing spider.

Interestingly, growing up in Yugoslavia the first 25 years of my life, I have not heard of Charlotte’s Web until I came to the States. But then I had kids. And kids loved to watch the movie over and over again. So I read the book.

And to this day, occasionally, spontaneously, I start singing “Isn’t it great that I articulate!” An important and heart-felt sentiment for a writer for whom words are toys.

Then I received in the mail (but am yet to read it, I promise I will), Michael Sims‘ book The Story of Charlotte’s Web, a biography of E.B.White and the story of the making of the book.

But not everything is fiction and myth. I am a scientist at heart. Each one of those invented characters always made me want to learn more about the real creatures.

Orb weaver (Argiope sp.) Members of this genus are found all around the world and spin large webs that often contain striking designs. Charlotte’s Web author E.B. White, who consulted with a Museum curator while writing the classic children’s book, named the main character Charlotte A. Cavatica after a common orb weaver, Araneus cavaticus. © AMNHR. Mickens

Orb weaver (Argiope sp.) Members of this genus are found all around the world and spin large webs that often contain striking designs. Charlotte’s Web author E.B. White, who consulted with a Museum curator while writing the classic children’s book, named the main character Charlotte A. Cavatica after a common orb weaver, Araneus cavaticus. © AMNHR. Mickens

A couple of months ago, I went to the American Museum of Natural History in New York City (thanks for the tickets, you know who!) to see their new exhibitSpiders Live. Yes, “Live” is a good description – there are plenty of living specimens in there, many quite fascinating.

As usually happens in museum exhibits, there was plenty to learn about what we know. Anatomy, physiology, ecology, evolution, geography, behavior. Sure, there were a couple of non-spiders there, like scorpions, but it was clearly explained exactly why they are not spiders and how they are related.

One could see a short video showing how Gladiator spider catches its prey by throwing a carefully counstructed web trap on it, like this:

And they mentioned the Bolas spider which catches its prey by lassoing it in with its bolas-like ball of silk:

Interesting – to me at least, as a chronobiologist – is that the Bolas spider uses its circadian clock for an interesting function – it produces different blends of chemicals in its pheromone at different times of night (pdf) to coincide with different times when two different species of moths are flying around, each species attracted to a specific mix of aromatic chemicals.

But beyond learning facts, I was also looking at the ways the exhibit tries to include the scientific process – how we know what we know about spiders? I was looking for, perhaps, descriptions of ingenious experiments on the courtship signaling in wolf spiders, or the research on unique social, colonial spiders. Nope.

There was a part, at the end, which described how scientists collect spiders in the field, how they catch them, preserve them and label them.

And then I saw what I was really looking for. Yes! They did it! The exhibit had a really nice description of my favorite spider research ever! And there it was, The Charlotte’s Web connection, and my own personal connection! I talked about it at the last #TriSciTweetup at the NC Museum of Natural Science in Raleigh NC, for the inaugural Lightning Talks with Brian Malow on Thursdays at the Daily Planet Cafe:

Back in 1948., zoologist H. M. Peters was studying how spiders spin webs. He was getting tired as he had to do all of his research late at night, when spiders spin their webs. So, he asked his friend Peter Witt, a pharmacologist, if there is anything that he could give to spiders that would make them spin during the day. Peter suggested amphetamines. It did not work. Spiders kept weaving at night. But, oh my, their webs looked crazy! They were like impressionist art!

Argiope spider web This real argiope spider web has been colored and preserved. Its most striking feature, an ‘X’ running through it, is something of a mystery. Many spiders embellish their webs with these designs, called stabilimenta, but the reason is unknown. Scientists think stabilimenta may attract insects by reflecting light, warn birds away, or camouflage the spider from predators. © AMNHD. Finnin

Argiope spider web. This real argiope spider web has been colored and preserved. Its most striking feature, an ‘X’ running through it, is something of a mystery. Many spiders embellish their webs with these designs, called stabilimenta, but the reason is unknown. Scientists think stabilimenta may attract insects by reflecting light, warn birds away, or camouflage the spider from predators. © AMNHD. Finnin

Peter Witt was an amazing person, a wonderful man. I had the fortune to meet him once, in 1998, just a couple of weeks before he died. He was the Head of the institute for brain and behavior at Dorothea Dix hospital in Raleigh, now unfortunately closed.

Intrigued by the results his friend Peters got when giving spiders amphetamines, he turned his own research into that direction, using spider webs as windows into the way different chemicals affected the nervous system. Some of those were pharmaceuticals of the day. Others were drugs found relatively easily on street corners back in the 1950s and 1960s. Both were of interest to science, of course, for different reasons.

Different drugs had different effects on the shapes of the web. In high doses, almost every drug resulted in highly irregular webs. But at carefully chosen lower doses, there were some interesting differences. For example, under the influence of caffeine, the webs were vertically shorter but horizontally wider, as spiders made larger angles between the radial spokes of the web.

The most striking was the effect of LSD-25. Yes, LSD. This is the only drug which resulted in webs being more carefully weaved and more perfect than the controls.

Charlotte? Is that you?

Many years later, I was teaching a lab at NCSU in animal physiology. Part of the lab was a project, done by students under my supervision. Some students did projects on humans – each other. But the other half used animals. Invertebrates, as there was no time to get an IACUC (institutional animal care and use committee) approval for use of vertebrates (that is a long and difficult process).

A spider web on pervitine

A spider web on pervitine

One of my students decided to use Peter Witt’s experimental protocol, applying a chemical that he never used way back then – serotonin. Result? Spiders made decent webs, but they took about twice as much time to make them. They went slow about it. They made perhaps half of the twists of the spiral before deciding that was the end, leaving about twice as much space between the loops of the spiral.

Spider brains are large and complicated. They are so large they can’t even fill just the head, a part of them fills the thorax. Of course, spider brains are difficult to study. Not to mention that we do not have a spider genome sequenced yet so we do not have the tools to monitor what is happening in a spider brain. Thus, this line of research has been largely abandoned.

But it was not all in vain. Apart from being able to categorize substances along the lines of their effects on spider webs (often corresponding to their effects on human brains), this method now has a place in agriculture. Placing a few spiders in a field or orchard overnight and taking a look at the webs in the morning can tell the researcher if there are pesticides there, and perhaps which class of pesticide if not the exact kind.

Perhaps there is something in the air that can induce a spider to write “Terrific” and I’d love to know how it does that.

Stumped by bed nets, mosquitoes turn midnight snack into breakfast

Anopheles mosquito (unknown source)

Anopheles mosquito (unknown source)

One of the most effective methods for the control of spread of malaria is the use of bed nets infused with insecticides. Most species of mosquitoes (the Anopheles genus) that carry the malarial parasite (Plasmodium falciparum) are considered to be strictly nocturnal – they are active only during the night.

Thus, sleeping under the net provides protection against getting bitten by the insect vectors of the disease. The net does it in two ways – by providing a mechanical barrier between the mosquito and the human, and by killing mosquitoes that get in contact with the infused insecticide.

As we have learned many times, often the hard way, evolution tends to find a way around such tricks. A number of Anopheles species or local populations have evolved resistance to pyrethroid insecticides usually used in the nets. Yet, the mechanical protection of the net should still be effective, right?

Not so fast! A new study published in September 21 in the Journal of Infectious Diseases documents a behavioral change in a local mosquito population that effectively works around the safety protection of bed nets. What do they do that’s new? They changed the time of day when they bite!

Malaria-carrying mosquitoes are thought to all be strictly nocturnal. Recently, this dogma has started to be questioned, mainly because the rates of malaria did not significantly diminish in areas where bed nets have been implemented. Perhaps they fly and bite during the day, yet nobody bothered to test that hypothesis yet? A previous study noticed a shift in timing of activity and biting from middle of the night into early night. This study was quite systematic – repeating the experiment in two locations in Benin at three time-points: before, during and after the full implementation of bed nets in both locations.

Chronogram of the experiment. Translation for humans: 'chronogram' is an "aren't we sophisticated in our clever use of silly, opaque, uneccessary jargon" version of 'timeline'.

Chronogram of the experiment. Translation for humans: 'chronogram' is an "aren't we sophisticated in our clever use of silly, opaque, uneccessary jargon" version of 'timeline'.

What did they do? They collected mosquitoes in large numbers and recorded the time of day they caught mosquitos. In addition, they used morphology to identify the genus, and PCR to identify the species. Every single mosquito was Anopheles funestus. They tested the caught mosquitoes for pyrethrin resistance and did not detect any – every single mosquito died. Thus all the changes were strictly behavioral.

How did they collect them? They placed humans in strategic places as living targets. It looks pretty much like this video, except they actually captured the insects into vials, then transferred them into small bags:

During the period of just a few years as the bed nets got implemented in the two villages, local mosquitoes dramatically shifted the timing of activity. Instead of 2 or 3am, they now predominantly bit humans around 5am:

Shift in timing in mosquito activity in two locations over three sampling periods.

Shift in timing in mosquito activity in two locations over three sampling periods.

What does that mean?

First, we don’t know yet if this was an evolutionary (i.e., genetic) change or a purely behavioral change. It is possible that there was quite a lot of genetic variation in timing of activity in the population a few years ago and that the bed nets provided a selective regimen that skewed the population to consist mainly of late night and dawn-active individuals. It is also possible that there is sufficient behavioral plasticity in the mosquito allowing it to learn the new best time of day to go out foraging. I’d love to see the mosquitoes placed in isolation chambers to monitor purely genetic patterns of circadian rhythms of activity.

But let’s think more in ecological terms. There are several players here: the Plasmodium parasite, the Anopheles vector, the human host, and predators that eat mosquitoes, notably bats. I have written at length about this a few years ago. Here’s a simple schematic of how the system works when undisturbed:

A crude schematic of possible timing of activity in this ecological system

A crude schematic of possible timing of activity in this ecological system

If the mosquito shifts to almost dawn, what happens?

First, the humans are up and about, outside of nets, readily available to bite. If the humans are healthy but mosquitos are carriers, this is a good way to transmit malaria to them.

But the humans who are sick, the sources of malaria, are still not available. At the times when they undergo “quaternary fevers”, which are the times when malarial parasites are present in their blood (I explained this in great detail before), they are safely hidden by the nets in the middle of the night and they are not bitten by late-biting mosquitos.

Second, a mosquito that bites a human around dawn is much more likely to get detected by that human and be swiftly turned into a small, bloody mush.

Third, while a mosquito that flies around dawn may be able to avoid some of the bats (though not all of them – many bats hunt until the break of dawn), they are now increasingly vulnerable to other predators – frogs, lizards and birds – that tend to hunt at dawn.

As it often happens, there are pros and cons when it comes to evolving new adaptations. The bed nets are now selecting for new adaptations in mosquitoes. It is hard to predict what will be the pros and cons of those adaptations for human health, or the pros and cons of those adaptations for mosquitoes and their survival, or pros and cons of these adaptations to insects’ predators. Future research on this will be both very interesting to watch and very useful for control of malaria.


Nicolas Moiroux, Marinely B. Gomez, Cédric Pennetier, Emmanuel Elanga, Armel Djènontin, Fabrice Chandre, Innocent Djègbé, Hélène Guis and Vincent Corbel, Changes in Anopheles funestus Biting Behavior Following Universal Coverage of Long-Lasting Insecticidal Nets in Benin, J Infect Dis.(2012) doi: 10.1093/infdis/jis565

The Scienceblogging Weekly (August 26th, 2012)

The week was too busy to finish this on Friday. Then on Saturday the news broke that Neil Armstrong died – something I wanted to highlight as a special topic – so I decided to wait another day and give people a chance to wrote posts and articles about Neil. So, with a delay, the weekly linkfest is here!


Blog of the Week:

We are all in the gutter is a an astronomy and astrophysics group blog. The title of the blog comes from the quote “We are all in the gutter, but some of us are looking at the stars.” from Lady Windermere’s Fan by Oscar Wilde. Emma, Niall, Rita and Stuart are astronomers, astrophysicists, star-gazers and space geeks at various career stages, having fun with their blog, exploring the universe from every angle they can possibly think of.


Top 10:

Unless They’re Zombies, Fossils Don’t Live by Brian Switek:

I hate the phrase “living fossil.” The term should be eradicated from the vocabulary of science writers, and anyone who employs it should be promptly encased in Carbonite. “Missing link” is the only slogan that pisses me off more. My acute allergic reaction to the idiom may be a little overwrought, I admit. But, to me, “living fossil” is nonsense that obscures more than it elucidates. Take the coelacanth, for example….

Hyenas Eschew Lent, Chew Donkeys Instead by Anne-Marie Hodge:

Anyone who has ever attended a holiday parade or gone on a summer vacation knows that cultures tend to create their own seasonal patterns. In much of Western culture, December is a time of much celebrating and feasting, while similarly wintry January is relatively dreary and dull (after New Year’s celebrations subside). This raises a question: how do the behaviors and culture of a society affect the animals that depend upon that society’s garbage for their food? The progressive encroachment of human settlements into the habitats of wild animals has opened opportunities for animals to avail themselves of human refuse. A raccoon in North America is likely to find a juicy watermelon rind in July and leftover turkey remains in November. Perhaps equally enticing for a roving dumpster-diver, but by no means nutritionally equivalent….

Why Is the Night Sky Turning Red? by Amy Shira Teitel:

The idea of a red sky at night used to invoke beautiful images of vibrant sunsets, the product of warm sunlight bathing the sky near the horizon. The adage of “red sky at night, sailor’s delight” refers to a calm night ahead; a red sunset suggests a high-pressure system in the west is bringing calm weather. But red skies at night have taken on a new meaning in recent decades. As outdoor lighting become increasingly prominent, our night skies are gradually turning from black to red….

When will we find life in space? by Phil Plait:

One of the reasons I love astronomy is that it doesn’t flinch from the big questions. And one of the biggest is: are we alone? Another reason I love astronomy: it has a good shot at answering this question…

Paleo-politics: The really long view by Will Femia:

…..The other explanation is that the Cretaceous ended when, 65 million years ago, an asteroid (or asteroids) slammed into the earth, right across the future-Gulf of Mexico at the tip of the Yucatan Peninsula. Not only did the impact and resulting fallout from that asteroid kill the dinosaurs, it also wiped out huge quantities of marine life, including many of the “tiny marine plankton with carbonate skeletons” (I’m guessing some version of Coccolithophore? Anyone?) that would become the rich soil that slaves would farm on land their ancestors would inhabit in voting districts that would favor Democratic candidates around the turn of the second millennium of the Common Era……

What the Dark Knight knows about holding our urban lives together by Scott Huler:

There’s a lot not to love about The Dark Knight Rises, the crazyish new chapter in the latest Batman cycle: a series of actions and explosions so unconnected that they make a Rorschach test look like a syllogism by comparison; Marion Cotillard’s death scene, which lacked only her eyes rolling up and her tongue lolling sideways from her mouth to equal those put on by toddlers on playgrounds; and Christian Bale’s Batman growl — close your eyes and you think Cookie Monster is saving Gotham City….One thing the movie got right, though, is its focus on the infrastructure systems that serve as the beating and vulnerable heart of our urban existence. Every major plot point directly relates to the built environment and the networks that make every element of our lives possible….

Science For Princesses by Janet Stemwedel:

I have always known that I loved science, that delicious alliance of imagination and methodical testing that could help you figure out something about how a piece of the world worked. However, being born at the tail-end of the 1960s, I grew up in a culture that wanted me to know that girls were not supposed to like science. In fact, between toy commercials and TV shows, teachers and peers, I got the message pretty quickly that science is not something for girls. Rather, girls should turn their attention to more important matters . . . like being properly feminine. There was a way that girls were supposed to be—neat and tidy and pretty and pink and quiet and well-behaved. I was not any of those things. I didn’t want to be any of those things. I didn’t know how to be any of those things. And, as far as I could tell, trying to be those things was not going to help me get my hands on the science-y stuff that I wanted. So what was the point?….

How to Annoy E.O. Wilson by Michelle Nijhuis:

…….During a panel at the Aspen Environment Forum in Colorado, as she describes here, Emma piqued Wilson with her talk of making more nature — of expanding our definition of the natural world to include places humans have invaded, altered, and restored. Spending billions trying to return coastal areas like the Everglades to pre-Columbian “purity,” she added, is a lost cause. Better to invest in upslope reserves, and perhaps even learn to admire the tenacity of invasive species…..

Father’s age dictates rate of new mutations by Virginia Hughes:

With every passing year, men are increasingly likely to transmit new mutations to their children, according to the largest study yet of the so-called paternal age effect, published yesterday in Nature. The findings could help explain why older men are more likely to have a child with autism or schizophrenia than are younger men, the researchers say….

I Am Science…and a Nerd by Craig McClain:

I am a nerd. I was a nerd. I will be a nerd. Perhaps in kindergarten I wasn’t, where nerdom had difficulty establishing itself among the simple lessons of the alphabet, counting, and colors. In kindergarten, we are more or less the same in deficiencies and achievements. But after that, I am pretty confident my geek flag flew. I cannot remember ever being a bad student. Repeated straight A’s and the honor role defined me….


Special topic 1: Neil Armstrong

Neil Armstrong’s message to the future by Amy Shira Teitel

Neil Armstrong: Ace Engineer and Hotshot Test Pilot by Amy Shira Teitel

Neil Armstrong’s legacy went to waste but a new space race is on the cards by Alok Jha

Neil Armstrong: 1930 – 2012 by Phil Plait

Pow! ZOOM! To the Moon! by Phil Plait

Debunking myths about Neil Armstrong by James Oberg

Rocks remember, and so do we by Ethan Siegel

What Neil Armstrong Knew Is What We Never Will by Charles P. Pierce

Keep in mind as you put together your Neil Armstrong packages tonight… by Charles Apple

The Man and the Moon by Anthony Lane

As We Say Goodbye to Neil Armstrong, Should We Also Let Go of Our Space Fantasies? by John Horgan

For Neil Armstrong, the First Moon Walker, It Was All about Landing the Eagle by Andrew Chaikin

Neil Armstrong by Babbage

Neil Armstrong Talks About The First Moon Walk by Robert Krulwich

Neil Armstrong by Neil Gaiman

Neil Armstrong’s Last Interview by Jeff Marlow

RIP Neil Armstrong, star of the first big story of my news career by Steve Buttry

The Cold War Push Behind Neil Armstrong’s ‘One Small Step’ by Andrew C. Revkin

Rest in Peace, Neil Armstrong by Matthew Francis


Special topic 2: rape and pregnancy

Rep. Todd Akin (R-MO) serves on House Committee on Science, Space, and Technology by David Kroll

Here is Some Legitimate Science on Pregnancy and Rape and What Do You Do When There is No Best Dataset? A follow-up on pregnancy and rape statistics by Kate Clancy

The sperm don’t care how they got there, Rep. Akin by Emily Willingham

Sure, women cannot get pregnant from rape. Also, all mean people are ugly and puppies are immortal. by Melanie Tannenbaum

Legitimate rape, seminal priming, and preeclampsia by Jon Wilkins

Unfamiliar sperm, Tibetans, and cheese: Why evolutionary biology doesn’t excuse Todd Akin by Jeremy Yoder

What people who talk about “legitimate rape” really mean by Naomi McAuliffe

Todd Akin and the Anti-Science House Science Committee by Brandon Keim

‘Legitimate rape’ – a medieval medical concept by Vanessa Heggie

Backstory: the reporter who interviewed Akin by Mike Hoyt

A letter to Paul Ryan about forcible rape by Dr. Jen Gunter

Pregnancy Flowchart by Adam Weinstein

Hard words: Do we know what we’re talking about when we talk about rape? by Kathryn Blaze Carlson

The Crackpot Caucus by Timothy Egan

Why Sex Education Helps End Rape by Erica Grigg

Akin breakin’ science by Phil Plait

It’s trigger warning week by Laurie Penny

Rape exceptions aren’t legitimate by Irin Carmon

Where Akin got the idea that rape victims rarely get pregnant by Tim Townsend and Blythe Bernhard

An Open Letter to Rep. Akin From a Woman Who Got Pregnant From Rape by Shauna Prewitt

Todd Akin’s Abortion Position Reflects GOP Platform by Laura Bassett

Conservative Media Dismiss Akin “Rape” Comments As “Dumb,” But Rhetoric Is Reflected In GOP Policies by MIKE BURNS & SOLANGE UWIMANA

The Problem With Men Explaining Things by Rebecca Solnit

Todd Akin and the Right’s False Fact Machine by Josh Barro

Words and deeds by David Wescott

Rep. Todd Akin’s statements have a familiar ring to them… by Sassquach

Legitimate takedown: Todd Akin meets the women of the Internet by Virginia Heffernan

A Canard That Will Not Die: ‘Legitimate Rape’ Doesn’t Cause Pregnancy by Garance Franke-Ruta

The Official Guide to Legitimate Rape by Katie J.M. Baker

Todd Akin’s “Legitimate Rape” Comment Was Not a Misstatement. It Was a Worldview. by Laura Helmuth

Rep. Todd Akin’s Rape Remark At Odds With Science Of Pregnancy by Jeanna Bryner

What Does Todd Akin Think “Legitimate Rape” Is? by Amy Davidson


Special topic 3: superbug at NIH

The “NIH Superbug”: This Is Happening Every Day by Maryn McKenna

Genome detectives unravel spread of stealthy bacteria in a hospital by Ed Yong

Not a failure, a lesson. The NIH Clinical Center KPC Outbreak by Eli Perencevich

The NIH Superbug Story—a Missing Piece by Judy Stone

Hunting a Superbug by Deborah Blum

‘Superbug’ stalked NIH hospital last year, killing six by Brian Vastag

NIH should have notified it of superbug outbreak, Montgomery County official says by Brian Vastag

Like a Game of Clue, Genomics Tracks Outbreak, Revealing Evolution in Action by Ricki Lewis

Genome Detectives Solve a Hospital’s Deadly Outbreak by Gina Kolata

Govt. Gene Sleuths Stop Superbug That Killed 6 by The Associated Press


Best Images:

Drake equation: How many alien civilizations exist? by IIBStudio

Sunday Morning Anole Cartoon: When Lizard Biologists Compete by Rich Glor

If you were to summarise the world into 100 people, how would the population turn out? by Charlie Hilton

Conventional Wisdom by Randy Yeip

Are those pictures of Mars from the Curiosity rover? by Is Twitter Wrong?

Miss Insomnia Tulip’s Anatomical Macaroons by AnatomyUK

Votive Ear by Jai Virdi

Glow-in-the-dark cockroaches look like Jawas by Jess Zimmerman

London Zoo animal audit – in pictures by The Guardian

Animals in the News by Alan Taylor


Best Videos:

How Did Apollo-era Astronauts Sleep in Space? and Learning to Land on the Moon by Amy Shira Teitel

Amazing Color Differences In Lizard Populations Separated By Little Distance by Jonathan Losos

Can dinosaurs still be badass with feathers? by Charlie Jane Anders

Camera shutter speed synchronized with helicopter blade frequency by whataboutlarry1

Why Insect Wings Don’t Fracture by Sid Perkins

The High-Resolution Life of a Neuron by Brandon Keim

Curiosity Drops in on Mars in High-Res by JPLnews

Doodling in Math Class: Connecting Dots by Vi Hart

Jessica Wise: How fiction can change reality by TEDEducation

Learning By Play by Nadja Popovich



Three Ways of Looking at the Great Pacific Garbage Patch by Miriam Goldstein

Thomas Kuhn: the man who changed the way the world looked at science by John Naughton

Kuhn the Irrationalist by Peter Coles

A brief history on how I became an Animal Behaviourist… by Kate Mornement

How Domed Dinosaurs Grew Up by Brian Switek

Microbes manipulate your mind by Mo Costandi

Kissing bug – the real vampire of Latin America by Samantha Price

Is solidarity a thing of the past? by Kurt Cobb

No, immunology should get the same scrutiny as psychiatry. And vice versa. by Tim Skellet

So, you’ve dropped a vial or lost a sample box in your liquid nitrogen container…now what? by Brian Krueger

Breeder by Melissa Wilson-Sayres

‘Beam Us Up, Mr. Scott!’: Why Misquotations Catch On by Maria Konnikova

Superbug Summer Books: EXPERIMENT ELEVEN by Maryn McKenna

Chemical Free Dirt (for the Fairytale Garden) and Smoked Out and No, no. Not Nicholas Kristof on Chemicals Again by Deborah Blum

Why are languages so different—and disorderly? by Philip Ball

Aphids, carotenoids and photosynthesis by Ian Le Guillou

Do Be a Dick (sometimes): Emotions and Skeptics by Ashley F. Miller

Tesla’s Revenge: Filmmakers Kickstart Electrifying Docudrama About Cult Genius by Hugh Hart

The neurology of Psalm 137 by Vaughan Bell

Book review: Connectome by Sebastian Seung by Moheb Costandi

TGIPF: Penis in My Head by Christie Aschwanden

First US stem cell trial for autistic children launches today by Kathleen Raven

Stem cell clinical trial for autism: proceed with caution by Emily Willingham

Is a trial of stem cell therapy in autism scientifically and ethically justified? by Orac

Would Rachel Carson Embrace ‘Frankenfoods’? – This Scientist Believes ‘Yes’ by Pamela Ronald

Debunking the Hunter-Gatherer Workout by Herman Pontzer

Morality and Basketball by Sean Carroll

Republican spending plan casts shadow on science by Amy Maxmen

Making Liquor Recommendations by Dr24hours

Richard Dawkins in Playboy by Faye Flam

Amateur Scientists Discover Asian Needle Ant Has Expanded its Range by Thousands of Miles, Unnoticed by Rob Dunn

Dogs Chasing Their Tails Are Akin to Humans With OCD and Celebrating 1,447 Years of the Loch Ness Monster and Go to Sleep, All-Nighter Cram Fests Don’t Work and Want to Avoid a Mid-Life Crisis? Get Friends and Crafty Bonobo Shows Humans Aren’t the Only Stone Tool-Makers by Rachel Nuwer

Asperger’s Doesn’t Make You an Asshole by Heina

Bodies in art, art in bodies by John Hawks

NASA’s Amazing Gliding Gemini Capsules by Amy Shira Teitel

Can Identical Twins Get Away With Murder? by Brian Palmer

What can survive on Mars? by Steven A. Edwards

How to Learn a Language Nobody Speaks and Lance Armstrong Surrenders Against Doping Charges and Will be Banned for Life by Rose Eveleth

Rockstars, Ethograms and Behavior (Problems) by Julie Hecht

Planetary alignment pyramid scheme by Phil Plait

We Can Save the World by Eating Bugs and Drinking Urine by Erin Biba

Clothes Make the Man—Literally and The Neuroscience of Optimism by Jordan Gaines

Wasps Follow Order of Succession When Queen Dies and The Shambulance: Zero-Calorie Noodles? by Elizabeth Preston

Friday Weird Science: This quail has a cloth fetish by Scicurious

Vowel Movement: How Americans near the Great Lakes are radically changing the sound of English. by Rob Mifsud

How to Teach a Horse the Rules of the Road by Miriam Kramer

Remnants of a stellar suicide pact and The Terrible, Horrible, No Good, Very Bad Scientific Talk by Matthew Francis

Helium-Breathing Gibbons Sing Like Human Sopranos by Tanya Lewis

Siberian Princess reveals her 2,500 year old tattoos by The Siberian Times reporter

The birthplace of English? by Tim De Chant

Anti-Terrorism Campaigns and the Criminalization of Public Non-Conformity by Gwen Sharp

Hormones Explain Why Girls Like Dolls & Boys Like Trucks by Natalie Wolchover

The Nature of Consciousness: How the Internet Could Learn to Feel by Steve Paulson

New Morbid Terminology: Coffin Birth by Katy Meyers

Are You a Hero or a Bystander? by Sue Shellenbarger

Invasive species provide important lessons for surviving climate change and New species of barbet discovered in Peru by GrrlScientist

Just how big were dinosaurs? by Dave Hone

How Plantain Trees Could Become an Energy Source by Rhitu Chatterjee

Night Thoughts of a Classical Physicist by Ann Finkbeiner

WWWTP? Time’s Aspirin Structure Causes Headache by See Arr Oh

Candidates clam up on climate by Curtis Brainard

Overlooked and Underfoot: Sidewalk Cleaning in New York City by Ashley Taylor

Spawning coral monitored for effects of climate change by Melissa Gaskill

10 Myths About Space Travel That Make Science Fiction Better by Charlie Jane Anders

Goo-eating snakes and the eggs that evade them by Andrew Durso

Bonobo Stone Tales: The Making Of A Story by Charles Choi

Replacement Parts and Newly discovered rat that can’t gnaw or chew by Ed Yong

Artist Patricia Olynyk inspired by light pollution by Casey Rentz

Scoop: A preview of Romney’s energy plan by Philip Bump

Neuroscience: Solving The Hard-On Problem by Neuroskeptic

Every Step You Take by Wendy Lovelady

Fighting the stereotype that math is only for boys by Patricia Valoy

The Wall Street Journal Does It Again: Another Whopper Of A Lie On Climate Science by Dana Nucitelli

It’s all about objective multiples… by Mia Cobb

Medieval Women as Physicians by Tracy Barrett

Was Vincent van Gogh Color Blind? It Sure Looks Like It by Colin Schultz

Ego v. Efficiency at the U.S. National Science Board by Jeffrey Mervis

The Science of Bad Neuroscience by Neurobonkers

Social Position Drives Gene Regulation of the Immune System by Daniel Lende

Q&A: Alexandra Cousteau by Emily Fisher

The evolutionary history of dragons, illustrated by a scientist by Annalee Newitz

Egg-ceptionally Bad by Cassandra Willyard

The Free Will Confusion (1): On “My Brain Made Me Do It!” by Stephan Schleim

Should we teach algebra? by Paul Raeburn

The Rats of War: Konrad Lorenz and the Anthropic Shift by Liam Heneghan

Why College Binge Drinkers Are Happier, Have High Status by Maia Szalavitz

How many species are there? by Zen Faulkes


Media, Publishing, Technology and Society:

How to Succeed in Journalism when You Can’t Afford an Internship by Alexandra Kimball

Who are the offline-academics? by Katie Wheat

Sick of Impact Factors: Coda by Stephen Curry

Taking the Impact Factor seriously is similar to taking creationism, homeopathy or divining seriously by Bjoern Brembs

There are cons to open acces? Really? by Bjoern Brembs

“You’re not entitled to your own facts” vs. That’s your opinion. Kiss my ad. by Jay Rosen

Twitter rewrites the script for political conventions by Martha T. Moore

Barbara Mack: best media lawyer I ever worked with by Steve Buttry

Ask A Writer: “How Do I Write What The Audience Wants To Read?” by Chuck Wendig

The End of My Writing Career / Author Sharon Potts by Clay Stafford

Research As You Go by Steven Johnson

The ridiculous SVP embargo is back again by Ross Mounce

Intellectual power and responsibility in an age of superstars by Daniel W. Drezner

Coming in the side door: The value of homepages is shifting from traffic-driver to brand by Adrienne LaFrance

Google Hiring Data Reveals Two Things Women Can Do To Get Hired And Promoted More by Nicholas Carlson

A Day In My Life As A Freelance Science Writer by Charles Choi

Turn Off the Phone (and the Tension) by Jenna Wortham

Adulthood, Delayed: What Has the Recession Done to Millennials? by Derek Thompson

Why Are Young People Ditching Cars for Smartphones? by Jordan Weissmann

The Cheapest Generation by Derek Thompson and Jordan Weissmann

How Wikipedia Manages Sources for Breaking News by Heather Ford

Ex-NPR Hill reporter: Lied to daily by Patrick Gavin

Report: Social network demographics in 2012 by Pingdom

6 questions journalists should be able to answer before pitching a story by Tom Huang

Plagiarism, defamation and the power of hyperlinks and The billion-dollar question: What is journalism for? and Why it’s better for fact-checking to be done in public by Mathew Ingram

Rutgers Professor’s Research Shows Social Network Sites Foster Close and Diverse Connections by Lisa Intrabartola

Don’t blame Twitter when journos tweet stupid things; blame stupidity by Steve Buttry

How long-form journalism is getting ‘a new lease of life’ in the digital world by Rachel McAthy

Why fact-checking matters by Emily Willingham

Rotary Dial by Ftrain

The closing of American academia by Sarah Kendzior

Be More Productive. Take Time Off. by Jason Fried

Journalist Of The Day: SciAm’s Bora Zivkovic talks about the evolution of social by Chao Li


Blogs of the Week so far:

May 11, 2012: Academic Panhandling
May 18, 2012: Anole Annals
May 25th, 2012: Better Posters
June 1st, 2012: Vintage Space
June 8th, 2012: Tanya Khovanova’s Math Blog
June 15th, 2012: Russlings
June 22nd, 2012: Parasite of the Day
June 29th, 2012: March of the Fossil Penguins
July 6th, 2012: Musings of a Dinosaur
July 13th, 2012: Contagions
July 21th, 2012: Life is short, but snakes are long
July 27th, 2012: Science Decoded
August 11th, 2012: Powered By Osteons
August 18th, 2012: Do you believe in dog?

The Scienceblogging Weekly (August 18th, 2012)

Blog of the Week:

Do you believe in dog? is a brand new blog. It is written by two dog researchers, one in New York City, the other in Yarra Valley just outside of Melbourne, Australia. Julie Hecht you may already know from her wonderful blog Dog Spies, her writing in The Bark, or her research which we covered here at SciAm. She studies (and teaches about) dog cognition. Mia Cobb, the Australian, did her research in animal behavior on birds and ants, but now works on issues of dog shelters, welfare and performance science of working dogs. What is the coolest thing about the blog is that the two of them write for each other, addressing each other in each post, thus teaching and learning from each other in a dialogue to which we are all invited to participate in and contribute.


Top 10:

Tales from the OR by Summer Ash:

WARNING: This post contains my blood and guts, literally. If you’re squeamish, I recommend skipping this one. What follows is my journey through the operating room at Columbia-Presbyterian on July 18, 2012. Apologies, but I couldn’t help starting off with yet another pop culture reference (this time from Wes Anderson’s Rushmore)….

An example of why it is important to distinguish evolution as fact, theory, and path. by T. Ryan Gregory:

I, and others, have pointed out that there are three aspects of evolution: evolution as fact, evolution as theory, and evolution as path. Evolution as fact refers to the historical reality that species are related through common ancestry. This is supported by a massive amount of evidence from a wide array of independent sources. Evolution as theory refers to the proposed explanations for how “descent with modification” occurs — mutation, natural selection, genetic drift, etc. Evolution as path refers to the actual patterns that have occurred during the history of life, such as when certain events (e.g., branching points, extinctions, etc.) took place, how lineages are related, when and how many times certain traits evolved, and such. The important point is that these three components are largely independent…

The Childhood Aquatic by John Romano:

There is a structurally integral part of my psyche that is the keystone to my existence. I am not sure how it was placed in such a vital position, but it seems this part of me is embedded in my DNA. Something that I can never remember being without. The absolute and total fascination with the natural world….

Abraham Lincoln and The Embalmer by Romeo Vitelli:

The assassination of Abraham Lincoln on April 15, 1865 shocked a nation still recovering from four years of bloody civil war. Along with the hunt for his killers and the uncovering of the assassination plot against the President and several other members of his administration, there was also the logistic nightmare of his funeral and the need to transport the President’s body by train from Washington D.C. to his final resting place in Springfield, Illinois. Since the funeral train would retrace the route that Lincoln had traveled to Washington following his election, the body would be viewed by millions of mourners along the way during the numerous planned stops. All of which raised the question of how to keep the body preserved long enough to reach its destination. Considering the fact that funeral embalming was a relatively new development at that time, some very special arrangements needed to be made…

Inspiration from bassist Victor Wooten shows me a new way to deal with my “child-as-scientist” frustrations by Marie-Claire Shanahan:

I have a confession to make: I cringe a little every time I see a school science or science outreach program justified by saying something like, “Young children are natural scientists, truly curious about the world” (That particular quote is from the Delaware Museum of Natural History). I feel like a curmudgeon about it because it often comes with really good intentions to get students actively involved in doing science (something I definitely support)….

How a Tick Bite Made Me Allergic to Meat by Helen Chappell:

The last time I ate a hamburger, I spent the night in the emergency room. There wasn’t anything wrong with the hamburger itself—aside from being a bit overdone—but it sent me into anaphylactic shock. It wasn’t always this way…

Are wolves really all that? by DeLene Beeland:

Have conservation scientists become carried away, touting the ecological benefits of wolves where there are perhaps — dare I say it? — not as many as we believe there to be? Perhaps some people in the media, and even some in science, have gotten carried away with the ecological changes that wolves are actually capable of mediating, says globally-renowned wolf biologist L. David Mech in his most recent paper “Is science in danger of sanctifying the wolf?” …

Losing One’s Head: A Frustrating Search for the ‘Truth’ about Decapitation by Lindsey Fitzharris:

If you ever find yourself in a pub with me, chances are that at some point, the conversation will turn to death. Not just death, but the terrifying and horrible ways people have succumbed to it in the past. I have often heard a story retold about a man who attended the execution of his friend during the French Revolution. Seconds after the guillotine fell, the man retrieved the severed head and asked it a series of questions in order to determine whether or not it was possible to retain consciousness after decapitation. Through a system of blinking, the victim allegedly communicated his message back to his friend. The ending to this story changes according to the whims of the narrator… or perhaps the number of drinks he or she has consumed by that time. I wondered: was this the 18th-century equivalent to an urban legend? Or could there, in fact, be a degree of truth in this ghastly tale?….

A Dirty, Deadly Bite by Brian Switek:

Dragons aren’t real. At least, the fire-breathing wyverns and coiling wyrms of medieval lore aren’t. Those reptilian menaces were products of superstition and pre-scientific ideas about prehistoric creatures. They were ugly amalgamations inspired by our fears and actual fossil remains of long-extinct mammals and dinosaurs. But in the early 20th century, reporters excitedly relayed the discovery of what quickly became known as the Komodo dragon – ten foot long lizards that had coexisted with humans on South Pacific islands for thousands of years, but had only just been recognized by western science….

The Itsy Bitsy Drummer by Helen Shen:

Rrrr… RRR… Thack! Thack! Thrusting his front legs skyward, the male jumping spider shakes his rear end to send thumps, scrapes, and buzzes through the ground. He’s playing for a female’s attention, dazzling her eight eyes with semaphore while drumming out seductive seismic signals. A few missteps could turn the spider’s performance into a dinner show—with the star as the main dish. The ferocious female demands precise choreography, set to a groovy beat that UC Berkeley behavioral ecologist Damian Elias is working to decipher….

Best Images:

On Cephalopods and Science Fiction by Jen Richards

Beautiful periodic table from LIFE magazine’s 1949 special on the atom by Frank Swain

Curiosity’s photos (cartoon) by Viktor Poór

A bacterium on a diatom on an amphipod on a frog on a bump on the log in the hole in the bottom of the sea!<!–

The Spider Wars by bonybones

UNDERCOVER by Jun Takahashi

The Olympics Are Over and Here Are the Best Infographics by Rose Eveleth

They fell out of the sky! by Bill Harding

Elgar’s Explosion by Eva Amsen

Teaching history by Zach Weinersmith

Old Friends by Beatrice the Biologist

Tasting the rainbow: The ants whose multi-coloured abdomens show exactly what they’ve been eating by Mohamed Babu

Anole Raids A Hummingbird Feeder by Karen Morris

Unicorn Blood Parasite by The-Episiarch

Cures of all Kinds by Jai Virdi


Best Videos:

The GMO Song: “OMG GMOs!” by Andrew Bean, David Holmes, Sharon Shattuck, and Krishnan Vasudevan

Do watch this – probably the best ever debris flow video, from Austria last week by Dave Petley

Tricky Mister! Indirect Sperm Transfer in Primitive Hexapods by The Bug Chicks

Helmet Cam Strapped to Hunting Falcon Captures “Birds-Eye-View” Footage by Michael Zhang

Seat vibration test: oscillate the human by Marc Abrahams

Lice on a Bird: Convergent Evolution in action! by Bug Girl



Where Fire Meets the Sea by Tanya Lewis

Curiosity Landing: What’s With All the Peanuts? and Apollo’s Youthful Glow and The Soviets’ First Space ‘Rendezvous’ by Amy Shira Teitel

The benefits of seeing a “challenge” where others see a “threat.” and Why do swimmers hate Lane 8? and The psychology of doping accusations: Which athletes raise the most suspicion? by Melanie Tannenbaum

Could you be an Olympic athlete? by Catherine de Lange

Mysterious Tides: Toxic blooms of marine algae are getting worse, and some think we’re to blame. by Marissa Fessenden

Astrobiology: Worth It? by GunnarDW

Olympics Physics: The Long Jump and Linear Regression by Rhett Allain

Diseases That Just Won’t Quit by Tim Wall

Think Like a Doctor: A Peculiar Heartbeat Solved! by Lisa Sanders

The Bullying Culture of Medical School by Pauline Chen

Two Tales of Symbiosis by Elio Schaechter

Where the Minutes Are Longer: The Weird Science of Telling Time on Mars by Rebecca J. Rosen

Stop Calling Sherlock a Sociopath! Thanks, a Psychologist. by Maria Konnikova

Why cocaine users should learn Bayes’ Theorem by Precocity

Science on crack, 2: Walter White & cooking crystal meth by Puff the Mutant Dragon

We live in a geocentric world! by Thony C.

Murder by Physics by Matthew Francis

In Vietnamese community, treating taboos on cancer by Erin Loury

Years After Slash and Burn, Brazil Haunted by ‘Black Carbon’ and Science Takes Fat Out Of Chocolate, Replaces It With Fruit and Defending a Sanctuary With Paint and Song by Rachel Nuwer

Why We Need Ecological Medicine by Rob Dunn

Is PTSD A Product of War, or Of Our Times? by David Dobbs

A very modern trauma by Vaughan Bell

Curious about Curiosity: the Science Lab on Mars (Part I) and Search for Water (Part II) and Life on Mars (Part III) by Claire.W

Popping up trouble with butter and Alzheimer’s by biochembelle

A New Species Discovered … On Flickr by Adam Cole

Cells = drugs = government regulation? by Ada Ao

On the loss of a mentor: Al Malkinson, lung cancer researcher, scholar, gentleman by David Kroll

The Hidden Power of Whale Poop by Brandon Keim

What do you do when you’re sick? by Jai Virdi

Choice of Wood in Cremation Pyres by Katy Meyers

Food and trust of science and Does a Ph.D. train you to head a lab? by Zen Faulkes

Africa Grows Too Hot to Grow Chocolate by Mollie Bloudoff-Indelicato

Community health workers help HIV patient change attitude, life by Helen Shen

Hyenas Show It’s Better to Be Creative than Try, Try Again and Close Look at Bison DNA Reveals Our Dirty Fingerprints by Elizabeth Preston

CDC: Pretty Much Everyone Is Fat by Maryn McKenna

Why did people start mummifying their dead in the driest place on Earth? by Ed Yong

Found in translation: where do cures come from? by Jenny Rohn

Mouse Eyes Come With Built-In Bird Detectors by Sophie Bushwick

Atop Everest, two Sherpas and a watchmaker forged a friendship that changed their lives by Samantha Larson

Here’s an Omical Tale: Scientists Discover Spreading Suffix by Robert Lee Hotz

Flavors of Uncertainty: The Difference between Denial and Debate by Wendee Holtcamp

Tracks of an Oak Killer by Erin Loury

What is fair in the Olympics? Is sex a special case? and What is DNA? by Genegeek

That Eternal Question by Nicholas Suntzeff

Choosing the Paths Less Traveled? There’s an App for That by Henry Grabar

“Canopy” Meg Lowman (forest ecologist) – podcast by Samantha Larson

Scientific reproducibility, for fun and profit by John Timmer

Good Scientist! You Get a Badge. by Carl Zimmer

Reproducing Scientific Results – On Purpose by Derek Lowe

Common Lab Dye Found to Interrupt Formation of Huntington’s Disease Proteins by Kathleen Raven

No, that’s not a picture of a double sunset on Mars and An unreal Mars skyline by Phil Plait

How to Patch the PhD Problem by Alison McCook

Lead’s Everlasting Legacy by Meghan D. Rosen

Tweeting my genome #twenome and “Run away!”: a one-size-fits-all solution by Alex Brown

The Rise of the Three-Parent Family by Annalee Newitz

The Political Benefits of Taking a Pro-Climate Stand in 2012 by Connie Roser-Renouf, Anthony Leiserowitz, Edward Maibach

The Circadian Advantage: How Sleep Patterns Benefit Certain NFL Teams by David K. Randall

Book Review: Newjack Guarding Sing Sing by Erin Podolak

Dear HigherEd Communicators: John Tesh is Kicking Our Asses by Elizabeth Monier-Williams

When Yellow Fever Came to the Americas by Michelle Ziegler

The Mind of a Flip-Flopper and Cow Week: Angry cows vs. angry mothers by Maggie Koerth-Baker

PhD2.0 and anecdotes from the trenches by Jeanne Garbarino

The Sea Longs for Red Devils by Daniela Hernandez

Cooperating For Selfish Reasons by Miss Behavior

The Mix-Up that Ended the World by Erik Vance

Intimate Life of Mosquitoes by Lowell Goldsmith

What Anti-Trafficking Advocates Can Learn from Sex Workers: The Dynamics of Choice, Circumstance, and Coercion by danah boyd

Confessions of a Fake Scientist by Phil Edwards

Baby, You Light Up My World Like Nobody Else by Rachel Wang

Nothing Says Baby-Makin’ Like Desiccated Bacon and Scientists create a “Dow Jones” for ocean health by Allie Wilkinson

The Evolution of Shark Week, Pop-Culture Leviathan by Ashley Fetters

The Smell of Fear (No Tweets Necessary) by Natalie Angier

Post-Antipsychiatry by The Neurocritic

Where Have All The Cults Gone? and Is Poker A Game of Skill or Luck? by Neuroskeptic

Brain’s Drain: Neuroscientists Discover Cranial Cleansing System by Daisy Yuhas

This Woman Wants You to Buy Her, Piece by Piece by Rose Eveleth

My Brain Made Me Do It: Psychopaths and Free Will and How PTSD and Addiction Can Be Safely Treated Together and Couples Therapy Can Help PTSD and Improve Relationships by Maia Szalavitz

On quack cancer cures, and “alternative medicine” as religion by Xeni Jardin

Scientists can block heroin addiction now? and Offbeat tales: The summer heat takes its toll and Morning wrap-up by Paul Raeburn

How to Put a Curator in a Box: Part 1 and Ask an Exhibitionist #1: What’s the fake water? by Helen Chappell

Sharks and lasers, not just for entertainment! by Craig McClain

Giant cluster phenomenally fertile by Nadia Drake

Emma Marris: In Defense of Everglades Pythons and A Song Tries to Go Beyond the ‘OMG’ Reaction to GMOs by Andrew Revkin

The Emerging Revolution in Game Theory by The Physics arXiv Blog

“A simple feat… only expensive”: The Oatmeal tries saving Tesla’s lab by Casey Johnston

How many colors are really in a rainbow? by Ethan Siegel

Spiders Weave Better on LSD-25 by Clyde

Are Drug Companies Faking an Innovation Crisis? Uh, No. by Derek Lowe

Gorilla Joy Without a Doubt by Marc Bekoff

Turning Trauma Into Story: the Benefits of Journaling by Jordan Gaines

A Lesson in Rocketry by Marie-Claire Shanahan

PhD what is it good for? #leavingacademia by Jerry Nguyen

Contraception, healthcare and the costs women will leave behind by Katie Rogers and Ruth Spencer

The problem with poker by Pete Etchells

Rare Discovery: Hook-Legged Spider Found in Oregon Cave by Douglas Main

Why I’m Working Toward my Ph.D. at a Museum by Alejandro Grajales

How not to criticize psychiatry, part 1 by Tim Skellet

Book Review: The Wolverine Way, by Douglas Chadwick by DeLene Beeland

On Sciences and Humanities: Reflections on Coyne and Konnikova by German Dziebel

Citizen scientists may beat the pros in identifying at-risk species by Kate Shaw

The Long-Lived Legacy of the Cambrian’s “Wonderful Life” by Brian Switek

Bigger and Smaller by Lucy E. Hornstein

Scissor Sisters by Sally Adee

Brain network: social media and the cognitive scientist (pdf) by Tom Stafford and Vaughan Bell


Media, Publishing, Technology and Society:

Sick of Impact Factors by Stephen Curry

A smear campaign against Impact Factors…and the Sheep of Science by Drugmonkey

Deep impact: Our manuscript on the consequences of journal rank by Bjoern Brembs

Chess ratings and Impact Factor and Self archiving science is not the solution by Zen Faulkes

On publishing in PLoS One, and what’s the matter with ecology? by C. Titus Brown

Should supreme court justices use Google? by Paul Raeburn

Geneticists eye the potential of arXiv and Neanderthal sex debate highlights benefits of pre-publication by Ewen Callaway

9 ways to find helpful people and organizations to follow on Twitter by Steve Buttry

Instead of a press release: Options to add to your press release diet by Denise Graveline

Jonah Lehrer and the Problems with “Pithy” Science Writing by Karthika Muthukumaraswamy

Using Links as Citations Helps Gizmodo Defeat a Defamation Claim–Redmond v. Gawker Media by Eric Goldman

Discover magazine moving to Wisconsin and Discover magazine update by Paul Raeburn

New! New! New! (not yet) and If I were making a Twitter clone… and Making a Twitter clone, day II by Dave Winer

Magazines Don’t Have a Digital Problem, They Have a Bundling Problem by Hamish McKenzie

Should journalists specialize? by Kallen Dewey Kentner

Science Outreach in North Carolina by Russ Campbell

Stop Publishing Web Pages by Anil Dash

Author Platform Lessons from #1 New York Times Bestseller Rebecca Skloot by Dan Blank

To Think, To Write, To Publish by Maria Delaney

Do We Need Another Information Sharing Platform? by Jalees Rehman

How The American University was Killed, in Five Easy Steps by Debra Leigh Scott

13 ways of looking at Medium, the new blogging/sharing/discovery platform from @ev and Obvious by Joshua Benton

How To Lose Twitter Followers by Neuroskeptic

What to Do With Political Lies by Garance Franke-Ruta

Science Communication in the PhD process by Heather Doran

Science News staffers complain about misappropriation of their copy by UPI and UPI’s second response on misuse of copy by Paul Raeburn

UPI shirks responsibility by Curtis Brainard

News stories that aren’t news by John L. Robinson

Student Paper Editors Quit at University of Georgia by RICHARD PÉREZ-PEÑA

Letter from the Editor in Chief by Polina Marinova

Students walk out on University of Georgia newspaper by Andrew Beaujon

UGA Red & Black staff walks out today in protest. Is it now Red & Dead? by Maureen Downey

Witness describes confrontation between Grady NewSource Reporter and Red & Black Publisher by Grady Newsource

Study: Journalists’ lousy understanding of fair use leads to self-censorship by Andrew Beaujon

Five types of problem writer by Ann Friedman

Jonah Lehrer’s Mistake — And Ours by Peter Sims

Making Studies Out of Nothing at All by Taylor Kubota

On being a journalist, getting quotes by Razib Khan

Mendeley Acquires SciLife, a Social Network for Scientists and Researchers by Darrell Etherington

Nikola Tesla museum campaign earns $500,000 online in two days by Adam Gabbatt

Lessons on the Internet for LAMs from The Oatmeal: Or, Crowdfunding and the Long Geeky Tail by Trevor Owens

Further Decline in Credibility Ratings for Most News Organizations by Pew

The Update by Matt Thompson

Metrics, metrics everywhere: How do we measure the impact of journalism? by Jonathan Stray

Why we are poles apart on climate change and Doing science is different from communicating it — even when the science is the science of science communication by Dan Kahan

Hey, Twitter — shouldn’t it be about the users? by Mathew Ingram

The first steps towards a modern system of scientific publication by Joe Pickrell

Reflections on science blogging by Puff the Mutant Dragon


Blogs of the Week so far:

May 11, 2012: Academic Panhandling
May 18, 2012: Anole Annals
May 25th, 2012: Better Posters
June 1st, 2012: Vintage Space
June 8th, 2012: Tanya Khovanova’s Math Blog
June 15th, 2012: Russlings
June 22nd, 2012: Parasite of the Day
June 29th, 2012: March of the Fossil Penguins
July 6th, 2012: Musings of a Dinosaur
July 13th, 2012: Contagions
July 21th, 2012: Life is short, but snakes are long
July 27th, 2012: Science Decoded
August 11th, 2012: Powered By Osteons

The Scienceblogging Weekly (August 11th, 2012)

Blog of the Week:

Kristina Killgrove (Twitter) is a bioarchaeologist. Her blog Powered By Osteons covers a wide spectrum of topics on archaeology, bioanthropology, and the classical world. But what it has the most, and is most exciting, are bones. Lots of bones. Human bones. Skulls and femurs and pelvises and what we can learn about the past from studying them.


Top 10:

Satisfying Curiosity: preparing for the Mars landing by John Rennie:

…All the Mars rovers so far, from the trailblazing Sojourner to the overachieving twins Spirit and Opportunity, have been extraordinary exploratory robots, but Curiosity represents an ambitious new extreme. Most obviously, it’s much bigger: Curiosity weighs almost a ton and is the size of a small car, whereas Spirit and Opportunity were half as long and a fifth as massive and Sojourner was not much bigger than a large cat….

Muscles and the Lactic Acid Myth by Larry Moran:

…It’s all a myth. Lactic acid has nothing to do with acidosis (the buildup of acid in the muscles). In fact, it’s not even clear that acidosis is the problem, but let’s deal with that another time….

Is a PhD required for good science writing? by Emily Willingham:

…..In fact, as someone who has a PhD in science but has been a writer longer than I’ve been a scientist, I’d argue that it might be better not to have specific training in science if you’re reaching for an audience of nonscientists, depending on what your goal as a writer is. If your goal is to tell a great science story that keeps the nonscientist reading and thinking, “wow” or “I get it,” then scientific training might be an anti-requisite. If your target is critique and analysis of science, then scientific training could be quite useful as long as you don’t let your deep background blind you to what your readers might not understand as well as you…..

What Grown-Ups Can Learn From Kids’ Books by Maria Konnikova:

….The little prince isn’t alone in carrying insights that are lost on a child. What of Alice in her wonderland and mirrored adventures? Alice’s story may have been born from a tale told to children one lazy afternoon, but it became much more: a deep philosophical meditation….

Olympic Physics: Air Density and Bob Beamon’s Crazy-Awesome Long Jump by Rhett Allain:

Even now, there are those who claim that the long-jump record of 8.9 meters that Bob Beamon set in 1968 was so crazy awesome because he accomplished it in Mexico City, which is almost 8,000 feet above sea level. The argument is that the air is thinner, and so there is less air resistance, and Mexico City is further from the center of the earth, and so the gravitational forces are smaller. Does any of this have any impact? And if so, does it really matter?…

Is corn the new milk? Evolutionarily speaking, that is. by Jeremy Yoder:

It is a widespread misconception that, as we developed the technology to reshape our environment to our preferences, human beings neutralized the power of natural selection. Quite the opposite is true: some of the best-known examples of recent evolutionary change in humans are attributable to technology. People who colonized high-altitude environments were selected for tolerance of low-oxygen conditions in the high Himalayas and Andes; populations that have historically raised cattle for milk evolved the ability to digest milk sugars as adults….

In the Bronx, Rights Get Fuzzy by Cassie Rodenberg:

I’ve been working with photographer Chris Arnade to document stories in Hunts Point, Bronx and often-ignored areas of New York City. Over the course of the last year, we have noticed the impact the city’s Stop and Frisk policy has on the neighborhood. Recently, we made the decision to start documenting that in action should we see it. This Sunday, we did:…

What do Christian fundamentalists have against set theory? by Maggie Koerth-Baker:

I’ve mentioned here before that I went to fundamentalist Christian schools from grade 8 through grade 11. I learned high school biology from a Bob Jones University textbook, watched videos of Ken Ham talking about cryptozoology as extra credit assignments, and my mental database of American history probably includes way more information about great revival movements than yours does. In my experience, when the schools I went to followed actual facts, they did a good job in education. Small class sizes, lots of hands-on, lots of writing, and lots of time spent teaching to learn rather than teaching to a standardized test. But when they decided that the facts were ungodly, things went to crazytown pretty damn quick….

Stop Calling Sherlock a Sociopath! Thanks, a Psychologist. by Maria Konnikova:

I’d like to get something off my chest. It’s been bugging me for a very, very long time. Sherlock Holmes is not a sociopath. He is not even a “high-functioning sociopath,” as the otherwise truly excellent BBC Sherlock has styled him (I take the words straight from Benedict Cumberbatch’s mouth). There. I’ve said it…

What’s the difference between “transparency” and “invisibility”? by Greg Gbur:

In writing my previous post on The Murderer Invisible, I started thinking again about the relationship between something being “transparent” and something being truly “invisible”. Most of us can appreciate that, under the right circumstances, a transparent object like a glass window can be very hard to see, but most of us also appreciate that glass is not even close to fitting the popular perception of invisibility. In fact, though we encounter plenty of transparent things in nature, we don’t encounter invisible things….


Special topic: Curiosity:

Mars needs rovers! (and it just got a big one) by Matthew Francis

What Curiosity Will and Won’t Teach Us About Martian Life by Jeffrey L. Bada

A lifetime of curiosity: An interview with JPL director Charles Elachi by Nadia Drake

How Did We Get That Incredible Photo of Curiosity’s Descent on Mars? by Alexis Madrigal

Landing Curiosity on Mars was Way Harder and Way Less Expensive than the Olympics by Rose Eveleth

Watching Curiosity’s Mars Landing Live on a 53-Foot Screen in Times Square by Laura Geggel

Me and Curiosity by Taylor Kubota

“Curiosity” Driven Science by Larry Moran

Long day at the office as scientists get in sync with Mars by Bridie Smith

Curiosity’s first color photo of Mars is only its second-most exciting photograph yet by Robert T. Gonzalez

Meanwhile in Mars…. by Shibin Dinesh

Curiosity Rover: Driving Lessons on Mars by Tamara Krinsky

Engineering Life to Survive on Mars and Aid Human Colonization by Tanya Lewis by Eyder Peralta

See what it’s like to be a flight controller for Curiosity by Ruth Suehle

SCUBA Diving through the Endless Martian Desert by Thomas Hayden

Poet Laureates of Mars: Meet the NASA Team Behind Curiosity’s Twitter by Benjamin Soloway


Best Images:

Mars orbiter catches Curiosity by the tail by Eric Hand

Mars orbiter catches pic of Curiosity on its way down! and Curiosity landing site: the whole mess by Phil Plait

Curiosity Rover’s Home on Mars: A Powers-of-Ten Visual Explainer by Alexis Madrigal

Classic Scientific Illustrations by Ian Wang

Stickleback by Simone


Best Videos:

The only existing video footage of Mark Twain, as filmed by Thomas Edison by Robert T. Gonzalez

3D-printed exoskeleton gives a little girl use of her arms by Sean Ludwig

Curiosity’s Descent by JPLnews

Fred Guterl by The Daily Show

Forget Wireless Keyboards and Touch Your Plant Instead by Katie Pratt

The Scienceline music video awards by Kelly Slivka

How Math Comes to Mind: Intuition, Visualization, and Teaching by Stanislas Dehaene and Steven Strogatz

High Speed Video of Flipping Cats by destinws2

Mark Achtman on Plague Genetics by Michelle Ziegler



Superbug Summer Books: THE POWER OF HABIT by Maryn McKenna

Olympic Greatness: Biology or Motivation? by Melanie Tannenbaum

Backpacking Lizards For Science: Radio-Tracking Puerto Rican Anoles by Jonathan Losos

Will Climate Doubt Dry Up with the Drought? by Bob Deans

Undead: The Rabies Virus Remains a Medical Mystery by Monica Murphy and Bill Wasik

In Antarctica, Dreaming of Mars by Alexander Kumar

How to Unstick a Gecko and Mom’s Genes Make Males Die Sooner by Elizabeth Preston

Laboratory dye repurposed against protein clumps found in Huntington’s disease by Kathleen Raven

Stress Is a Real Killer—for Dragonflies by Douglas Main

Only Young Scientists Overthrow Old Concepts? and What Does “pH” Mean? by Larry Moran

Award-winning teacher Michael Lampert: WHY I LOVE SCIENCE by Casey Rentz

Sandpipers forgo sleep for days because there’s too much sex to be had and Prisoners pitch in to save endangered butterfly and A circuit for aggression in the brains of angry birds by Ed Yong

The Largest Waves in the Sea Aren’t at the Beach by Kim Martini

Plants with Personality by Emily Anthes

What’s up with social psychology? by Thom Baguley

The Molecular Olympics by Stuart Cantrill

Free online tool helps identify bat calls by Mark Kinver

New Forensics Tool for Catching Elephant Poachers and Man Wears Artificial Uterus for Science & His Wife and Celebrating 80 Years of LEGO by Rachel Nuwer

Historiography of the Market for Health by Jaipreet Virdi

Sleep research reveals keys to health by Lydialyle Gibson

Olympic Diving Physics by Paige Brown

Apollo 15’s Bizarre Contraband Stamp Debacle and How NASA Engineered the Enduring Apollo Flags by Amy Shira Teitel

Explaining Risk: Know Your Aristotle by Trisha Greenhalgh

Species Traits and Community Assembly by Jacquelyn Gill

First-Ever National Survey on Genetically Engineered Mosquitoes Shows Mixed Support by Matt Shipman

A Cult of Quantity by Will

Nope, these birds are not lesbians by Annalee Newitz

The Spruce Street Swamps by David H.

Psychology and Its Discontents by Carol Tavris

The Kangaroo’s Tale: How an errant elevator door ended an odd form of popular entertainment by Jack El-Hai

Ehux: The Little Eukaryote with a Big History by Jaime E. Zlamal

A New Generation of “Digital Ornithologists” by Abby McBride

The story behind “Scaling Metagenome Assembly with Probabilistic de Bruijn Graphs” by C. Titus Brown

What Lurks In Logs by Carl Zimmer

The Sham Ph.D. by Dave G Mumby

In Defense of Algebra by Nicholas Warner

A Mysterious “Alien” Creature Identified by NC Museum Researchers by jasoncryan

Fear of a Black Hole by Matthew Francis

Skeletons in the Closet by Heather Pringle

Serbian entity in Bosnia and Herzegovina pledges to revolutionise its “unsatisfactory” science by Mićo Tatalović

TGIPF: Slug Sex Redux by Cassandra Willyard

Anorexia nervosa, neurobiology, and family-based treatment by Harriet Brown

Ten clues to the modern poisoner by Deborah Blum

Cheetah Sets New Land Speed Record, Beats Bolt by 4 Seconds by Tanya Lewis

Science settles some decades-old debates about the best way to swim by Michael Ann Dobbs

Seven climate-change diseases to ruin your day by James West

Anolis sagrei (Cuban Brown Anole) in Valdosta, Georgia! 04 August 2012 by Janson Jones

Stiletto snakes by Andrew Durso


Media, Publishing, Technology and Society:

Judge Posner: Embedding Infringing Videos Is Not Copyright Infringement, And Neither Is Watching Them by Mike Masnick

Everything That’s Wrong with Political Journalism in One Washington Post Item by Jay Rosen

Scientific Communication As Sequential Art by Bret Victor

How to Write a Malcolm Gladwell Book by Zach Weiner

Where peer-review went wrong and Some more of peer-review’s greatest mistakes and What is this peer-review process anyway? by Mike Taylor

Chipping away at “hard” — for the poets and What has podcasting accomplished? by Dave Winer

Oracles, Big Answers, & Pop Sci’s Neglect of Mystery by David Dobbs

Journalism at the speed of bytes – a timely report by Lawrie Zion

Advice and examples on how and what journalists should tweet by Steve Buttry

PeerJ: are we reinventing the wheel? by Eduardo Santos

Blogging about blogging, and tweeting about tweeting: what I have learnt after 100 tweets by Michael McCarthy

Whither Science Publishing? by Bob Grant

Beware, Tech Abandoners. People Without Facebook Accounts Are ‘Suspicious.’ by Kashmir Hill

Downgrading Facebook. Tech Abandoner? Or Rational Lifestyle Choice? by Haydn Shaughnessy

Security Questions: The Biggest Joke in Online Identity Verification by Rebecca J. Rosen

All in a Single String by Maria Konnikova

Who’s That Woman In The Twitter Bot Profile? by Jason Feifer

Why Cartoons, sex and music are necessary in science communication by Emily Coren

Social Media for the Physiologist – A Modern Utopia or a Brave New World? by Dr. Isis with contributions from Danielle Lee, Pascale Lane, and Kristy Meyer

An Unexpected Ass Kicking and 7 Things I Learned From My Encounter With Russell Kirsch by Joel Runyon

Enter an Elevator with Confidence by Heather R.

Evidence-based, informative and on YouTube? How to communicate science in the Internet age by Dorothy Bishop

The Future of the Internet is…a la Carte by Matt Shipman

If #Google Plus is “Deserted” I Hope It Stays That Way by Tinu Abayomi-Paul

The false-balance trap by Paul Raeburn

Cheating in Online Courses by Dan Ariely

There’s only one truly open platform — the web by Mathew Ingram

The balance trap by Natasha Loder

Knit Together by Mindy Weisberger


Blogs of the Week so far:

May 11, 2012: Academic Panhandling
May 18, 2012: Anole Annals
May 25th, 2012: Better Posters
June 1st, 2012: Vintage Space
June 8th, 2012: Tanya Khovanova’s Math Blog
June 15th, 2012: Russlings
June 22nd, 2012: Parasite of the Day
June 29th, 2012: March of the Fossil Penguins
July 6th, 2012: Musings of a Dinosaur
July 13th, 2012: Contagions
July 21th, 2012: Life is short, but snakes are long
July 27th, 2012: Science Decoded

The Scienceblogging Weekly (August 4th, 2012)

Blog of the Week:

Beatrice the Biologist says this about itself: it is “part science blog, part comic, and part incoherent rambling: science edutainment at its finest.” Written – or rather drawn – by Katie McKissick, each post is a visual delight and will make you chuckle…and learn.


Top 10:

Gavin’s Story: Whole Exome Sequencing Finds Mystery Mutation by Ricki Lewis:

In a hotel ballroom on the campus of the University of Pennsylvania on a midsummer Saturday in 2010, an unusual roll call was under way at the Family Conference for the Foundation for Retinal Research. Betsy Brint, co-head of organization, was calling out what sounded like code words – CEP290, GUCY20, LRAT – and for each one, a few people would stand up, excited, then form little groups. After all 18 abbreviations had been called, representing the genes known to cause Leber congenital amaurosis (LCA), a few sets of parents were left standing. Troy and Jennifer Stevens, of Chino, California, were among those whose childrens’ genes and mutations were still a mystery….

Alain de Botton Tries Hand at Sex, Fails by AV Flox:

…..The next sections jump into “evolutionary-biological interpretation,” which we took to mean science, and which gave us the distinct impression that the author’s research of sex stopped at the work of William H. Masters and Virginia E. Johnson instead of starting there. That’s not surprising, though. ….

Even Deadly Snakes and Monkey Shit Couldn’t Stop Me From Excavating Maya Ruins in the Jungle by Charles Choi:

Snakes. In the ancient Maya ruins where I’m working at with archaeologists, the creatures we fear most are probably the snakes. That fact might sound like the punchline to an Indiana Jones joke, until you hear about the most dreaded serpent here in the jungles of Belize. The fer-de-lance is likely the deadliest snake in Latin America, packing an amputate-if-you’re-lucky bite if it goes untreated. Its long fangs can go right through a boot, and it’s aggressive – unlike many snakes that seem more afraid of us than we are of them, the fer-de-lance won’t hesitate to strike. ….

The importance of being Aquaman, or how to save the Atlantean from his briny fate by Andrew Thaler:

….There’s no way around it. Even with the huge amounts of heat Aquaman would produce as he burned through his daily 48,000 Calories, he is going to get cold. With little body fat and no fur to speak of, his heat retention potential is pitiful. Fortunately, there are plenty of simple solutions to the thermal problem. Unfortunately, almost all of them involve visible changes to his physique….

Moths, Memory, and Motivation by James Hathaway:

….We quickly found out that something that seemed simple – catching a bunch of pretty colored insects and putting them in boxes – was actually demanding and nearly endlessly complex and mysterious. A lot of the butterflies that were the coolest, the rarest, the most beautiful, lived in strange places – treetops, the edges of swamps and streams, sunlit clearings in deep woods – and only flew in certain seasons and specific times of the day – early spring, late afternoon. We learned why – mating rituals, foodplant availability, lifecycle requirements. We didn’t just read, we observed. We learned that the books were not always right – insects are really variable and behave differently in different locales. We developed hypotheses, collected information that supported or contradicted them. We learned, at least concerning a couple dozen species of butterflies in the part of upstate New York where we lived, how nature worked. Nature taught us the science we needed to use, and science taught us what there was to know. (Not that we knew enough to call it “science, “ of course.) It was like the world had opened up. ….

Pain Control by Shara Yurkiewicz:

She had only been in the hospital twice in her life: once when she was nine and now, 60 years later. She had gotten tonsils out then. She was getting tumors out now. Her abdomen hurt when she was awake. Her abdomen would also hurt during exploratory surgery, although she wouldn’t be able to feel it under general anesthesia. Her body would feel it, though, and could respond by dangerously spiking or plunging her vitals. She needed an epidural before surgery to keep the pain under control…..

Bad Chemistry by Deborah Blum:

The start of the story is this: In December 2008, a 23-year-old research assistant named Sheri Sangji accidentally set herself on fire while working in a chemistry laboratory at the University of California, Los Angeles. She died 18 days later in a hospital burn unit….

Is Childhood Pertussis Vaccine Less Effective Than We Thought? by Maryn McKenna:

Delicately and cautiously, health authorities in the United States and other countries are beginning to open up a difficult topic: Whether the extraordinary ongoing epidemic of whooping cough, the worst in more than 50 years, may be due in part to unexpected poor performance by the vaccine meant to prevent the disease….

Meet the people who keep your lights on and Blackout: What’s wrong with the American grid by Maggie Koerth-Baker:

Power was restored today in India, where more than 600 million people had been living without electricity for two days. That’s good news, but it’s left many Americans wondering whether our own electric grid is vulnerable. Here’s the good news: The North American electric grid is not likely to crash in the kind of catastrophic way we’ve just seen in India. I’m currently interviewing scientists about the weaknesses in our system and what’s being done to fix them and will have more on that for you tomorrow or Friday….

New OCD Symptom: Tail Chasing by Elizabeth Preston:

…Dogs with compulsion may pace, chase imaginary flies, or lick their flanks until they get sores, despite their owners’ best efforts to make them stop. Certain breeds are especially vulnerable. A staple of canine compulsion is tail chasing, which frequently strikes bull terriers and German shepherds. On one forum, user MatrixsDad complains that his German shepherd “is constantly chasing and barking at her tail…She comes up and puts her backside against anyone who’s standing around so she can get a better view of her tail before she starts chasing it.”…


Special topic 1: Jonah Lehrer

Jonah Lehrer’s Deceptions by Michael C. Moynihan

Jonah Lehrer Resigns From The New Yorker After Making Up Dylan Quotes for His Book by JULIE BOSMAN

The deception ratchet by Bradley Voytek

Jonah Lehrer, Bob Dylan, and journalistic unquotations and More unquotations from the New Yorker by Mark Liberman

Neuroscience author resigns from The New Yorker after admitting to fabricating Dylan quotes. by Paul Raeburn

Jonah Lehrer’s Grievous Oraculism by Ta-Nehisi Coates

Jonah Lehrer throws it all away by Roxane Gay

How we decide (to falsify). by Janet D. Stemwedel

Original thoughts? by Eva Amsen

Can cheaters repent? by Christie Aschwanden

Jonah Lehrer debacle lesson: Do your homework by Randy Lewis

‘It’s hard to start at the top,’ says Sharon Waxman of Jonah Lehrer by Steve Myers

What Jonah Lehrer reveals about popular science writing by Daniel Bor

Jonah Lehrer Turned His Back On Science by Khalil A. Cassimally

15 Minutes of Meaning for Jonah Lehrer by Alexis Madrigal

Why I Still Really Like Jonah Lehrer by J.S. Adams

On Bob Dylan And Jonah Lehrer, Two Fabulists by Ann Powers

Jonah Lehrer’s missing compass by Seth Mnookin


Special topic 2: Algebra

Abandoning Algebra Is Not the Answer by Evelyn Lamb

Does mathematics have a place in higher education? by Cathy O’Neil

When Andrew Hacker asks “Is Algebra Necessary?”, why doesn’t he just ask “Is High School Necessary?” by Rob Knop

Yes, algebra is necessary by Daniel Willingham

Why Algebra Matters (and Why Andrew Hacker is Off-Target) by RiShawn Biddle

“Is Algebra Necessary?” Are You High? by Blake Stacey

A modest proposal by PZ Myers

Algebra Is Necessary, But What About How It’s Taught? by Melanie Tannenbaum

It’s Not the Algebra, It’s the Arithmetic by Mike the Mad Biologist

On Algebra, High Expectations, and the Common Core by Dana Goldstein

The end of algebra by Alexandra Petri

Mathematical Illiteracy in the NYT by Mark C. Chu-Carroll

In Defense of Algebra by Evelyn Lamb

Scientific American Math Doc Defends Algebra Ed by Steve Mirsky

Why We Need m(x)+b: A Response to “Is Algebra Necessary?” by Erik Kimel


Best Images:

Macro photographs of snails and insects in the rain by Vadim Trunov

An ant that protects herself with… um… butt foam and More hanging larvae by Alex Wild

URI Sci Comms Day with Bora Zivkovic by Katie, PhD

Teaching Molecular Biology with Watercolors by Rachel Nuwer

Could a Whale-Powered Bus Be the Future of Transportation? by Rachel Nuwer

Hypogean Wildstyle: Dominik Strzelec’s Byzantine Geology by Paul Prudence

Quite Possibly the Cutest (Accurate) Dinosaur Illustration Ever by Annalee Newitz


Best Videos:

Watch 131 Years of Global Warming in 26 Seconds by Climate Central

Women in science … on television?!? Evidently not by Emily Willingham

Is There Life On Mars? by KPCC

Ben Goldacre at TEDMED 2012 by TEDMED

London Plague of 1665 by Michelle Ziegler

Field Biology: setting and baiting traps by DNLee

Twitter Algorithm Predicts When You’ll Get Sick (8 Days In Advance, With 90% Accuracy) [STUDY] by Shea Bennett

Curiosity (the New Mars Rover) Explained by phdcomics

100 Gallons: Reflections From A Nation Powered By Water by Powering A Nation

Best Anole Documentary Ever by Jonathan Losos

Sight by Eran May-raz and Daniel Lazo

How Did Apollo Astronauts Learn to Land on the Moon? by Amy Shira Teitel



Antibodies found in Peruvians suggest natural resistance to rabies in local vampire bats and NIH emerges with new emergency medicine research hub by Kathleen Raven

What’s next for scientific teaching? by Zen Faulkes

Deep-sea squid can break off all its arms onto an enemy by Ed Yong

Catching Fraud: Simonsohn Says and Why Don’t Social Scientists Want To Be Read? and Social Science and Language, Again and DSM-5 R.I.P? by Neuroskeptic

If You Compare Yourself With Michael Phelps, Will You Become A Better Swimmer? and We Won. They Lost. by Melanie Tannenbaum

A trustworthy guide to black hole astronomy by Matthew Francis

Velcro Hairs Allow Ants to Hang Their Larvae by Alex Wild

I, For One, Welcome Our New Fishy Overlords by Ian O’Neill

Is this study the bane of crypto-zoologists? by Esther Inglis-Arkell

Vacation Adventure: The La Brea Tar Pits by Erin Podolak

Are climate sceptics more likely to be conspiracy theorists? by Adam Corner

Michael Phelps, Losing the 400IM, and His Taper by Daniel Lende

What Is the Nocebo Effect? by Joseph Stromberg

Why do women leave science? by Zinemin

Muller is still rubbish by William M. Connolley

Breakthrough: The First Complete Computer Model of a Living Organism by George Dvorsky

How The Fukushima Exclusion Zone Shows Us What Comes After The Anthropocene by Colin Schultz

Interdisciplinarity, Heritability, and Public Policy by Kris Hardies

Why Dogs Chase Laser Beams (and Why It Can Drive Them Nuts) by Natalie Wolchover

The Hunter Hunted: Searching for the Body of an Anatomist by Lindsey Fitzharris

The Devil’s Technology by Ross Chapman

Lives of the Deaf by Jaipreet Virdi

Clouding the Olympic issue, China style by Claire

I want to ration your health care by PalMD

Galápagos Redux: When Is It OK to Kill Goats? by Virginia Hughes, Michelle Nijhuis and Jason G. Goldman

Broken heartland: The looming collapse of agriculture on the Great Plains by Wil S. Hylton

Why Experts are Almost Always Wrong by Rose Eveleth

Work-Life Balance for Whom? by Athene Donald

Stiletto snakes by Andrew Durso

New Lights to Help ISS Astronauts Stay Alert by Liat Clark

The Vomit-Inducing Gemini 8 Mission and NASA’s Manned Grand Tour of the Inner Planets by Amy Shira Teitel

Artificial Beginnings: Understanding the Origin of Life by Recreating It by Eric Sawyer

To know a tiger is at least to start tolerating them, study shows and Tigers, people, and finding ways for both to thrive by Sue Nichols

Higgs Discovery: Personal Reflections by Matt Strassler

Did Gymnast Jordyn Wieber Perform Too Soon? In Olympic scoring, the last shall be first. by Karla Starr

Chop Like A Girl by Michelle Nijhuis

Curiosity readies for dramatic entrance and Mission control before the party and Curiosity to look for habitable environs by Nadia Drake

Why is Pluto not a planet? by Tristan Avella

Once upon a time: The possible story of viruses by Audrey Richard

How to pronounce “Muller’s Ratchet” by Jon Wilkins

The evolution of music by James Gaines

Sex testing and the Olympics: myths, rumours and confirmation bias by Vanessa Heggie

Light Pollution’s Potentially Harmful Effects Highlighted In New Film by Lynne Peoples

Taking the scenic route by Kelly Slivka

wesome Harry Potter Fan Decodes Wizarding Genetics: It’s All About Trinucleotide Repeats by Susana Polo

How the Elephant Makes Its Rumble by Veronique Greenwood

Swiss sheep to be outfitted to cry ‘wolf’ by text message by Agence France-Presse

TGIPF: Sex When You Can’t Hang On by Erik Vance

Human cycles: History as science by Laura Spinney

A HOT topic in transit by Taylor Kubota

Stiletto snakes by Andrew Durso


Media, Publishing, Technology and Society:

Imagining a ‘World Without Patents’… by Mark Summerfield

Five years as a science blogger – my experiences and how it began by Stephan Schleim

9 Reasons Why Running A Science Blog Is Good For You by Julio Peironcely

Top ten tips for blogging for scientists by Paul Knoepfler

The art and craft of science blogging by Daniel Blustein

Science Reporting Gone Wrong by Paige Brown

Reddit as a Science Outreach Tool by Brian Kahn

Setting Sail Toward a Science Communications Career by Liz Neeley

Journalists slow the environmental debate by Mari Kildahl

The journalistic method: Making the jump from science to journalism by Jessica Morrison

Does journalistic ‘balance’ hurt America? by Trudy Lieberman

The missing millions of Kibera and Kidnapped at birth and Grandma Obama’s support for domestic violence by Martin Robbins

#riscweet! How to Effectively Communicate Science on the Web by Viet Le

A New Age for Truth by Craig Silverman

Big data is our generation’s civil rights issue, and we don’t know it by Alistair Croll


Blogs of the Week so far:

May 11, 2012: Academic Panhandling
May 18, 2012: Anole Annals
May 25th, 2012: Better Posters
June 1st, 2012: Vintage Space
June 8th, 2012: Tanya Khovanova’s Math Blog
June 15th, 2012: Russlings
June 22nd, 2012: Parasite of the Day
June 29th, 2012: March of the Fossil Penguins
July 6th, 2012: Musings of a Dinosaur
July 13th, 2012: Contagions
July 21th, 2012: Life is short, but snakes are long
July 27th, 2012: Science Decoded

The Scienceblogging Weekly (July 27th, 2012)

Blog of the Week:

Science Decoded is a wonderful mix of science, book reviews, and thoughts about the media, written by Erin Podolak, alumna of the University of Wisconsin program for Science Journalism, and now a science writer for The Dana-Farber Cancer Institute.


Top 10:

A Killer Without Regret by Deborah Blum:

In the summer of 1920, a 29-year-old son of Minnesota farmers docked his boat (acquired with stolen money) at a small island in New York City’s East River. One by one he hired out-of-work sailors to crew for him. And one by one, he shot them in the head with a Colt .45 and dumped their bodies in the water. Before he was executed in 1930, Carl Panzram put the sailor body tally at 10 although he estimated that was only about half his total murder count. “For all these things, I am not in the least sorry,” he wrote in a jail house confessional. “I was so full of hate that there was no room in me for such feelings as love, pity, kindness or honor or decency.”…

The marathon & Olympic movement on Huffington Post by Greg Downey:

Many people think they know the story of the very first ‘marathon.’ Pheidippides, reputedly the fastest man in the Greek army, allegedly ran from the battlefield at Marathon twenty-five miles to Athens in 490 BCE to announce a Greek victory over the invading Persians. Bolting into the Athenian assembly, he shouted, νικωμεν (nikomen), ‘We have won!’ and promptly keeled over dead….

Galápagos Monday: The People Problem by Virginia Hughes:

…Two-thirds of the jobs on the islands are in the service sector. The tourists come, of course, because of the amazing plants and animals. They contribute money directly to conservation efforts, and their patronage boots the economy and allows the government to set up its own conservation management systems. That’s all great, except — more people also means more: ships, construction, roads, vehicles, hotels, restaurants, water and energy use, garbage, and sewage. All of that threatens the habitats and health of the plants and animals. In other words, the whole thing is unsustainable. The growing economy in the Galápagos is simultaneously supporting more science and conservation efforts and destroying the things that need to be studied and conserved. The economy is eating itself….

Geometry Proves Sheep Are Selfish Jerks by Elizabeth Preston:

Sometimes what looks like friendly behavior is really an attempt to get one’s neighbor eaten by a wolf before oneself. Sheep, for instance, seem cozy enough in their flocks. What’s a better way to travel than surrounded by 100 percent merino? But the real reason they stick close to their neighbors is to save their own woolly rear ends…

Noisy sex means death for flies if bats are listening by Ed Yong:

Some folks just can’t help being loud in bed, but noisy liaisons can lead to a swift death… at least for a housefly. In a German cowshed, Natterer’s bats eavesdrop on mating flies, homing in on their distinctive sexual buzzes….

Wisconsin frac sand sites double by Kate Prengaman:

Tucked behind a hill in rural Trempealeau County, farmland undergoes an industrial transformation. Outside this city of 1,300, Preferred Sands turns Wisconsin’s sandy soil into a hot commodity. A wall of green trees opens to a vast expanse of sand buzzing with activity. Excavators mine and conveyors carry the sand from towering stockpiles up into the processing plant. Every week, this facility ships 7,500 tons of sand by rail to oil and gas fields in Texas, North Dakota and Pennsylvania. …

Language Serves the Group by Edmund Blair Bolles:

Steven Pinker has posted an important essay on group selection. You can gather its thesis from the title, “The False Allure of Group Selection.” Since I am on record saying that group selection (really, multilevel selection) was critical to the evolution of language, I read the essay with strong interest. Let me say right off that I was astonished to find that the essay makes no remarks about the evolution of language. Pinker is a famous proponent of language’s evolutionary origins and biological basis, but he says nothing of group selection and language. Instead he criticizes ideas that group selection explains religion, culture, and nations. I am skeptical of those claims too. Pinker is a fine writer and I got several chuckles out of his examination of various shallow appeals to group selection. Was I laughing at my own doom?…

Ending the AIDS epidemic by John Rennie:

Thirty-one years into the HIV epidemic, health authorities are finally starting to sound hopeful about the prospects for curbing it. If that sentence sounds bitter or sarcastic, it isn’t meant to be. Rather, it’s an honest assessment of how long and frequently depressing the era of HIV and AIDS has been, and of how much misery it has spawned. But it also acknowledges reasons to think that maybe, just maybe that’s beginning to change….

Ending U.S. chimpanzee laboratories will save chimpanzee research by Brian Hare:

…The non-lab research model has now become the dominant research model. In my area of research a collection of just five zoos and African sanctuaries recently published more scientific papers in higher impact journals than all five active U.S. chimpanzee laboratories. These non-lab researchers contributed data relevant to fighting HIV, Malaria, Parkinson’s, Autism, Alzheimer’s, and a myriad of other human ailments. They did this while studying chimpanzees that live life freely in extremely enriched environments. …

One way to successfully invade a habitat: eat the competition by Jeremy Yoder:

The Asian Harlequin ladybug, Harmonia axyridis, eats aphids like they’re Popplers, and it’s been repeatedly introduced into the U.S. and Europe to do exactly that. But since it was first introduced, H. axyridis has spread of its own accord, and displaced native ladybugs. This isn’t just because the Harlequin ladybug eats more aphids, or breeds faster, than the locals; it looks like part of the Harlequin’s success is due to the fact that it eats its native competition….


Special topic: Sally Ride

American Astronaut Sally Ride Dies at 61 by John Matson

Remembering Sally Ride by Nadia Drake

Sally Ride’s Astronaut Class Completely Changed NASA’s Demographics by Amy Shira Teitel

What Sally Ride Did For STEM Education by Austin Carr

Sally Ride’s Space Flight Was Not Exactly A Great Moment for Feminism by Laura Helmuth

The Women Who Would Have Been Sally Ride by Alexis Madrigal

Rest in peace, Sally Ride by Matthew Francis

First Female U.S. Astronaut, Sally Ride, Comes Out In Obituary by Chris Geidner

Sally Ride by The AstroDyke

Why Aren’t There Any Openly Gay Astronauts? by Natalie Wolchover

Thank you, Sally Ride by Meg Urry


Best Images:

Sketching at the American Museum of Natural History by Marissa Fessenden

Manatees by Jen Richards

Sunday Morning Anole Cartoon by Rich Glor

Anole Photo Of The Day by Jonathan Losos

Sharks, Art, and Conservation by Heather Goldstone

Dapper Days in China by peacay


Best Videos:

MIT video models airports most likely to spread diseases by Kathleen Raven

Leprosy Facts: Ancient Disease Still In Our Midst by Cara Santa Maria

The Art of Hatching by Allison DeVan

Bear Cam: Watch Brown Bears Catch Salmon in Alaska by Tanya Lewis

Why Whales are Weird by Joy Reidenberg

Ask Jay Rosen Anything: What Does Political Journalism Get Wrong? Get Right? by Andrew Sullivan

Olympicene – Periodic Table of Videos by periodicvideos



Science on crack: the chemistry of illegal drugs, 1 by Puff the Mutant Dragon

The International AIDS Conference Returns: So Much Still To Do by Maryn McKenna

“We took a rat apart and rebuilt it as a jellyfish.” and Aging termites put on suicide backpacks full of chemical weapons by Ed Yong

How Do You Choke Away the British Open? The Science of the Tight Collar by David Dobbs

A Brief History of the Eustachian Tube and The Catheter by Jaipreet Virdi

The Secret Life of Western Corn Rootworm Beetles by James Hamblin

Soccer’s Big Data Revolution by Khalil A. Cassimally

FDA advisory panel looks positively on new eye drug by Kathleen Raven

Autism Outreach on Wheels: Students Design Mobile Clinic for A.J. Drexel Autism Institute by Rachel Ewing

Batman Movies Don’t Kill. But They’re Friendly to the Concept. and Batman Returns: How Culture Shapes Muddle Into Madness by David Dobbs

Inside the Minds of Mass Killers by Daniel Lende

How Urban Parks Enhance Your Brain by Eric Jaffe

World’s Coolest Animal Bridges and Should Dolphins and Whales Have Human Rights? by Rachel Nuwer

How Aldous Huxley, 118 Today, Predicted the Present Far More Accurately than George Orwell and Mapping Afghanistan’s Geology from Really, Really Far Away by Rose Eveleth

There is no greenhouse effect by Robert Grumbine

And Finally the Hounding Duck Can Rest by Carl Zimmer

What’s next for scientific teaching? by Zen Faulkes

Speciation in Bears by Larry Moran

Scientists make curing HIV a priority by Erin Loury

New Study Suggests Humans, Not Climate, Killed Off Neanderthals by Colin Schultz

When Bad Theories Happen to Good Scientists by Matt Ridley

Lemurs Most Threatened Mammals on the Planet by Karl Leif Bates

A year of anarchy in science by Michael Brooks

The Secrets of Geek Mating Rituals by Annalee Newitz

On Leaving Academia by Terran Lane

How Not to Counsel Smokers by Lucy E. Hornstein

The Colorado shooting suspect: how “smart?” by David Kroll

Why don’t we consume dairy products from mammals that aren’t cows? by Benjamin Phelan

Can Sleep Deprivation Cause Psychotic Behaviour? by Romeo Vitelli

Is Mythology Like Facebook? by John Bohannon

Crossing valleys in fitness landscapes by Bjørn Østman

How NFL and NBA cheerleaders and citizen scientists came together. by Darlene Cavalier

Unraveling the left brain/right brain theory by Amanda Mascarelli

The Aurora Shootings and The Mean World Syndrome by David Ropeik

What is this “Mass Spectrometer”? by Penny Higgins

Shark Teeth Have Built-In Toothpaste by Jennifer Viegas

Meet the Skeptics: Why Some Doubt Biomedical Models – and What it Takes to Win Them Over by Kristin Sainani

The Stoneflies: Old or New? by Christopher Taylor

Wrong for the Right Reasons by Matthew Martyniuk

Search Trends Reveal Sexual Seasons and A Case Study in Voodoo Genetics by Neuroskeptic

The brewer’s yoke, the domestication of microbes by A Schooner of Science

The horrible truth about Spiderman’s Anatomy by Bug Girl

Nixon’s Contingency Plan for a Failed Apollo 11 by Amy Shira Teitel

Once an Archaeologist…? Plan B Careers in Archaeology by Becky Wragg Sykes

Diagnosing the Killer in Colorado by Deborah Blum

Olympic Physics: Tennis and Olympic Physics: Diving by Matt Shipman

It Takes an 8-Year-Old to Outsmart a Crow by Elizabeth Preston

Why You Can’t Fake A Good Horn by Carl Zimmer

“The Redder the Better” . . . Sometimes by Anne-Marie Hodge

Exploring the Mind of the Mountain Gorilla by Kimberly Gerson

Cuts loom for US science by Ivan Semeniuk & Helen Thompson

Skepticism And The Second Enlightenment by Kyle Hill

Greenland Melt Was Predicted In Advance By Paper Awaiting Publication by Dan Satterfield

Drought hurts shipping industry, raises prices by Mollie Bloudoff-Indelicato

Olympic Pseudoscience by Steven Novella

Velcro Hairs Allow Ants to Hang Their Larvae by Alex Wild

Circadian Rhythms: Our Eyes, Our Rhythms by Anita Slomski

Scientists in North Carolina will take close look at ants from Chicago by Jessica M. Morrison

DIYBio: Placenta Stem Cells for Research and More by Ada Ao

Beginnings – three simple words by Pete Etchells

Why climate change doesn’t spark moral outrage, and how it could by David Roberts

TGIPF: The Bed Bug and His Violent Penis by Brooke Borel


Media, Publishing, Technology and Society:

The Making of PeerJ and Open Science, SciBarCamp and Les Horribles Cernettes by Graham Steel

Thomas Friedman’s Lessons for Anthropologists by Daniel Lende and Greg Downey

ABC News: armchair psychologist: The network offers irresponsible speculation about the Colorado shooter by Curtis Brainard

How We Play Today by Jamie Rosenberg and George Myers

Anatomy of a Zombie Lie… by Tom Levenson

Grief in the Age of Social Media by Callie Schweitzer

A Self-Made Man Looks At How He Made It by John Scalzi

Another science startup that’s changing how research is done. An interview with Elizabeth Iorns of Science Exchange. by William Gunn

If you email it, they will comment and No Comment? by Ethan Perlstein

Blogging expertise by Zen Faulkes

Explaining the news through song: A personal case study by David Holmes

Taming the Impact Factor by Iddo Friedberg

The dark side of data by Mike Loukides

The Death Of SEO: The Rise of Social, PR, And Real Content by Ken Krogue

Blogging, Tweeting, and Other Digital Activities: A Beginner’s Guide to the Internet for Early-career Scholars by Melinda Baldwin

Enduring lessons from being fired 20 years ago by Steve Buttry

Social Media and the Science Classroom, a Twitter Discussion by Michele Arduengo

What Users do with PLOS ONE Papers by Martin Fenner

The Great Sieve: This Is What Browsing Scientific Research Looks Like by Rebecca J. Rosen

Content Factor: A Measure of a Journal’s Contribution to Knowledge by Joseph Bernstein and Chancellor F. Gray

Meet Lena Groeger: @ProPublica’s newest news app developer by Elizabeth R. Miller

Who should see what when? Three principles for personalized news by Jonathan Stray

Predicting the growth of PLoS ONE by Najko Jahn

UK government will enforce open access to development research by Alok Jha

Who’s Talking About ScienceOnline? Interactive Map Of 1000 #Scio13 Twitterers by Mary Canady

An open Twitter-like ecosystem by Dave Winer

A new era for the Nature Network blogs by Lou Woodley

Why a high Google rank is becoming ‘worthless’ by Brad Shorr

BuzzFeed’s strategy by Chris Dixon

ScienceOnline Project Postcard by Karyn Traphagen

Bunch of Fives – Why Blogging is Great, and Tips for Starting by Suzi Gage

How BuzzFeed wants to reinvent wire stories for social media by Justin Ellis

The State of Educational Blogging in 2012 by Sue Waters

How journalists can do a better job of correcting errors on social media by Craig Silverman

Sharing stories with sources before publication is risky, but can improve accuracy and To show or not to show? by Steve Buttry

Quantifying impact: A better metric for measuring journalism by Greg Linch

Going paperless: eliminate stacks of paper by converting paper magazine subscriptions to digital subscriptions by Jamie Todd Rubin

Are You Reading These 17 Science Blogs? You Should by Julio Peironcely

No credit for Uncle Sam in creating Net? Vint Cerf disagrees by Charles Cooper

They Didn’t Build That by Paul Krugman

So, who really did invent the Internet? by Michael Hiltzik

WSJ mangles history to argue government didn’t launch the Internet by Timothy B. Lee



Blogs of the Week so far:

May 11, 2012: Academic Panhandling
May 18, 2012: Anole Annals
May 25th, 2012: Better Posters
June 1st, 2012: Vintage Space
June 8th, 2012: Tanya Khovanova’s Math Blog
June 15th, 2012: Russlings
June 22nd, 2012: Parasite of the Day
June 29th, 2012: March of the Fossil Penguins
July 6th, 2012: Musings of a Dinosaur
July 13th, 2012: Contagions
July 21th, 2012: Life is short, but snakes are long

The Scienceblogging Weekly (July 21th, 2012)

Blog of the Week:

Life is short, but snakes are long is written by Andrew Durso who is a PhD student at Utah State University, where he studies the behavior, physiology, and ecology of toad-eating snakes. So, everything on his blog is about snakes. And every post on his blog has something about snakes that you have not known before.


Top 10:

Global Warming’s Terrifying New Math by Bill McKibben:

If the pictures of those towering wildfires in Colorado haven’t convinced you, or the size of your AC bill this summer, here are some hard numbers about climate change: June broke or tied 3,215 high-temperature records across the United States. That followed the warmest May on record for the Northern Hemisphere – the 327th consecutive month in which the temperature of the entire globe exceeded the 20th-century average, the odds of which occurring by simple chance were 3.7 x 10-99, a number considerably larger than the number of stars in the universe…

The Mystery of the Missing Chromosome (With A Special Guest Appearance from Facebook Creationists) by Carl Zimmer:

There’s something fascinating about our chromosomes. We have 23 pairs. Chimpanzees and gorillas, our closest living relatives, have 24. If you come to these facts cold, you might think this represented an existential crisis for evolutionary biologists. If we do indeed descend from a common ancestor with great apes, then our ancestors must have lost a pair after our lineage branched off, some six million years ago. How on Earth could we just give up an entire chromosome….

Are Warnings About the Side Effects of Drugs Making Us Sick? by Steve Silberman

Your doctor doesn’t like what’s going on with your blood pressure. You’ve been taking medication for it, but he wants to put you on a new drug, and you’re fine with that. Then he leans in close and says in his most reassuring, man-to-man voice, “I should tell you that a small number of my patients have experienced some minor sexual dysfunction on this drug. It’s nothing to be ashamed of, and the good news is that this side effect is totally reversible. If you have any ‘issues’ in the bedroom, don’t hesitate to call, and we’ll switch you to another type of drug called an ACE inhibitor.” OK, you say, you’ll keep that in mind…..

Battling antivaccinationists at FreedomFest by Orac:

Like so many other skeptics, I just returned from TAM, which, despite all the conflict and drama surrounding it this year, actually turned out to be a highly enjoyable experience for myself and most people I talked to. As I’ve been doing the last few years, I joined up with Steve Novella and other proponents of science-based medicine to do a workshop about how difficult it is to find decent health information on the Internet, and how the “University of Google” all too frequently puts quackery on the same level as reliable sources of medical information because all that matters for most search engines when it comes to ranking search results is the number and kinds of sites that link to a given site…..

Epic fraud: How to succeed in science (without doing any) by John Timmer:

Running scientific experiments is, frankly, a pain in the ass. Sure, it’s incredibly satisfying when days or weeks of hard work produce a clean-looking result that’s easy to interpret. But often as not, experiments simply fail for no obvious reason. Even when they work, the results often leave you scratching your head, wondering “what in the world is that supposed to tell me?” The simplest solution to these problems is obvious: don’t do experiments….

One Molecule for Love, Morality, and Prosperity? by Ed Yong:

Imagine a molecule that underlies the virtues that glue societies together. Imagine that it brought out the better angels of our nature with just a sniff and could “rebond our troubled world.” Imagine that it was the “source of love and prosperity” and explained “what makes us good and evil.” Well, carry on imagining. This is a story about oxytocin, and oxytocin is not that molecule….

How We Changed Penguins Just by Watching by Elizabeth Preston:

If a penguin falls in the forest and no one is there to hear it, I don’t know what kind of forest that is—but everyone who’s interested in penguins is probably hanging out a lot closer to the South Pole. The charismatic birds let scientists and tourists alike get a close look without too much trouble. And all that familiarity has the potential to change penguins, and other closely watched animals, for good….

What Would Happen If a Lion Fought a Tiger? by Natalie Wolchover:

This ultimate cat fight has happened more times than you might expect. The Romans pitted African lions against Asian tigers in the Coliseum, to the rip-roaring pleasure of the Plebeians. A few fights were also staged in the early decades of the 20th century, and on several modern occasions, accidental cross-species encounters at zoos have quickly developed into gruesome scenes guaranteed to scar any nearby schoolchildren for life. But how do these lion versus tiger showdowns go down?…

In Search of Grote Reber by Matthew Francis:

Unlike most sites where the business of cosmology is done, Fermi National Accelerator Laboratory—known colloquially as Fermilab—isn’t in a remote spot. The facility is in Batavia, Illinois, part of the sprawling metroplex of Chicago, and it’s just a short drive from two major tollways. The Standard Model describes a plethora of particles, but it has nothing on the number of fast-food joints and auto shops within ten minutes’ drive of the Fermilab gates. My friend hosting me during my stay in Illinois wasn’t even aware of the lab’s location, despite having friends living close by—the area around it is that dense…

Dancing in digital immortality: The evolution of Merce Cunningham’s “Loops” by Ashley Taylor:

The modern dancer and choreographer Merce Cunningham died in 2009, and his company gave its final performance at the end of last year. Many of his dances will live on in the memories of former company members who go on to restage them. But there’s one solo, “Loops,” that Cunningham never taught to another dancer. This piece lives on through a different medium: digital motion capture…


Special topic: Science of Superheros

Batman and Gotham: A Deeply Dysfunctional Love Story by Adam Rogers

The horrifying physiological and psychological consequences of being Aquaman by Southern Fried Scientist

Dear Science, leave Aquaman alone! by AmasianV

Why Aquaman is the best damn superhero in comic history by Cyriaque Lamar

Physics Shows Batman’s Cape Is Suicide Machine by Liat Clark

The Fall and Rise of the Dark Knight-the Difficulties of Batman’s Life While He Exists by E. Paul Zehr

Science sways superheroes by Alan Boyle


Best Images:

The Goddamned Particle by Perrin Ireland

Your Skeleton – on the Internet by Daniel Lende

Animals With Misleading Names by Rosemary Mosco

The Bizarre, Breathtaking Science Photos of Fritz Goro by Tanya Lewis

American World War II Plague Posters by Michelle Ziegler

Beautiful biodiversity illustrations by Becca Stadtlander


Best Videos:

Friday Science Cinema by Justine E. Hausheer

When astronomers get video cameras…… by Niall

NSF Rhode Island Video Boot Camp participant Dr. Sunshine Menezes delivers her message. by NSFMessengers

Tagging Giants: Studying Whale Sharks in Cendrawasih Bay by Mark Erdmann

Variety is the Spice of Lice by TheFieldMuseum

Five Men Agree To Stand Directly Under An Exploding Nuclear Bomb by Robert Krulwich

Chuck Norris, tapeworms, and the future of science: video of my keynote talk by Carl Zimmer



Patients, Prisoners, and Mass Shootings — A Timeline by David Dobbs

Gorilla Youngsters Seen Dismantling Poachers’ Traps—A First by Ker Than

Life on the Leg of a Crab by Craig McClain

Can you Shoot an Arrow Backwards – into Space? by David Dilworth

How to “downplay the achievements of science” by Eoin Lettice

Why Facial Disfigurements Creep Us Out by Joseph Bennington-Castro

Wisconsin’s Sand Rush by Kate Prengaman

A Way to Trap Carbon Deep in the Ocean and City Officials Declare War on Lawn Gardens by Rachel Nuwer

From Living Room to Lily Pad: Is the Fatal Amphibian Chytrid Fungus Spread via Pet Frogs? by Sarah Fecht

Just good friends? Attraction to opposite-sex friends is common but burdensome by Christian Jarrett

Just My Luck (or is it?) by David Nussbaum

The Bra Is 500 Years Older Than We Thought and 400 Years Worth of Water Discovered in Sub-Saharan Namibia by Colin Schultz

Learning from the Tubeworm by Michelle Nijhuis

The Real Life of Pi by Noby Leong

How would you like to sleep with the fishes? by aranyak

‘Get Over It’: Climate Change Is Happening by Eric Roston

Recycling the Seasons by Erin Gettler

Fusing chromosomes by John Hawks

No sweet outcome for PhD worker bees by Elizabeth Gibney

Q&A With Mariette DiChristina: Born a Scientist by Jeanne Garbarino

Lion’s Mane Jellyfish Image: This Is (Literally) How Things Blow Up On The Internet! by Anthony Wing Kosner

The Endless Summer by Mark Bittman

Performance enhancement: Superhuman athletes by Helen Thompson

Discovery of ‘God particle’ has UNC roots by Samuel Mason

Just the facts ain’t enough, ma’am by Wilson da Silva

Artificial Volcanoes Aren’t the Solution to Warming by Erik Klemetti

Dolphins May Be Math Geniuses by Jennifer Viegas

New Science Emboldens Long Shot Bid for Dolphin, Whale Rights by Brandon Keim

What it’s Like to Witness a Grunion Run by Jason Goldman

Everything Is a Remix: The Sound of Horses Racing on TV Is Actually a Sample of Buffaloes Charging and Exploding Chocolate, Poisoned Scuba Suits, and the Bulgarian Umbrella: A Survey of Strange Assassination Tech by Alexis Madrigal

Secrets of the clam tongue: a case study in opportunistic science outreach and New nightmare fuel: the giant scaleworm Eulagisca by Miriam Goldstein

Pardon me–is this stool taken? by Bug Girl

10 species named after famous people by Bethan Jinkinson

Pancakes, served with a side of science by Aatish Bhatia

One fish, two fish and 400,000 zebrafish by Kathleen Raven

The Dirty Dozen: A wish list for psychology and cognitive neuroscience by Chris Chambers

Brain Scanning… Or Vein Scanning? by Neuroskeptic

What was the oldest Olympic sport? by Greg Laden

Dr Hornstein hasn’t gone the way of the dinosaur by Lucy Hornstein

Science Metaphors (cont.): Sub-Grid Physics by Ann Finkbeiner

Will we ever run the 100 metres in 9 seconds? by Ed Yong

Dinosaur Aunts, Bacterial Stowaways, & Insect Milk by Katie Hinde

Geneticists Evolve Fruit Flies With the Ability to Count by Liat Clark

Scientists take a bird’s eye view to prevent bird-aircraft collisions by Allie Wilkinson

Technique gets clear images from light reflected off blank paper by Matthew Francis

Vitamin D gets frequent testing, but the results are a bit quizzical by Jessica M. Morrison

How Placebo’s Evil Twin Makes You Sicker by Elizabeth Preston

Galápagos Monday: When Conservation Means Killing by Virginia Hughes

‘Canopy Meg’ wants you to care about the rainforest by Samantha Larson

Person With Autism Manages To Do Something by Zoe

Using zombies to teach science by Tara C. Smith

Ecomorphs Converge On Suites Of Correlated Traits by Yoel Stuart

Is Society Becoming Over-Medicalized? Interview with Executive Editor of Reuters Health, Dr. Ivan Oransky by Shiv Gaglani

How land-inefficient is organic agriculture? by Mark Lynas

Record Heat Wave Pushes U.S. Belief in Climate Change to 70% by Mark Drajem


Media, Publishing, Technology and Society:

That plan to archive every tweet in the Library of Congress? Definitely still happening by Andrew Phelps

More on the Library of Congress and Twitter by Dave Winer (also see my Science Blogs – definition, and a history)

v1 by Rethink Digg

Example Visualizations using the PLoS Search and ALM APIs and More fun with Visualizations by Martin Fenner

ScienceWriters2012: The NC Scouting Report by Rosalind Reid

Could the iPad save magazines? by Molly Mirhashem

The techies in journalism are not the problem by Anna Tarkov

Readership of papers vs. blog posts by Jeremy Fox

Why Flip The Classroom When We Can Make It Do Cartwheels? by Cathy N. Davidson

Higgs this, boson that by Richard Panek

Beginner Blogging – The Prequel by Renee Dobbs

Power to the People (When it Comes to Funding Research) by Aurélie Coulon

Curation techniques, types and tips by Steve Buttry

No Internet For One Year: Tech Writer Tries Life Offline by Joanna Stern

Why Dave Winer Invented the Blog and How blogging came to be by Dave Winer

Introducing #smarttakes: pop-up aggregation from the Guardian by Ruth Spencer

‘False Balance’ in Some Coverage of Carolina Sea-Level Controversy by Sara Peach

Brought to book: Academic journals face a radical shake-up by The Economist

All’s Not Fair in Science and Publishing by Frederick Southwick

Let journalists do their jobs by David Wescott

How Academics Face the World: A Study of 5829 Homepage Pictures by Owen Churches, Rebecca Callahan, Dana Michalski, Nicola Brewer, Emma Turner, Hannah Amy Diane Keage, Nicole Annette Thomas and Mike Elmo Richard Nicholls

MIT Economist: Here’s How Copyright Laws Impoverish Wikipedia by Robinson Meyer

Why ‘future of journalism’ confabs fail by Alan D. Mutter

Why paywall journalism is changing how journalists write by Tim Burrowes

ProPublica gets $1.9 million from Knight to expand its efforts in data journalism by Adrienne LaFrance

The trouble with content by Jeff Jarvis

The Scholar’s Frenemy by PHLane

Dealing with Edits and Comments by hurleybirds

Don’t Have Time to Tweet-bollocks! Twitter can even save you time as a scientist. by Scott Wagers

Communicating science in the age of the internet by Deevy Bishop

Laptops in Lecture? by Rhett Allain

What was the first science blog? by Paul Raeburn

Scientific particles collide with social media to benefit of all by Marie Boran

On science blogs this week: Scandal by Tabitha M. Powledge

Standing on the Shoulders of Bloggers: Carnival frustration searing my soul. by Thony Christie

The Rise of Open Science by Roger Câmara

The Web Is Not the Internet (You’re Probably Getting That Wrong) by Abraham_Riesman

Delete the Save Button by Farhad Manjoo

How Reddit Became the Internet’s Vigilante Voltron by Wylie Overstreet



Blogs of the Week so far:

May 11, 2012: Academic Panhandling
May 18, 2012: Anole Annals
May 25th, 2012: Better Posters
June 1st, 2012: Vintage Space
June 8th, 2012: Tanya Khovanova’s Math Blog
June 15th, 2012: Russlings
June 22nd, 2012: Parasite of the Day
June 29th, 2012: March of the Fossil Penguins
July 6th, 2012: Musings of a Dinosaur
July 13th, 2012: Contagions

The Scienceblogging Weekly (July 13th, 2012)

Blog of the Week:

Contagions is a blog written by Michelle Ziegler (Twitter, Facebook, the other two blogs by Michelle – Heavenfield and Selah – are focused entirely on history and not on medicine or science). In Contagions, Michelle explores infectious disease – there is a lot about the Plague – from history to epidemiology to most recent scientific papers. Sometimes gruesome, always fascinating.


Top 10:

Is Autism an “Epidemic” or Are We Just Noticing More People Who Have It? by Emily Willingham:

In March the US Centers for Disease Control and Prevention (CDC) the newly measured autism prevalences for 8-year-olds in the United States, and headlines roared about a “1 in 88 autism epidemic.” The fear-mongering has led some enterprising folk to latch onto our nation’s growing chemophobia and link the rise in autism to “toxins” or other alleged insults, and some to sell their research, books, and “cures.” On the other hand, some researchers say that what we’re really seeing is likely the upshot of more awareness about autism and ever-shifting diagnostic categories and criteria….

New technique identifies magnetic cells in animals by watching them spin by Ed Yong:

A migrating robin can keep a straight course even when it flies through a cloudy night sky, devoid of obvious landmarks. That’s because it can sense the Earth’s magnetic field. Something in its body acts as a living compass, giving it a sense of direction and position. This ability – known as magnetoreception – isn’t unique to robins. It’s been found in many other birds, sharks and rays, salmon and trout, turtles, bats, ants and bees, and possibly cows, deer and foxes. But despite more than 50 years of research, the details of the magnetic sense are still elusive….

The Sex Scholar by Kara Platoni:

Decades before Kinsey, Stanford professor Clelia Mosher polled Victorian-era women on their bedroom behavior—then kept the startling results under wraps….

Bloggers and Bowerbirds by Erin Kissane:

There are still a lot of elbows being thrown in the squabble about “creation” versus “curation,” and it seems to be getting worse. As humans tend to do, we’re talking past each other and pretending to simplicity in the face of the complex and the weird. Here’s what I think is going on. I think we’re getting tripped up by two things: clumsy language and a misapprehension about competition for limited resources….

Citations, Social Media & Science by Morgan D. Jackson:

This morning I was reading a newly published paper that I found intriguing, not only for its content1 but also for who it cited — sort of. Among the regular cadre of peer-reviewed journal articles supporting the author’s findings were two blog posts by University of Glasgow professor Roderic Page. Rod is a major proponent for digitizing and linking biodiversity literature with all aspects of a species’ pixel-trail across the internet, so I was excited to see his blog being “formally” recognized. As I finished reading the paper and reached the References section, I skimmed through to see how a blog citation might be formatted. Much to my dismay, after breezing through the L’s, M’s, and N’s I found myself within the R’s, with nary a Page in sight…

Investigation: Drug Resistance, Chicken And 8 Million UTIs by Maryn McKenna:

…I’ve been working with a great new group, the Food and Environment Reporting Network — one of the grant-funded journalism organizations that have arisen in the wake of the collapse of mainstream journalism — on an important, under-reported topic. Which is: Over the past decade, a group of researchers in several countries have been uncovering links between the use of antibiotics in chicken production and the rising occurrence of resistance in one of the most common bacterial infections in the world. The infection in question is UTI, which just about every woman I know will recognize: It stands for urinary tract infection, and on average one out of every 9 women in the United States suffers one at least once per year. There are 6 million to 8 million UTIs in the US each year, costing at least $1 billion in healthcare spending….

The hows and whys of human attraction by Barbara J. King:

Robin Dunbar may not be a household name, but some of his thinking has reached the status of household ideas. You’ve heard that 150 is an approximate upper limit on the number of our family-and-friend relationships because that’s how many connections we can track? That’s Dunbar. You’ve read the theory that language evolved as a sort of replacement for hands-on grooming among our primate relatives when group size got big? That’s Dunbar too. Now, in The Science of Love and Betrayal, Dunbar, who is Professor of Evolutionary Anthropology at Oxford, asks seductive questions about love and friendship. Why do men and women pair-bond when so many other animals don’t? How do biology and sociality intersect in explaining human attraction to others? …

Crimes and Misdemeanors: Reforming Social Psychology by Dave Nussbaum:

The recent news of Dirk Smeesters’ resignation is certainly not good news for social psychology, particularly so soon after the Diedrik Stapel case, but I believe it can serve as an opportunity for the field to take important steps towards reform. The reforms that are needed the most, however, are not restricted to preventing or detecting the few instances of fraud by unscrupulous researchers who are intentionally falsifying data. What we should be more concerned about are the far less egregious, but much more common offenses that many of us commit, often unknowingly or unintentionally, and almost never with fraudulent intent….

The Vampire of Venice Returns, or What Is that Brick Doing in that Skull’s Mouth? by Kristina Killgrove:

It seems like every spring there is renewed coverage of a partial skeleton that was found on the island of Lazaretto Nuovo (one of two 15th-16th century leper colonies near Venice) in 2009. I’ve never covered it here, but since I was alerted to an airing of a documentary about the skeleton on Italian TV this week, I thought it may be time to track the progress of the so-called Vampire of Venice (“il vampiro di Venezia” in Italian, and not to be confused with a similarly named Dr. Who episode)….

How the Deaf Brain Rewires Itself to ‘Hear’ Touch and Sight by Nadja Popovich:

Our experiences help shape our brains. So it might make sense that for a person born without hearing, the part of the brain that’s meant to process audio would be underdeveloped. But according to a new study, those who have been deaf since birth actually use the sound-related part of the brain — known as the primary auditory cortex — to do even more heavy lifting than their hearing counterparts. …


Special topic 1: #arseniclife:

The Case (Study) of Arsenic Life: How the Internet Can Make Science Better by Rebecca J. Rosen

Live-blogging Arsenic Life by Carl Zimmer

Discovery of an arsenic-friendly microbe refuted and Q and A: Critical ‘Arseniclife’ studies released by Dan Vergano

Pair Of Studies Rebuts Arsenic-Based Life by Carmen Drahl

Arsenic Death by ChemBark

“Arsenic bacteria”: Coffin, meet nails by Ashutosh Jogalekar

Arsenic Life, Cold Fusion, and the Allure of Wishful Thinking by Matthew Francis

Another chink in the Ingelfinger armor? Arsenic life talk forces Science to release paper early, without embargo and Science has “not asked for a correction or retraction” of arsenic life paper, and why situation is unlike XMRV-CFS by Ivan Oransky

Arsenic-Life Discovery Debunked—But “Alien” Organism Still Odd by Richard A. Lovett

Consider the publication embargo… and NASA’s cowardly responses to their #arseniclife FAIL by Rosie Redfield

New research points toward “no” on arsenic life by Phil Plait

Annoying Arsenic Claim Debunked for Good – We Hope. by Faye Flam

Notorious Arsenic-Tolerant Bacterium Needs Phosphorus After All by Quirin Schiermeier

Despite refutation, Science arsenic life paper deserves retraction, scientist argues by David Sanders

Two studies show ‘weird life’ microbe can’t live on arsenic by Alan Boyle

Latest on #ArsenicLife by Jonathan Eisen

Journal retreats from controversial arsenic paper by Marc Kaufman

New Science Papers Prove NASA Failed Big Time In Promoting Supposedly Earth-Shaking Discovery That Wasn’t by Matthew Herper


Special topic 2: glut of PhDs:

WaPo: Not enough jobs for science PhDs by David Kroll

The STEM PhD Glut Makes the Mainstream Media by Mike the Mad Biologist

Subtleties of the Crappy Job Market for Scientists by Julianne Dalcanton

The wages of a life science Ph.D. (not high!) and More on jobs & Ph.D.s by Razib Khan

“Alternate careers” is just the next exploitation strategy? by DrugMonkey

Too many scientists? by Puff the Mutant Dragon

Washington Post: “U.S. pushes for more scientists, but the jobs aren’t there.” by Chemjobber

Life as PhD student by Elf Eldridge


Best Images:

TICKS ON A SNAKE by teresa.frog.applause

On Writing by Abstruse Goose

Here’s Something You Don’t See Every Day by Jonathan Losos

Arctic Biologist Shares Astonishing Sea Creatures With the World by Pete Brook

Visual Field by xkcd


Best Videos:

Nobel laureate occasionally hangs out on street corners, answering physics questions by Maggie Koerth-Baker

Snake Stunt: Drinking While Dangling by Andrew C. Revkin

Talent Search » TED@Vancouver » Carin Bondar: Reproduction and survival in the animal kingdom

Talent Search » TED@Sydney » James Byrne: How plants have sex

Stomach Bacteria Show Early Human Travels by skepTV

Piecing together Patagonia’s ancient vegetation by Melanie Connor

Opening Keynote from Cameron Neylon – Network Enabled Research by Open Repositories 2012

‘Big Ass Shark’ Unexpectedly Swipes Fish Off Girl’s Line Like Something Out of a Movie by Neetzan Zimmerman

The Higgs Boson, Part II: What is Mass? by MinutePhysics

Alan Turing: His Mind, His Life (VIDEO, Part Two) by Cara Santa Maria

This is What Snake Venom Does to Blood! by fragrancemad

Is Apollo 18 Real? by Amy Shira Teitel

#CurlyHairMafia on the Secret of NIMH by DNLee

From Galileo to Galaxy Zoo: Astronomy in the Digital Age by Alessandro Mangiafico



No, the web is not driving us mad and Why I am always unlucky but you are always careless by Vaughan Bell

Where are the Canadian media in analysing the Death of Evidence protest? by Marie-Claire Shanahan

The Dead Sea is Dying: Can
A Controversial Plan Save It?
by Dave Levitan

Trajectory of a falling Batman by Ben Goldacre

The mundaneness of science by Christie Aschwanden

Brain Scans Predict When Poker Players Will Bluff and Why Successful Leaders Share Their Harems by Elizabeth Preston

Egg-eating snakes and This blog is supposed to be about snakes, but if you can’t make exceptions for family, then you’re a jerk by Andrew Durso

Doubt Is Good for Science, But Bad for PR by Stuart Firestein

When you throb with pain…are you feeling the beat? by scicurious

Little fellah bums by Michael Wellan

Silk cages preserve vaccines and antibiotics for months without refrigeration and Urban noise can turn sparrow females into bad mums and Chicken vaccines merged to form live viruses and caused outbreaks of irony and Uncertainty shrouds psychologist’s resignation by Ed Yong

South Carolina Governor Nikki Haley slashes funding for coastal science and sustainable development by David Shiffman

Daily Mail, HuffPo Dumb Down Dinosex by Brian Switek

Q&A With Deborah Berebichez: Seeing the World Through Physics Glasses by Double Xpression

Mathematics and HIV by Jessica Wapner

Thai Farmers Fight ‘Global Warming Fines’ by Prangtip Daorueng

Why Crowds Can Turn Deadly by Emily Badger

You can hide those lying eyes by Zen Faulkes

You can’t ban redheaded sperm by David Winter

Zombies and Volleyball: The Benefits of the Bystander Effect by Melanie Tannenbaum

Q: Why Do We Wear Pants? A: Horses by Alexis Madrigal

There is something and not nothing by Roger Ebert

Want to Get Teens Interested in Math and Science? Target Their Parents by Anna Mikulak

Scientific History and the Lessons for Today’s Emerging Ideas by The Physics arXiv Blog

A striking experiment shows how you can run on quicksand and Black hole shines a light on dark galaxies by Matthew Francis

Why Canada’s scientists need our support by Alice Bell

Why Eugenics Will Always Fail by Esther Inglis-Arkell

Gnathia marleyi — or not by Susan Perkins

Will We Ever Find All the Dinosaurs? by Brian Switek

Should we all be guinea pigs? by John Rennie

Pipes, Reins, & the Cerebral Winepress: Mechanical Metaphor in Vesalius’ Fabrica by Marri Lynn

The climate of the climate change debate is changing by Myles Allen

Lizards Can’t Take The Heat – But Can They Take The Cold? by Martha Munoz

Crackpots, geniuses, and how to tell the difference by Maggie Koerth-Baker

Relativistic Baseball: What would happen if you tried to hit a baseball pitched at 90% the speed of light? by xkcd

I saw the (negative) sign: Problems with fMRI research by Dana Smith

Nikola Tesla and the magic of science by Danica Radovanovic

Why George Will Is Wrong About Weather And Climate by Jocelyn Fong

If “Fifty Shades of Grey” Had Been Written by a Biology Textbook Author by Ricki Lewis

Keeping Parkinson’s Disease a Secret by Kate Yandell

Distrusting Scientific Research by Kelsey Tsipis

Weird Fiction Monday: Mass Effect: Apocalypse by Greg Gbur

Could the S.H.I.E.L.D. Helicarrier Fly? by Rhett Allain

Planet of the Mega Disasters by Faye Flam

Dr. Drew Cashes In by Charles Seife

Galápagos Monday: The Sad Sex Life of Lonesome George by Virginia Hughes

Crowdfunding Questions With Co-founder Matt Salzberg by Travis Saunders

Roid Age: steroids in sport and the paradox of pharmacological puritanism by Greg Downey

Traditional Sexual Values Challenged in Classic Animal Study by Brandon Keim

Painless Injections by Tianyou Xu

Down, boy! The politics of humping by jwoestendiek

Notes on Some of Those 79 “New” Shark Species by Chuck Bangley

What’s the difference between “Opossum” and “Possum”? by Jason Bittel

A Brief History of Money by James Surowiecki

Tree Rings and Climate: Some Recent Developments by Michael E. Mann, Gavin Schmidt, and Eric Steig

The American Heat Wave and Global Warming by MarkCC

Brain Time by David Eagleman

Increase in wildfire frequency and severity – is it real? by Kelly Ramirez


Media, Publishing, Technology and Society:

If Mitt Romney were running a “post-truth” campaign, would the political press report it? by Jay Rosen

Chronicling Mitt’s Mendacity, Vol. XXV by Steve Benen

SPARC Europe’s response to the inaccuracies in the article by the Daily Mail’s City Editor on 18 June by Alma Swan

Wheeler: Spoken word, handwritten letters make lasting impressions by Burgetta Wheeler

The Blogfather on science blogging by NASW

Twitter and the Arab Spring: New Evidence by Henry Farrell

Predatory Open-Access Journals? by Sarah Hird

Academic blogging: minority scholars cannot afford to be silent by Denise Horn

Should Applied Funding Go To Academia Or Startups? by Elizabeth Iorns

The Importance of Open Access: An Interview with Patient Advocate Graham Steel by PatientsLikeMe

Are you sure that’s true? Truth Goggles tackles fishy claims at the moment of consumption by Andrew Phelps

The Dreamers’ dreams: young immigrants tell their stories by Ruth Spencer

Retraction tracking by Zen Faulkes

J-school grads turn to startup scene by Anne Field

Thoughts on the Finch Report, part 1 and Part 2 by Mike Taylor

A history of science blogging and Reflections on 10 years in science blogging by Razib Khan

A History of Science Blogging and Communicating Science to Society by Larry Moran

Bora’s Science Blogging Post by Eva Amsen

Video Tip of the Week: ScienceSeeker for science blogging by Mary Mangan

Sharpening ideas: From topic to story by Dan Ferber

Challenging ‘He Said, She Said’ Journalism by Linda Greenhouse

Are we stuck in filter bubbles? Here are five potential paths out by Jonathan Stray

Alan Alda warms up science communication with the Flame Challenge and The Flame Challenge winners, and other attempts to get science communication out of its rut by Peter Linett

Darpa Wants You to Be Its Hackathon Guinea Pig by Arikia Milikan

Science journalism through the looking glass by Chris Chambers and Petroc Sumner

How the byline beast was born by Jack Shafer

The left’s gone left but the right’s gone nuts: Asymmetrical polarization in action by David Roberts

Confessions of an Internet Addict by Alexis Madrigal

Science, Blogging and Plagiarism by Michael McBurney

How future-safe was the first Harvard blogging site? by Dave Winer

Why Blogs Fail by Neuroskeptic

Takes Two to Tango by Karen McLeod

How to live-tweet from an event by Tia Fisher

Is Open Access a Moral or a Business Issue? A Conversation with The Pennsylvania State University Press by Prof. Hacker

Reflections on Games For Change by Eric Martin

All’s Not Fair in Science and Publishing by Frederick Southwick

The ultimate geek road trip: North Carolina’s mega data center cluster by Katie Fehrenbacher and 10 reasons Apple, Facebook & Google chose North Carolina for their mega data centers and The controversial world of clean power and data centers and The story behind how Apple’s iCloud data center got built and That’s a wrap: The 4-part series on North Carolina’s mega data centers

What should society journals do about open access? and What does it cost to publish a paper with Elsevier? by Mike Taylor

The Blob versus the blog: arguing how social media is changing science and Transformative idea for peer review: reviewing & grading the reviewers by Paul Knoepfler

Three Keys to Clearing Two Social Media Hurdles by Farris Timimi

How the iPad helps scientists do their jobs by Joel Mathis

Reforming Copyright Is Possible by Pamela Samuelson

Piecemeal existence: For today’s young freelancers, what will traffic bear? by Ben Adler

The significance of plot without conflict by Still Eating Oranges

The Scienceblogging Weekly (July 6th, 2012)

Blog of the Week:

Musings of a Dinosaur is a blog written by a physician, family practitioner, Lucy E. Hornstein, author of the book Declarations of a Dinosaur: 10 Laws I’ve Learned as a Family Doctor. Having a small general family practice is different from beeing a specialist in a large hospital. Approach to patients is different. The way one runs the business is different. The thoughts about electronic medical records (a frequent topic of the blog) are different. A valuable perspective, wry and funny and insightful.


Top 10:

Maxwell’s demon goes quantum, can do work, write and erase data by Matthew Francis:

At any temperature above absolute zero, particles in a system move randomly, an effect known as thermal fluctuation. The random character of the fluctuations means they cannot be put to work in a mechanical sense (the measure of the energy unavailable for work is called entropy). 19th century physicist James Clerk Maxwell proposed a tiny intelligent “demon” that could harvest the thermal fluctuations to restore their usefulness; later work in the 20th century showed that the demon itself would have entropy, which would keep the thermodynamic books balanced.

Interesting by Shara Yurkiewicz:

I pull up a test result for my patient, and the senior resident standing behind me lets out an excited squeal. “I’ve never seen the imaging come back positive for this,” she says. Our two-week-old infant, who already has a rare infection, also has a rare associated structural abnormality. It’s not benign, but it is fixable. The fix usually requires surgery. As we walk over to the patient’s room to update her mother, my senior gushes about the zebra that was uncovered on the ultrasound. She asks me if I’m excited. “I dunno,” I mutter, which is somewhat more diplomatic than my disgust that she is. ”Her kid has to get surgery now.”

The world’s smallest fly probably decapitates really tiny ants by Ed Yong:

…Even though flies as a group aren’t exactly giants, the new species was around half the size of the previous smallest species. Brown named it Euryplatea nanaknihali after Nanak Nihal Weiss, a young boy from Brown’s home town in Los Angeles. Weiss is an entomology fanatic and Brown hopes that the name will help to keep his interest for years to come….

Creationists and Climate “Skeptics” – Separate Species or Just Different Breeds? by Faye Flam:

Several of the regular readers of this column have told me that since I’ve been brave enough to tell the truth about evolution, I should do the same for climate change and expose it as a hoax. In one case I replied that in my stories I always strive to reflect the truth to the best of my abilities. He wrote that he was “disappointed.” These evolution-accepting climate change “skeptics” are an interesting breed, revealing some key differences in the ways they and creationists approach science. Self-described climate skeptics are much more scattered in their views than are creationists, but they are better organized and together speak with a louder, and angrier voice….

Printing dinosaurs: the mad science of new paleontology by Laura June:

In April of this year, I headed out to a marl pit in Clayton, New Jersey to watch a team of Drexel University students and their teacher, Professor Kenneth Lacovara, dig for fossils. Marl, a lime-rich mud, had been mined and used as the 19th century’s leading fertilizer, but since around World War II (with the development of more advanced, synthetic fertilizers), demand for it has steeply lessened, and there aren’t many marl mining businesses left in the US. The marl pits of Southern New Jersey are famous for something else, though: they have been incredibly rich in fossil finds. In February, Dr. Lacovara had announced that the Paleontology department at Drexel would team up with the Engineering department for what would largely be a novel new project: scanning all of the fossils in the University’s collection (including some previously unidentified dinosaurs of Lacovara’s own finds in other parts of the world) using a 3D scanner. The Engineering department would then take those scans and use a 3D printer to create 1/10 scale models of the most important bones. But, he reported, that wouldn’t be the end of it: they intended, he said, to use those scale polymer “printouts” to model and then engineer fully working limbs, complete with musculature — to create, in effect, a fully accurate robotic dinosaur leg or arm, and eventually, a complete dinosaur….

Childbirth and C-sections in pre-modern times by Kristina Killgrove:

Basically since we started walking upright, childbirth has been difficult for women. Evolution selected for larger and larger brains in our hominin ancestors such that today our newborns have heads roughly 102% the size of the mother’s pelvic inlet width (Rosenberg 1992). Yes, you read that right. Our babies’ heads are actually two percent larger than our skeletal anatomy…

Self help: forget positive thinking, try positive action by Richard Wiseman:

For years self-help gurus have preached the same simple mantra: if you want to improve your life then you need to change how you think. Force yourself to have positive thoughts and you will become happier. Visualise your dream self and you will enjoy increased success. Think like a millionaire and you will magically grow rich. In principle, this idea sounds perfectly reasonable. However, in practice it often proves ineffective….

The Uncertainty Principle for climate (and chemical) models by Ashutosh Jogalekar:

A recent issue of Nature had an interesting article on what seems to be a wholly paradoxical feature of models used in climate science; as the models are becoming increasingly realistic, they are also becoming less accurate and predictive because of growing uncertainties. I can only imagine this to be an excruciatingly painful fact for climate modelers who seem to be facing the equivalent of the Heisenberg uncertainty principle for their field. It’s an especially worrisome time to deal with such issues since the modelers need to include their predictions in the next IPCC report on climate change which is due to be published next year….

The living rainbow: A fatal flaw in a classic study of sexual selection by Jeremy Yoder:

A key component of classical sexual selection theory is the idea that males maximize their evolutionary fitness—the number of children they ultimately have—by mating with lots of females, while females maximize their fitness by selecting only one or a few high-quality partners. It’s pretty clear that this model works well for some species (like ducks), but also that there are many it doesn’t fit so well. Now it looks like one of the “classic” experimental examples of sexual selection may actually fall into the latter category….

Dr. Google and Mr. Hyde by David Gorski:

….Like all major new technologies, the Internet has a good side and a bad side. In many cases, the same property is both good and bad, and one place that this is particularly true is in medical information. The Internet has an abundance of medical information, all there for the reading and learning, and various discussion forums that began with online BBS services and the now mostly obsolete global discussion community of Usenet allow people from all over the world who would never have communicated directly with each other before to share information and experiences. Unfortunately, there is a dark side to this. Regular readers of this blog know what that dark side is, too. The same technology that allows reputable scientists and doctors to publish reliable medical information to the world at very low cost also allows quacks and cranks to spew their misinformation, nonsense, pseudoscience, and quackery to the whole world at very little cost. And, boy, do they ever! In many ways, the quacks are a far more effective online presence than skeptics and supporters of science-based medicine. I mean, look at SBM itself. We’re still using a generic WordPress template. Now look at an antivaccine website like The International Medical Council on Vaccination or Generation Rescue or the antivaccine blog Age of Autism. Look at quack websites like The comparison, at least when it comes to web and blog design, is not flattering…..


Special topic: Higgs boson:

What is the Higgs boson? – video by Ian Sample and Laurence Topham

What Is the Higgs Boson? [Video] by George Musser

Higgs Boson VIDEO: A Metaphor To Explain The Particle, Or Further Confuse You by Cara Santa Maria and Henry Reich

Sonnet on a Higgs-Like Particle (video) by Vi Hart

New Particle Resembling Long-Sought Higgs Boson Uncovered at Large Hadron Collider by John Matson

If You Want More Higgs Hype, Don’t Read This Column by John Horgan

Beyond Higgs: On Supersymmetry (or Lack Thereof) by Glenn Starkman

Mr Boson, I presume…? by Charles Ebikeme

Live-Blogging the Higgs Seminar by Sean Carroll

Science Friday by Sean Carroll

Higgsteria: We Didn’t Need No U.S. Super Collider by Gary Stix

Pros and Cons of building particle accelerators – Werner Heisenberg by Beatrice Lugger

Higgs? Probably not tomorrow and Discovering a boson and Linux at CERN and The mysterious Mr. Higgs by Gianluigi Filippelli

Who gives a Higgs? by Jacqui Hayes

What If the New Particle Isn’t the Higgs Boson? by Natalie Wolchover

Why the Higgs Particle Matters by Matt Strassler

The Best Analogies Scientists and Journalists Use To Explain the Higgs Boson by J. Bryan Lowder

High on Higgs by Subhra Priyadarshini

Stop calling it “The God Particle!” by Dr. Dave Goldberg

The Higgs Boson explained by PhD Comics by Jorge Cham, via Nathan Yau

Scientists’ search for Higgs boson yields new subatomic particle by Brian Vastag and Joel Achenbach

The Higgs Boson – Certainly, certainly (?) there! (at least, I am pretty certain it is) by Julian Champkin

Gallery: how Wired readers picture the Higgs Boson by Ian Steadman

The Art of Science – Particle Accelerator Art by Michele Banks

Gettin’ Higgy With it: A Roundup of Higgs Boson Jokes on Twitter by Xeni Jardin

Higgs! by Phil Plait

Higgs Boson: the jokes edition by Khalil A. Cassimally

Scientists might have found the Higgs Boson by Maggie Koerth-Baker

Higgsdependence Day! by Matthew R. Francis

Physicists Find Elusive Particle Seen as Key to Universe by DENNIS OVERBYE

How the Discovery of the Higgs Boson Could Break Physics by Adam Mann

CERN Announces Discovery of Higgs-like Particle by PRI The World

What It Means to Find “a Higgs” by Mariette DiChristina

So What’s the Big Deal About the Higgs Boson, Anyway? A Physics Double Xplainer by Matthew Francis

A Moment for Particle Physics: The End of a 40-Year Story? by Stephen Wolfram

Higgs-like discovery from the inside by Jon Butterworth

The Higgs Boson and my mom by Laura Jane Martin

What Higgs Boson Evidence Looks Like by Ira Flatow

Higgs boson: Prof Stephen Hawking loses $100 bet by Nick Collins

Physicists Detect New Heavy Particle by Virat Markandeya

Hipster Pop Quiz: What is the Higgs Boson? by Motherboard

These Hipsters Have No Idea About the Higgs Boson by Megan Garber

CERN Finds New Particle (And it Might be the Higgs Boson!) by Miriam Kramer

Does 5-sigma = discovery? by Hyperspace

It’s true, they say they have the Higgs in the bag. Big news. Just imagine the hubbub were it deemed imaginary. and Goldarned god particle by Charlie Petit

So the Higgs boson walks into a… by Eryn Brown

Lighter side of the Higgs boson by Alan Boyle

Nobel Laureates in Physics React to the Higgs-Like Particle News [Video] by Nature magazine

Do You Understand The Higgs Boson? by Fake Science

It’s kind of a Higgs deal by Zen Faulkes

Field Day by Rheanna Sand


Best Images:

Snake Oil? The scientific evidence for health supplements by David McCandless and Andy Perkins

Unusual Bridges For Animals – Wildlife Overpasses by THE WORLD GEOGRAPHY

Horoscoped by David McCandless

The complete history of philosophy visualized in one graph by Simon Raper, via George Dvorsky

Paper birds – now with some internal anatomy by Diana Beltran Herrera

How Do We Know by The Census Bureau


Best Videos:

Curiosity’s Seven Minutes of Terror by NASA

Hermit Crab in Glass Shell turning over by Robert DuGrenier

Virtual Pigeon Attracts, Baffles Randy Males by Rachel Nuwer

Stephen Colbert Interviews Neil deGrasse Tyson at Montclair Kimberley Academy – 2010-Jan-29 by teridon

Fracking by Carin Bondar

Watch a giant African land snail enjoying a nice cool shower by Lauren Davis

Science Is A Girl Thing: Chris Hardwick, Cara Santa Maria Talk Women In STEM On G4’s ‘Attack Of The Show’ by Cara Santa Maria

Speed Comparison: GT vs. F1 cars by mclaren777

Why We Need to Broaden Participation in Science by RMCRSLDM

Science Writing in the Age of Denial, April 23, 2012 videos by University of Wisconsin-Madison

What Happens Inside the Large Hadron Collider? by George Musser and Rose Eveleth

Som Sabadell flashmob by Banco Sabadell

Octopus ‘vulgaris’ hatchlings hatching by Richard Ross

Ophiarachna Predatory Brittle Star FEEDING ACTION! by ChrisM

Deep-Sea Cephalopods Hide Using Light by AMNHorg



The Good-Old Days of Contraception: Lemon-Peel Diaphragms and Beaver-Testicle Tea by Sophie Bushwick

TGIPF: Iceland’s Phallological Museum by Alex Witze and Jeff Kanipe

The Myth of the Rational Scientist by Byron Jennings

Do scientists need an equivalent of the Hippocratic Oath to ensure ethical conduct? by Lou Woodley

Will We Ever Find Dinosaurs Caught in the Act? and Pterosaurs Done Wrong by Brian Switek

Trees, grass, carbon dioxide and the battle for dominance by GrrlScientist

Franz Boas and Neuroanthropology by Daniel Lende

Altmetrics and the Future of Science by Samuel Arbesman

Lunch: An Urban Invention by Nicola Twilley

The Making Of Meat-Eating America by Dan Charles

How To Start Your Own Farm by Forrest Pritchard

Foie Gras Hypocrisy by Matt Pressberg

U.N. Report from Rio on Environment a ‘Suicide Note’ by Mark McDonald

A “rule-of-forearm” for collecting data in Botswana by Andrew J King

Microbiomes mediating microevolution by Zen Faulkes

Dietary supplements: Manufacturing troubles widespread, FDA inspections show by Trine Tsouderos

Grizzlies move into Polar bear territory by Rebecca Deatsman

The Unsung Scientist, Louis-Antoine Ranvier by Cynthia McKelvey

Turning trauma into story: the benefits of journaling by Jordan Gaines

The tyranny of π: A semirational rant on an irrational number by Jonathan Chang

Draining the Desert? by Kate Prengaman

BOOK REVIEW: Companions in Wonder: Children and Adults Exploring Nature Together by Michael Barton

Ancient impact crater may be largest ever found by Stephen “DarkSyde” Andrew

Rising Heat at the Beach Threatens Largest Sea Turtles, Climate Change Models Show by Rachel Ewing

You Can See Poor From Space by Philadelinquency

Maya Lin: A Memorial to A Vanishing Natural World by Diane Toomey

The Problems With Forecasting and How to Get Better at It by Nate Silver

Ray Bradbury and the Lost Planetarium Show by David Romanowski

Opossums: Survival Machines and Opossum Reproduction by Jason Bittel

Conducting Cells in Mosses by Jessica M. Budke

What’s the difference between one kid with a fever and one without? by Connor Bamford

You want to cut me where? by Steven Salzberg

Birds of the Sun by Christopher Taylor

Coffee: a caffeinated chronicle by Jordan Gaines

Inner Ears Reveal Speed of Early Primates and The Shambulance: Ab Toning Belts (or, Muscle Tone Is All in Your Head) and Flightless Giant’s Flower Diet Revealed by Poop Fossils by Elizabeth Preston

Reviving the ‘apparently dead’ in Georgian Britain by Alun Withey

Don’t trust the religious by P.Z.Myers

Mother Nature Wants to Eat You, or: The Trouble With Alternative Med by Puff the Mutant Dragon

Galápagos Monday: World Within Itself by Virginia Hughes

Not in Our Genes by Bryan Appleyard

On the merits of science literacy by Alice Bell

Defining a hybrid species by Retrieverman

Sleep Research in the Blind May Help Us All by Steven Lockley, Ph.D.

Male Lactation- there’s probably something wrong with you by Noby Leong

Bill McKibben on the Global Warming Hoax by Bill McKibben

Why the Left-Brain Right-Brain Myth Will Probably Never Die by Christian Jarrett

Do Bears Sense That Hunters Are Afoot? and Thinking About Your Own Demise Inspires Environmentalism by Rachel Nuwer

Infrastructure and You by Marie-Claire Shanahan, Scott Huler and Tim De Chant

Bottles Full of Brain-Boosters by Carl Zimmer

New Study: Climate Deniers Are Emoting–Especially the Conspiracy Theorists and The Politics of Ice and Fire by Chris Mooney

What’s Behind The Record Heat? by Douglas Main

Jungle Science and the Future of Conservation by Mireya Mayor

A Poison for Assassins and Tiny Fireworks by Deborah Blum

“Why Do We Have to Learn This Stuff?”—A New Genetics for 21st Century Students by Rosemary J. Redfield

Darwin, Darwinism, and Uncertainty: book review by Matt Young

You’re Not as Happy as You Think You Are, Behavioral Scientists Report by Thomas Hayden

Strange sounds: How the brain makes sense of degraded speech by Julia Erb

Do We Need “Evolutionary Medicine”? by Harriet Hall

What the Germs in Your Bellybutton Say About You by Jason Tetro

Just a Reminder by Mike Haubrich

Night Shift by Rob Dunn

When Killer Whales Attack by Kieran Mulvaney

Voyager 1: The Little Spacecraft That Could by Amy Shira Teitel

Marriage is a tool society uses to reproduce by Greg Laden

Supplements: Something Smells Fishy by Cassandra Willyard

Cost of scientific research – and political naivity by Ken Perrott

The time has come: public participation in science policy making. and Harnessing Citizen Scientists: Let’s Create a Very Public Office of Technology Assessment by Darlene Cavalier

Get to know the narwhal! by Heidi Smith

Worm kills insects by vomiting Hulk-like bacteria by Ed Yong

The Tasmanian Echidna’s Four-Headed Penis by Lucy Cooke

Why Do Flamingos Stand On One Leg? by Matt Soniak

The First Poem Published in a Scientific Journal by Maria Popova

Truth and Reconciliation for Group Selection (pdf) by David Sloan Wilson

With a snail’s help a fish transitions from dying to dead by Craig McClain

Can You Learn To Be Synaesthetic? and False Positive Neuroscience? by Neuroskeptic

The Psychologist: Vladimir Nabokov’s understanding of human nature anticipated the advances in psychology since his day by Brian Boyd


Media, Publishing, Technology and Society:

The Geek Poet Strikes Back by Beth McNichol

A field guide to ocean science and conservation on twitter by Andrew Thaler

How to solve impossible problems: Daniel Russell’s awesome Google search techniques by John Tedesco

Should Google and Amazon be allowed to control domains? by Mathew Ingram

Calling Dr. Google by Jeff Jarvis

Belated thoughts on the Finch Report on achieving Open Access by Mike Taylor

The ‘Busy’ Trap by Tim Kreider and Have You Fallen Into The Busy Trap? by Brad Feld and Do We All Work Too Much? And Do We Really Have a Choice? by Walter Frick

The Death and Rebirth of Television News: “All of Life is Reduced to the Common Rubble of Banality” by Steven Lloyd Wilson

The Enlightenment project could inspire our media by Matthew da Silva

What Twitter could have been by Dalton Caldwell

A manifesto for the newspaper’s public editor in the social media era by Dan Gillmor

Why Google Plus isn’t dead — well, yet by John D. Sutter

SciWriteLabs 8.3: Adjudicating the Lehrer plagiarism accusations. Plus: Do Arianna and Oprah deserve lifelong bans? by Seth Mnookin

The Great American Novel by Maria Konnikova

Of Flying Cars and the Declining Rate of Profit by David Graeber (also see reactions by Henry Farrell and Cassiodorus)

Journatic worker takes ‘This American Life’ inside outsourced journalism by Anna Tarkov

Positive signs from Wiley on open access and Dear Wiley: please use Creative Commons Attribution for your open-access activities by Mike Taylor

On Tides, Visibility, and Quiet Revolutionary Acts by Dana Hunter

The View from Nowhere Interviews Trenberth by Michael Tobis

Social Networking For Scientists – The Wiki by Christie Wilcox

Save your darlings: Blank on Blank gives new life to old tape by Adrienne LaFrance

Hooray for the Awesome Wave of Lady Scientists in Action Movies by Alyssa Rosenberg

Long-form journalism project Matter aiming for September launch by Rachel McAthy

The Predictable Comment by The Digital Cuttlefish

Dramatic Growth of Open Access by Heather Morrison

The 2012 presidential election: what voters want – the community agenda by Jay Rosen and Nadja Popovich

Website Tests How Political Opposites Actually Discuss Differences by Marissa Alioto

Sorry, Your Tweets Can Still Be Subpoenaed by Adam Martin

Why You Should Be An Open Notebook Scientist by Anthony Salvagno

Startups that Catalyze Science by Samuel Arbesman

The Scienceblogging Weekly (June 29th, 2012)

Blog of the Week:

This week’s choice was easy – March of the Fossil Penguins, written by Dr. Daniel Ksepka. What is there not to like? Penguins! Fossils! Straight from the keyboard of the leading world expert on the topic. Enjoy!


Top 10:

How presidential elections are impacted by a 100 million year old coastline by Craig McClain:

Hale County in west central Alabama and Bamberg County in southern South Carolina are 450 miles apart. Both counties have a population of 16,000 of which around 60% are African American. The median households and per capita incomes are well below their respective state’s median, in Hale nearly $10,000 less. Both were named after confederate officers–Stephen Fowler Hale and Francis Marion Bamberg. And although Hale’s county seat is the self-proclaimed Catfish Capitol, pulling catfish out of the Edisto River in Bamberg County is a favorite past time. These two counties share another unique feature. Amidst a blanket of Republican red both Hale and Bamberg voted primarily Democratic in the 2000, 2004, and again in the 2008 presidential elections. Indeed, Hale and Bamberg belong to a belt of counties cutting through the deep south–Mississippi, Alabama, Georgia, South Carolina, and North Carolina–that have voted over 50% Democratic in recent presidential elections. Why? A 100 million year old coastline….

The Curious Case of the Poisoned Cows by Deborah Blum:

On a bright morning in early June, a Texas rancher named Jerry Abel turned his small herd of cattle out to graze. The 18 cows moved hungrily into that field of fresh grass. Within a few hours, only three were still alive. Abel’s 80 acre ranch sits just a little east of Austin and the story was strange enough that on Sunday a local CBS affiliate picked it up. “There was nothing you could do,” Abel told KEYE about his desperate efforts to save the animals. “Obviously, they were dying.”…

In the Steps of a Hungry Acrocanthosaurus by Brian Switek:

Compared to mounted dinosaur skeletons, fossil footprints might seem like mundane objects. They only record one small part of a fantastic creature, and it is harder to envision a whole dinosaur from the ground up than the wrap flesh around a skeletal frame. But we should not forget that dinosaur footprints are fossilized behavior—stone snapshots of an animal’s life. And sometimes, trackways record dramatic moments in dinosaur lives….

When It Comes to Numbers, We’re All Late Bloomers by Elizabeth Preston:

Good news for aspiring jelly-bean jar estimators who are under 30! Your intuitive grasp of numbers may not have peaked yet. Unlike other cognitive skills, the ability to approximate keeps improving well into adulthood. Since the skill is tied to mathematical smarts, this news might bring hope to struggling students….

Summer of Smoke by Christie Aschwanden:

June 8, 2012, Cedaredge Colorado—It was an ordinary Friday afternoon. I was at my desk writing when I looked out the window and saw an enormous plume of smoke billowing from the back of our property. It was the kind of moment when you’re supposed to remain calm and remember all the wise things you learned in first aid class or girl scouts. (Stop! Drop! Roll!) Instead, I panicked.

Plague at the Siege of Caffa, 1346 by Michelle Ziegler:

The first stage of the Black Death among Europeans was said to begin with the whoosh of a Mongol trebuchet. Gabriele De’ Mussi, a lawyer from near Genoa writing in about 1348, is believed to have recorded the account of the earliest use of plague as weapon of war at Caffa in 1346….

New flu gene found hiding in plain sight, and affects severity of infections by Ed Yong:

I could write the entire genome of a flu virus in around 100 tweets. It is just 14,000 letters long; for comparison, our genome has over 3 billion letters. This tiny collection of genetic material is enough to kill millions of people. Even though it has been sequenced time and time again, there is still a lot we don’t know about it….

‘Man-sheep-dog’: inter-species social skills by Paul Keil and Greg Downey:

Paul, the lead author, interviewed sheepdog trialer Damian Wilson about his interactions with his dog, a border collie named Yandarra Whiskey. Damian and Whiskey gave Paul a demonstration of the techniques used in sheepdog competitions as they together tried to move a mob of three sheep. In a competition in New South Wales, a trainer and dog have to move three sheep who have never been herded through a difficult obstacle course, and the trainer loses points if he (or, less frequently, she) breaks from a slow, measured pace walking the course. The rules mean that the dog itself must be trained until it anticipates the sheep’s reactions, and understands, on some level, what dog and trainer, together, are trying to accomplish. Although the trialer may give commands, the dog, too, is a kind of expert….

Preview: 3-D Space Shuttle Movie Will Bring the Launch Pad to Your Living Room by Tanya Lewis:

If you missed the final launch of the Space Shuttle, or the first private spacecraft rendezvous with the International Space Station, fear not. A new documentary to be released late this year promises you a fiery, 3-D, launch-pad view of these historic flights…

A Wartime Medical Dispenser by Jaipreet Virdi:

The Napoleonic Wars brought John Harrison Curtis’ studies to a standstill, as he became one of thousands of young men conscripted to fight against Napoleonic advances towards Britain. With his medical learning in hand, Curtis enlisted in the Royal Navy in 1808, to obtain his qualifications as surgeon and extend his medical skills. Since 1745, the Royal College of Surgeons in London, Edinburgh and Dublin, and the Navy held close associations with each other as the College was responsible for examining naval surgeons for active service. To be admitted as surgeon in the navy, candidates had to obtain a certificate of competence from the College and then be subjected to a two-hour oral examination at Somerset House….


Special topic #1: Getting young journalists and scientists to become savvy on the Web:

#Realtalk for the j-school graduate on the first five years of your career by Ann Friedman

Young journalists don’t seem to care about the Web: Why not? by Phillip Smith

Few Tweet successes as Generation Y fails to use blog-standard tools by Elizabeth Gibney

British Ph.D. Students Don’t Tweet by Elizabeth Gibney


Special topic #2: Wicked Problems:

Covering Wicked Problems by Jay Rosen

Overcoming Wicked Problems by Michael Shellenberger and Ted Nordhaus

Andrew Revkin on the Super Wicked Problem of Climate Change by Amanda Frank

David Roberts on the Simple Climate Problem by Andrew Revkin

Wicked Problems by UpLook


Best Images:

Global Distribution of Nobel Prizes Reflects Great Shifts in Modern History [Infographic] by Scientific American Magazine


Best Videos:

Mathematically Correct Breakfast by George Hart

A Song About A Circle Constant by Vi Hart

Oldest Sound Recording Resurrected from Paper by Eric Olson

A Glass Act — Harry Potter Theme Played on Wine Glasses by murayu74

What does traffic have to do with fluid dynamics? by FY! Fluid Dynamics

Milestone for WINS by The Academy of Natural Sciences of Drexel University

Beautiful Black Art by Tony Barnhart

Making the Invisible Visible in Video by MITNewsOffice

How Many Men Does it Take to Pull an Astronaut Out of the Ocean? by Amy Shira Teitel

Scraps to soil: New Yorkers carry compost to Greenmarkets instead of tossing it in the trash by Laura Geggel and Virat Markandeya

Instant Egghead – Do Cosmic Rays Spark Lightning? by Phil Yam



Beware Stimulus Effects in Psychology by Neuroskeptic

Do cephalopods dream of aquatic sheep? and Big in Japan by Zen Faulkes

TGIPF: The Weird World of Banana Slug Sex by Cassandra Willyard

How to Spot Pseudoneuroscience and Biobunk by APS

Bad science not about same-sex parenting by Andrew Perrin

Adrenaline Junkies Look to the Moon for Great New Fix by Amy Shira Teitel

Snakes that chew their food by Andrew Durso

The Anthropocene, and the tech that might save humans by Christie Nicholson

Far out in North Carolina by Stefan Rahmstorf

Ostrich! Get your ostrich here! The man behind the Greenmarket ostrich stand by Taylor Kubota

S.O.S. Save Our Seagrass by Whitney Campbell

What does the way you count on your fingers say about your brain? by Corrinne Burns

Size and evolution by Anthony King

Madness over sea level rise in North Carolina by John Bruno

How Will Global Warming Affect Lizards? A Detailed Physiological Study On Puerto Rican Anoles by Jonathan Losos

Seven sins of scientists part 5: snobbery by Paul Knoepfler

Tidal massaging reveals a hidden ocean on Saturn’s moon, Titan by Matthew Francis

How did the remote control get so awful and confusing? by Daniel Engber

Thoughts on Obamacare by Pal MD

Why supermarket tomatoes look great but taste bland and Exposed: the severe ethical breaches of superhero journalists and Mystery of the flatfish head solved *cough* four years ago *cough* and Why a new case of misconduct in psychology heralds interesting times for the field and Californian condor not extinct yet, but still regularly poisoned by lead by Ed Yong

Shiny! Top 10 reasons why seafarers love Joss Whedon’s Firefly by Miriam Goldstein and Craig McClain

Mysterious Fairy Circles Are ‘Alive’ by Rachel Nuwer

The Dolomite Problem – Peeking Under The Hood by Suvrat Kher

The Curse of the Lead Bullet by Deborah Blum

Should Linus Pauling’s erroneous 1953 model of DNA be retracted? by Jeff Perkel

How to trick people into eating dog food and H*MPING: Why do they do it? by Julie Hecht

The New ExxonMobil: Has the Tiger Changed Its Stripes? and A Court’s Scientific Smackdown: The D.C. Circuit Trashes Science Deniers on Global Warming and the EPA by Chris Mooney

America’s Other Audubon: A Victorian Woman’s Radical Journey of Art, Science & Entrepreneurship by Maria Popova

CDC proposes testing baby boomers for hepatitis C by Jessica M. Morrison

Climate-Studying Seals Bring Back Happy News by Elizabeth Preston

Brave New Worlds by Cameron Walker

Your Color Red Really Could Be My Blue by Natalie Wolchover

Science Denied by Phil Primack

A New Satellite Tool Tracks Deforestation by Rachel Nuwer

Sleeper Sharks Slurp Snoozing Seals by Brian Switek

The Lessons (and Echoes) of Silent Spring by Keith Kloor

The curse of the gingers by PZ Myers

The Higgs Boson is a Liberal Conspiracy To Get The Government More Involved In Mass* by Tom Levenson

Poland’s wolves trot across key wildlife overpasses by DeLene Beeland

In defense of pink microscopes by TheCellularScale

In Defense of #sciencegirlthing by Ben Young Landis

Social Justice in Animals and Animals in Visual Media by Marc Bekoff

Of wanton plants and prudish immune systems: late-night thoughts for National Pollinator Week by Leafwarbler


Media, Publishing, Technology and Society:

SciWriteLabs 8.1: The Lehrer affair, consequence-free plagiarism, and rules for blogging and SciWriteLabs 8.2: Is it kosher to re-use wording from Facebook updates in your journalism? And: do we need a Son of Sam law for media miscreants? by Seth Mnookin

Disrupting journalism education, too by Jeff Jarvis and Disrupting education by Dave Winer

Open Notebook Series: What is an Open Notebook? by Anthony Salvagno

Genius writing – or can a good lab journal help you become smarter? by Eric-Wubbo Lameijer

On Blogging, Direction And Ben Radford’s “Still Skeptical of Blogs” by Kylie Sturgess

Launching version 2.2: Twitter Integration by ScienceSeeker

A bad bad week for access by Richard Smith

Social Networking Concept May Have Emerged During Renaissance, Researchers Say by Tara Kelly

Wellcome Trust will penalise scientists who don’t embrace open access by Alok Jha

Shaking Up Israel’s National Archives: A conversation with Israel’s new chief archivist by Yair Rosenberg

Google’s One-Gender-Fits-All T-Shirts Don’t Fit by Ryan Tate

Library of Congress Acquires Carl Sagan Papers by Audrey Fischer

Putting People at the Center of Journalism by Josh Stearns

How do you tell when the news is biased? It depends on how you see yourself by Jonathan Stray

All A’Twitter: How Social Media Aids in Science Outreach – Discussion and Conclusions by Caitlyn

Did you just tell me to go fuck myself? by Ian Mulvany

Scientists On Twitter: 30 Biologists And Chemists To Follow by Rebecca Searles

Measuring and Visualizing Interdisciplinarity by Samuel Arbesman

Why Porn and Journalism Have the Same Big Problem by Jordan Weissmann

Can you go on the press release diet? A 12-step program by Denise Graveline

How the New York Times technology blog, Bits, perpetuated the myth of a mental illness due to mobile phone use: Or, Follow the money by Les Posen

The Scienceblogging Weekly (June 22nd, 2012)

Blog of the Week:

Like clockwork, almost every day for more than two years, Tommy Leung and Susan Perkins bring you Parasite of the Day. Sometimes gross, but always fascinating. And considering how most of us don’t pay much attention to parasites these days, there is something cool to learn every single day.


Top 10:

The only good abortion is my abortion by Maggie Koerth-Baker:

…Of course, we don’t call it an abortion. We call it “a procedure” or a D&C. See, my potential abortion is one of the good abortions. I’m 31 years old. I’m married. These days, I’m pretty well off. I would very much like to stay pregnant right now. In fact, I have just spent the last year—following an earlier miscarriage—trying rather desperately to get pregnant…

Defending Jonah Lehrer by Bradley Voytek (about criticisim of neuroscience, not “self-plagiarism”):

Cognitive neuroscience grew out of experimental psychology, which has decades of amazing observations to link psychology and behavior. But with this legacy comes a lot of baggage. Experimental psychologists observed that we have the capacity for memory, attention, emotion, etc. and they sought to piece those phenomena apart. With the advent of neuroimaging techniques, psychologists put people in brain scanners to see where in the brain behaviors “were”. But this is the wrong way of thinking about these concepts.

The genius myth by Zen Faulkes:

…This myth of destiny and inevitable triumph of genius is, to me, completely the opposite of what science is. The scientific method leveled the playing field for discovering truth. Anyone could follow the methods and get to the bottom of things, so truth was no longer subject to tricky things like personal revelation….

Climate change is simple: We do something or we’re screwed by David Roberts:

…The challenge I took on was to convey the gist of my “brutal logic of climate change” post in a reasonably short amount of time, using as little scientific jargon as possible. Just: there is a problem that calls for urgent action. Business-as-usual means disaster. This is all gloom and doom — not even much humor. I know that turns people off or shuts them down. I know people need to feel a sense of hope and efficacy. I know — indeed, have recently been writing — that we need a vision of a sustainable future. But I needed to do my own version of “Danger Will Robinson!” Just to get it on the record…

Tunes without composers: music naturally evolves on DarwinTunes by Ed Yong:

…The tunes embedded above weren’t written by a composer, but fashioned through natural selection. They are the offspring of DarwinTunes, a program which creates bursts of noise that gradually evolve based on the preferences of thousands of human listeners. After hundreds of generations, tracks that are boring and grating soon morph into tunes that are really quite rhythmic and pleasant (even if they won’t be topping charts any time soon)….

Snake-eating beetles by Andrew Durso:

So little is known about the parasites of snakes that we tend to discount them all together, but the ecological and evolutionary interactions between hosts and their parasites can be very strong. This is a story about how two enterprising snake biologists solved a mystery that had been puzzling entomologists for decades…

Test-Tube Piggies: How did the guinea pig become a symbol of science? by Daniel Engber:

…To call someone or something a guinea pig may suggest a mere experiment (“Joe Biden was put out as a guinea pig for the White House”), or it can invoke the specter of exploitation (the U.S. Army wanted “to use young men as guinea pigs and throw them away”). The image either describes the scientific process or condemns it. It’s a totem or a scarecrow. What makes this wording more curious is the fact that guinea pigs, real ones, don’t mean much to working scientists. For all their rhetorical importance, the animals scarcely register in the lab…

What’s changed in evolution and ecology since I started my Ph.D. by Jeremy Yoder:

Last month, I filed my PhD dissertation, bringing to an end an intellectual and personal journey that began seven years ago in the summer of 2005. I know a lot more now than I did then, and I know a lot more about the boundaries of what I don’t know, too. But not only has my knowledge changed—evolution and ecology looks a lot different now than it did seven years ago when I was planning my dissertation research. At some point, and often multiple points, in the process of getting a PhD, everybody wonders whether what they’re doing is already out of date. Some of the transformations in the field I think I could see coming. For instance, it was clear in 2005 that computational power would keep increasing, phylogenetics would be used more and more to ask interesting questions, more and more genomes would be available for analysis, and evolutionary developmental biology was on the rise. It was unfortunately also predictable that it would be possible to study climate change in real time over PhD-length timescales. And although the 2008 global financial crisis didn’t help, it was clear that funding and jobs were going to be more competitive than they had been for our predecessors….

Drawing sharp boundaries in a fuzzy world by Chris Rowan:

Humans are natural splitters. We have an innate tendency to look at the world and mentally sort everything into different categories, and grades, and entities: this is one thing, that is another; it was this, now it’s that. Our perception of colour is a good example of how our brains automatically split a continuum into discrete boxes. We’ve incorporated our love of classification deep into science, trying to formalise and quantify the dividing lines we want to draw on everything: it’s this when conditions A and B are met, it’s that when we see Y and Z. But nature doesn’t often make it easy for us to draw our sharp dividing lines….

Why the Scientist Stereotype Is Bad for Everyone, Especially Kids by Michael Brooks:

To many – too many – science is something like North Korea. Not only is it impossible to read or understand anything that comes out of that place, there are so many cultural differences that it’s barely worth trying. It’s easier just to let them get on with their lives while you get on with yours; as long as they don’t take our jobs or attack our way of life, we’ll leave them in peace…


Special topic #1: Science: It’s a Girl Thing

“Science: It’s a Girl Thing”: Lab Barbie, Extra Lipstick by Maryn McKenna

Hey girl! Science wants YOU – but don’t forget the lipstick by Gozde Zorlu

Girls! Be A Scientist! You too Can Dance in the Lab in High Heels! by Deborah Blum

Friday Sprog Blogging: You’ve made it clear “it’s a girl thing,” but is “it” science? and Science For Princesses and How do we make room for pink microscopes? (More thoughts on gendered science kits.) by Janet D. Stemwedel

#sciencegirlthing: the PR guy’s take by David Wescott

E.U.’s ‘Science, it’s a girl thing’ campaign sparks a backlash by Olga Khazan

Science – It’s a Girl Thing (Insert Facepalm Here) by Carin Bondar and Joanne Manaster

Why “Pinkifying” Science Does More Harm Than Good by Noisy Astronomer

Hey Science, “How YOU doin’?” by Summer Ash


Special topic #2: Turtles

Turtle Anatomy, in Stunning Images from 1820 by Maria Popova

Galápagos Monday: Lynn’s Tortoises by Galápagos Monday: Lynn’s Tortoises

Terrifying sex organs of male turtles by Darren Naish

Turtles Have Horrifying Penises by Erin Gloria Ryan

Sex locked in stone: Fossil turtle pairs provide first direct evidence of prehistoric vertebrate mating. by Brian Switek

What Remains in the Rock by Brian Switek

Friday Weird Science: Why, you DIRTY LITTLE HERPS! by Scicurious

Preserved in the Act and Fossilized Turtle Whoopie by Craig McClain


Best Videos:

Eating on a Green Roof: New York’s Buildings Provide Food, Habitat for Wildlife by Rachel Nuwer, Chris New and Brennan Kelley

How do Spaceships Landing in Water Not Hit Boats? by Amy Shira Teitel

Must-watch video on rip currents by Miriam Goldstein

Whale Rainbow by rsean9000

Charged Gold Nanoparticles “Unzip” DNA by N.C.State

World Science Festival Fascinates With Robotic Animals, World’s Lightest Material, Quantum Levitation by Cara Santa Maria


Best Images:

Human Microbiome Project by Perrin Ireland

Greek octopus forms coalition with dolphin’s genitals by Rowan Hooper



The Difference Between Science ‘Skills’ and ‘Knowledge’ by Emily Richmond

How To Stop Science Alienation Syndrome by Deborah Blum

How to Determine If A Controversial Statement Is Scientifically True by Alan Henry

Numeric Pareidolia and Vortex Math by MarkCC

Tech-Based Dollhouse Inspires Future Girl Scientists by Kellie Foxx-Gonzalez

Med Student Rescues Body Part From Airport Security by Robert Krulwich

Things I Learnt from my (Unscientific) Experiences with Crowdsourcing. by David Ng

In Defense of Genetically Modified Crops by Sarah Zhang

When Did Americans Lose Their British Accents? and Why Do People Feel Phantom Cellphone Vibrations? by Matt Soniak

NASA Astronauts Brought Playmates to the Moon and Valentina Tereshkova Was the First Woman in Space and NASA and FAA Agree on the Future of Spaceflight and Vintage Space Fun Fact: NASA’s Canadian Contingent and Mars Rover Curiosity’s Retro Parachute by Amy Shira Teitel

Brains are Different on Macs by Neuroskeptic

Putting Fear In Your Ears: What Makes Music Sound Scary by Jessica Stoller-Conrad

Former Quantitative Trader Spurns Wall Street to Explore the Final Frontier by Patrick Clark

Can Anoles With Differently Shaped Genitals Interbreed? and Territorial And Thermoregulatory Behavior Of Sri Lankan Otocryptis Lizards by Jonathan Losos

How can scientists communicate to the public if they can’t even explain their work to each other? by Maggie

On this Father’s Day, let’s remember the allofathers, too by Emily Willingham

Are Fathers an Endangered Species? by Paul Raeburn

A shot to the head by Vaughan Bell

Get Ready, Because Voyager I Is *This Close* to Leaving Our Solar System by Rebecca J. Rosen

Does All Wine Taste the Same? by Jonah Lehrer

The Blind Spot: A Requiem by Megan Garber and Driving without a Blind Spot May Be Closer Than It Appears by Rachel Ewing

Notebooks Shed Light on an Antibiotic’s Contested Discovery by Peter Pringle

10-year-old solves science riddle and co-authors paper by Jon White

Keeping strong during a long winter nap by Zen Faulkes

What did Galileo ever do to you? by Ken Perrott

End the macho culture that turns women off science by Athene Donald

What’s in a (Gene) Name? by Hillary Rosner

Darwin, Worm Grunters, and Menacing Moles by Anthony Martin

Growing Up on Zoloft – Talking Drugs, Depression, and Identity With Katherine Sharpe by David Dobbs

ANAL CONES! Diadematid sea urchin mysteries! and Follow up on the Anal Cone! (thanks to the New Scientist) by Christopher Mah

How to find good sperm by Kristian Sjøgren

It has long been a mystery why flamingos in captivity suffer foot lesions. A Danish study now claims to have solved a part of this mystery. by Jeppe Wojcik

Black bears show counting skills on computers by Matt Bardo

DIY biology by Laura H. Kahn

Same Old Story: Too Many Graduate Students by Rob Knop

Scientists Find Weak Evidence That Unhealthy Lifestyles Lead to Weak Sperm by Allie Wilkinson

Sound Scholarly Communication by David De Roure

Sports doping, Victorian style by Vanessa Heggie

Welcome to the Anthropocene by David Biello

Goat Moms Recognize Their Kids Saying “Ma!” and The Shambulance: Ionic Foot Detox Baths by Elizabeth Preston

Thoughts on Tarbosaurus, Part 1. and Part 2 by Victoria Arbour

An Abstemious Home by Jessa Gamble

Crowdfunding: It’s not a grant … or is it? by Rebecca Rashid Achterman

The monthly ring: Expanding HIV prevention options for women by Dr. Zeda Rosenberg

Experiments hint at a new type of electronics: valleytronics and Quantum fluctuations may uncover a clue to high-temperature superconductivity by Matthew Francis

Reinventing the Wheel by Meagan Phelan

When Mammals Ate Dinosaurs by Brian Switek

The Rise of the Fork: Knives and spoons are ancient. But we’ve only been eating with forks for a few centuries. by Sara Goldsmith

‘Silent Spring’ is 50. The Credit, and the Blame, It Deserves. by David Ropeik

As America grows more polarized, conservatives increasingly reject science and rational thought by Amanda Marcotte

In the year 2023, and humans are on Mars for all to see by Kevin Orrman-Rossiter

Scalia’s Republican Brain: Why He’ll Come Up With a Reason to Overturn the Healthcare Mandate by Dylan Otto Krider

Does art-from-science really add anything? by Jon Butterworth

Prairie Ridge Ecostation by Christine L. Goforth

Let’s not get carried away by Markus Pössel


Media, Publishing, Technology and Society:

The Slow Web by Jack Cheng

Using Storytelling in Blogs by Maximilian Majewski

I’ll ask the questions here! by M.S.

Lawyer attacking The Oatmeal shocked by big mean Internet’s reaction and Lawyer tries and fails to shut down The Oatmeal’s charitable fundraiser by Casey Johnston and The Oatmeal v. FunnyJunk, Part IV: Charles Carreon Sues Everybody by Ken and The Guy Continues to Mess With The Oatmeal by Kevin Underhill and Funnyjunk’s Lawyer Charles Carreon Just Keeps Digging: Promises He’ll Find Some Law To Go After Oatmeal’s Matt Inman by Mike Masnick

Journalism education cannot teach its way to the future by Howard Finberg and Why Professors Value Journalism Degrees More Than Professionals (Beyond the Obvious) by Carrie Brown-Smith

How would you engage the community in a vagina discussion? by Steve Buttry

Socialising Research: How to get your research results noticed and used. by Jo Hawkins

All A’Twitter: How Social Media Aids in Science Outreach – Chapter 11: Set of Best Practices for Social Media Use by Caitlyn Zimmerman

Teachers and Administrators, Don’t Be Scared of Technology: It Won’t Replace the Classroom by Jody Passanisi and Shara Peters

Is it ok to get paid to promote Open Access? by John Dupuis

Pay attention to what Nick Denton is doing with comments by Clay Shirky

Watergate mythology invites pushback, ignores journalism’s messy nature by Andrew Beaujon

Why Women Still Can’t Have It All by Anne-Marie Slaughter and No One ‘Has It All,’ Because ‘Having It All’ Doesn’t Exist by Lindy West

When Twitter Stumbles, Sites Across the Web Go Down With It by Alexander Furnas

Open Access and Science Communication. Reflections on the need for a more open communication environment by Alessandro Delfanti

A step-by-step approach for science communication practitioners: a design perspective by Maarten C.A. van der Sanden and Frans J. Meijman

Does the technical staff at the World Health Organization (WHO) tweet? by Nina Bjerglund

An Open Letter To Conference Organizers and Panel Moderators by Sean Bonner

Twitterror by Oliver Reichenstein

To create a new social network or not to? Scientists weigh in. by Upwell

The Perfect Technocracy: Facebook’s Attempt to Create Good Government for 900 Million People and Inside Google’s Plan to Build a Catalog of Every Single Thing, Ever by Alexis Madrigal

Why Pen Names Might Be a Bad Idea for Most Bloggers by Ryan Matthew Pierson

Blogging relieves stress on new mothers by Victoria M Indivero

Should We (And Can We) Regulate What We Do Not Understand? by Kathleen Wisneski

Scholars are quickly moving toward a universe of web-native communication by Jason Priem, Judit Bar-Ilan, Stefanie Haustein, Isabella Peters, Hadas Shema, and Jens Terliesner

Bill Marriott: Chairman of the Blog by Michael S. Rosenwald

Apps I Want to Go Away by Sam Grobart

Some Thoughts on Peer Review and Altmetrics by Ian Mulvany


Extra: On the Finch report on Open Access:

Open access is the future of academic publishing, says Finch report by Alok Jha

The Finch Report on open access: it’s complicated by Stephen Curry

First thoughts on the Finch Report: Good steps but missed opportunities by Cameron Neylon

U.K. Panel Backs Open Access for All Publicly Funded Research Papers by Kai Kupferschmidt

Finch Report, a Trojan Horse, Serves Publishing Industry Interests Instead of UK Research Interests by Stevan Harnad


Extra: On the “self-plagiarism” saga:

On science blogs this week: Jonah Lehrer by Tabitha M. Powledge

Jonah Lehrer: The issues are simple by Paul Raeburn

This Week in Review: The potential of Microsoft’s Surface, and keeping blogging ideas fresh by Mark Coddington

Jonah Lehrer, Hypertext Author by Dorian Taylor

Jonah Lehrer “Self-Plagiarism” Brouhaha is Crap by Matthew E May

New Journalistic Workflow by Bora Zivkovic

Blogging and recycling: thoughts on the ethics of reuse. by Janet D. Stemwedel

How Jonah Lehrer should blog by Felix Salmon

The ethics of recycling content: Jonah Lehrer accused of self-plagiarism by Jonathan M. Gitlin

A (Partial) Defense of Jonah Lehrer by Robert Wright

The Tyranny of Novelty by Matthew Francis

Jonah Lehrer, self-borrowing and the problem with “big ideas” by Laura Hazard Owen

The Scienceblogging Weekly (June 15th, 2012)

Blog of the Week:

Russ Williams is the Director of the North Carolina Zoological Society and, as far as I know, the only “director of a zoo” who blogs. And does he ever – Russ has been blogging up a storm ever since 2005 when Ed Cone taught him how (you may call me The Blogfather, but Ed Cone is the blogfather for many of us in North Carolina). On his blog Russlings, Russ covers plenty – what is new at the N.C.Zoo in Asheboro, what is new in other zoos around the country and the world, what is new in policy and politics of animal conservation, plus cool pictures and videos of wildlife. But where the value really comes up is at the times of natural disasters – Russ is “in the know” and often the first and/or the only person to blog about the status of zoos and aquaria, as well as farm animals, wildlife preserves etc, in the affected areas. During disasters, Russlings is the Go-To place for such coverage.


Top 10:

How Our Disinterest in ‘The Environment’ Signals the End of Nature by Christopher Mims:

No one reading this has the slightest fucking clue what “nature” is, and in 1995 fisheries scientist Daniel Pauly proved it. In the paper that introduced the term “shifting baselines,” Pauly described how experts who determined how many fish should be caught often started with whatever the baseline state of the ecosystem was when they started their careers, instead of considering what a fishery might have looked like in the past, when it wasn’t nearly as degraded….

Getting used to being in charge of the planet by David Roberts:

…Nonetheless, like evolution, the dominance of human beings on Spaceship Earth is a profound and terrifying threat to all sorts of traditional worldviews. If Darwin showed us that God is not our author, the Anthropocene shows that He is not our caretaker. There’s no parent to supply us with endless resources and endless room to dispose of our waste. There’s no one to protect us or prevent us from screwing it all up….

Walking the Line: How to Identify Safe Limits for Human Impacts on the Planet by David Biello:

Is preserving the general environmental conditions that allowed civilization to flourish—a moderate climate, a rich array of species, rivers that reach the sea—necessary to ensure humanity endures? Or is minimizing alterations to the global environment introduced by human activity—rising levels of CO2 from fossil-fuel burning, widespread extinction, dams that impound water—more important to our success? Choosing the right approach is vital as the scale of human impact on the planet becomes so large that scientists are calling this new epoch in Earth’s history the Anthropocene (when human activity alters global climate and ecosystems)…

#GMOFAQ: Transferring genes from one species to another is neither unnatural nor dangerous by Michael Eisen:

Last week I wrote about the anti-science campaign being waged by opponents of the use of genetically modified organisms in agriculture. In that post, I promised to address a series of questions/fears about GMOs that seem to underly peoples’ objections to the technology. I’m not going to try to make this a comprehensive reference site about GMOs and the literature on their use and safety (I’m compiling some good general resources here.) I want to say a few things about myself too…

Sea level rise 101 by John Bruno:

Based on the NC legislature’s decree about the science of sea level rise projections and some of the related propaganda we have seen from climate change deniers, I get the sense there is a lot of confusion about sea level rise. So here is a primer on what we know about sea level and climate change…

Dirty soil and diabetes: Anniston’s toxic legacy by Brett Israel:

The Rev. Thomas Long doesn’t have neighbors on Montrose Avenue anymore. Everyone is gone. Widespread chemical contamination from a Monsanto plant was discovered in this quiet city in the Appalachian foothills back in the 1990s. In West Anniston, behind Long’s home, a church was fenced off, and men in “moon suits” cleaned the site for weeks. Nearby, boarded windows and sunken porches hang from abandoned shotgun houses. Stray dogs roam the narrow streets. A red “nuisance” sign peeks above the un-mowed lawn of one empty house. Bulldozers will be here soon…

Pollution, Poverty, People of Color: No beba el agua. Don’t drink the water. by Liza Gross

Jessica Sanchez sits on the edge of her seat in her mother’s kitchen, hands resting on her bulging belly. Eight months pregnant, she’s excited about the imminent birth of her son. But she’s scared too. A few feet away, her mother, Bertha Dias, scrubs potatoes with water she bought from a vending machine. She won’t use the tap water because it’s contaminated with nitrates…

The crayola-fication of the world: How we gave colors names, and it messed with our brains (part II) by Aatish Bhatia:

Lately, I’ve got colors on the brain. In part I of this post I talked about the common roads that different cultures travel down as they name the colors in their world. And I came across the idea that color names are, in some sense, culturally universal. The way that languages carve up the visual spectrum isn’t arbitrary. Different cultures with independent histories often end up with the same colors in their vocabulary. Of course, the word that they use for red might be quite different – red, rouge, laal, whatever. Yet the concept of redness, that vivid region of the visual spectrum that we associate with fire, strawberries, blood or ketchup, is something that most cultures share….

How the Chicken Conquered the World by Jerry Adler and Andrew Lawler:

The chickens that saved Western civilization were discovered, according to legend, by the side of a road in Greece in the first decade of the fifth century B.C. The Athenian general Themistocles, on his way to confront the invading Persian forces, stopped to watch two cocks fighting and summoned his troops, saying: “Behold, these do not fight for their household gods, for the monuments of their ancestors, for glory, for liberty or the safety of their children, but only because one will not give way to the other.” The tale does not describe what happened to the loser, nor explain why the soldiers found this display of instinctive aggression inspirational rather than pointless and depressing. But history records that the Greeks, thus heartened, went on to repel the invaders, preserving the civilization that today honors those same creatures by breading, frying and dipping them into one’s choice of sauce. The descendants of those roosters might well think—if they were capable of such profound thought—that their ancient forebears have a lot to answer for….

‘Sexual depravity’ of penguins that Antarctic scientist dared not reveal by Robin McKie:

It was the sight of a young male Adélie penguin attempting to have sex with a dead female that particularly unnerved George Murray Levick, a scientist with the 1910-13 Scott Antarctic Expedition. No such observation had ever been recorded before, as far as he knew, and Levick, a typical Edwardian Englishman, was horrified. Blizzards and freezing cold were one thing. Penguin perversion was another….


Special topic #1: stimulants in school:

The Questions About ADHD Drugs The New York Times Didn’t Ask by Matthew Herper

The labels change, the game remains the same by Vaughan Bell

The NY Times: When Stimulants Are Bad by Robert Whitaker

The Horror of Drug-Boosted Grades and SAT Scores by Jacob Sullum

Should Ritalin Be Distributed To Everyone Taking the SATs? by Gary Stix.


Special topic #2: Prometheus and science in the movies:

The biology of Prometheus by Zen Faulkes

The Science of Prometheus – a review, containing a lot of spoilers by Frank Swain

Prometheus: an archaeological perspective (sort of). by Henry Rothwell

Ridley Scott’s Prometheus Examines the Roots of Alien’s Mythology by Larry Greenemeier

‘Prometheus’ Offers a Creationist Indulgence for Science Geeks by James Gorman

Prometheus: what was that about? Ten key questions by Ben Walters

Stealing fire by Zen Faulkes

Space: The Science of Prometheus by Discovery News

What’s Wrong With Prometheus (a Partial List) by Julian Sanchez

Best Videos:

Instant Egghead – What Causes Brain Freeze? by Ferris Jabr and Eric Olson

The Fabulab’s Flame Challenge by Jeanne Garbarino, Perrin Ireland and Deborah Berebichez

Curly Haired Mafia – Prometheus SPOILERS!!! (video) by Lali DeRosier, DNLee and Dr.Rhubidium

Best Image:

UCD worker wins award for rare photo of bee sting in action by Andrea Gallo


Sensory Ecology of the Third Eye by Ashli Moore

Lovely Lysenko by Dominic Berry

Assuming the Doctor’s a ‘He’ by Danielle Ofri, M.D.

Why We (Accidentally) Name Babies for Hurricanes by Elizabeth Preston

What is a vagina? by Emily Willingham

Imaginary Numbers are Real by Matthew Francis

Curious Experiments by Archbishop Marsh’s Library. “‘Curious Experiments’ for ‘The Amusement and Entertainment of Ladies, as well as Gentlemen’ which took place before a paying audience in Dublin in 1743.” recreated by high school students 270 years later.

Crowdfunding: A New Opportunity for Science and Innovation by John R. Platt

Old Books that Guided Science by Samuel Arbesman

Why you probably won’t experience your own traumatic death by George Dvorsky

June Gloom by Cameron Walker

Dear Slate: America Needs More Artists by See Arr Oh

Negative results and dodgy papers: keep quiet or publish? by Tom W. Phillips

Our Animal Natures by Barbara Natterson-Horowitz and Kathryn Bowers

‘I’m Not Your Wife!’ A New Study Points to a Hidden Form of Sexism by Gayle Tzemach Lemmon

Achtman on Plague Evolution by Michelle Ziegler

Would You Call Me A Scientist? by Sheril Kirshenbaum

Visiting “Brains. The Mind as Matter” at the Wellcome Collection by The curious neuron

Food Trade Too Complex to Track Food Safety by Maryn McKenna

The Johannes Kepler Defense by Romeo Vitelli

Taking the colour out of light. by Thony C. “The man who didn’t invent the achromatic lens” John Dollond born 9 June 1706.

Carnivorous plants respond to increased soil nitrogen, eco-news websites completely miss the point by Andrew Thaler

Virginia Lawmaker Says ‘Sea Level Rise’ Is A ‘Left Wing Term,’ Excises It From State Report On Coastal Flooding by Rebecca Leber

Teaching Neuroanatomy With A Showercap by Neuroskeptic

Fungus Inside Us: A New Health Frontier? by Brandon Keim

The Top Ten Strangest Self-Experiments Ever by Alex Boese

G r e a t e r / l e t t e r / s p a c i n g / helps reading in dyslexia by The Neurocritic

Dangerous Interventions: MMS and Autism by Emily Willingham

Cholera vaccine deployed to control African outbreak by Gozde Zorlu

Bath salts and… zombies? by Donna

You Don’t Have What it Takes by Lucy E. Hornstein MD

What they didn’t tell you about the transit of Venus by Rebekah Higgitt

Science Outreach: What Do You Need? by Matt Shipman

Double Xpression: Liz Neeley, Science Communicator Extraordinaire by Jeanne Garbarino

Overeating Makes Flies Obese, Diabetic, Dead by Elizabeth Preston

Creationism Uses Dinosaurs to Lure Kids Into Radical Ideas, But Scientists Should Not Care Too Much by Cameron English

No, America Does NOT Need More Scientists and Engineers by Derek Lowe

Plant uses chemical weapons to make mice spit out its seeds and To control cannibal toads, you just need the right bait and Fear of spiders changes bodies of grasshoppers and makes plants decay more slowly and Microbial Menagerie and Male spider castrates himself and gets more stamina by Ed Yong

Where have I been? Or, science outreach’s place in science. by Lauren Meyer

The culinary adventures of a cuttlefish by Jonas

Science Communication: A sort-of-kind-of Carnival, and some more thoughts of mine by Scicurious

Scientists map ‘Facebook for birds’ by Alan Boyle

Double Xpression: Debbie Berebichez, PhD Physicist by Jeanne Garbarino

The anthropologist and the kurgans by John Hawks

Scientists Tackle The Geography Of Nature Vs. Nurture In Maps Of U.K. by Ted Burnham

Does Acceptance of Evolution Matter? by Ed Brayton

Did Neanderthals Produce Cave Paintings? by Sarah Everts

Media, Publishing, Technology and Society:

Sorry, Young Man, You’re Not the Most Important Demographic in Tech by Alexis Madrigal

Online Seniors: Tech-Savvier Than You Think by Frederic Lardinois

Open access to research is inevitable, says Nature editor-in-chief by Alok Jha

A Serious Look at Funny Faces by Henry Adams – on the history of cartoons.

An Anarchist Constitution for Twitter by Rebecca Greenfield

Why Twitter Matters: Tomorrow’s Knowledge Network by Nigel Cameron

Learning To Write From Chopin by Murr Brewster

An alternative to the college degree? by Amy Scott

From scrubbing floors to Ivy League: Homeless student to go to dream college by Vivian Kuo

11 dreams for the publishing debate — #1 fewer papers and 11 dreams for the publishing debate — #2 get real credit for surveys and exposition and 11 dreams for the publishing debate — #3 get real credit for refereeing and #4 get real credit for communicating and
#5 sharing all our work every way we can by Peter Krautzberger

All A’Twitter: How Social Media Aids in Science Outreach – Chapter 8: Talking with the Social Media Experts and Chapter 9: Gathering Survey Results, and Chapter 10: Coming to Conclusions by Caitlyn Zimmerman

Why the World’s Most Perfect News Tweet Is Kind of Boring by Megan Garber

Do Journo Watchers Ignore Environmental Beat? by Keith Kloor

Exhausted With The Same by Erika Napoletano

Why you should be excited about vector-based maps in iOS 6 by Tim De Chant

Pitch Perfect – a primer for scientists reaching out to journalists by Liz Neeley

Social media and Google Analytics – who’s interested in botany? by Alun Salt

Paying for information versus *access* to information: A key distinction for news publishers by Robert Niles

Please RT by n+1 editors

The Scienceblogging Weekly (June 8th, 2012)

Wow – this was hard! I could have had at least Top 20 instead of Top 10 (but you’ll find them all listed down there anyway)…


Blog of the Week:

Tanya Khovanova’s Math Blog is a blog by Tanya Khovanova, a Visiting Scholar and Research Affiliate at MIT, a 1976 gold medalist (and 1975 silver medalist) at the International Mathematics Olympiad. What she does the most (though there is occasionally other stuff there) is to pose difficult (and some not to so difficult) mathematical problems and puzzles for her readers to try to solve in the comments. Go ahead and give it a try yourself!


Top 10:

Sea Level Rise Is Tied to Prevalence of Homosexuality by Craig McClain:

Although only two years old and previously unrecognized by the scientific establishment, Global Draining (GD) has now become a widely accepted theory. GD states that sea level is falling not rising (Southern Fried Science, 2010a). Current rates of GD indicate the entire world’s ocean will be empty by 2026 (Southern Fried Science, 2010a). Local-scale observation of in situ draining combined with a robust theoretical model firmly place the rate of draining at 40 Gigatons of water per year (Dr. M, 2010). It has been argued that both one and multiple holes occur in the ocean floor that allow for GD (i.e. the monoclavis versus polyclavis hypotheses via McCay, 2010; Southern Fried Science, 2010b). However, the impacts and causes of GD are not clearly understood. Despite this, GD is a fundamental tenet of nearly every facet of science and likely correlated with many aspects of biology, economics, sociology, religion, and politics. For example, GD is likely to lead to massive die offs of sharks and reduce global atmospheric oxygen levels (Shark Diver, 2010)…

The crayola-fication of the world: How we gave colors names, and it messed with our brains (part I) by Aatish Bhatia:

In Japan, people often refer to traffic lights as being blue in color. And this is a bit odd, because the traffic signal indicating ‘go’ in Japan is just as green as it is anywhere else in the world. So why is the color getting lost in translation? This visual conundrum has its roots in the history of language…

Arsenic Life Wrap-Up: The Good, the ‘Not-So-Good’ by See Arr Oh:

“Arsenic Life,” a hot-button issue for much of the past year, reemerged this week with two new papers, one propitious, and one, well…not so much….

In defense of frivolities and open-ended experiments by Bradley Voytek:

My first child was born just about nine months ago. From the hospital window on that memorable day, I could see that it was surprisingly sunny for a Berkeley autumn afternoon. At the time, I’d only slept about three of the last 38 hours. My mind was making up for the missing haze that usually fills the Berkeley sky. Despite my cloudy state, I can easily recall those moments following my first afternoon laying with my newborn son. In those minutes, he cleared my mind better than the sun had cleared the Berkeley skies…

Women’s Work by Virginia Hughes:

I write mostly about neuroscience, genetics and biotechnology. That means I spend most of my time talking to and writing about men.

In May of 2011 (chosen arbitrarily just because it was a year ago and I’m pretty sure I wasn’t thinking about this gender gap then), 89 percent of my phone interviews were with men.

I can think of a few reasons for this…

The Mechanics and Meaning of That Ol’ Dial-Up Modem Sound by Alexis Madrigal:

Of all the noises that my children will not understand, the one that is nearest to my heart is not from a song or a television show or a jingle. It’s the sound of a modem connecting with another modem across the repurposed telephone infrastructure. It was the noise of being part of the beginning of the Internet…

I’m not a speciesist, but… by Jack Scanlan:

Is it a paradox to hate your own species? Is such a feeling the product of a broken and conflicted mind? Or could it perhaps be the signature of psychopathy? Every day these questions run through my mind and I feel guilty. Why? Well, because I do hate my own species. Homo sapiens is terrible, and I’m surprised more people don’t recognise this…

The science and ethics of voluntary amputation by Mo Costandi:

…In January 2000, the mass media ran several stories about Robert Smith, a surgeon at the Falkirk and District Royal Infirmary who had amputated the legs of two patients at their own request and was planning a third amputation. The news stories incorrectly described the patients as suffering from Body Dysmorphic Disorder. They further stated that the director of NHS trust running the hospital at which Smith works described the amputation of healthy limbs as “inappropriate”; since then, no British hospital has performed a voluntary amputation…

In Defense of Mickey Mouse Science by Byron Jennings:

…I suppose one could hook up the computers directly to the experiments and have them generate models, test the models against new observations and then modify the experimental apparatus without any human intervention. However, I am not sure that would be science. Science is ultimately a human activity and the models we produce are products of the human mind. It is not enough that the computer knows the answer. We want to have some feeling for the results, to understand them. Without the simple models, Mickey Mouse science, that would not be possible: the big news made ever so small…

From plaster to programming: How borrowed technologies are changing paleontology by Justine E. Hausheer:

In popular culture, paleontologists are like Indiana Jones. Rugged men wandering through rocky deserts, wearing wide-brimmed leather hats and multi-pocketed khaki vests. Rock-hammers hang nonchalantly from their belt-loops, maps and note-pads protrude from pockets. On a whim, they brush aside some sand to reveal a ferocious skull and massive vertebrae, and then they puzzle out the mysteries of dinosaurs just by staring at the rocks. But in contemporary science, paleontologists are biologists, computer programmers, and engineers…


Special topic: Scientists, Journalism and Outreach

Eh, the whole week started with The Unwritten Rules of Journalism by Adam Ruben and then the blogosphere exploded – see for yourself:

Make Me Feel Something, Please by Soren Wheeler

Will Scientists Ever Get Science Writing? by Deborah Blum

Science Careers Magazine: A platform for a funny guy who says he really hates science journalism by Charlie Petit

Keep Cool Science Journalists by Khalil A. Cassimally

Congratulations! You’re Dumb! by Matthew Francis

Science is more than freaks and circuses by Paul Livingston

A KISS for communicating science by biochembelle

Scientists Engaging With The Public: Let’s Get Started and Talking About Science: Why Do You Do What You Do? by Matt Shipman

Summary of the #ReachingOutSci Series by Communities Team

On Outreach: something’s got to give by scicurious

A Call To Arms For Young Science Journalists by Khalil A. Cassimally

Which came first, rewarding outreach or doing it? On chickens, eggs, and overworked scientists by Kate Clancy

The root of problems by Zen Faulkes

Quick thoughts on the what and why of science outreach by Cedar Riener

Where Have All the Scientists Gone? by Magdeline Lum

Why are scientists trapped in the ivory tower and what can be done to escape? by Jeanne Garbarino

Speak Up, Scientists! by Tom Bartlett

So You Want To Communicate Science Online: The Flowchart by Miriam Goldstein

Some Scattered Thoughts on Outreach Work by Eight Crayon Science

One Venus transit – but many kinds of scientific outreach by Chris Rowan


Best Videos:

A Wildlife Rescue Center for New York City by Rachel Nuwer, video by Kelly Slivka and Kate Yandell.

The Curious Sex Lives Of Animals (VIDEO) by Cara Santa Maria and Carin Bondar

What we didn’t know about penis anatomy (video) by Diane Kelly

CreatureCast – Ginko (video) by Casey Dunn

Fruitfly Development, Cell by Cell (video) by Joe Hanson



How Our Disinterest in ‘The Environment’ Signals the End of Nature by Christopher Mims

Dramatic impacts on beach microbial communities following the Deepwater Horizon oil spill by Holy Bik

I Point To TED Talks and I Point to Kim Kardashian. That Is All. by Carl Zimmer

NASA’s Manned Venus Orbital Mission and This Is What Happens When Galaxies Collide and The X-15′s First Glide by Amy Shira Teitel

North Carolina’s attempted ban on sea level rise is a boon for Global Draining researchers by Southern Fried Scientist

How Intuition and the Imagination Fuel Scientific Discovery and Creativity: A 1957 Guide by Maria Popova

Battleship Earth: Does the Pentagon have the right weapons to fight off an alien invasion? by Cara Parks and Joshua E. Keating

Is Arsenic the Worst Chemical in the World? and The Arsenic Diet by Deborah Blum

Bad Reaction: The Toxicity of Chemical-Free Claims by Sharon Hill

Peptide shows potential to reverse skin fibrosis and Turning down the heat revs up brown fat by Kathleen Raven

Mermaids Embodies the Rotting Carcass of Science TV and Time for a Dinosaur Attack? by Brian Switek

David Dobbs and science storytelling: Lost in your brain. by Paul Raeburn

Piscine Geriatrics and Update on the iFish by whizbang

“HULK SMASH GM” – mixing angry Greens with bad science by Martin Robbins

For an Isolated Tribe, Time Follows the Terrain, and the Future is Uphill by Valerie Ross

Turning Scientific Perplexity into Ordinary Statistical Uncertainty by Cosma Shalizi

Credible Amelia Earhart Signals Were Ignored by Rossella Lorenzi and More Amelia Earhart Nonsense by Brian Dunning

“How do you feel about Evidence-Based Medicine?” by Harriet Hall

Wind-aided birds on their way north by Liz O’Connell

Transit of Venus through the ages by Jonathan Nally

Attempts to predict earthquakes may do more harm than good by David Petley

Reporting Preliminary Findings by Steven Novella

What makes sea-level rise? by Stefan Rahmstorf

Detectable but not hazardous: radioactive marine life of Fukushima by Miriam Goldstein

Elaine Fuchs: “There’s no comfortable route for a scientist” by Rachel Zwick

Why the GOP distrusts science and Conservatives Attack Scientific Findings About Why They Hate Science (Helping to Confirm the Science) by Chris Mooney

Jumping Vampire Spiders Choose Victims by Headwear and Why You Can’t Kill a Mosquito with a Raindrop and Rare Blooms by Elizabeth Preston

To study vampire spiders, build Frankenstein mosquitoes and Cockroaches and geckos disappear by swinging under ledges… and inspire robots and Giant insects disappeared thanks to falling oxygen levels and agile birds and Bacteria turn themselves into living electric grids by sending currents down mineral wires and How to weigh dinosaurs with lasers and Will we ever… clone a mammoth? by Ed Yong

New species are found all the time, even in Europe. by Tim Parshall

Sunday morning musings by PalMD

Winning the climate culture war and The top five things voters need to know about conservatives and climate change by David Roberts

Genetic Modification – What’s the big deal? by Donna

Cancer on the Brain by David Ropeik

Learning by Making: American kids should be building rockets and robots, not taking standardized tests. by Dale Dougherty

“Arsenic bacteria”: If you hadn’t nailed ‘im to the perch ‘e’d be pushing up the daisies by Ashutosh Jogalekar

BP Demands Scientist Emails in Gulf Oil Spill Lawsuit by Brandon Keim

Will Lex Luthor save North Carolina from climate change? by Michael Yudell

Coordinated Hunting in Red Devils by Craig McClain

Use it or lose it? by Levi Morran

Natural voyeurism: Animal webcams make peeping Toms of us all by Kelly Slivka

Why We Don’t Believe In Science by Jonah Lehrer

Mermaids do not exist, and five other important things people should, but do not, know about the ocean by WhySharksMatter

Transits of Earth from Other Planets by John Rennie

Bend me, shape me: flexible electronics perform under punishing conditions by Matthew Francis

The Invasivore’s Dilemma by Michelle Nijhuis

Beware Of The Branches: The Impacts Of Habitat Structure On Locomotion And Path Choice by Timothy Higham

Science Hubris, or Shame on You, Mayim Bialik by Lucy E. Hornstein MD

Your guide to zombie parasite journalism by Carl Zimmer

Science Gallery Pushes Art With A Social Conscience by Lucas Kavner

This Is Your Quail on Drugs, Behaving Badly by Neda Semnani

Making neuroscience public: Neurohype, neuroscepticism and neuroblogging by Brigitte Nerlich

Dictators Turn Strangely Benevolent in Online Game by Dave Mosher

The Platypus Fallacy. by T. Ryan Gregory

What You Know About the Difference in Dolphins and Porpoises is Wrong by SoundingTheSea

Has the public’s understanding of science devolved into a perverse worship of uncertainty? by Pamela Ronald

Darwin’s ‘clumsy’ prose by Angelique Richardson

Life and science challenges: flames, Hawkeye, the needle and the damage done by Jeanne Garbarino

Mars One: The Martian Chronicles or Big Brother Live on Mars? by Danica Radovanovic

Driving without a Blind Spot May Be Closer Than It Appears by Rachel Ewing

I love waking up to bad science in the morning paper by Rachel Felt

Interloper of the Venus Transit by Phil Plait

Brian: The Typographical Error that Brought Early Career Neuroscientists and Artists Together by Megan J. Dowie, Erin Forsyth and Leah Forsyth

How can I stop…… stammering? by Stuart Farrimond

Identical Twins, Different Lives by Neuroskeptic

That Antidepressants In Water Cause Autism Study by Neuroskeptic, and Fish, Antidepressants, Autism and a Problematic Research Premise by Dorothy Bishop, and Taking the Bait: A Fish (and autism) Story by Deborah Blum

Zombies are not a health problem (for us). Should they be a solution? by Jonathan Purtle

Portrait of the Archaeologist as Young Artist by Heather Pringle

Building a Shadow CV by Jacquelyn Gill

WHO adopts global vaccine action plan by Gozde Zorlu

The Republican Brain: The perils and promise of taking a stand. by Paul Raeburn

N. Carolina Senate decides to include science in sea level projections after all by John Timmer


Media, Publishing and Technology:

Lessons in blogging (and tweeting) from Samuel Pepys by Justin Ellis

Social Networks Over Time and the Invariants of Interaction by Samuel Arbesman

This I believe about journalism, newspapers and the future of media by Tim J. McGuire

Beyond citations: Scholars’ visibility on the social Web by Judit Bar-Ilan, Stefanie Haustein, Isabella Peters, Jason Priem, Hadas Shema and Jens Terliesner

Wi-Fi and Amtrak: Missed Connections by Ron Nixon – obviously written by someone who’s never boarded anything but Acela, which is notorious for bad wifi. I find wifi perfectly usable on the Carolinian route of Amtrak.

The North West London Blues by Zadie Smith

SPARC Open Access Newsletter, issue #164 by Peter Suber

Facebook will sell me to you, and you to me by Scott Rosenberg

A brief history of Car Talk: “They’ve changed the way people see public radio in America” by Andrew Phelps

Ebook revolution can kindle a passion for publishing by Ed Victor

My Gettysburg oration: A vision for journalism that can long endure by Steve Buttry

All A’Twitter: How Social Media Aids in Science Outreach – Chapter 6: Struggles of Facebook for the Multipurpose Marine Cadastre and Chapter 7: Survey Design by Caitlyn Zimmerman

Not a fan of the big Bitly revamp? Here are 9 alternatives by Nancy Messieh and A little free advice for Bitly by Dave Winer

Added Value: I do not think those words mean what you think they mean and 25,000 signatures and still rolling: Implications of the White House petition by Cameron Neylon

Sustainable quality by Dan Conover

Revisiting the View from Nowhere by John L. Robinson

How Writing A Science Blog Saved My PhD and 3 Mandatory Tools For Digital Scientists by Julio Peironcely

How the Internet Became Boring by Christopher Mims

“Dear Author” by Ted C. MacRae

What Is a Blog Post? by Rob Jenkins

Startup Culture: Values vs. Vibe by Chris Moody

Ask TON: Organizing notes by Jeanne Erdmann and Siri Carpenter

Why Reporting Is Ripe For Innovation by Vadim Lavrusik

Guys! I Have the Next Big Thing: A Social Network for Hermit Crabs by Alexis Madrigal

Arianna Huffington says HuffPo’s ‘sideboob’ news page is meant as a joke by Ruth Spencer

Does your newsroom have a smart-refrigerator strategy? by Adrienne LaFrance

How to improve environmental coverage? by Curtis Brainard

10 Timeframes by Paul Ford

It’s a Googly World: A Map of the Planet’s Most Visited Websites by Country by Rebecca J. Rosen

Twitter Gives you the Bird by Armin and Twitter’s new bird logo by Dave Winer

The great newspaper liquidation by Jack Shafer

The Scienceblogging Weekly (June 1st, 2012)

Blog of the Week:

Vintage Space is a blog by Amy Shira Teitel, science writer and historian of space exploration living in Arizona. She has been busy lately, contributing articles to Discovery News, Motherboard, Spaceflight Observer podcasts, Scientific American Guest Blog, Soapbox Science blog, Timeline Magazine, AmericaSpace and Universe Today, among else. Vintage Space is her writing laboratory, where she first explores topics she may subsequently expand into longer pieces for other venues. And she links to all of her articles as they go live in various places so you can keep up with her prolific output. Those of you regular readers of Scientific American blogs may remember her guest posts, and for those of you not familiar, those can give you the taste of her fascinating forays into the history of space: Sky Crane – how to land Curiosity on the surface of Mars and Apollo 1: The Fire That Shocked NASA and John Glenn: The Man Behind the Hero.

Top 10:

Nicotine and the Chemistry of Murder by Deborah Blum:

The 1850 murder of Gustave Fougnies in Belgium is not famous because of the cleverness of his killers. Not at all. They – his sister and brother-in-law – practically set off signal flares announcing their parts in a suspicious death.

It’s not famous because it was such a classic high society murder. The killers were the dashing, expensive, and deeply indebted Comte and Countess de Bocarmé. The death occurred during a dangerously intimate dinner at their chateau, a 18th century mansion on an estate in southern Belgium.

Nor it is remembered because the Comte died by guillotine in 1851 – so many did after all.

No, this is a famous murder because of its use of a notably lethal poison. And because the solving of this particular murder changed the history of toxicology, helped lay the foundation for modern forensic science. The poison, by the way, was the plant alkaloid nicotine….

Richard Dawkins, Edward O. Wilson, and the Consensus of the Many by David Sloan Wilson:

…I mean Dawkins and Wilson no disrespect by calling them two among many. I trust that they would agree and would defer to others especially when it comes to mathematical models, which is not their area of expertise. If the public is going to become literate on the issues at stake—as well they should, because they are fundamental to the study of human sociality—then they will need to realize that both Wilson and Dawkins get some things right and other things wrong. Moreover, the entire community of scientists is in more agreement than the infamous exchange in Nature seems to indicate. Taking the argument from authority seriously can lead to a breakthrough in the public’s understanding of social evolution. …

The protein makes the poison: Dancing fruit flies and terfenadine by Ashutosh Jogalekar:

…Dose-specific toxicity is indeed of paramount importance in medicine, but if you delve deeper, the common mechanism underlying the toxicity of many drugs often has less to do with the specific drugs themselves and more to do with the other major player in the interaction of drugs with the human body – proteins. Unwarranted dosages of drugs are certainly dangerous, but even in these cases the effect is often mediated by specific proteins. Thus in this post, I want to take a slightly different tack and want to reinforce the idea that when it comes to drugs it’s often wise to remember that “the protein makes the poison”. I want to reinforce the fact that toxicity is often a function of multiple entities and not just one. In fact this concept underlies most of the side-effects of drugs, manifested in all those ominous sounding warnings delivered in rapid fire intonations in otherwise soothing drug commercials…

The trouble with brain scans by Vaughan Bell:

Neuroscientists have long been banging their heads on their desks over exaggerated reports of brain scanning studies. Media stories illustrated with coloured scans, supposedly showing how the brain works, are now a standard part of the science pages and some people find them so convincing that they are touted as ways of designing education for our children, evaluating the effectiveness of marketing campaigns and testing potential recruits…

Cloaking the rainbow by Rose Eveleth:

Invisibility cloaks aren’t just for Harry Potter anymore. Last year, researchers made one that cloaked things in time. Now they’ve made thousands of tiny invisibility cloaks that trap a rainbow. That’s right, 25,000 invisibility cloaks trapping a rainbow. The first question you might be asking is: why? Why does it take 25,000 invisibility cloaks to trap a rainbow? Or maybe, why trap a rainbow in the first place?

An Analysis of Blaster Fire in Star Wars by Rhett Allain:

You have no idea how long I have been planning to look at the blasters in Star Wars. No idea. Finally, the 35th Anniversary of Star Wars has motivated me to complete my study (which I haven’t actually started). Here is the deal: What are these blasters? How fast are the blaster bolts? Do the blasters from the spacecraft travel at about the same speed as the handheld blasters? Why do people still think these are lasers?…

Don’t worry so much about being the right type of science role model by Marie-Claire Shanahan:

What does it mean to be a good role? Am I a good role model? Playing around with kids at home or in the middle of a science classroom, adults often ask themselves these questions, especially when it comes to girls and science. But despite having asked them many times myself, I don’t think they’re the right questions…

Evolutionary psychology: A dialogue by Jeremy Yoder:

A Biologist went down to the coffee shop one day, because the walk out to the edge of the University campus provided some brief respite from the laboratory. Along the way the Biologist encountered an Evolutionary Psychologist, who was also going to the coffee shop, and they fell to walking together…

How I Stopped Worrying (about science accuracy) And Learned to Love The Story by Phil Plait:

When I was a kid – and who am I kidding; when I was an adult too – I made fun of the science in movies. “That’s so fakey!” I would cry out loud when a spaceship roared past, or a slimy alien stalked our heroes. Eventually, my verbal exclamations evolved into written ones. Not long after creating my first website (back in the Dark Internet Ages of 1997) I decided it would be fun to critique the science of movies, and I dove in with both glee and fervor. No movie was safe, from Armageddon to Austin Powers…

The Fantastic Gliding Stegosaurus by Brian Switek:

Stegosaurus is undoubtedly one of the most perplexing dinosaurs. What was all that iconic armor for? (And how did amorous stegosaurs get around that complication?) Paleontologists have been investigating and debating the function of Stegosaurus ornamentation for decades, but without much consensus. The dinosaur’s spectacular plates were certainly prominent visual signals, but could they also have been used for regulating body temperature? Or might there be some evolutionary impetus we’re not thinking of?



The Anatomy of a Videogame-Scare Story by Brian Fung

My Favorite Toxic Chemical by John Spevacek:

Urban trees reveal income inequality and Home Income inequality, as seen from space by Tim De Chant

Neuroscientists should study Zombie Ants by TheCellularScale

Octopuses Host a Masterclass on Hiding by Elizabeth Preston

Toxic Carnival: Day Three and Toxic Carnival: Day Four and Toxic Carnival: Day Five by Matthew Hartings

Social Sauropods? by Brian Switek

Birds Have Juvenile Dinosaur Skulls by Brian Switek

Ecological complexity breeds evolutionary complication by Jeremy Yoder:

Fire-chasing beetles sense infrared radiation from fires hundreds of kilometres away by Ed Yong:

Crowdfunding as the future of science funding? by Anthony Salvagno

Revisiting why incompetents think they’re awesome by Chris Lee. “Dunning-Kruger study today: The uninformed aren’t as doomed as the Web suggests.”

Lost in your brain by David Dobbs – “When science writer David Dobbs is suddenly unable to remember how to drive his kids to school, he sets off on a quest to understand his own brain, and makes a shocking discovery.”

Earth took ten million years to recover from Permian-Triassic extinction by Duncan Geere

Of Darwin, Earthworms, and Backyard Science by Anthony Martin

The great Pacific garbage reality by Usha Lee McFarling – “The great Pacific garbage reality. It’s not tsunami debris we should fear; it’s the trash clogging our oceans.”

The snakes that eat caviar by Andrew Durso

On the humanity (or lack thereof) of the X-Men by Megan M. McCullen

Tuatara reptile slices food with ‘steak-knife teeth’ by Victoria Gill

Traumatized animal radically changes diet and behavior in an unhealthy way: the real story of the “vegetarian shark” by David Shiffman

Reaching Out: Why are scientists trapped in the ivory tower and what can be done to escape? by Jeanne Garbarino

Keep shouting. You never know who is listening. by Emily Finke

Media, Publishing and Technology:

We need to reinvent the article by Sean Blanda

Blogonomics, ten years on by Henry Copeland

The 10 Biggest Social Media Lies by Mike Elgan

The Floppy Disk means Save, and 14 other old people Icons that don’t make sense anymore by Scott Hanselman

Wikipedia as an explainer by Dave Winer

Libre redistribution – a key facet of Open Access by Ross Mounce

Amid Tweets and Slide Shows, the Longform Still Thrives: How the form survives in this digital era by Emma Bazilian

Making More Scientists by John Wilbanks

What is it that journalists do? It can’t be reduced to just one thing by Jonathan Stray

Why “We the People” should support open access by Bill Hooker

Live chat today at noon about science blogging, circadian rhythms, sleep, metabolism and evolution

Join Robin Lloyd and myself today at 12 noon EDT for the first edition of the Scientific American Fast Chat. Log in and ask questions, and we’ll try to answer. The whole thing will last about 30 minutes.

Clocks, metabolism, evolution – toward an integrative chronobiology

The biannual meeting of the Society for Research on Biological Rhythms happened last week. Unfortunately, I could not attend, so will have to wait another two years for the next opportunity.

I am not sure how this stuff happens, but there was a flurry of new papers in the circadian field just preceding the event. Several of them have already received quite a lot of attention in both old and new media, and rightfully so, but I decided not to cover them one at a time just as the embargo lifted for each one of them.

Instead, I will just very briefly describe and explain the main take-home messages of each one of them, link to the best coverage for those who want more detail (“Cover what you do best. Link to the rest.“), and then try to come up with more of a ‘big picture’ summary of the current state of the field.

I apologize in advance for covering and linking to some of the papers that are not published in Open Access journals. I am not as strict about this policy as some other bloggers are (“if my readers cannot access it, they cannot fact-check me”), and will occasionally cover non-OA papers. Even if most of my readers cannot access them, I gather that a miniscule proportion can access and, if I got something wrong, can alert the other readers in the comments. And speaking of Open Access, I am not one to sign many online petitions, but this one is worth it so please sign if you have not done it already.

So, let’s see what new and exciting in chronobiology these days…



Article: Ben Collins, Elizabeth A. Kane, David C. Reeves, Myles H. Akabas, Justin Blau, Balance of Activity between LNvs and Glutamatergic Dorsal Clock Neurons Promotes Robust Circadian Rhythms in Drosophila, Neuron, Volume 74, Issue 4, 706-718, 24 May 2012

What is it about: Robustness of daily rhythms and their flexible, adaptive responses to the environment, require a feedback loop between a cluster of clock cells in the brain and another cluster of non-clock cells in the brain of Drosophila melanogaster.

What is new: Feedback loops between two or more brain centers (or tissues, or organs) as necessary for either existence of some circadian rhythms, or for the rhythms’ robustness and fine-tuned response to the environment, have been studied mostly in vertebrates, especially birds and lizards, and to some extent mammals. Such feedback loops have been found in the fruitfly as well. This paper finds out a lot of detail about this feedback loop, including the use of glutamate as a neurotransmitter in one half of the loop. As Drosophila is still the lab organism with the most developed techniques for precise genetic manipulations, this is an important advance.

Take-home message: How core clock genes turn each other on and off within a cell over 24 hours is just the beginning, a small part of the story. To work properly, to be adaptive, and to respond well to environmental cues, circadian rhythms require organization at a higher level, with fine-tuned communication among clock-cells and between clock and non-clock tissues.

Some more thoughts: This is a technical tour-de-force. Fruitfly genetics techniques today are so powerful and this paper appears to use them all: inserting, deleting, downregulating and upregulating genes of choice in precisely targeted cells in the brain. As every behavioral biologist knows, once introduced into an experiment animals do whatever the heck they please. The behavior measured in this paper was a simple light-avoidance test – fruitfly larvae (and in the last experiment, also adults) are placed in a petri dish that is half in light, half in darkness, and the movement and position of the larvae is monitored. Considering how messy such behavioral data tend to be, the results in this paper are quite impressive.

The Abstract/Summary, the Introduction, and the (far too short) Discussion are very clear, straighforward and easy to read and understand. They are also upfront and direct about their main take-home message. The many pages in-between, though, are clearly meant to be read only by Drosophila clock geneticists who can actually wade through the essentially endless litany of acronyms in hope of replicating or following up on this study. Clocks are my field, but I am not a geneticist or drosophilist, so much of the Materials & Methods and Results sections in this paper are over my head. Maddeningly, some of the most important stuff is hidden in the Supplemental Materials, including this model for how the whole thing works (shouldn’t this image be up front, on the top of the whole thing?):

Drosophila neuron model

Drosophila neuron model

Note: If I remained in research, I would have done something like this, not necessarily in fruitflies, but definitely looking at neural networks, feedback loops and higher-level organization of the circadian system, within ecological and evolutionary contexts. This may bias me toward liking this paper as much as I do.

Good coverage elsewhere: None that I can find. Only a warmed-up (and not that good) press release at Futurity and ScienceDaily.



Article: Rachel S. Edgar et al., Peroxiredoxins are conserved markers of circadian rhythms, Nature, Published online 16 May 2012, doi:10.1038/nature11088

What is it about: A protein (peroxiredoxin) that is found in almost all living organisms has two states/conformations that cycle at approximately 24 hours. Presence and proper function of core circadian clock genes is not necessary for the cycling of this protein. An Archea species that does not live on the surface does not have the clock and does not have this protein.

What is new: This finding in human red blood cells and a Protist (O.tauri) was published last year. This paper adds similar data for a whole bunch of other organisms: cyanobacteria, archaea, fungi, plants, insects and vertebrates.

Take-home message: There are really two take-home messages, one physiological, one evolutionary. First, this demonstrates that circadian clocks are properties of the entire cells (or assemblages of cells in case of multicellular organisms), not just the transcription/translation loops of core clock genes.

Second, the protein in question, the peroxiredoxin, could be akin to “scaffolding”, something that allows a cell to keep cycling while genes come and go, mutate and change and duplicate, while being fine-tuned by natural selection. Over billions of years, this can result in major groups of organisms (e.g., animals vs. plants vs. fungi vs. bacteria, vs. several different groups of protists) having entirely different circadian genes, yet all of them using the same “logic” (transcription/translation feedback loops).

Both the peroxiredoxins and the circadian clocks are thought to have originated as defense from UV radiation of the early oceanic surfaces (Pittendrigh, C.S., 1967. Circadian rhythms, space research, and manned space flight. In: Life Sciences and Space Research 5:122-134. North-Holland, Amsterdam.), or defense against other kinds of demage, including that from oxidation, so it makes sense that they co-originated and co-evolved only once in the history of the planet, perhaps around 2.5 million years ago when photosynthetis bacteria introduced lots of molecular oxygen into the Earth’s atmosphere. It also makes sense that they both are missing in organisms that have never lived close to the oceanic or terrestrial surface (e.g., many Archaea).

Essential reading: When the two papers (on red blood cells and the protists) came out last year, I wrote a very comprehensive post that places this research direction into historical, philosophical, methodological and even media context. There is not much in that post that would change with the publication of this new paper apart from additional confirmation in several new species. So just go and read it again.

Some more thoughts: Peroxiredoxins cycle in all kinds of different cells with an approximately 24 hour period. This makes them, almost by definition, circadian clocks. Last year’s papers also show that the peroxiredoxin clock dominates its phase over the clock driven by core circadian genes. But there is something still to find out, and it is important: can the peroxiredoxin clock drive any other rhythms? For it to work as a biological pacemaker, it is not sufficient for it to cycle itself, it also need to drive timing of other events in the cell (and the entire organism). I am assuming that this research group will look at this problem next.

Mammals have six peroxiredoxin genes. In an experiment (Zhang et al., Cell , 2009), human cell lines were engineered in such a way that each culture had a different peroxiredoxin gene knocked out. None of the knock-outs had any effect on the regular circadian expression of the core clock gene Bmal1. Of course, having six genes indicates redundancy in function. One would need to knock out all six simultaneously in order to see an effect on other rhythms in the cell, but there is a question if cells with all peroxiredoxins knocked out can survive at all. Someone should try this.

Also, that experiment was done in mammalian cells. Mammals are probably the worst model system for studying this question. Vertebrates have undergone several events of gene (and genome) duplication, and mammals got at least another one. If you look at mammals, every clock gene exists in multiples (e.g,. Per1, Per2, Per3). Poor peroxiredoxin probably cannot do much in such a massively genetically determined system.

Gene duplication allows for evolutionary experimentation. As long as one copy of the gene keeps working, the others are free to mutate. Some mutations will be selected against (e.g., if they mess up the clock function) and others will be selected for (e.g., if they fine-tune the circadian function, making it more flexible and adaptable, or start performing some other valuable function instead). This means that functions formerly in the domain of higher-level organization or the domain of phenotypic plasticity, are now under control of genes. This process is called Genetic assimilation (and sometimes Baldwin effect, though that term is usually reserved for genetic assimilation of learned behaviors). So it is quite possible that the clock in mammals is over-determined by genes, making it useless for the study of peroxiredoxins as scaffolding for circadian evolution.

If I was doing this research, I would stay away from these vertebrate oddballs for at least the next five or ten years, and focus my time, funds and energy on the study of bacteria, archaea, protists, fungi and perhaps some plants – smaller the genome the better.

Good coverage elsewhere: Great coverage by Ed Yong, Megan Scudellari and Ewen Callaway. Was also covered by Debora MacKenzie.

Additional reading: Whence Clocks? and Clock Evolution


Article: Faure, S., Turner, A.S., Gruszka, D., Christodoulou, V., Davis, S.J., von Korff, M. & Laurie, D.A. Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley (Hordeum vulgare) to short growing seasons, Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1120496109

What is it about: In barley cultivars from Northern Europe a mutation in a gene responsible for flowering feeds back on the circadian clock genes, greatly reducing the amplitude of the gene cycling, effectively shutting down the clock. Without proper clock function, barley does not use the clock to measure seasonal changes in daylength (photoperiodism) but instead matures at the fastest rate its development permits. This allows barley to mature and flower early in the season, as well as to photosynthetise throughout the long days of summer in the North.

What is new: Yet another organism in which some of the clock function is temporarily or permanently eliminated. Good news: unlike the other such organisms which tend to be not-well-studied inhabitants of extreme environments, barley is a domesticated plant, well researched and easy to use in the lab.

Take-home message: one has to be careful with interpreting studies like these – just because an organism does not show a couple of well-studied rhythms in physiology and behavior, and does not show cycling in expression of core clock genes does not mean that all circadian function is gone. Ensembles of cells, or feedback loops between tissues, or cytoplasmic factors like peroxiredoxin may still be working in the organism, it’s just that this cannot be detected with the techniques used in the study.

Good coverage elsewhere: As far as I know, I am the only one who covered this paper.



Article: Summa KC, Vitaterna MH, Turek FW (2012) Environmental Perturbation of the Circadian Clock Disrupts Pregnancy in the Mouse. PLoS ONE 7(5): e37668. doi:10.1371/journal.pone.0037668 (Open Access)

What is it about: Female mice kept in 24 cycles get and remain pregnant easily. Female mice kept in rotating shifts (either advances or delays of the 24 hour cycle by 6 hours every several days) do not. Difference is striking!

What is new: Interactions between circadian rhythms and reproductive cycles have been studied for decades in many different organisms. Last year, a study with already pregnant mice moved to rotating shifts did not result in spontaneous losses of pregnancy. This study suggests that rotating shifts prevent pregnancy to begin in the first place, probably by interfering with implantation of the egg in the uterus.

Take-home message: Another example how clock is not just about timing of downstream events, but also plays part in them more directly. While this study was done in rodents, it works well together with epidemiological data from humans working on rotating shifts. As the light-dark cycle is shifted, the brain clock resets itself pretty quickly, over a period of a couple of days. But peripheral clocks in all the other organs will reset slower, each at its own rate. This include the ovaries, uterus etc, which may not be ready for egg implantation at the time of day when the brain send the relevant signal. In essence, internal desynchronization of clocks prevents all the parts of the system to work in synchrony – this is the main negative effect of jet-lag, and it applies to reproduction as much as it does to digestion and other functions.

circadian phaseshift pregnancy

Effect of entrainment on success of pregnancy

Some more thoughts: Both the paper and the media coverage are clear, straightforward and readable. But if one wanted to explain these data by building a formal/conceptual or mathematical model this could easily get mind-bogglingly complicated: one would have to take into account multiple feedback loops between repeatedly desynchronized oscillators, plus potential effects of photoperiodism.

Good coverage elsewhere: Sarah Fecht did a great job. Most of the rest of the media just regurgitated the press release. Oh, this was even covered by Daily Mail 😉

See also: Oxytocin and Childbirth. Or not.



Article: Johnni Hansen, Christina F Lassen, Nested case–control study of night shift work and breast cancer risk among women in the Danish military. Occup Environ Med doi:10.1136/oemed-2011-100240

What is it about: A large-scale study of Danish female soldiers found a higher incidence of breast cancer in those who had to work night shifts. Longer the period of night-shift work, greater the incidence. Also, early risers were more susceptible to this negative effect of night shift work.

What is new: Earlier studies were mostly done in nurses in the USA. This provides a much larger data-set of women followed over a long period of time in a different profession in a different country. Military environment also controls for many other aspects of life (food, quality of medical care, physical fitness, etc.) which tends to be more uniform than in the general population.

Take-home message: Prolonged night shift work, especially if you are an early bird, may be bad for your health.

Some more thoughts: Internal desynchronization between various body clocks, especially long-term, is bound to have negative consequences. Suffering from jet lag occasionally when traveling is fine. But getting jet-lagged every day for years is seriously impairing all sorts of body functions (see reproduction above).

Good coverage elsewhere: Steven Reinberg



Article: Yuta Fuse, Akiko Hirao, Hiroaki Kuroda, Makiko Otsuka, Yu Tahara and Shigenobu Shibata, Differential roles of breakfast only (one meal per day) and a bigger breakfast with a small dinner (two meals per day) in mice fed a high-fat diet with regard to induced obesity and lipid metabolism. Journal of Circadian Rhythms 2012, 10:4 doi:10.1186/1740-3391-10-4 (Open Access)

What is it about: Three groups of mice were fed a high-fat diet, each group getting exactly the same amount of food each day (and eating it all up each day). One group had free access to food at all times (and ate all the time). The second group was given food in a limited time regimen: a large breakfast and a small dinner. The third group was given all the food to gobble up in one large brekfast. The group that got only a large breakfast got obese, had other metabolic problems and had a disrupted expression of circadian genes.

What is new: Another interesting paper showing that timing of meals determines how the food is processed by the body.

Take-home message: Eating one big meal per day is bad for your health – spread it out a little.

Some more thoughts: The paper is interesting as the data suggest something different from most of the other papers in this line of research (see the next two papers below).

Good coverage elsewhere: I could not find any.


Article: Megumi Hatori, Christopher Vollmers, Amir Zarrinpar, Luciano DiTacchio, Eric A. Bushong, Shubhroz Gill, Mathias Leblanc, Amandine Chaix, Matthew Joens, James A.J. Fitzpatrick, Mark H. Ellisman, Satchidananda Panda, Time-Restricted Feeding without Reducing Caloric Intake Prevents Metabolic Diseases in Mice Fed a High-Fat Diet. Cell Metabolism, 17 May 2012 doi:10.1016/j.cmet.2012.04.019

What is it about: Groups of mice were fed either normal or high-fat diet either with continuous free access to food or with feeding time limited to 8 hours during the night (remember that mice are nocturnal – this is their active period, i.e., their “day”). The results appear to be opposite from the paper above (by Fuse at al.) – it is the mice with unlimited feeding that got obese and developed metabolic problems, as well as reduced amplitude of the circadian gene expression.

What is new: Hmmm, which one of the two papers is “more right” than the other? The devil is in the details, so we’ll have to look there.

There are two obvious differences between the two papers. The Hatori paper gave full volume of the normal daily intake of food, while the Fuse paper gave mice only 80% of the normal food quantities per day – which is calory restriction in itself. This may explain why the free-feeding mice in Hatori paper got obese and developed problems, while the mice in the Fuse paper did not.

Second, there is a difference in timing of meals in time-restricted groups. There is “time-restricted feeding” and then there is “time-restricted feeding”! The Hatori paper restricted feeding to an 8-hour period starting one hour after lights-off and ending three hours before lights-on. The Fuse group gave breakfast at the moment of lights-off (the paper does not say for how long – presumably with reduced diet the hungry mice just ate it all very fast) and a smaller “dinner” at the moment of lights-on. These are very different timing schedules!

In many ways, the two-meal schedule of the Fuse paper is similar to the time-restricted schedule of the Hatori paper. Note that these two schedules did the best in regard to obesity and metabolism. Both the free-feeding (especially with the full diet in the Hatori paper) and extremely restricted feeding (brief but huge breakfast in the Fuse paper) resulted in bad metabolic effects. One can perhaps conclude that extremes are bad – one huge meal is bad as is continuous grazing, but that the spread of feeding over two or more smaller meals does better.

Take-home message: The perennial “more research is needed”….until then it is wise to eat your meals at normal times, more than once per day, no grazing in-between, and no midnight snacks…

Hatori image

Effect of feeding regimen on body weight and metabolism

Some more thoughts: Hatori paper is….overwhelming! There is so much work done. As I was reading it all, my thought was that ten pages in the middle of the paper could be completely cut out of the paper and the result would still remain exactly the same – just weigh the mice! All sorts of things were measured in a variety of ways, from gene expression patterns, to standard metabolic tests to histology. All that work strengthens the notion that obesity and metabolic problems are correlated, so the work is definitely not for nothing, and is very impressive. It certainly adds a lot of information to the notion that circadian clock is not just a timer, but intimately involved in regulation of metabolism.

Good coverage elsewhere: Peter Janiszewski, Ph.D. and Garth Sundem. Also see Michael Coston. There was plenty of coverage in mainstream media, mostly OK, some bad…


Article: Till Roenneberg, Karla V. Allebrandt, Martha Merrow, Céline Vetter, Social Jetlag and Obesity. Current Biology, Volume 22, Issue 10, 939-943, 10 May 2012. doi: 10.1016/j.cub.2012.03.038

What is it about: A huge number of Europeans from various ages, latitudes and longitudes were assessed for a variety of circadian, sleep and health parameters. It turns out that most suffer from “social jet-lag” – an internal desynchronization between various body clocks as a result of continuous mismatch between the natural body rhythms and societally and culturally imposed wake-up, school, work and bed-time schedules. During the school/work week, people are massively sleep deprived. They then make up for it, “paying off the sleep debt”, over the weekends. The difference between the amount of sleep one gets on work/school nights and the amount of sleep one gets during the weekend is especially stunning in adolescents, whose internal clocks are naturally phase-delayed and thus most dramatically out of sync of what the society is forcing them to do:

roenneberg image

Average sleep time by age and gender (top) and discrepancy between workday and weekend sleep (bottom)

One of the most remarkable results is that people with the largest workday/weekend discrepancy, the most socially jet-lagged individuals, are also most prone to smoking, drinking, obesity and other health problems. Naturally thin people (B) did not get obese if they were more sleep deprived, but those somewhat prone to obesity became obese if they were also sleep deprived due to social jet-lag:

roenneberg image2

Effect of social jetlag on obesity in obesity-prone people (top) and thin people (bottom)

What is new: Bits and pieces of this were known for a while. But nobody has ever done such a tremendous study on such a large number of people, controlling for so many factors and measuring so many parameters and so many outcomes. This is definitely a tour-de-force paper of the year in this field and is appropriately matched with a brand new book by the lead author – Internal Time: Chronotypes, Social Jet Lag, and Why You’re So Tired – which I am currently reading.

Take-home message: Socially imposed school and work schedules are messing with our health. Political will is needed to change the mindset, change the culture, and change the way we use time in the society.

Some more thoughts: This paper goes together well with the several papers described above – living a life outside of synchrony with the light-dark cycle of the natural environment (and no, artificial indoor light cannot match it) has serious health consequences, leading to metabolic, physiological, reproductive and psychological problems that negatively affect billions of people on Earth, and cost the society billions of dollars of lost productivity, unnecessary medical care, and loss of educational potential in teenage students. Watch the video:

Note: Again, and infuriatingly so, most of the interesting stuff is in the Supplemental Materials.

Good coverage elsewhere: Maria Popova, Jamie Condliffe, Robert T. Gonzalez, Allison Aubrey, Kate Southam and many others.

Additional readings: When Should Schools Start in the morning? and Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask) and Sun Time is the Real Time.



Genes are, for the most part, invisible to natural (and sexual) selection.

What evolution can work on are phenotypes – composites of anatomical, physiological and behavioral traits as they change during the development and lifetime of an organism. Genes are selected for, indirectly, inasmuch as they contribute to the phenotype. While in different organisms and in different cases selection may act on a number of different levels – genes, embryos, cells, organs, organisms, groups, species – usually the most important unit of selection is the individual organism.

How a gene contributes to the phenotype is affected by many factors – multiples ways of splicing it, multiple ways of post-translational modification, which other genes are present, where and when is it expressed during development, interactions between cells, tissues and organs, and interactions between the organism and its environment. As genes, chromosomes and genomes sometimes get duplicated, this provides more opportunities for traits, previously resulting from higher-level interactions, to get incorporated into the genetic instructions via the process of genetic assimilation.

The basic unit of life is the cell. A single-celled organism has to have all of its internal processes coordinated in order to display adaptive responses to the environment in order to survive and reproduce. In multi-celled organisms, each cell type has to behave properly, communicate properly with the other cells, and coordinate its activities with all the other cells in the body for the organism to display adaptive responses to the environment in order to survive and reproduce.

Molecules that do all, or almost all of the work are proteins. They build structures, they catalyze reactions, break down food, store and use energy, control communication between cells, regulate the expression of the genes, and more.

But proteins are hard to study! Nucleic acids are much easier – they are stable, inert, the 3D conformation does not matter, and laboratory techniques have been developed to discover, sequence and study snippets of DNA and RNA in ways that today can be done by middle-schoolers or in DIY science projects. When you have the hammer, everything is a nail. When you have genetic tools, your graduate students are instructed to use them. And then sometimes they forget why they are doing this in the first place…

We study nucleic acids because they are markers, or proxies, for proteins. We locate genes and hope that the processes of transcription, splicing and translation do not confound too much what the resulting proteins are and what they do. This means that study of genes – their sequences and patterns of expression – is a reasonable first step in studying a biological phenomenon as it provides us with tools and information needed to study proteins, cells and higher-order phenomena that are evolutionarily relevant.

Of the Big Four – anatomy, biochemistry, physiology, behavior – it is behavioral traits that are the furthest removed from the underlying genes. It is really difficult to find genes directly involved in behavior. Big screens for genes for behaviors usually come up with genes for kinases, neurotransmitter receptors, neuronal development factors and other generalized components of the nervous system.

Circadian clock is an exception. While one may argue that the clock is not actually a behavior but a physiological mechanism that regulates many other behaviors, it is still the closest to a behavioral trait we ever got in discovering underlying genetics. Most people in the field agree that all major genes involved in clock function have been discovered (mostly during the 1990s) and that it is not productive to search for more.

Sure, the Abstract book of last week’s SRBR meeting still contains some posters and blitz-sessions by students with a detailed genetics work (well, the students need to learn the techniques, right?), but most of the Big Honchos of the field have moved on – to properties of the entire cells, neural networks, properties of multi-clock systems, and interactions with the environment. In a sense, after a detour of the 1990s when all the focus and energy was placed into gene discovery (“opening the black box”), the field of chronobiology is going back to its roots – a historically incredibly comparative and integrative subdiscipline of biology.

For a long time we have thought of circadian clocks as simply timers – something that determines when other downstream functions happen. But evidence over the last couple of decades has accumulated that clocks are much more intimately involved in some of those functions, beyond just timing.

Ten years ago, when I was exiting the field, the interaction between clocks and metabolism was just starting to be explored. We learned that fruitfly clock-gene timeless is involved in cocaine addiction. We learned that mutations in clock genes that change circadian period also change other aspects of timing, from frequencies of fruitfly courtship songs, to developmental timing in nematodes, to photoperiodic responses, to reproductive cycles.

Today, involvement of the circadian clock in many aspects of metabolism is probably the most exciting and most heavily studied area in the field. And this is shown by all the papers I highlighted today. The focus away from identification of genes and moving on to proteins, cells, neural networks, multi-oscillatory systems, and interactions with the environment are making the field as exciting as ever, and in vanguard of much of the rest of biology which is still overly focused on DNA. And the findings have obvious and stark implications not just for our better understanding of Life, but also for understanding of adaptation of organisms to the changing climate, and for understanding the consequences on human health.

The Scienceblogging Weekly (May 25th, 2012)

Blog of the Week:

Over the years, Better Posters blog has become the “Go To” place to send students when they start preparing posters for their first scientific meetings. Updated weekly, on Thursdays, this blog by Dr. Zen Faulkes (who also blogs at his other two awesome blogs NeuroDojo and Marmorkrebs, as well as on the #SciFund blog) provides ideas, suggestions, underlying theory, and thorough, fair critiques of poster design for scientific conferences. It is a link I (and I am sure many others) send whenever asked what is the best resource for preparing a good poster. Zen Faulkes also has a broader category of posts about presentations in general, both oral and poster, under the Zen of Presentations tag on his other blog.

Top 10:

Phineas Gage’s connectome by Mo Costandi:

Anyone who has studied psychology or neuroscience will be familiar with the incredible case of Phineas Gage, the railroad worker who had a metre-long iron rod propelled straight through his head at high speed in an explosion. Gage famously survived this horrific accident, but underwent dramatic personality changes afterwards. In recent years researchers reconstructed his skull and the passage of the rod through it, to try to understand how these changes were related to his brain damage. Now, neuroscientists from the University of California, Los Angeles have produced Gage’s connectome – a detailed wiring diagram of his brain, showing how its long-range connections were altered by the injury.

Replication studies: Bad copy by Ed Yong:

Positive results in psychology can behave like rumours: easy to release but hard to dispel. They dominate most journals, which strive to present new, exciting research. Meanwhile, attempts to replicate those studies, especially when the findings are negative, go unpublished, languishing in personal file drawers or circulating in conversations around the water cooler. “There are some experiments that everyone knows don’t replicate, but this knowledge doesn’t get into the literature,” says Wagenmakers. The publication barrier can be chilling, he adds. “I’ve seen students spending their entire PhD period trying to replicate a phenomenon, failing, and quitting academia because they had nothing to show for their time.” These problems occur throughout the sciences, but psychology has a number of deeply entrenched cultural norms that exacerbate them. It has become common practice, for example, to tweak experimental designs in ways that practically guarantee positive results. And once positive results are published, few researchers replicate the experiment exactly, instead carrying out ‘conceptual replications’ that test similar hypotheses using different methods. This practice, say critics, builds a house of cards on potentially shaky foundations…

Plan X; or, Planning White’s Small Step by Amy Shira Teitel:

In 1964, the launch schedule for the Gemini program was set and it was tight. Missions with new objectives would launch every eight to ten weeks taking NASA a step closer to the Moon each time. But hardware setbacks and some surprising feats by Soviet cosmonauts took a toll on the schedule. In the first half of 1965, NASA developed a plan that would see Gemini match and begin to overtake the Soviet Union in space. It was done largely in secret and known internally as Plan X….

Against the Infantilization of the Natural History Museum by Justin Erik Halldór Smith (and related: Relics With Much to Tell About Bird Diets May Be Lost to Time by Sarah Fecht):

…The project of exhaustively collecting and describing the basic kinds of large animal, and analyzing and displaying these animals’ bodily parts and systems, is a project that gained momentum in the late Renaissance and that was largely completed by the end of the 19th century. Like, say, realist painting in the Western tradition, it is a project that has a bounded history (indeed the two histories fairly closely overlap one another). This means that an alpaca intestine displayed in formaldehyde is a sample of a part of a South American camelid; but it is also an artefact of a modern European knowledge project. In this respect a proper natural history museum, that is to say an unreconstructed adult natural history museum, is really two museums at once: it is a museum of nature, but also a museum of the history of a very singular attempt to know nature quite literally inside-out….

What a Physics Student Can Teach Us About How Visitors Walk Through a Museum by Henry Adams:

….To devise a good layout requires some understanding of what museum visitors do, and there’s surprisingly little literature on this topic. Most of the studies of museum-goers that I’ve seen rely on questionnaires. They ask people what they did, what they learned, and what they liked and didn’t like. No doubt there are virtues to this technique, but it assumes that people are aware of what they’re doing. It doesn’t take into account how much looking depends on parts of the brain that are largely instinctive and intuitive and often not easily accessible to our rational consciousness. Was there another mode of investigation and description that would illuminate what was actually taking place?…

Lies You’ve Been Told About the Pacific Garbage Patch by Annalee Newitz:

You’ve probably heard of the “Pacific garbage patch,” also called the “trash vortex.” It’s a region of the North Pacific ocean where the northern jet stream and the southern trade winds, moving opposite directions, create a vast, gently circling region of water called the North Pacific Gyre — and at its center, there are tons of plastic garbage. You may even have seen this picture of the garbage patch, above — right? Wrong….

The (misunderstood) language of DNA by Genegeek:

I love analogies and use them often to get people to think about scientific concepts in new ways. I’ll share some of my favourite ones on the blog but today, I want to talk about Analogies Gone Bad….There is a lovely analogy to help people understand DNA code: DNA can be seen as a language…

Killers that sux by DrRubidium:

You might notice the sting of the injection. Within seconds you’d realize you’re having trouble moving your eyes and fingers, followed by your arms and legs. If you were standing, you’d collapse. In a heap on the floor, you’d realize nearly every muscle in your body was paralyzed. Being fully conscious, your sense of panic would be rising as rapidly as the paralysis was spreading. Swallowing and breathing has become more and more difficult. Slipping into unconsciousness, your last conscious thought may well be “I am going to die.”…

What Is the “Bible of Psychiatry” Supposed to Do? The Peculiar Challenges of an Uncertain Science by Vaughan Bell:

The American Psychiatric Association have just published the latest update of the draft DSM-5 psychiatric diagnosis manual, which is due to be completed in 2013. The changes have provoked much comment, criticism, and heated debate, and many have used the opportunity to attack psychiatric diagnosis and the perceived failure to find “biological tests” to replace descriptions of mental phenomena. But to understand the strengths and weaknesses of psychiatric diagnosis, it’s important to know where the challenges lie….

Do Plants Smell Other Plants? This One Does, Then Strangles What It Smells by Robert Krulwich:

“Plants smell,” says botanist David Chamovitz. Yes, they give off odors, but that’s not what Chamovitz means. He means plants can smell other plants. “Plants know when their fruit is ripe, when their [plant] neighbor has been cut by a gardener’s shears, or when their neighbor is being eaten by a ravenous bug; they smell it,” he writes in his new book, What a Plant Knows. They don’t have noses or a nervous system, but they still have an olfactory sense, and they can differentiate. He says there’s a vine that can smell the difference between a tomato and a stalk of wheat. It will choose one over the other, based on…smell! In a moment I’ll show you how….

Special topic: pigeons

Why Aren’t Cities Littered With Dead Pigeons? by John Metcalfe:

Any fair-sized city in the United States is lousy with pigeons, hoovering up bread crumbs from public squares and head-bobbing so much they look like little Jay Zs groovin’ to some fresh beats. The favorite rumpus room of the pigeon, New York City, is thought to contain anywhere between 1 and 7 million of the flapping rats of the sky. So where are all the dead ones?

Big Bird: Are New York’s pigeons getting fatter? An investigation into animal obesity. by David Merritt Johns

Pigeon GPS Identified by Megan Scudellari: “A population of neurons in pigeon brains encodes direction, intensity, and polarity of the Earth’s magnetic field.”

Pigeons have tiny compasses in their heads by Greg Laden.

Speaking pigeon by Kelly Slivka: Keeping up with New York City’s feathered underdogs.


The Zebra Neuron by TheCellularScale – Von Economo Neurons discovered in more and more species, lose the “human specialness” role.

Is the Purpose of Sleep to Let Our Brains “Defragment,” Like a Hard Drive? by Neuroskeptic. Or is it “Disk Cleaner”, or “Reboot”?

Gaming and Exercise: Will Diablo III Derail Your Discipline? by Melanie Tannenbaum – from the horse’s mouth – this research was done in her lab.

It’s supposed to hurt to think about it! by Ethan Siegel: “One of the most fundamental questions about the Universe that anyone can ask is, “Why is there anything here at all?””

Legal highs making the drug war obsolete by Vaughan Bell:

The Drachma and the Euro as a Cybernetic Question by Michael Tobis:

Life Traces as Cover Art and The Ichnology of Peeps by Tony Martin.

Copulatory vocalizations of chacma baboons (Papio ursinus), gibbons (Hylobates hoolock), and humans. by NCBI ROFL. Sonograms, thus it is science!

Putting the ‘Fear’ in Climate Change by Paige Brown – “Do scientists and climate communicators really need the ‘scary’ headlines and alarming facts to get media coverage?”

Energy Drinks: What’s the Big Deal? by Dirk Hanson: “The sons of Red Bull are sporting record concentrations of caffeine.”

Failure – what doesn’t get published in Psychology (for good reason?) by Åse Kvist Innes-Ker.

Uncertainty overdone by Bryan Walker: “As a concerned human being I don’t want scientists to soft-pedal on that evidence.”

A Sensitive Subject, on quantifying uncertainties in modeling climate change and its impacts, by Tamsin Edwards:

Could Angry Birds lead to mass murder? by Martin Robbins: “Attempts to link last year’s Norway shootings to Call of Duty are spectacularly misguided. Moral panic about violent video games is based on prejudice, ignorance and the selective use of flawed research.”

Chemistry at the hairdresser by JessTheChemist.

Our Favorite Toxic Chemicals and Toxic Carnival: Day One and Toxic Carnival: Day Two and Pain, Undoubtedly, Comes with the Cure by Matthew Hartings.

Neurons are like equations by TheCellularScale .

Persuasion and the Brain by David R. Gruber:

New sense organ helps giant whales to coordinate the world’s biggest mouthfuls by Ed Yong

In The Beginning Was the Mudskipper? by Carl Zimmer

Virtual resurrection shows that early four-legged animal couldn’t walk very well by Ed Yong

The Positively Biased Life by Matthew Chew on non-publication of negative data, and on ecology as a discipline.

Will you explain the differences (and similarities) between endemic and epidemic diseases? by Emily Willingham. Eeeek – imagine a pandemic of iguanas!

It is a mistake to eliminate government science. Part I and Part II by Simon Goring

Carpenter versus Aurora 7 by Amy Shira Teitel

You scientist, we want you to get ahead….but not too FAR ahead! by Anne Buchanan

Birding from parking level five: Suburban ospreys in Florida by Justine E. Hausheer

The smokeless stove: A partnership between academics and designers in New York City has produced a stove that could reduce child deaths in Africa by Emma Bryce

Media, Publishing and Technology:

Your 5-minute, 5-day orientation to Twitter by Anton Zuiker

Web Design Manifesto 2012 by Jeffrey Zeldman

The teacher I hated who changed my life by General Tso:

How to Deal with Information Overload by Walter Jessen and Simon Franz.

Can Blogs Be Used to Resolve Conflicts? by Greg Laden:

Data journalism research at Columbia aims to close data science skills gap by Emily Bell and Alex Howard

The Facebook Fallacy by Michael Wolff: “For all its valuation, the social network is just another ad-supported site. Without an earth-changing idea, it will collapse and take down the Web.”

How Amy O’Leary live-tweeted her own speech — and won the #backchannel by Andrew Phelps

The verdict: is blogging or tweeting about research papers worth it? and When was the last time you asked how your published research was doing? by Melissa Terras

Who gives a tweet? After 24 hours and 860 downloads, we think quite a few actually do by Kaisa Puustinen and Rosalind Edwards

Why newspapers need to lose the ‘view from nowhere’ by Mathew Ingram

Buzz Bissinger: Newspaper editors are “very cautious — too cautious” by Adrienne LaFrance

How obsession can fuel science blogging: The story of Retraction Watch by Ivan Oransky

Text mining: what do publishers have against this hi-tech research tool? by Alok Jha

Copy editing: It’s taught me a lot, but it has to change by Steve Buttry

Chossat’s Effect in humans and other animals

This post was originally published on April 09, 2006.

This April 09, 2006 post places another paper from my old lab (Reference #17) within a broader context of physiology, behavior, ecology and evolution. The paper was a result of a “communal” experiment in the lab, i.e., it was not included in anyone’s Thesis. My advisor designed it and started the experiment with the first couple of birds. When I joined the lab, I did the experiment in an additional number of animals. When Chris Steele joined the lab, he took over the project and did the rest of the lab work, including bringing in the idea for an additional experiment that was included, and some of the analysis. We all talked about it in our lab meetings for a long time. In the end, the boss did most of the analysis and all of the writing, so the order of authors faithfully reflects the relative contributions to the work.

What is not mentioned in the post below is an additional observation – that return of the food after the fasting period induced a phase-shift of the circadian system, so we also generated a Phase-Response Curve, suggesting that food-entrainable pacemaker in quail is, unlike in mammals, not separate from the light-entrainable system.

Finally, at the end of the post, I show some unpublished data – a rare event in science blogging.

If you know what Chossat’s Effect is, I guess you are a) a physiologist, b) expert in thermoregulation, and c) old. This is term that got expunged from the scientific lexicon a few decades ago, in an effort – correct me if I am wrong on this – spearheaded by the U.S. textbook companies, to replace scientific terminology named after the discoverers (and sometimes even Latin and Greek terms) with bland English neologisms.

But I love Schwann’s Cells, Fallopian Tubes (or Mullerian Ducts), Purkinje Fibers, Brocca’s Area and the amazing Bundle of His! Those terms are memorable, make it easy to sneak in some historical context into teaching science, and have an emotional effect of bringing forth images of ancient scientists working under candlelight, sacrificing their eyesight and health, their social standing and sometimes even their lives, in the feverish hunger for knowledge.

So, what is Chossat’s Effect? It comes from a 19th century French scientist who was studying the physiology of starvation [1]. The ‘modern’ term for this effect is “fasting-induced nocturnal hypothermia” (doesn’t that sound like something that would prompt the students in the classroom to immediatelly stop paying attention to the teacher and instead pick-up their cell-phones and start text-messaging their friends?).

Actually, this is a very interesting area of research that is very tightly connected to circadian biology. This post is likely to be long, so feel free to skim and just focus on the first part if you are into birds, second part if you are interested in mammals, and the last part if you are into humans.


All warm-blooded animals (and yes, that includes at least some reptiles, not to mention a few heat-producing plants like stink-cabbage) exhibit a daily rhythm of body temperature. If an animal is active during the day (diurnal) and sleeps during the night, reducing the metabolic rate during the night is a good way to save energy.

Some of the smallest birds, like swifts and hummingbirds, need to feed continuously in order to stay alive. At night, when they are not able to forage (flowers are closed, it’s hard to see, and owls are hunting at the time), they drop their metabolic rate, and thus body temperature, quite dramatically. The body temperature gets down as low as the environmental temperature, sometimes daringly close to the freezing point. The total drop can be as large as 40 degrees Celsius in some instances! This is called daily torpor (yup, click on that link – it is an excellent blog post) and the metabolic rate drops as much as 95% [2, 3]. This is like full-scale winter hibernation EVERY DAY!

Chossat’s effect does not refer to daily torpor, though. It describes a drop in temperature during the night that is larger than the usual circadian fluctuation, in animals undergoing fasting, e.g., during spells of very bad weather (e.g., hurricanes).

Normal amplitude (daily maximum minus nightly minimum) of body temperature in birds with normal access to food ranges between about 1 and 2 degrees Celsius. For instance, a daily maximum may be 41 degrees and the nightly minimum may be 39 degrees (yes, the birds are much warmer than mammals, which makes them inhospitable to microbes that cause many mammalian diseases), which calculates to 2 degrees of amplitude.

During fasting (or food deprivation in the laboratory), the nightly minima drop down to lower levels than in fed birds. The minimum gets lower and lower with each additional night. Importantly, the daily maxima do not change at all. It is thought that it is advantageous for birds to retain their normal metabolic rates during the day so they can immediately resume foraging once the bad weather subsides. Also, if the bad weather persists for too long, the birds need the daytime metabolic rates in order to fly away [4].

According to John Wingfield’s “Emergency Life-History Stage” hypothesis [5], an individual’s perception of inclement weather directly affect the levels of stress hormones (e.g., corticosterone). An individual who does not perceive the bad weather to be “too bad”, will reduce daytime activity and reduce night-time temperature in order to save energy – this individual has made a decision to sit it out.

On the other hand, an individual who perceives bad weather to be “really bad” (or if it lasts too long) will have higher levels of stress hormones and will attempt to fly away during the day. This is not the same mechanism as the seasonal migration, which is usually a nocturnal flight, i.e., they do not experience Zugunruhe, just stress. Stressed birds do not attempt to escape at night, at which time they have allowed their body temperature to drop by several degrees.

Nocturnal hypothermia has been studied in a large number of species of birds (see, for examples, references # 6-12), but most of the work was performed on pigeons [13-15] and quail [16]. Not all avian species exhibit this response. Laurilla at al. [18] write:

“On the other hand, many large birds that are adapted to long fasting periods as a part of their life histories, e.g. penguins and geese (Cherel et al., 1988; Castellini andRea, 1992), owls (Hohtola et al., 1994) and some raptors (McKechnie andLovegrove, 1999) do not show marked hypothermia during fasting. Some species enter hypothermia upon food restriction only when isolated from conspecifics in a laboratory environment, while in the field they remain normothermic by huddling. These observations have even led some authors to question the usefulness of the concept of hypothermia (Lovegrove and Smith, 2003).”[8]

Here is a graphic example of a fasting-induced nocturnal hypothermia in quail (from[17]). The period between the two triangles is the time (3 days) during which the birds had water but no food. Before and after, birds were fed ad libitum. Below is a graph that shows the difference between the temperature minima during the first, second and third day (top) and night (bottom) of food deprivation in comparison to the last three days and nights of normal feeding prior to the fasting treatment:

Much of the more recent research is looking at other environmental cues that can modify the Chossat’s effect, as well as the involvement of the circadian clock in this time-specific form of thermoreguluation.

For instance, some of the ambient cues that affect the response include ambient temperature [16, 20], ambient light [17], photoperiod [18, 19], single vs. repeated fasting [18, 19], caloric food restriction vs. complete food deprivation [13], social situation, e.g., opportunity for huddling [8] and presence of stationary vs. flying predators [19, 20]. Here is an example of an effect of ambient temperature on nocturnal hypothermia in fasted pigeons (from [20]). Lower the ambient temperature, deepeer the Chossat’s effect:

Here is the effect of the presence of a predator (from [2]). In the presence of a perched hawk (P), nocturnal hypothermia reached normally low levels. In the presence of the flying hawk (F), temperature did not drop as much. Presumably, the pigeons kept the metabolic rate high enough to be able to fly fast if needed:

As stated above, hypothermia occurs only during the night while the temperature during the days remains normal. However, all the studies are performed either in natural conditions of day and night or in light-dark cycles in the laboratory. In constant darkness, the circadian rhythm of temperature persists and hypothermia is apparent. Moreover, the temperature drops both at the minima during the ‘subjective night’ and at the maxima during the ‘subjective day’ (from [17]):

This suggests that light has a direct (or “masking“) effect on body temperature during the light-phase of the cycle. But is this effect acting directly on the thermoregulatory centers in the hypothalamus or is it mediated by the circadian clock that drives the rhythm of body temperature? In Japanese quail, the circadian pacemakers are located in the eyes. When the eyes are removed [17], both the daily maxima in the light-phase and the nightly minima during the dark phase drop, suggesting that the effect is mediated via the circadian clock, as the light perceived by the photoreceptors in the pineal gland and in the deep brain is incapable of keeping the daily maxima from dropping:


Some small mammals, such as smallest rodents and shrews, exhibit a full-blown daily torpor either normally [21] or in response to fasting [22]. Here is an example of a daily torpor of a mouse-opposum:

In nocturnal animals, which many mammals are, body temperature is high at night when the animals are active and it drops during the day when the animals are sleeping. In rats, fasting induces diurnal hypothermia, i.e., drop of the daily minimum during the day (black circles, compared to pre- and post- treatment values in white symbols) while the nightly maxima remain unaffected [23]:

Chronic caloric food restriction leads to the drop in both the daily minima and nightly maxima of temperature [24]. All the studies until recently have studied responses in relatively small animals (both birds and mammals) with high metabolic rates and high energy needs.

But do larger animals, like humans, also exhibit Chossat’s effect? After all, the first documented case, that by Chossat himself, was in a dog. This was repeated recently [25]. But even dogs are pretty small compared to humans.

Recently, researchers have addressed this question in a number of species of large mammals, including sheep, goats, horses and yaks [26-29]. Some additional environmental cues were also studied, including the effects of shearing on the circadian temperature rhythm in sheep [30]. Here is a record from a goat:

Notice that, unlike in birds, both the maxima and minima gradually go down.

But, as far as I could find by digging through the literature, nobody has ever performed a similar study in humans. I am assuming that it has been noticed if body temperature drops in fasted humans, but I am not aware of a study systematically addressing this question.


More than a decade ago I was teaching one of many sections of an Animal Anatomy and Physiology Course. This course requires students to perform a research project. One group of students studied the effects of fasting on body temperature and blood pressure in humans.

They found 8 subjects, all healthy, athletic, non-drinking, non-smoking students ages 19-23. They were instructed to eat normally during the Day1 of the experiment. They subsequently spent 36 hours in a house drinking only water and eating nothing. Every four hours, temperature and pressure were measured. By using kids’ digital ear thermometers and manual sphigmomanometers they managed, for the most part, not to awaken the subjects during the night. Here are examples of body temperature of three of the subjects – Night1, followed by Day2 and Night 2:

Here are the pooled data for all eight subjects, starting with Day2 and followed by Night1 and Night2 plotted on top of each other for comparison:

Obviously, body temperature of Night2, after a day of fasting, was lower than that of Night1, after the day of normal feeding. I do not have their raw data any more, but if I remember correctly, the data for blood pressure looked very similar. I heard they had a huge breakfast, courtesy of the young researchers, at the end of the experiment.

So, Chossat’s Effect appears to be operating in humans as well. Now, this is cool in itself, and I sure hope that someone with access to good clinical lab repeats this study, but there is something else about these data that really excites me. This finding can be used as a tool for studying something entirely different!

The Hypothesis

One of the first demonstrations that humans have daily rhythms involved the time-of-day dependence of time perception. In other words, our subjective “feel” of the speed of passage of time changes systematically with the time of day. At the same time, it has been known for a couple of centuries now that the subjective time perception is also altered during fever. And we know that circadian clock governs daily rhtyhms of body temperature.

So, what affects the time perception: time of day or body temperature? If the time passes faster in the evening than at dawn, is it because of the circadian clock acting on the time-perception brain-centers directly, or because we are warmer at the time (which is also driven by the circadian clock)?

This question has haunted circadian researchers for decades and they have devised ever more elaborate experiments to tease the two hypotheses apart, with no avail – we still do not know. But, if by depriving the subjects of food, we can dissociate clock-time from temperature, perhaps we can address this question after all. If the subjective perception of 1 minute (do not use 1 second or 1 hour – those are durations unsuited for this experiment) is similar between the night after a fed day and the night after the fasting day, then the perception is directly driven by the circadian clock.

If, on the other hand, perception of a minute changes systematically between the two nights, then we conclude that it is body temperature that affects subjective time perception. Please, someone do this! And if you do, or even if you just want to replicate the Chossat’s Effect in humans, I would appreciate it if you would properly cite this post:

Bora Zivkovic, Chossat’s Effect in humans and other animals (2006), A Blog Around The Clock,


[1] M. Chossat, Sur l’inanition, Paris, 1843
[2] Hiebert, S.M. 1990. Energy costs and temporal organization of torpor in the rufous hummingbird (Selasphorus rufus). Physiological Zoology . 63:1082-1097.
[3] Hiebert, S.M. 1991. Seasonal differences in the response of rufous hummingbirds to food restriction: body mass and the use of torpor. Condor 93:526-537.
[4] Tobias Wang, Carrie C.Y. Hung, David J. Randall, THE COMPARATIVE PHYSIOLOGY OF FOOD DEPRIVATION: From Feast to Famine, Annual Review of Physiology, January 2006, Vol. 68, Pages 223-251
[5] Wingfield, JC; Maney, DL; Breuner, CW; Jacobs, JD; Lynn, S; Ramenofsky, M; Richardson, RD, Ecological bases of hormone-behavior interactions: The “emergency life history stage”, American Zoologist [Am. Zool.]. Vol. 38, no. 1, pp. 191-206. 1998.
[6] Tracy A. Maddocks, Fritz Geiser, Energetics, Thermoregulation and Nocturnal Hypothermia in Australian Silvereyes, Condor, Vol. 99, No. 1 (Feb., 1997) , pp. 104-112
[7] Randi Eidsmo Reinertsen and Svein Haftorn, The effect of short-time fasting on metabolism and nocturnal hypothermia in the Willow Tit Parus montanus, Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology, Volume 154, Number 1 (January 1984): 23 – 28
[8] Barry G. Lovegrove and Gary A. Smith, Is ‘nocturnal hypothermia’ a valid physiological concept in small birds?: a study on Bronze Mannikins Spermestes cucullatus, Ibis, Volume 145, Issue 4, Page 547 – October 2003
[9] MacMillen RE, Trost CH., Nocturnal hypothermia in the Inca dove, Scardafella inca, Comp Biochem Physiol. 1967 Oct;23(1):243-53.
[11] Waite, TA, Nocturnal hypothermia in gray jays Perisoreus canadensis wintering in interior Alaska, ORNIS SCAND. Vol. 22, no. 2, pp. 107-110. 1991.
[12] Cécile Thouzeau, Claude Duchamp, and Yves Handrich, Energy Metabolism and Body Temperature of Barn Owls Fasting in the Cold, Physiological and Biochemical Zoology, volume 72 (1999), pages 170-178
[13] Rashotte ME, Henderson D., Coping with rising food costs in a closed economy: feeding behavior and nocturnal hypothermia in pigeons, J Exp Anal Behav. 1988 Nov;50(3):441-56.
[14] R. Graf, S. Krishna and H. C. Heller, Regulated nocturnal hypothermia induced in pigeons by food deprivation, Am J Physiol Regul Integr Comp Physiol 256: R733-R738, 1989
[15] Michael E. Rashotte, Iuri F. Pastukhov, Eugene L. Poliakov, and Ross P. Henderson, Vigilance states and body temperature during the circadian cycle in fed and fasted pigeons (Columba livia), Am J Physiol Regul Integr Comp Physiol 275: R1690-R1702, 1998
[16] Hohtola E, Hissa R, Pyornila A, Rintamaki H, Saarela S., Nocturnal hypothermia in fasting Japanese quail: the effect of ambient temperature, Physiol Behav. 1991 Mar;49(3):563-7.
[17] Herbert Underwood, Christopher T. Steele and Bora Zivkovic, Effects of Fasting on the Circadian Body Temperature Rhythm of Japanese Quail, Physiology & Behavior, Vol. 66, No. 1, pp. 137-143, 1999
[18] Mirja Laurila, Tiina Pilto, Esa Hohtola, Testing the flexibility of fasting-induced hypometabolism in birds: effect of photoperiod and repeated food deprivations, Journal of Thermal Biology 30 (2005) 131-138
[19] MIRJA LAURILA, THERMOREGULATORY CONSEQUENCES OF STARVATION AND DIGESTION IN BIRDS, PhD Dissertation, Faculty of Science, Department of Biology, University of Oulu, 2005 (
[20] Mirja Laurila, Esa Hohtola, The effect of ambient temperature and simulated predation risk on fasting-induced nocturnal hypothermia of pigeons in outdoor conditions, Journal of Thermal Biology 30 (2005) 392-399
[21] Francisco Bozinovic, Gricelda RuÍz, Arturo CortÉs & Mario Rosenmann, Energetics, thermoregulation and torpor in the Chilean mouse-opossum Thylamys elegans (Didelphidae), Revista Chilena de Historia Natural 78: 199-206, 2005
[22] Lovegrove BG, Raman J, Perrin MR., Daily torpor in elephant shrews (Macroscelidea: Elephantulus spp.) in response to food deprivation, J Comp Physiol [B]. 2001 Feb;171(1):11-21.
[23] Kei Nagashima, Sadamu Nakai, Kenta Matsue, Masahiro Konishi, Mutsumi Tanaka, and Kazuyuki Kanosue, Effects of fasting on thermoregulatory processes and the daily oscillations in rats, Am J Physiol Regul Integr Comp Physiol 284: R1486-R1493, 2003.
[24] Yoda T, Crawshaw LI, Yoshida K, Su L, Hosono T, Shido O, Sakudara S, Fukuda Y & Kanosue K (2000) Effects of food deprivation on daily changes in body temperature and behavioural thermoregulation in rats. Am J Physiol 278: R134-R139.
[25] G. Piccione, G. Caola and R. Refinetti, Daily Rhythms of Blood Pressure, Heart Rate, and Body Temperature in Fed and Fasted Male Dogs, J. Vet. Med. A 52, 377-381 (2005)
[26] Giuseppe Piccione, Giovanni Caola, Roberto Refinetti, Circadian rhythms of body temperature and liver function in fed and food-deprived goats, Comparative Biochemistry and Physiology Part A 134 (2003) 563-572
[27] Piccione, G., Caola, G., Refinetti, R., 2002a. Circadian modulation of starvation-induced hypothermia in sheep and goats. Chronobiol. Int. 19, 531-541.
[28] Piccione, G., Caola, G., Refinetti, R., 2002b. The circadian rhythm of body temperature of the horse. Biol. Rhythm Res. 33, 113-119.
[29] Xing-Tai Han, Ao-Yun Xie, Xi-Chao Bi, Shu-Jie Liu and Ling-Hao Hu, Effects of high altitude and season on fasting heat production in the yak Bos grunniens or Poephagus grunniens, British Journal of Nutrition (2002), 88, 189-197
[30] Giuseppe Piccione, Giovanni Caola, and Roberto Refinetti, Effect of shearing on the core body temperature of three breeds of Mediterranean sheep, Small Ruminant Research 46 (2002) 211-215

When Should Schools Start in the morning?

This is not really a new post. But it is not exactly a re-publishing of an old post either. It is a lightly edited mashup or compilation of excerpts from several old posts – I hope it all makes sense this way, all in one place. The sources of material are these old posts:

Sleep Schedules in Adolescents (March 26, 2006)
ClockNews – Adolescent Sleep (March 28, 2006)
More on sleep in adolescents (April 01, 2006)
When Should Schools Start in the morning? (April 02, 2006)
All Politics Is Local (June 29, 2006)
Adolescent Sleep Schedule (September 10, 2006)
Books: “Snooze…Or Lose! – 10 “No-War” Ways To Improve Your Teen’s Sleep Habits” by Helene A. Emsellem, MD (May 15, 2008)


I am glad to see that there is more and more interest in and awareness of sleep research. Just watch Sanjay Gupta on CNN or listen to the recent segment on Weekend America on NPR.

At the same time, I am often alarmed at the levels of ignorance still rampant in the general population, and even more the negative social connotations of sleep as an indicator of laziness.

Nothing pains me more than when I see educators (in comments) revealing such biases in regards to their student in the adolescent years. Why do teachers think that their charges are lazy, irresponsible bums, and persist in such belief even when confronted with clear scientific data demonstrating that sleep phase in adolescents is markedly delayed in comparison to younger and older people?

In short, presumably under the influence of the sudden surge of sex steroid hormones (and my own research gently touched on this), the circadian clock phase-advances in teen years. It persists in this state until one is almost 30 years old. After that, it settles into its adult pattern. Of course, we are talking about human populations, not individuals – you can surely give me an anecdote about someone who does not follow this pattern. That’s fine. Of course there are exceptions, as there is vast genetic (and thus phenotypic) variation in human populations. This does not in any way diminish the findings of population studies.

Everyone, from little children, through teens and young adults to elderly, belongs to one of the ‘chronotypes’. You can be a more or less extreme lark (phase-advanced, tend to wake up and fall asleep early), a more or less extreme owl (phase-delayed, tend to wake up and fall asleep late). You can be something in between – some kind of “median” (I don’t want to call this normal, because the whole spectrum is normal) chronotype.

Along a different continuum, one can be very rigid (usually the extreme larks find it really difficult to adjust to work schedules that do not fit their clocks), or quite flexible (people who find it easy to work night-shifts or rotating shifts and tend to remain in such jobs long after their colleagues with less flexible clocks have quit).

No matter where you are on these continua, once you hit puberty your clock will phase-delay. If you were an owl to begin with, you will become a more extreme owl for about a dozen years. If you are an extreme lark, you’ll be a less extreme lark. In the late 20s, your clock will gradually go back to your baseline chronotype and retain it for the rest of your life.

The important thing to remember is that chronotypes are not social constructs (although work-hours and school-hours are). No amount of bribing or threatening can make an adolescent fall asleep early. Don’t blame video games or TV. Even if you take all of these away (and you should that late at night, and replace them with books) and switch off the lights, the poor teen will toss and turn and not fall asleep until midnight or later, thus getting only about 4-6 hours of sleep until it is time to get up and go to school again.

More and more school districts around the country, especially in more enlightened and progressive areas, are heeding the science and making a rational decision to follow the science and adjust the school-start times accordingly. Instead of forcing teenagers to wake up at their biological midnight (circa 6am) to go to school, where invariably they sleep through the first two morning classes, more and more schools are adopting the reverse busing schedule: elementary schools first (around 7:50am), middle schools next (around 8:20am) and high schools last (around 8:50am). I hope all schools around the country eventually adopt this schedule and quit torturing the teens and then blaming the teens for sleeping in class and making bad grades.

No matter how much you may wish to think that everything in human behavior originates in culture, biology will trump you every now and then, and then you should better pay attention, especially if the life, health, happiness and educational quality of other people depends on your decisions.


Recently, Lance Mannion wrote an interesting post on the topic, which reminded me also of an older post by Ezra Klein in which the commenters voiced all the usual arguments heard in this debate.

There are a couple of more details that I have not touched upon in the previous posts.

First, lack of sleep can lead to obesity and even diabetes, as the circadian clock is tightly connected to the ghrelin/leptin system of hormonal control of hunger, feeding and fat-deposition.

Second, lack of sleep discourages exercise. Put these two pieces of data together, and you get a national epidemic of obesity, not just a bunch of sleep-deprived children.

Third, lack of sleep has a well-documented effect on mood. No, teenagers are not naturally that moody – at least not all of them. They are just barely “functional” (instead of “optimal”) and walk through life like zombies because they are operating on 4-8 hours of sleep instead of 9 hours (optimal for teens, it goes down to about 8 for adults). Of course they are moody.

Fourth, chronic sleep deprivation can have long-term consequences, ranging from psychiatric diseases to cancer. Remember that teens in high-school (and college students are faring worse!) are constantly jet-lagged!

There is even a hypothesis floating around that sleep-delay in adolescence may affect the onset of picking up smoking.

Fifth – and I did not think of this although it is obvious – teenagers above a certain age, still in high school, are allowed to drive. If they are driving themselves to school at 6 or 7am, when their circadian clocks think is it 3 or 4am, it is as if they are driving drunk. There is actually a scale devised by one of the sleep researchers that tells which time of the night corresponds to what number of bottles of beer. Driving at 4am (or driving a ship, like Exxon Valdez, or operating a power-plant, like one in Chernobyl) is the equivalent of driving drunk – way over the legal limits. Teenagers driving at 7am are equally “drunk”.

One of the reasons for the resistance to healthy initiatives to change school-start schedules stems from the fact that the world is organized by adults and adults want to have the world run according to schedules that fit their moods and are unwilling to change it – they may not know that teens feel differently, or they defend their preferences nonetheless.

A large proportion of adults in this country still subscribe to barbaric notions that sleep is a shameful activity, a sign of laziness, and that teens need to be tortured in order to “steel” them to grow into “real men”. This has roots all the way back to the Puritan so-called “work-ethic” which is really a “no fun for anyone” punitive ethic long ago shown to be physically and emotionally debilitating.

When I was a kid, back in old now-non-existent Yugoslavia, most schools in big urban areas worked in two shifts. All the kids started school at 8am and ended at 1:15pm for one week, then started at 2pm and ended at 7:15pm the next week, and so on…

If a school had, let’s say, twelve classes of the seventh grade, six of those would be in the A-shift and the other six in the B-shift. Each shift had its own complete set of teachers, assistants, nurses…everything except the one shared Principal and the school psychologist.

The time between 1:15pm and 2pm was for supplementary classes (either for those who needed extra help, or for those preparing for Math Olympics and such) and clubs. That was also time for kids from two shifts to meet and get to know each other (it is amazing how many kids from opposite shifts started dating each other after the year-end Big Trip to the Coast). There was no such thing as the American hype for high-school competitive sports, which I still find strange and curious after 15 [now 20] years in this country.

Thus, you get to sleep in for a week (but miss out on afternoon activities), then have to get up relatively early for a week but have the afternoon free to gallivant around town. Nobody there understands what’s the American fuss over kids being home alone – of course they are home alone, cleaning the house, fixing meals, doing homework and BETTER be getting to school on time!

Teachers were pretty understanding about sleeping types. I do not recall ever having a big test, quiz or exam being given at the extremes of the day (around 8am or around 7pm). As an owl myself, I was much more likely to raise my hand, participate in discussions, or volunteer for oral examinations during the week when I was in school in the afternoon, and that was fine with most of my teachers.

Transportation was not an issue. Most kids lived close enough to their neighborhood school to walk. For those who lived a little farther away – hey, no problem, that’s Europe, so Belgrade has a huge and pretty efficient public transportation system. I do not remember ever seeing any of my friends ever being dropped off to school by a parent driving a car! Or being brought to or picked up from school by a parent beyond fourth grade at all – period. And the minimum driving age being 18, nobody drove themselves to school either.

In rural areas, there was no need for two shifts – something like 9am-2:15pm was good enough to accommodate all of the kids.

I do not think that this kind of system can be implemented in the USA. It relies on an efficient public transportation which, with exception of a few oldest East Coast cities, is practically non-existent. American cities have been built for cars.

But some things can be done.

First, swap the starting times so elementary kids go to school first, middle school next and high school last (e.g., around 8am, 8:30am and 9am respectively). Studies show that teens do not go to sleep later if their school starts later. Some cynics claim that is what teens will do. But they do not. Actually, they fall asleep at the same time, thus gaining an additional hour of sleep.

Teens are almost adults. The current generation of teens, perhaps because of a closer and tighter contact with their parents than any generation before, is the most serious, mature and responsible generation I have seen. Give them a benefit of the doubt. Just because you were into mischief and hated your parents when you were their age does not mean that today’s kids are the same.

Second, start the school day – for all kids every day – with PE (or some kind of exercise), preferably outdoors, as both exposure to daylight and the exercise have been shown to aid in phase-shifting the circadian clock.

Third, let them eat breakfast afterwards (sticking to a meal schedule also helps entrain the clock). Follow up with the electives which kids may be most interested in.

By the time they hit math, science and English classes around 11 or so, their bodies are finally fully awake and they can understand what the teacher is saying, and do the tests with a clear mind instead of in a sleepy haze.

Do not permit any caffeine to be sold in schools. Advise parents not to allow TV or any other electronics to be in kids’ bedrooms. Let them enjoy those activities in the living room. Bedroom is for sleeping, and sleeping alone. A book before bed is fine, but screens just keep them awake even longer.

Finally, rethink all those extra activities you are forcing the teens to do: sports, art, music, etc. In teen’s minds, the day does not start with the beginning of school in the morning. We may think that we are at work most of our day. Teens do not – they consider their day to begin at the time school-day is over. Their day begins in the afternoon. School is something they have to deal with before they can have their day. Realize this and give them time and space to do with their day what they want. Do not push them to do things that you think they’ll need to get into Harvard. Let them be – leave them alone. Then they’ll go to sleep at a normal time.

Concern for our kids’ physical and mental health HAS to trump all other concerns, including economic costs, cultural traditions and adult preferences. We have a problem and we need to do something, informed by science, to fix the problem. Blaming the messenger, proposing to do nothing, and, the worst, blaming the kids, is unacceptable.


All of this targets high-schoolers. However, there is barely any mention of college students who are, chronobiologically, in the same age-group as high-school students, i.e., their sleep cycles are phase-delayed compared to both little kids and to adults.

In a way, this may be because there is not much adults can do about college students. They are supposedly adults themselves and capable of taking care of themselves. Nobody forces (at least in theory) them to take 8am classes. Nobody forces them to spend nights partying either.

They are on their own, away from their parents’ direct supervision, so nobody can tell them to remove TVs and electronic games out of their bedrooms. The college administrators cannot deal with this because it is an invasion of students’ privacy.

Forward-looking school systems in reality-based communities around the country have, over the last several years, implemented a policy that is based on science – sending elementary school kids to school first in the morning, middle-schoolers next, and high-schoolers last. This is based on the effects of puberty on the performance of the human circadian clock.

For teenagers, 6am is practically midnight – their bodies have barely begun to sleep. Although there have been some irrational (or on-the-surface-economics-based) voices of opposition – based on outdated notions of laziness – they were not reasonable enough, especially not in comparison to the scientific and medical information at hand, for school boards to reject these changes.

I am very happy that my kids are going to school in such an enlightened environment, and I am also happy to note that every year more school systems adopt the reasonable starting schedules based on current scientific knowledge.

Yet, college students are, from what I heard, in much worse shape than high-schoolers. Both groups should sleep around 9 hours per day (adults over thirty are good with about 8 hours). High-schoolers get on average 6.9 hours. College students are down to about five! The continuous insomnia of college students even has its own name in chronobiology: Student Lag (like jet-lag without travelling to cool places). Is there anything we, as a society, can do to alleviate student lag? Should we?


This kind of ignorant bleating makes me froth at the mouth every time – I guess it is because this is my own blogging “turf”.

One of the recurring themes of my blog is the disdain I have for people who equate sleep with laziness out of their Puritan core of understanding of the world, their “work ethic” which is a smokescreen for power-play, their vicious disrespect for everyone who is not like them, and the nasty feeling of superiority they have towards the teenagers just because they are older, bigger, stronger and more powerful than the kids. Not to forget the idiotic notions that kids need to be “hardened”, or that, just because they managed to survive some hardships when they were teens, all the future generations have to be sentenced to the same types of hardships, just to make it even. This is bullying behavior, and disregarding and/or twisting science in the search for personal triumphalism irks me to no end.

I hated getting up early, too. I still hate it, and I’m so far beyond growth hormones that I don’t even remember how they felt. But I do remember that in middle and high school, I dragged myself out of the house at 5 a.m. every day of the week to deliver papers before I caught the 6:45 a.m. bus to school. I never fell asleep in class. Neither did anybody else. And something caused me to grow 6 inches and add 35 pounds between sophomore and junior year. At the end of that kind of day, complete with cross-country, basketball or track, I had no trouble falling asleep at 10 p.m.

He said that he grew up in height and weight when he was in high school. Who knows how much more he would have grown if he was not so sleep deprived (if his self-congatulatory stories are to be believed and he did not slack off every chance he had). Perhaps he would not grow up to be so grouchy and mean-spirited if he had a more normal adolescence.

I don’t know where he got the idea that growth hormone is a cause of the phase-delay of circadian rhythms in adolescence. It could be, but it is unlikely – we just don’t know yet. But, if a hormone is a cause, than it is much more likely to be sex steroids. Perhaps his sleep-deprived and testosterone-deprived youth turned him into a sissy with male anxiety he channels into lashing at those weaker than him?

In previous centuries, adolescents in an agrarian society got up at 4:30 or 5a.m. with their parents to milk the cows or do any other of a long list of chores. Did growth hormones pass them by? Where were the “studies” that showed they really needed to go to bed after midnight and sleep until 10? And why weren’t their parents all being reported to the DSS? Oh, that’s right, there was no DSS. How did that generation survive?

He assumes that in times before electricity, teenagers used to wake up and fall asleep at the same time adults did. Well, they did not. Studies of sleep patterns in primitive tribes show that adolescents are the last ones to wake up (and nobody bashes them for it – it is the New Primitives with access to the media that do that) and the last ones to fall asleep – they serve as first-shift sentries during the night watch.

Even in this, the 21st century, kids who enter the military at 17 find that they can fall asleep easily at 9:30 or 10, because they know they’re going to be getting up at 4:30 or 5. Apparently the Army hasn’t read the study on circadian rhythms.

Actually, the military being the most worried by this problem is funding a lot of research on circadian rhythms and sleep and has been for decades. Because they know, first hand, how big a problem it is and that yelling sargeants do not alert soldiers make.

Kids, if you need more sleep, my study shows there’s a simple way to get it. Turn off – I mean “power down” – the cell phone, the iPod and the computer sometime before 11 p.m. Turn off the TV. Turn off the light. Lie down in bed and close your eyes.

…and sit in the dark for the next four hours, heh?

What especially drives me crazy is that so many teachers, people who work with adolescents every day, succumb to this indulgence in personal power over the children. It is easier to get into a self-righteous ‘high’ than to study the science and do something about the problem. It is easier to blame the kids than to admit personal impotence and try to do something about it by studying the issue.


My regular readers are probably aware that the topic of adolescent sleep and the issue of starting times of schools are some of my favourite subjects for a variety of reasons: I am a chronobiologist, I am an extreme “owl” (hence the name of this blog), I am a parent of developing extreme “owls”, I have a particular distaste for Puritanical equation of sleep with laziness which always raises its ugly head in discussions of adolescent sleep, and much of my own past research was somewhat related to this topic.

So, I was particularly pleased when Jessica of the excellent Bee Policy blog informed me of the recent publication of a book devoted entirely to this topic. Snooze…or Lose! by Helen Emsellem was published by National Academies and Jessica managed to get me an advanced reading copy to review.

You can also read the book online (or buy the PDF). Much more information on the topic can be found on the book webpage, on the National Slep Foundation website, on Dr.Emsellem’s homepage and the Start Later for Excellence in Education Proposal (S.L.E.E.P.) website. I strongly encourage you to look around those webpages.

Her daughter Elyssa wrote one of the chapters in the book and is promoting the book and the information relevant to teenagers at the place where teenagers are most likely to see it – on MySpace (you see – it’s not just music bands who caught onto this trick – serious information can be promoted at MySpace as well).

The main audience for this book are teenagers themselves and their parents – I think in this order although officially the order is reversed. Secondarily, the audience are teachers, administrators and officials in charge of school policy. Who this book is not targeted to are scientists and book reviewers because there are no end notes!

Anyway, considering that the main audience are teens, their parents and teachers (i.e., laypeople), the book is admirably clear and readable. The book starts out with presenting the problem – the chronic sleep deprivation of adolescents in modern society – and provides ample evidence that this is indeed a wide-spread problem. It continues with a simple primer on physiology of sleep and circadian rhythms, followed by a review of the current knowledge of the negative consequences of chronic sleep deprivation: from susceptibility to diseases, through psychological and behavioral problems, to problems of physical and mental performance.

A whole chapter – the one I found most interesting – is devoted to the role of sleep in various kinds of memory and the negative effects of sleep deprivation on learning – both declarative and episodic memory, as well as kinesthetic memory needed for athletic performance and safe driving. This is where I missed the end notes the most.

Throughout the book, Dr.Emsellem makes statements of fact about sleep that are obviously derived from research. I’d like to see the references to that research so I can evaluate for myself how strong each such statement is. Although my specialty is chronobiology (physiology, development, reproduction, behavior, ecology and evolution) of birds, and secondarily that of mammals, reptiles, invertebrates and microorganisms (I could never quite get excited about clocks in fish, fungi and plants, or molecular aspects of circadian rhythms, or medical aspects of human rhythms), I am quite familiar with the literature on sleep, including in humans.

Thus, I know that the statements in the book reflect scientific consensus but that the meaning of “consensus” is quite elastic. In some cases, it means “there is a mountain of evidence for this statement and no evidence against it, so it is highly unlikely that this will change any time soon”. In other cases it means “there are a few studies suggesting this, but they are not perfect and there are some studies with differing results, and this can stand for now but is likely to me modified or completely overturned by future research”.

Having end notes would help the expert reader see how weak or strong each one of these findings is, and would also be suggestive to lay readers that the statements in the book are supported by actual research and are not just the author’s invention as seen in so many self-help books. End notes and references add to the believability of the text even if one does not bother to check the papers out.

The book then turns to variety of factors, both biological and social, that conspire to deprive our teens of sleep, both from the perspective of a sleep researcher and from the perspective of teenagers. Little snippets of teenagers’ thoughts on the topic are included throughout the book and add an important perspective as well as make the book more fun to read. Otherwise, the “case studies”, the bane of so many psychology books, are kept to the minimum, discussed very briefly, and used wisely..

In the next section, Dr.Emsellem turns to solutions. First, she present several tests of sleep deprivation that readers can administer themselves in order to self-diagnose the problem. She then describes ten different strategies that parents and teens can work on together in order to solve the problem of sleep deprivation and all the concomittant negative effects (and Alyssa adds her own chapter on the teen perspective on how those can work). If that does not work, she describes additional methods that a sleep doctor may prescribe to help solve the problem. There is also a short chapter describing a couple of other sleep disorders, e.g., sleep apnea, that also contribute to sleep deprivation in affected individuals.

The last portion of the book addresses the social aspects of sleep deprivation and changes that parents and teens can make in their homes, as well as broader community, towards solving the problem. For adults, being a role model for the child is important and this requires paying attention to one’s own sleep hygiene.

The very last portion is really the raison d’etre of the book – how to make one’s community change the school starting times. The author presents a couple of examples of school districts in which such change was enacted, the strategies parents used to force such changes and the incredible positive results of such changes. The whole book is really designed to provide information to parents and teens who are working on changing their local attitudes toward school starting times.

The schools used to start about 9am for most of the century (and before). Then, due to the pressure from business and economic (read “busing”) woes of school districts, the school starting times started creeping earlier and earlier starting back in 1970s until they reach the horribly early times seen today in many places, requiring kids to get up as early as 5am in order to catch the school bus on time. As a result, high schoolers (and to some extent middle schoolers and college students) sleep through the first two periods in school, feel weak and groggy all day long, more easily succumb to diseases, have trouble learning and performing well in school and the athletic field, and are in too bad mood to be pleasant at home – this is not the natural state of things as much as the stereotype of the “grouchy teen” is prevalent in the society, it is mainly due to sleep deprivation and the biggest factor causing sleep deprivation are early school starting times.

In places in which enlightened and progressive school boards succumbed to the wishes of parents and students, i.e., in places in which parents and students used smart diplomatic tactics to engender such change, the positive results are astounding. The grades went up. The test scores went up. The students are happy. The parents are happy. The teachers are happy. The coaches are happy because their teams are winning all the state championships. There is a decrease in tardiness and absences. There is a decrease in sick days and even in numbers of diagnoses of ADD and depression in teens. There is a drop in teen crime. There is a drop in car accidents involving teens (by 15% in one place!). The whole county feels upbeat about it!

While the book makes me – a scientist – thirsty for end notes and references, it does remarkably well what it was designed to do – arm the parent and kids with knowledge needed to make a positive change in their communities – a change that is necessary in order to raise new generations to be healthy and successful, something we owe to our children.

We should do this no matter how much it costs, but the experiences from places in which the changes were made, contrary to doomsayers, is that there was no additional cost to this at all. The changes were implemented slowly and with everyone involved pitching in their opinion and their expertise until the best possible system was arrived at, adapted to the local community situation. No new buses were needed to be rented. No unexpected new costs appeared. And having a safe, happy community saved money elsewhere (e.g., accidents and crime rate decline). And it worked wonderfully everywhere.

So, get the book and let your child read it, you read it, give a copy to other people in your community: the teachers, the school principal, the pediatrician, the child psychologist, the school board members, the superintendent of education and the governor. This is something that is easy to do, there are no good reasons against it and the health and the future of our kids is at stake. It is something worth fighting for and this book is your first weapon.



Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask)
Sun Time is the Real Time
What is a ‘natural’ sleep pattern?
Lesson of the Day: Circadian Clocks are HARD to shift!
Circadian Rhythms in Human Mating
Seasonal Affective Disorder – The Basics
Data for #drunksci: Daily rhythm of alcohol tolerance
Basics: Biological Clock
Spring Forward, Fall Back – should you watch out tomorrow morning?
(Non) Adaptive Function of Sleep

(Non) Adaptive Function of Sleep

This was first published on November 01, 2005.

Here is a nice article in Washington Post – Ecological Niche May Dictate Sleep Habits – about the adaptive function of sleep.

It addresses some of the themes I am interested in.

First, the unfortunate fact is that sleep was initially defined by researchers of humans, i.e., medical researchers. Inevitably, the (electrophysiological) definition of sleep was thus saddled with unnecessary anthropocentric elements that for decades hampered the study of evolution of sleep.

I was present at the meeting (here in Biotechnology Center in RTP) several years ago when the bigwigs of the sleep research community were first exposed to some very new ideas via not one but two talks about sleep in fruitflies (by Marcia Belvin and Joan Hendricks). That was quite an earthshaking event as the definition of sleep was substantially changed right then and there. Interestingly, the new (behavioral) definition was received not with resistance but with enthusiasm. Everyone in the room understood the potential of the new way of thinking to break off the shackles that sleep research had to suffer in for so long.

Since then, the marriage of circadian and sleep research has resulted in sleep research taking off at a breathtaking speed. As a result, many old assumptions and dogmas had to be discarded. For many years sleep researchers shunned evolutionary explanations and focused on physiological and medical aspects of the phenomenon. However, progress in sleep medicine depends on a better understanding of what sleep is for – a decidedly evolutionary question.

Another theme is the old battle between adaptationism and the more sophisticated view of evolution that incorporates the phenomena of developmental and phylogenetic constraints, as well as the concept of exaptation. Just because a mechanism currently serves a particular function does not mean that this function is what the mechanism originally evolved for. In other words, current function is not necessarily the original function (bird wings were initially adaptations for thermoregulation and later got exapted for flight). Here is the adaptationist statement:

The theorists have long disagreed about one another’s ideas, but most agree on one thing: If nature makes people sleep away so much of their lives, the reason has to be something crucial. That seemed to be the only way to explain why sleep-deprived people crave sleep so badly that they doze off behind the wheel of a car going 60 mph, and why rats deprived of sleep die sooner than rats deprived of food.

The article then trots out a couple of currently favoured hypotheses about the adaptive function of sleep:

Yet a wealth of sleep research has regularly produced baffling paradoxes and conflicting lines of evidence about the uses, role and need for sleep. If sleep is primarily about providing mental rest, why do people’s brains remain so active during sleep, as research in recent decades has found?

If sleep is about providing the body with rest, why do couch potatoes need as much sleep as Olympic athletes? Moreover, animals such as horses, which perform far more physical labor than humans, need much less sleep than people do.

If sleep primarily hones cognitive functions, why do the intellectually lazy need as much sleep as Nobel Prize-winning physicists? Also, why do humans — who are a lot smarter than rats — sleep less than rodents?

Finally, while much conventional thinking suggests that Americans should be sleeping more, a very large 2002 study found that people who sleep eight hours or more a night are likely to die younger than those who sleep seven. (Don’t touch that alarm clock; the study did not find that deliberately sleeping less increases life span.)

Considering that a vast majority of sleep researchers are MDs, not neccessarily up to speed in evolutionary theory, such sentiments are not surprising. It takes an evolutionary biologist to move the ball forward:

Jerome Siegel, a psychiatrist at the University of California at Los Angeles who described these discordant findings in acomprehensive review of the available research, published in the journal Nature last week, said he began to question the notion that sleep performs some essential function after noting that species that sleep less than others do not sleep any deeper — as they would if they were making up for the shorter time. Animals that sleep fewer hours generally sleep less deeply, while animals that sleep longer usually sleep more deeply.

Siegel, a respected sleep researcher who is also affiliated with the Department of Veterans Affairs, said he came to the conclusion there was only one explanation that could explain the paradoxes: in a word, evolution.

Rather than being designed to perform some critical function, Siegel wrote in his paper, sleep may be the way various species, humans included, have adapted to their ecological niches. While many valuable functions probably take place during sleep, Siegel suggested that it is possible that those functions are not the reason for sleep.

“There is this huge variation in sleep across species, and it fits with this huge variation in the niches that animals occupy,” Siegel said in an interview.

“The analogy I make is between hibernation and sleep,” he said. “No one says, ‘What is hibernation for? It is a great mystery.’ . . . It’s obvious that animals hibernate because there is no food, and by shutting down the brain and body they save energy.”

Sleep, Siegel suggested, may play much the same role. As evidence, he cited research that has found systematic differences in the way carnivores, omnivores and herbivores sleep: Carnivores sleep longer; herbivores, shorter; and omnivores, including humans, are somewhere in the middle.

“If animals have to eat grass all day, they can’t sleep a lot, but if they eat meat and are successful at killing an antelope, why bother to stay awake?” he asked.

On the other hand, mammals at greater risk of being eaten — such as newborns — spend large amounts of time asleep, presumably safe in hiding places devised by their parents. Supporting the evolutionary explanation, Siegel’s own research has shown that when the luxury of safe hiding places is unavailable — in the ocean, for instance — baby dolphins and baby killer whales reverse the pattern found among terrestrial mammals. These marine mammals sleep little or never as newborns and gradually increase the amount they sleep as they mature.

Let me put it simply: sleep makes you sit still and be quiet at times when it is dangerous to move around and there is nothing else important to do. All the other functions were added later due to either timing (some things are better done at certain times of day that coincide with either sleep-time or wake-time and the two processes get linked) or particular brain states (i.e., some functions, for instance the consolidation of memory, are easier to perform at times when the brain is NOT receiving much input from the outside environment):

The theory does not so much contradict other theories about the role of sleep as much as place them in context: “What I am saying is that it is not that sleep has been adapted to allow some vital function to be fulfilled, but the core function of sleep is to adapt animals to their ecological niche,” Siegel said. “Given the animal is inactive for a certain period of the day, certain functions will migrate to that period because it is more efficient” to perform them at that time.

Interestingly, this hypothesis does not conflict with an old (and frankly quite unpopular) notion that mammals and birds did not evolve sleep as a new process (after all, insects sleep, we now know), but that they evolved wakefulness as a novel state of the mind.

Insects, fish, amphibians, reptiles etc., have periods of activity and periods of slumber. The period of slumber corresponds to mammalian/avian state of sleep. But, the active state in cold-blooded animals is more similar to sleep-walking than real wakefulness.

Did birds and mammals independently evolve wakefulness or was there a whole suit of (now extinct) reptilian and dinosaurian lineages who were also wide awake? Did evolution of wakefulness provide a substrate for the evolution of consciousness? Interesting speculations, but nothing close to an answer to date. At least, provocative hypotheses by Jerome Siegel and some others are prompting the sleep scientists to reconsider everything they hold dear and therein lies progress.

Siegel’s paper is available online (unfortunately, behind a paywall). Carl Zimmer has an article on this in New York Times.

The Scienceblogging Weekly (May 18, 2012)

Blog of the Week:

For the greatest portion of the history of biology, every organism was a “model organism”. One would pick a problem and then choose which organism would be most suited for answering those particular questions. Then, in the 1990s, everyone jumped onto the bandwagon of studying just a handful of organisms that could be genetically modified at the time: mouse, fruitfly, thale cress, zebrafish, African clawed frog, bread mold, brewer’s yeast, or E.coli. All the other organisms were all but abandoned, only studied by a small number of die-hard researchers and, increasingly, amateurs. Now that technology allows us to investigate (and to some extent manipulate) entire genomes of almost any species we’d like, researchers are going back and rediscovering the abandoned model organisms once again. One of these is Anolis, a large group of species of lizards, noted for their dewlaps, and known especially for their fast adaptive radiation on tropical islands.

And now there is a blog that covers everything about these lizards – Anole Annals. Posts are written both by veteran researchers and their students, from several laboratories, as well as other contributors. They cover both recent and historical papers on evolution, ecology, biogeography, behavior, physiology, biomechanics and genetics of this diverse group of reptiles. They also describe their own research, including anecdotes and adventures from field work, equipment they use in the lab, and successes in discovery. On top of that, they help people ID the species from pictures, pay attention to the appearance of anoles in art and in the popular culture and generally have a lot of fun doing all of this. A blog entirely devoted to just one group of animals sounds very ‘niche’, but what they did was build a blog that has something for everyone and is a great fun (as well as insightful and educational) read for everyone.


Top 10:

The secret molecular life of soap bubbles (1913) by Greg Gbur:

…Today we take for granted that all material objects in the universe are comprised of discrete “bits” of matter, which we call atoms; however, even up until the early 20th century there were still proponents of the continuum hypothesis, in which all matter is assumed to be infinitely divisible…

Motherhood, war, and attachment: what does it all mean? by Emily Willingham:

I’m sure many mothers can attest to the following: You have friends who also are mothers. I bet that for most of us, those friends represent a spectrum of attitudes about parenting, education, religion, Fifty Shades of Grey, recycling, diet, discipline, Oprah, and more. They also probably don’t all dress just like you, talk just like you, have the same level of education as you, same employment, same ambitions, same hair, or same toothpaste. And I bet that for many of us, in our interactions with our friends, we have found ourselves judging everything from why she insists on wearing those shoes to why she lets little Timmy eat Pop Tarts. Yet, despite all of this mental observation and, yes, judging, we still manage to get along, go out to dinner together, meet at one another’s homes, and gab our heads off during play dates. That’s not a war. That’s life….

As oxygen filled the world, life’s universal clock began to tick by Ed Yong:

The Earth’s earliest days were largely free of oxygen. Then, around 2.5 billion years ago, primitive bacteria started to flood the atmosphere with this vital gas. They produced it in the process of harnessing the sun’s energy to make their own nutrients, just as plants do today. The building oxygen levels reddened the planet, as black iron minerals oxidised into rusty hues. They also killed off most of the world’s microbes, which were unable to cope with this new destructive gas. And in the survivors of this planetary upheaval, life’s first clock began to tick and tock….

Poisoning the Dalai Lama. Or Not by Deborah Blum:

Earlier this week, the Tibetan Buddhist leader, the Dalai Lama, told British journalists that he’d been warned of an ingenious Chinese plot to assassinate him with poison. Very ingenious, according to the plot he laid out for the Sunday Telegraph. He’d learned, he said, of a plan to send out a squad of women, pretending to be followers, who would have poison spread through either their hair or headscarves. When he laid his hands on their heads for a blessing, a lethal dose could be absorbed through his skin…

The Brain Hidden Epidemic: Tapeworms Living Inside People’s Brains by Carl Zimmer:

….But sometimes tapeworms take a wrong turn. Instead of going into a pig, the eggs end up in a human. This can occur if someone shedding tapeworm eggs contaminates food that other people then eat. When the egg hatches, the confused larva does not develop into an adult in the human’s intestines. Instead, it acts as it would inside a pig. It burrows into the person’s bloodstream and gets swept through the body. Often those parasites end up in the brain, where they form cysts….

Why Octopuses Should Run Our National Security Infrastructure by Annalee Newitz:

Next time the government wants new ideas about how to protect our nation’s security, it should consult an octopus. That’s the unusual proposition of marine biologist Rafe Sagarin, a pioneer in the infant field of “natural security,” where experts use models from nature to help them come up with emergency responses to everything from terrorist attacks to pandemics. Sagarin has just published a book about his work called Learning from the Octopus: How Secrets from Nature Can Help Us Fight Terrorist Attacks, Natural Disasters, and Disease. Any scientific theory that involves the superiority of cephalopods is automatically intriguing, so I called up Sagarin to talk about it.

Solving the Mystery of the Placental Jellyfish by Craig McClain:

Yesterday the DSN crew first saw the video above. What is this large floating sheet of goo? Is it alive? Was it once alive? The two leading contenders seems to be that it is A) an old whale placenta or B) a rare and enigmatic deep-sea jellyfish. And the answer is…. B)

Physics’s PR problem: Moving beyond string theory and multiple universes by Ashutosh Jogalekar:

….The problem is that most of the popular physics that the public enjoys constitutes perhaps 10% of the research that physicists worldwide are engaged in. Again, count the number of physics books in your local bookstore, and you will notice that about 90% of them cover quantum mechanics, cosmology, particle physics and “theories of everything”. You would be hard-pressed to find volumes on condensed matter physics, biophysics, the physics of “soft” matter like liquids and non-linear dynamics. And yes, these are bonafide fields of physics that have engaged physics’s best minds for decades and which are as exciting as any other field of science. Yet if you ask physics-friendly laymen what cutting-edge physics is about, the answers will typically span the Big Bang, Higgs boson, black holes, dark matter, string theory and even time-travel. There will be scant mention if any of say spectroscopy, optics, polymers, magnetic resonance, lasers or even superconductivity….

Dear Media, Leave My Dinosaurs Alone by Brian Switek:

I wish I could take dinosaurs away from the media for a while. Someone certainly should. Lazy journalists and unscrupulous documentary creators have amply demonstrated that they just can’t play nice with Tyrannosaurus, Triceratops and kin…

Do Bonobos And Chimpanzees Offer A Path To Understanding Human Behavior? by Sheril Kirshenbaum:

What leads people to acts of violence and genocide? What triggers empathy and altruism? Duke evolutionary biologist Brian Hare and research scientist Vanessa Woods believe the answer may be found in the great ape known as the bonobo….


Special topic: snakes:

And the Cascabel will Fall Quiet… by John F Taylor. Rattlesnakes may actually be learning and they may become more dangerous if their roundups aren’t stopped.

Spore Dispersal by Snakes by Jessica M. Budke

The Secret to Success Is Giant-Jawed Snake Babies by Elizabeth Preston

Identifying snake sheds, part II by Andrew Durso



Pacific plastic, sea skaters, and the media: behind the scenes of my recent paper by Miriam Goldstein. Once you are featured in The Onion, your career has reached the peak. What more can one do after that?

In the wake of high-profile controversies, psychologists are facing up to problems with replication. by Ed Yong. Psychology example, applicable at least to some extent to other fields.

The Flavor of Neutrinos by Matthew Francis

Confusing messages about sugar are stupid by David Despain

Two Earths would be needed to sustain human activity by 2030, report finds by Meghan Neal

Science vs. PR by Robert McHenry. How a scientific paper about chemistry turned into mass media articles about alien dinosaurs.

Who hates cilantro? Study aims to find out by Cari Nierenberg

Microbiology at Sea: A tale of ballast, vomit, and cockroaches by Holly Bik

Is the U.S. Ready for Home HIV Tests? by Benjamin Plackett

Lessons from the Lab: How to Make Group Projects Successful by Annie Murphy Paul. “Megacollaboration is becoming the norm in science. Here’s what we can learn about what works when working together.”

Sometimes scientists have a duty to swap the pipette for the placard by Adam Smith

Academics on archosaurs: Jerry Harris by Dave Hone

Whistle Recognition in Bottlenose Dolphins by Tara Thean

The regulation of nonsense by Jann Bellamy on medical quackery and CAM.

What Happens to All That Volcanic Ash? by Erik Klemetti

Cannibalism? by Mark Crislip

Science Standards: The Next Generation by Rhett Allain

Is the holocaust denial/climate change denial comparison apt? by Mark Hoofnagle

The Coming Beepocalypse, It’s hard out there for a bee, and Bees and STDs by Bug Girl

Huge Turtle Was Titanoboa’s Neighbor by Brian Switek

De-caffeinating pills? Say it ain’t so, Think Geek by David Kroll

Human morality is evolving by Ken Perrott

5 Things the Science Doesn’t Say About the Conservative Brain by Chris Mooney

The Republican Brain by Chris Mooney by Chad Orzel

Turning Wolves into Hounds by Heather Pringle

Dendrites of Direction by TheCellularScale

LA smog: more cows than cars? by Scott K. Johnson

The New Atheism and Evolutionary Religious Studies: Clarifying Their Relationship by David Sloan Wilson

Opinion: Academia Suppresses Creativity by Fred Southwick

Methods for Studying Coincidences by Samuel Arbesman

Is misconduct more likely in drug trials than in other biomedical research? by Ivan Oransky

A rising tide of willful ignorance by Rob Schofield. Lobbyists pushing to dictate which data scientists are allowed to use.


Media, Publishing and Technology:

All A’Twitter: How Social Media Aids in Science Outreach a Master’s Thesis by Caitlyn Zimmerman about the pros & cons and strategies in using social media in Marine Conservation outreach.

Guest Editorial: It’s Time To e-Volve: Taking Responsibility for Science Communication in a Digital Age by Christie Wilcox

Young scientists ask: Is there room out there for one more science communicator? by Denise Graveline

The SA Incubator: Helping Hatch Science Writers Since July 2011 by Erin Podolak

Research Blogs and the Discussion of Scholarly Information by Hadas Shema, Judit Bar-Ilan and Mike Thelwall, a research paper about science blogs using the aggregator. Responses by Scicurious, Neurocritic, Jonathan Eisen, Caroline Tucker, Misha Angrist and Invader Xan.

Beyond a Trend: How Scientists Use Social Media by Jessica Rohde

Twitter is like… by dorkymum. A beautiful metaphor to try on n00bs.

Do I Write? Or Do I Tweet? by Geoff Brumfiel

Mom, this is how twitter works by Jessica Hische

Printed books existed nearly 600 years before Gutenberg’s Bible by Annalee Newitz

Digital Pagination by Nate Barham. The page-flip is just another in a long line of “unnecessary” features to help us poor humans understand the content.

My personal take: 3 reasons I don’t like newspaper paywalls by Mathew Ingram and a response to it, Paywalls are backward-looking by Dave Winer.

Commenting, Moderation, and Provocation by Marc Bousquet

Aggregation guidelines: Link, attribute, add value by Steve Buttry – a definitive guide.

Please Don’t Learn to Code by Jeff Atwood, and Should you learn to code? by Dave Winer, and Don’t tell me not to learn! by Eva Amsen.

The newsonomics of News U.: Journalism and education are both about knowledge. Could their post-disruption business models start to blur? by Ken Doctor.

See, this is why publishers irritate me so much and Publishers versus everyone by Mike Taylor

The government spends billions on research. Should we have to pay $20,000 more to see the results? by Suzy Khimm

The Tao of Shutterstock: What Makes a Stock Photo a Stock Photo? by Megan Garber

How Facebook Saved Us from Suburbia by Christopher Mims and Does Facebook Turn People Into Narcissists? by Tara Parker-Pope

The tip of the iceberg- what digital photography really costs by Brendan Moyle

A Brief History and Proposed Definition for ‘Attention Economics’ by Adrian J. Ebsary

How barley domesticated its clock

barleyMost organisms that live on or near the surface of the Earth or its oceans have evolved a circadian clock – a daily timer of all biochemical, physiological and behavioral functions.

Daily cycle of light and darkness in the environment is a selective factor – having an internal clock is an adaptation that allows organisms to predict and prepare for instead of passively react to cyclical changes in the environment. The regularity of the light-dark cycle is usually a good predictor for other (perhaps not as precise) cycles of temperature, availability of food, or activity of predators.

ResearchBlogging.orgIt gets trickier for organisms that live in places where the light-dark cycle may be missing for big chunks of the year (the polar regions), or where light-dark cycle is not a good predictor of other relevant events in the environment (e.g,. cannot predict rain in very arid regions), or where light cannot penetrate at all (deep ocean, caves, underground burrows). In such organisms the clock may get uncoupled from some of its functions, e.g., it may still time biochemical but not behavioral events. Or the clock may be temporarily or permanently turned off.

Even animals that constantly live in caves still tend to have functioning circadian clocks even if they are not used by these animals to drive rhythms in behavior. In animals that regularly travel into and out of the caves, like bats, the clock is robust.

A number of organisms have been studied in which the clock may temporarily be turned off. In the chestnut tree , circadian clock stops in winter. In reindeer in the high Northern latitudes, behavioral rhythms (and underlying clock) work only during the short springs and autumns, not during the long polar winters and summers. In social insects, castes that spend their time inside the hive and need to work around the clock also do not have a functioning circadian clock.

The organisms that live in extreme environments tend to be difficult to study. It may be a harsh environment for the human researchers to spend long periods of time in. The organisms may not be easy to bring into the lab to study under controlled conditions. Most of such organisms are far from being standard “laboratory models” which means that little is known about their genetics, biochemistry, physiology and behavior.

Thus, one is limited in choices as to which rhythms to study and what conclusions one can take from such studies. A limited number of overt rhythms can be easily monitored in a standardized manner even in the laboratory. A record of overall physical activity and movement is usually made. Additional measured rhythms may be daily fluctuations in hormones, e.g., melatonin. And tissue samples may be taken over a 24-hour period for analysis of patterns of expression of core clock genes.

This approach may miss stuff. For example, even if there is no cycling of clock genes or overt behavioral rhythms, this does not mean that the clock may not be working anyway – cytoplasmatic cellular clocks, or ensembles of neural cells producing weak rhythms, or hormonal feedback loops between endocrine glands could still be producing daily cycles in some aspects of metabolism not identified by the researchers. The adaptive function of the clock is so strong, if nothing else for coordinating internal events, that is is difficult to persuasively and definitively demonstrate that absolutely nothing in the body cycles around a 24-hours cycle.

An important function of the clock is also in measuring changes in daylength – days get longer in spring and shorter during fall. Even environments that have no daily cycles for a while, or no utility in using light-dark cycles, may have strong seasonality, and seasons are another important aspect of the environment related to time. Most organisms use their circadian clocks to measure the changes in daylength through a mechanism called photoperiodism. So even organisms that have no use for daily clocks, may still retain them for their higher-level function of fine-tuning the annual calendar of events.

Domestication also has an effect on circadian clock as one can argue that the lab and the farm are “extreme environments” in some sense. It is well known that many domesticated strains of laboratory mice, rats and nematodes have lost seasonality. Most of our domesticated animals have vastly prolonged breeding seasons – sometimes spanning the entire year, or adding a Fall season to the existing Spring one  – compared to their wild relatives. Domestication may be a strong selective force for abandoning seasonality, which reduces the need for a functional circadian clock as well, especially if human care – feeding, defense, etc. – replace the need for the organism to fend for itself in sync with the cycles of nature.

Now a new player is entering this line of research – barley (Hordeum vulgare). Last week, Faure et al, published an open access paper in PNAS showing that strains of barley from Northern Europe have mutations in one of their photoperiodic genes – EARLY MATURITY8 (EAM8) – and that this gene greatly reduces the amplitude of expression of the core circadian clock genes.

As a result, northern varieties of barley can start flowering early and fast in the season, completely ignoring daylength, just following the normal developmental program. At the same time the disrupted clock allows for much longer daily activity of photosynthesis during long summer days, as it does not shut it down before darkness arrives in the evening.

One can imagine how such mutants were prized in the earlier history of the domestication. As humans moved more and more north, only the barley that could be harvested early and produced large yields was valuable. Late harvest may have been too late: humans may have already moved on, driven by hunger, and left the field to be harvested by birds. Or the harvest, being so small and late, would have been used only for consumption (winter is coming – time to brew some beer!) and not for seed for the next year.

Plant circadian clocks are very complex at the molecular level, involving several different feedback loops in expression, some operating in the morning, others in the evening, etc. Importantly, some of the genes involved in photoperiodism and flowering are intricately connected to the clock and may be a part of some of the clock feedback loops. Most of the past research focused on the way clock genes regulate flowering genes. This is an unusual paper in that it discovers the opposite direction – how a gene involved in flowering feeds back on the clock genes and regulates the way the clock works.

What is exciting about this work is that barley is not a difficult organism to do research on. One does not need heroic efforts or expensive Arctic or speleological gear to study it – it is a domesticated plant, easily grown in fields, glasshouses and labs. Furthermore, much of its biology is already well known, including the similarity between its genes and those of Arabidopsis thaliana, the standard model for plant research.

As a number of strains of barley exist, some southern some northern, there is plenty of material to do comparative studies to figure out exactly which genes and processes were involved in the process of domestication – what was selected for as the humans took their crops with them on their northward migrations. This makes barley potentially a useful standard laboratory model for the general studies of evolution under domestication.


Faure, S., Turner, A.S., Gruszka, D., Christodoulou, V., Davis, S.J., von Korff, M. & Laurie, D.A. Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley (Hordeum vulgare) to short growing seasons, Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1120496109

Related at Scientific American:

Chestnut Tree Circadian Clock Stops In Winter
Evolutionary Medicine: Does reindeer have a circadian stop-watch instead of a clock?
Domestication – it’s a matter of time (always is for me, that’s my ‘hammer’ for all nails)
Why social insects do not suffer from ill effects of rotating and night shift work?
Clock Evolution
Whence Clocks?
Circadian clock without DNA–History and the power of metaphor
Basics: Biological Clock
Clock Classics: It All Started with the Plants

Image: Wikimedia Commons, public domain.

Domestication – it’s a matter of time (always is for me, that’s my ‘hammer’ for all nails)

I originally published this post on August 6, 2008.

Since this article came out in The American Scientist in early 1999 (you can read the entire thing here (pdf)) I have read it many times, I used it in teaching, I discussed it in Journal Clubs, and it is a never-ending fascination for me.

Back in the 1950s, Dmitri Konstantinovich Belyaev started an experiment in which he selectively bred Silver Foxes, very carefully, ONLY for their tameness (and “tameness” was defined very rigorously in terms of type and speed of response, distance that triggers aggression, etc.).

What happened really fast in this experiment is that many other traits showed up, seemingly out of nowhere, in the subsequent generations. They started having splotched and piebald coloration of their coats, floppy ears, white tips of their tails and paws. Their body proportions changed. They started barking. They improved on their performance in cognitive experiments. They started breeding earlier in spring, and many of them started breeding twice a year.

Most of the people reacting to this experiment invoked pleiotropy, i.e., how changes in one gene affect expression of many other genes. See this NYT article for instance. However, even while I was reading it for the first time, my mind screamed – development!

And not just development, but more specifically, heterochrony – change in timing of developmental event.

If you alter the expression of one of the genes that affects developmental timing, you affect all sorts of things.

For instance, when the neural crest cells migrate they become melanocytes in the skin – if due to changes in timing they are late to arrive to some distal parts, e.g., paws and tail-tips, those part will be white. Neural crest cells also migrate to become the adrenal medulla – that little part of the body that releases (nor)epinephrine (adrenaline). If fewer of those cells arrive there on time, less the animal will show stress-response later in life.

There appears to be tight correlation between timers that act on different scales, e.g., developmental and circadian timing, circadian and fast behavioral timing, circadian and seasonal timing, etc.

I always wished I could get a lab, some foxes, an IACUC approval and some money to run these animals through a battery of standard experiments comparing dogs, wild foxes and domesticated foxes on all sorts of parameters of circadian rhythms, photoperiodism (they did change their seasonality patterns of breeding, after all), etc.

The bottom line is that a subtle change in timing of expression of a single developmental gene, something one can select for by choosing one of the traits (in this case a behavioral trait), will affect the change in timing of expression in many other genes. The difference between wild and domesticated foxes may not be in any DNA sequence at all – it could presumably be all epigenetic (see also). Sequence differences would arise later, as the two populations are not inter-mixing any more (for over 60 years now).

When you put together development, genetics and evolution, you can see that big changes (or, really, any changes at the very beginning of the evolutionary change) in DNA sequence are not necessary for big changes in entire suites of phenotypic traits. But in the 1950s, the bean-bag deterministic genetics was the norm, so the Belyaev experiment was a big jolt to the scientific community in the West (not so much for the Russian evolutionary biologists, though), so we need to look at this experiment through a decent grasp of history.

Now, I’d like to know what is the state of the experiment today. Ten years ago, the project appeared doomed – they had to sell foxes for fur in order to keep going at a small scale. Has this been fixed? Has anyone from the West help finance the continuation of the project? Has anyone in the West acquired some of the foxes and continued with the project? What are the recent developments?

Related at Scientific American:

Man’s new best friend? A forgotten Russian experiment in fox domestication by Jason G. Goldman

Learning from Domesticated Foxes by The Dog Zombie

The Russian Fox Study by Jason G. Goldman

Why social insects do not suffer from ill effects of rotating and night shift work?

This post was first published on May 10, 2009

ResearchBlogging.orgMost people are aware that social insects, like honeybees, have three “sexes”: queens, drones and workers.

Drones are males. Their only job is to fly out and mate with the queen after which they drop dead.

Female larvae fed ‘royal jelly’ emerge as queens. After mating, the young queen takes a bunch of workers with her and sets up a new colony. She lives much longer than other bees and spends her life laying gazillions of eggs continuously around the clock, while being fed by workers.

Female larvae not fed the ‘royal jelly’ emerge as workers.

Workers perform a variety of jobs in the hive. Some are hive-cleaners, some are ‘nurses’ (they feed the larvae), some are queen’s chaperones (they feed the queen), some are guards (they defend the hive and attack potential enemies) and some are foragers (they collect nectar and pollen from flowers and bring it back to the hive).

What most people are not aware of, though, is that there is a regular progression of ‘jobs’ that each worker bee goes through. The workers rotate through the jobs in an orderly fashion. They all start out doing generalized jobs, e.g., cleaning the hive. Then they move up to doing a more specialized job, for instance being a nurse or taking care of the queen. Later, they become guards, and in the end, when they are older, they become foragers – the terminal phase.

This pattern of behavioral development is called “age polyethism” (poly = many, ethism = expression of behavior), or sometimes “temporal polyethism” (image from BeeSpotter):

This developmental progression in behavior is accompanied by changes in brain structure, patterns of neurotransmitter and hormone synthesis and secretion, and patterns of gene expression in the central nervous system.

Some years ago (as in “more than ten years ago”) Gene Robinson and his students started looking at daily patterns of activity in honeybees. The workers in their early stages are doing jobs inside the hive, where it is always dark. They clean the hive, take care of the eggs and pupae, and feed the larvae and the queen around the clock. Each individual bee sometimes works and sometimes sleeps, without any semblance of a 24-hour pattern. Different individuals work and sleep at different, apparently random times. The hive as a whole is thus constantly busy – there is always a large subset of workers performing their duties, day and night.

As they get older, they start doing the jobs, like being guards, that expose them to the outside of the hive, thus to the light-dark and temperature cycles of the outside world.

Finally, the foragers only go out during the daytime and have clear and distinct daily rhythms. Furthermore, the foragers have to consult an internal clock in order to orient towards the Sun in their travels, as well as to be able to communicate the distance and location of flowers to their mates in the hive using the ‘waggle dance’. As bees are social insects, it is difficult to keep individuals in isolation for longer periods of time, but it has been done successfully and, in such studies, foragers exhibit both freerunning (in constant darkness) and entrained (in light-dark cycles) circadian rhythms, while younger workers do not.

In the Robinson lab, then PhD student Dan Toma and postdoc Guy Bloch did much of the early and exciting work on figuring out how the rhythmicity develops in individual worker bees as they pass through the procession of ‘jobs’.

In an early study, they measured levels of expression of mRNA of the core clock gene Period (Per). The gene was expressed at low levels and no visible daily rhythm in early-stage workers, but at much higher levels and in a circadian fashion in foragers.

As the levels of expression were measured crudely – in entire bee brains – it was impossible at the time to be sure which of the two potential mechanisms were operating: 1) the cellular clock did not work until the bee became a forager, or 2) the cellular clocks were working, but different cells were not synchronized with each other, producing a collectively arrhythmic output: both as measured by gene expression of the entire brain and as measured by behavior of the live bee.

Either way, the study showed correlation: the appearance of the functional circadian clock coincided with other changes in the brain structure, brain chemistry and bee behavior. They could not say at the time what causes what, or even if the synchronicity of changes was purely coincidental. They needed to go beyond correlation and for that they needed to experimentally change the timing to see if various processes can be dissociated or if they are tightly bound to each other.

And there is a clever way to do this!

First, they took some hives and removed all the foragers from it. This disrupted the harmony of the division of labor in the hive – too many cleaners and nurses, but nobody is bringing the food home. When that happens, the behavioral development of other workers speeds up dramatically – in almost no time, some nurses and guards develop into foragers. And, lo and behold, the moment they became foragers, they developed rhythms in behavior and rhythms of the Per gene expression in the brain. So, as the development is accelerated, everything about it is accelerated at the same rate: gene expression, brain structure, neurochemistry, and behavioral rhythmicity.

Nice, but then they did something even better. They removed most of the cleaners and nurses from some hives. Again, the balance of the division of labor was disrupted – plenty of food is arriving into the hive but there is not enough bees inside to take care of that food, process it, feed the larvae, etc. What happened then?

Well, some of the foragers went back into the hive and started performing the house-keeping duties instead of flying out and about. And, interestingly, their brain structure and chemistry reverted its development to resemble that of cleaners and nurses. They lost behavioral rhythmicity and started working randomly around the clock. And the rhythm of clock-gene expression disappeared as well.

So, genetic, neural, endocrine, circadian and behavioral changes all go together at all times. Social structure of the colony, through the patterns of pheromones present in the hive, affects the gene expression, brain development and function, and behavior of individual bees. Just like the gene expression and behavioral patterns, the patterns of melatonin synthesis and secretion in honeybee brains is low and arrhythmic in young workers and becomes greater and rhythmic in foragers. With the recent sequencing of the honeybee genome, the potential for future research in honeybee chronobiology looks promising and exciting.

But are these findings generalizable or are they specific to honeybees? How about other species of bees or other social insects, like wasps, ants and termites? Are they the same?

Other species of socials insects have been studied in terms of age polyethism as well. The earliest study I am aware of (let me know if there is an older one) studying behavioral rhythmicity in relation to behavioral development was a 2004 Naturwissenschaften paper by Sharma et al. on harvester ants. In that study, different castes of worker ants exhibited different patterns – some were strongly diurnal, some nocturnal, some had strange shifts in period, and some were arrhythmic. Those with rhythms could entrain to light-dark cycles as well as display freerunning rhythms in constant darkness.

Just last month [April 2009], a new paper on harvester ants came out in BMC Ecology (Open Access). In it, Ingram et al. show that foragers have circadian rhythms (both in constant darkness and entrained to LD cycles) in expression of Period gene (as well as behavioral rhythms), while ants working on tasks inside the hive do not exhibit any rhythms either in clock-gene expression or in behavior, suggesting that the connection between age polyethism and the development of the circadian clock may be a universal property of all social insects.

We know that in humans, night-shift and rotating-shift schedules are bad for health as the body is in the perpetual state of jet-lag: the numerous clocks in our bodies are not synchronized with each other. We have evolved to be diurnal animals, entrained to environmental light cycles and not traveling over many time zones within hours, or working around the clock. Social insects have evolved a different strategy to deal with the potentially ill effects of shift-work: switch off the clock entirely until one develops far enough that time-keeping becomes a requirement.


Yang, L., Qin, Y., Li, X., Song, D., & Qi, M. (2007). Brain melatonin content and polyethism in adult workers of Apis mellifera and Apis cerana (Hym., Apidae) Journal of Applied Entomology, 131 (9-10), 734-739 DOI: 10.1111/j.1439-0418.2007.01229.x

Sharma, V., Lone, S., Goel, A., & Chandrashekaran, M. (2004). Circadian consequences of social organization in the ant species Camponotus compressus. Naturwissenschaften, 91 (8) DOI: 10.1007/s00114-004-0544-6

Ingram, K., Krummey, S., & LeRoux, M. (2009). Expression patterns of a circadian clock gene are associated with age-related polyethism in harvester ants, Pogonomyrmex occidentalis. BMC Ecology, 9 (1) DOI: 10.1186/1472-6785-9-7

The Scienceblogging Weekly (May 11, 2012)

In the flood of information, filters are invaluable – people you trust to pick the best so you can focus on that, only that, and ignore the less important stuff.

Editors (including Jason here at the network) at and editors (including Krystal here at the network) at filter the best science blog posts each week.

Ed Yong’s weekly linkfests (like this one) and monthly Top 10 choices he’d pay for (see this for an example) are must-bookmark resources.

Some other bloggers are occasional or regular sources of links I pay attention to, e.g., John Dupuis on academia, publishing, libraries and books, Chad Orzel on academia and science – especially physics, Mike the Mad Biologist on science and politics, and the crew at the Knight Science Journalism Tracker for the media coverage of science. And at the NASW site, Tabitha Powledge has a must-read On science blogs this week summary every Friday.

Most of the articles and blog posts I read every day are brought to my attention by my friends on Twitter, Google Plus and Facebook, I get some through email notifications, as well as gleaned from and science blog aggregators. I then share a LOT of those links to my followers on Twitter, Facebook and Google Plus every day.

Every workday around midnight I post a linkfest on The Network Central to make it easier to see our network posts if you missed them during the day. Khalil and I take turns highlighting the best work by up-and-coming science writers on The SA Incubator blog. Weekly posting of the ever-growing list of posts submitted for the Open Laboratory is another resource. SciAm homepage is also set as a collection of filters – we decide what goes into “Blogs” box, what in the “Latest News” feed, what in the “Science Agenda” on top of the page, and what to collect into “In-Depth Reports” over time.

Now I will also start a weekly collection of links that are “best of the best” of everything I read over a period of a week – not the posts from #SciAmBlogs, but the rest of the Web: other blogs and other media sites. That means a lot of cutting! I mean, I tweet TONS of links every day! Choosing the best will not come easy to me, so this is a good exercise for me as well, and I hope will become a useful resource to you.

I’ll try to do this every Friday, time of day dependent on travel, work, life etc. Let me know in the comments if you have suggestions for formatting, timing, etc.

Blog of the Week:

Academic Panhandling: The art of granting for your supper. Everything you ever needed to know about writing grant proposals, written by a professional grant writer.

Top 10:

The Moscow Rules – Science Edition: Part 1, Part 2, Part 3, Part 4, Part 5, Part 6, Part 7, Part 8, Part 9 and Part 10 by Zen Faulkes, guest-blogging at Scientopia:

The Moscow Rules were directives that undercover American intelligence agents allegedly used in the Cold War. The rules were there to increase agent’s chances of making it out safely.

Sometimes, being in academic science can feel like being enemy territory in a cold war. You are often in strange territory (new lab), with many unfamiliar people (other grad students, post-docs, faculty) whose motivations are unclear. You might not trust them completely (especially administrators). There might not be the risk of attempted assassination by having poison injected into you with a specially built umbrella, but there’s enough similarity that the Moscow Rules can still apply…

If You Want A Lizard To Run Fast, Yell At It by Jonathan Losos:

…“As you well know, some days things just don’t seem to go well when testing whole animal performance. On one of those days out of frustration, fatigue, etc., we simply yelled at an apparent “slacker” lizard in jest. Much to our surprise this seemed to make a difference. We were also aware of the two recent papers for other species of lizards in which sound appeared relevant to behaviors associated with detecting threats. So, we figured what the heck, why not test for such effects systematically. Unlike many of the studies that you and others have performed with anoles, unless we simply can’t get a lizards to run along the racetrack or they appear unhealthy, we include data from all of the individuals rather than subjectively rating the trials for their quantity. Perhaps, some of the gains in speed associated with our yelling were greatest for those individuals that otherwise might have been discarded after receiving a poor subjective quality rating. Of course, we lack a simple way of determining this. Similarly, we have not yet methodically tested for whether expletives are more effective that milder language.”…

Invisible aliens: they’re not life as we know it — yet by John Rennie:

Both publications posit that life, at its most abstract, involves a thermodynamic disequilibrium. That is, life involves physical structures that can only maintain their integrity with inputs of energy. These physical structures will require covalent bonds between atoms (to allow nontrivial chemical reactions), so the environment in which life appears must allow such chemistry to occur. Some kind of liquid, but not necessarily water, would therefore also be necessary to enable those reactions. Finally, some molecules in the living system would need to be capable of Darwinian evolution for the life to arise. (Take note, creationist doubters of evolution: it is now a useful part of the definition of life!)

From theory and experiments, both papers argue that life with these traits could evolve under a wide (but definitely limited) range of environments. Carbon-based life on worlds with liquid water might represent a particularly versatile and common set of solutions, but biochemistry could go in many directions even on Earthlike worlds. And on planets and moons where terrestrial life would perish instantly, life based on silicon instead of carbon or liquid hydrocarbons instead of water might thrive…

Plastic Lessons by Shara Yurkiewicz:

I always feel awkward when I talk to plastic patients. The simulation mannequins are impressive: their eyes blink, their chests expand as they breathe, they have pulses, they bleed, they burn. A screen monitors vital signs: I administer a pressor and a dipping blood pressure perks up, or I order a beta blocker and a racing heart rate slows. A physician in the next room lends her voice to play the patient, responding to what I do and say. A physician in the same room becomes a tech, relying results of my tests and nudging me through the next steps when I veer off course….

Twilight of the giants in taxonomy by Emmett Duffy:

In an important sense, nothing exists until it’s given a name. And in the living world of organisms, names—official, scientific names—are assigned by unique creatures called taxonomists, experts in the minutiae of structure and biology of particular groups of organisms, working according to a strict and arcane body of rules of biological nomenclature. These individuals tend to be specialists—sages of whales, anglerfishes, microscopic worms that live only between the grains of sand on beaches, microscopic algae, purple sulfur bacteria, and everything in between…

Is Technology Destroying Your Relationships? by A.V.Flox:

Social networks put a number on those weak ties, but we all have weak ties in our meatspace lives. Marche bemoans how we use machines to check out at the grocery store instead of waiting in line with other people to have our purchases rung up by an actual human. But I wonder — even if you were to speak to the woman giving you dirty looks because you were buying a product with a big carbon footprint, can you actually call that a meaningful relationship?

I talk to people all the time — cab drivers, waiters, flight attendants, the guy at the post office, my manicurist, my barista, the boys at the convenience store where I buy my cigarettes, the guy at the newsstand. I am there, in the flesh. Does this mean our connections are any more meaningful than a like or a plus on social media?

Weak ties exist. They’re everywhere. All we have to do to make them meaningful is take the chance to go deeper. This is as true online as it is offline.

What does it mean to say that something causes 16% of cancers? by Ed Yong:

…executives and policy-makers love PAFs, and they especially love comparing them across different risk factors. They are nice, solid numbers that make for strong bullet points and eye-grabbing Powerpoint slides. They have a nasty habit of becoming influential well beyond their actual scientific value. I have seen them used as the arbitrators of decisions, lined up on a single graphic that supposedly illustrates the magnitude of different problems. But of course, they do no such thing…

The Mysterious Case of the Vanishing Genius by Mike Martin:

Margie Profet was always a study in sharp contradictions. A maverick thinker remembered for her innocent demeanor, she was a woman who paired running shorts with heavy sweaters year-round, and had a professional pedigree as eccentric as her clothing choices: Profet had multiple academic degrees but no true perch in academe. In the late 1980s and early 1990s, Profet published original theories about female reproduction that pushed the boundaries of evolutionary biology, forcing an entire field to take note. Indeed, back then it was hard not to notice Margie Profet, a vibrant young woman who made a “forever impression” on grade school chums and Harvard Ph.D.s alike. Today, the most salient fact about Profet is her absence. Neither friends, former advisers, publishers, nor ex-lovers has any idea what happened to her or where she is today. Sometime between 2002 and 2005, Profet, who was then in her mid-40s, vanished without a trace…

Fear fans flames for chemical makers by Patricia Callahan and Sam Roe (see also Part 2 Big Tobacco wins fire marshals as allies in flame retardant push and Part 3 Distorting science):

Manufacturers of fire retardants rely on questionable testimony, front groups to push standards that boost demand for their toxic — and ineffective — products

Asymmetrical snakes by Andrew Durso:

Animals have a long tradition of being bilaterally symmetrical – that is, of the left side and the right being nearly identical. Sure, there are a few exceptions – the human heart is nearly always farther to the left side, for instance. Snakes and other elongate, limbless animals sometimes stagger their paired organs (gonads, kidneys) so that one is in front of the other, to better fit in their cylindrical bodies. Most snakes have even done away with one of their two lungs. But the basic external body plan, the bones and muscles on the left and the right, are always mirror-images of one another, right?

Enter the pareatid snakes…


Drop the base to make bagels more delectable by Raychelle Burks:

Sometimes, just hearing that certain chemicals are in food just puts people off. “I think that a lot of people would be really surprised about the precise chemicals that are used to make their favorite foods,” said Dr. Hartings. Take Cool Whip for example. One of its ingredients is polysorbate-60, a chemical that helps give Cool Whip its puffy appearance. Polysorbate-60 moonlights as an ingredient in sexual lubricants like K-Y YOURS+MINE. Our foods contain all kinds of chemicals that have more than one job. Thankfully, one of those jobs is making food delicious.

Insects that skate on the ocean benefit from plastic junk by Ed Yong:

Imagine a world of two dimensions, a world with no up or down… just across. No climbing, falling, jumping, or ducking… just shimmying and sidling. Welcome to the world of the sea skater.

Sea skaters, or ocean striders, are small bugs. They’re relatives of the pond skaters or water striders that zip spread-eagled across the surface of ponds and lakes. Except they skate over the open ocean, eating plankton at the surface…

Problems in the neurozone by Pete Etchells:

Having a scan of your brain is a uniquely odd experience. I had one done once. I was loaded, torpedo-like, into a claustrophobia-inducing, cocoon-like chamber for nearly an hour, the first few terrifying minutes of which I spent desperately trying to recall whether I had actually passed that metal ball-bearing I swallowed when I was a kid. The machines themselves are pretty damn loud, but something about repetitive clunking noises seems to lull me into a state of relaxation, so I spent the majority of my time in the launch chamber trying not to snooze. Honestly, it was all quite enjoyable…

Abandoment issues by Dr. Al Dove, guest-blogging at NeuroDojo:

There exists on my hard drive a folder into which I loathe copying files, but only slightly less than I would loathe deleting them all together. It is a folder called “Aborted Manuscripts” and it is this folder which is the source of my shame. It is a graveyard of stupid ideas and of great ones poorly executed, of unfinished cogitations, of journal rejections, of unresponsive colleagues and of frustrating students. It’s a roadmap documenting 15 years of science (read: “me”) not doing what science (read: “me”) is supposed to do – get published…

Put Away The Bell Curve: Most Of Us Aren’t ‘Average’ by Shankar Vedantam:

The bell curve powerfully shapes how we think of human performance: If lots of students or employees happen to show up as extreme outliers — they’re either very good or very bad — we assume they must represent a skewed sample, because only a few people in a truly random sample are supposed to be outliers.

New research suggests, however, that rather than describe how humans perform, the bell curve may actually be constraining how people perform. Minus such constraints, a new paper argues, lots of people are actually outliers.

Human performance, by this account, does not often fit the bell curve or what scientists call a normal distribution. Rather, it is more likely to fit what scientists call a power distribution…

The real CSI: what happens at a crime scene? by Craig Taylor:

From the diver who finds the body parts, to the forensic specialist who identifies flecks of paint on the victim and the handwriting expert who examines the killer’s notes… What happens behind the yellow tape of one crime scene

Of mice and Marmaduke (and dinosaur farts) by Mike Argento:

EDITOR’S NOTE: The following column contains sophomoric humor and references to the bodily functions of dinosaurs and the size of certain anatomical features of mice, all in the name of science. If this kind of thing offends you, please skip this and go right to Marmaduke. That dog, he cracks us up…

Spacesuit In A Cave by Sarah Everts:

Most visitors to the million-year-old Dachstein Giant Ice Cave prefer to wear standard winter coats during visits to its freezing, icy interior. But for five days the Dachstein cave systems were a temporary lab for a squad of space scientists. Some 50 scientists assembled from three continents to use the UNESCO World Heritage site as a proxy for Mars—a first for the cave system, which normally hosts jazz concerts, modern art exhibits, laser shows, and a steady stream of tourists….

Experimental Biology Blogging: Self-promotion and ‘self-promotion’ by Scicurious:

But of course, this is because academics have two different kinds of self-promotion. One is ok, and one is not. One takes place in the ivory tower, and one involves the dreaded public…

1859’s “Great Auroral Storm”—the week the Sun touched the earth by Matthew Lasar:

Noon approached on September 1, 1859, and British astronomer Richard Christopher Carrington was busy with his favorite pastime: tracking sunspots, those huge regions of the star darkened by shifts in its magnetic field. He projected the Sun’s image from his viewing device onto a plate of glass stained a “pale straw colour,” which gave him a picture of the fiery globe one inch shy of a foot in diameter…

The Physics of Spilled Coffee by Jon Cartwright:

…Krechetnikov and his graduate student Hans Mayer decided to investigate coffee spilling at a fluid dynamics conference last year when they watched overburdened participants trying to carry their drinks to and fro. They quickly realized that the physics wasn’t simple. Aside from the mechanics of human walking, which depends on a person’s age, health, and gender, there is the highly involved science of liquid sloshing, which depends on a complex interplay of accelerations, torques, and forces. …

Why Do Conference Talks Suck, and How Can We Change That? by Matthew R. Francis:

…Yes, some speakers are better than others, and a few of the 42 talks I heard were very good. Also, I know I used to commit many of the same sins I witnessed in talks yesterday and the day before, so as I list the problems, I’ll flag my own bad habits (current and former). Based on conversations with my friends, this is not a problem limited to particle physics conferences, much less to physics conferences in general: it’s endemic in science, and perhaps most academic fields…

Sleek, Smart Spacesuits Are on the Horizon by Amy Shira Teitel:

Spacesuits are poised to go the way of the cell phone – once bulky and cumbersome, researchers are working on making them slim and smart. In the future, astronauts might be wearing specially engineered garments that combine the life-preserving features of a spacesuit with augmented reality technology that could intuit the wearer’s needs…

How and Why Neuroscience should be taught in School by TheCellularScale:

…Neuroscience is sort of where genetics was 20-30 years ago: The scientific frontier, fascinating to the public, changing the general worldview, raising ethical questions, science fiction’s closest reflection in reality. This has its benefits and its downfalls. There is currently strong general enthusiasm for neuroscience for just these reasons, but because everything ‘neuro’ is so exciting, the risk of media misrepresentation is high and the misuse of neuroscience concepts and terms by pseudo-science is common. …

Fetal Attraction by Robert Krulwich:

…Dr. Johnson says cells from fetal boys and girls have been found in mothers “four to five decades following the last pregnancy.” That fetus may have grown into a middle aged pharmacist, and still his cells are inside his mother. Cells wouldn’t persist in foreign body for NO reason. They must be doing something, but what?…

On Biocultural Anthropology by Daniel Lende:

…what brings many students into anthropology, and still impassions me about the field, is that it does approach the question of “What does it mean to be human?” in the broadest, most interdisciplinary way. And it strikes me that we have some core analytical approaches to that question that matter, and that this style of thinking is what really makes up the holism of anthropology, rather than a particular commitment to four-fields and working across the different sub-disciplines. This human lens includes a comparative approach, an attention to variation across time and space, a recognition that we as researchers inevitably bias our own data, and, yes, a commitment to drawing on multiple strands of research…

94 Elements by The 94 Elements team:

There are 94 naturally occurring elements, from Hydrogen to Plutonium, and together they make up everything in the world. The stories of the elements are the stories of our own lives, revealing the details of our personal lives, the patterns of our economies, and our relationships with our natural resources.

94 Elements is a new global filmmaking project, exploring our lives through the lens of the elements. The project is producing a collection of stories by different filmmakers about the endless ways the elements touch our daily lives. Each filmmaker takes one element as the basis for a film around how it’s used. The films are surprising and moving human stories – this is not about science, but about our human relationships with our mineral resources.

How Does the FDA Monitor Your Medical Implants? It Doesn’t, Really by Lena Groeger:

Each prescription drug you take has a unique code that the government can use to track problems. But artificial hips and pacemakers? They are implanted without identification, along with many other medical devices. In fact, the FDA doesn’t know how many devices are implanted into patients each year – it simply doesn’t track that data.

The past decade has seen numerous high profile cases of malfunctioning medical devices, which have led to injury or even death. Critics say the FDA’s minimal monitoring of devices contributes to these problems….

Leptin: Linking Malnutrition and Vulnerability to Infection by Michelle Ziegler:

As long as leptin levels stay within normal levels, all of the functions displayed above function normally. As the leptin levels drop, many of these functions are adversely effected. It is a wide-spread trigger for a starvation response. Why cripple the immune response during starvation? My best guess would be because of the huge energy expenditure required to keep the immune response running normally, especially in cellular proliferation.

Experts debate what makes a healthy vagina by Anna Salleh:

New US findings suggest our accepted definition of a healthy vagina could be ethnically biased, say some researchers, but others caution against over-interpreting the data.

A new study published today in Science Translational Medicine found, what an accompanying commentary describes as, an “unexpected and astonishing” variability over time in the vaginal bacterial communities of apparently healthy women….

The Ph.D. Now Comes With Food Stamps by Stacey Patton:

…A record number of people are depending on federally financed food assistance. Food-stamp use increased from an average monthly caseload of 17 million in 2000 to 44 million people in 2011, according to the U.S. Department of Agriculture’s Web site. Last year, one in six people—almost 50 million Americans, or 15 percent of the population—received food stamps.

Ms. Bruninga-Matteau is part of an often overlooked, and growing, subgroup of Ph.D. recipients, adjunct professors, and other Americans with advanced degrees who have had to apply for food stamps or some other form of government aid since late 2007….

Nicholas Kristof and the Bad, Bad Chemical World by Deborah Blum:

…Because his secondary crusade of the last few years, you know, the one against evil industrial chemicals, is really starting to annoy me. This is not saying that he’s entirely wrong – there are evil industrial chemicals out there. And, in many cases, they aren’t as well researched or as well regulated as they should be.

But if we, as journalists, are going to demand meticulous standards for the study and oversight of chemical compounds then we should try to be meticulous ourselves in making the case. And much as I would like it to be otherwise, I don’t see enough of that in Kristof’s chemical columns. They tend instead to be sloppy in their use of language, less than thorough, and chemophobic enough to undermine his legitimate points….

How Academic Biologists and Physicists View Science Outreach by Elaine Howard Ecklund, Sarah A. James and Anne E. Lincoln:

Scholars and pundits alike argue that U.S. scientists could do more to reach out to the general public. Yet, to date, there have been few systematic studies that examine how scientists understand the barriers that impede such outreach. Through analysis of 97 semi-structured interviews with academic biologists and physicists at top research universities in the United States, we classify the type and target audiences of scientists’ outreach activities. Finally, we explore the narratives academic scientists have about outreach and its reception in the academy, in particular what they perceive as impediments to these activities. We find that scientists’ outreach activities are stratified by gender and that university and disciplinary rewards as well as scientists’ perceptions of their own skills have an impact on science outreach. Research contributions and recommendations for university policy follow.

Blue-eyed-people-are-all-related zombie news by Jon Wilkins:

…So, to recap, 1) Cool paper. 2) Sex between blue-eyed people is not incest. 3) We have no idea when or where this mutation came from, but it is now conceivable that we could ask the question. 4) Embarrassingly bad science reporting spontaneously rises from the grave four years later and tries to eat your brain.

Conceptual Replication by Dave Nussbaum:

There is no substitute for direct replication – if you cannot reproduce the same result using the same methods then you cannot have a cumulative science. But conceptual replication also has a very important role to play in psychological science. What is conceptual replication? It’s when instead of replicating the exact same experiment in exactly the same way, we test the experiment’s underlying hypothesis using different methods…

Replicating Dissonance by Dave Nussbaum:

Another reason conceptual replication is so important is that if the field relies exclusively on direct replication then they risk replicating the same mistakes as well. Today I wanted to illustrate this risk by looking back at the history of one of social psychology’s most influential theories: cognitive dissonance. The richness and depth of Cognitive Dissonance Theory is a result of dozens of conceptual replications. I suggest that, had it not been for conceptual replication – had dissonance only been tested and re-tested in the original paradigm (Brehm’s Free Choice Paradigm) – the theory may not have stood up to recent criticisms directed at that particular paradigm…

Chimp acts like jerk, gets praised by scientists by Eoin O’Carroll:

A chimpanzee at Furuvik Zoo in Sweden has been lauded for his ‘innovation’ and ‘sophisticated cognitive skills,’ after behaving like a complete schmuck.

What is Peru’s dolphin and pelican die-off telling us? by Al Dove:

As many as 900 dolphins and over 4,000 pelicans have washed up dead on the beaches of northern Peru in the last couple of months, (see news coverage here, here and here), leading to a flurry of activity as various authorities and other interested parties move to find out what is going on. Experts cited in the news coverage suggest that unusually warm surface waters (10F higher than the season average) are changing the swimming patterns of the huge anchovetta schools off the coast of Peru, driving them deeper and out of the diving range of pelicans. In other words, the pelicans appear to be starving. The dolphins on the other hand, have shown a high prevalence of infection with morbilivirus, which is an infectious disease…

Why a Sperm Cell Is Like a Roomba by Elizabeth Preston:

A sperm cell, much like an expensive robotic vacuum cleaner, is a minimally intelligent body on a mission. Both the Roomba and the male gamete have to navigate a walled space without much idea where they’re going or why. And although it won’t clean your floors on the way, the sperm cell uses some of the same strategy as the robot vacuum…

In the Spring, Bat Moms Choose Girls by Elizabeth Preston:

Naturally a mother bat is happy to welcome into the world a bouncing baby whatever, as long as it has all its fingers and toe-claws. But she also wants her little one to have every advantage she can give it. So when spring comes early, big brown bats prefer to keep their female embryos. Unwanted males are reabsorbed into their mothers’ bodies as if they never existed…

Media, Publishing and Technology:

Science and Truth: We’re All in It Together by Jack Hitt:

…By now, readers understand that the definitive “copy” of any article is no longer the one on paper but the online copy, precisely because it’s the version that’s been read and mauled and annotated by readers. (If a book isn’t read until it’s written in — as I was always told — then maybe an article is not published until it’s been commented upon.) Writers know this already. The print edition of any article is little more than a trophy version, the equivalent of a diploma or certificate of merit — suitable for framing, not much else.

We call the fallout to any article the “comments,” but since they are often filled with solid arguments, smart corrections and new facts, the thing needs a nobler name. Maybe “gloss.” In the Middle Ages, students often wrote notes in the margins of well-regarded manuscripts. These glosses, along with other forms of marginalia, took on a life of their own, becoming their own form of knowledge, as important as, say, midrash is to Jewish scriptures. The best glosses were compiled into, of course, glossaries and later published — serving as some of the very first dictionaries in Europe.

Any article, journalistic or scientific, that sparks a debate typically winds up looking more like a good manuscript 700 years ago than a magazine piece only 10 years ago. The truth is that every decent article now aspires to become the wiki of its own headline. …

Neuroscience: Bloggers rule? by Paul Raeburn:

..We might be hard put to find any area of science coverage that hasn’t been subject to those kinds of distortions. Coverage of Lipitor and its ilk was certainly as likely to contain dramatic headlines, and particular agendas, including those of pharmaceutical companies. And ideological arguments? It depends upon what the meaning of “ideological” is…

Brain waves by Curtis Brainard:

From advice about “exercising your mind” to treatises on “the gay brain,” media coverage of neuroscience in the UK often pushes “thinly disguised ideological arguments” and reinforces artificial divisions between social groups, according to a new study….

What Will Become of the Paper Book? by Michael Agresta:

…In the past several years, we’ve all heard readers mourn the passing of the printed word. The elegy is familiar: I crave the smell of a well-worn book, the weight of it in my hands; all of my favorite books I discovered through loans from a friend, that minor but still-significant ritual of trust; I need to see it on my shelf after I’ve read it (and I don’t mind if others see it too); and what is a classic if not a book where I’m forced to rediscover my own embarrassing college-age marginalia?

Luddites can take comfort in the persistence of vinyl records, postcards, and photographic film. The paper book will likewise survive, but its place in the culture will change significantly. As it loses its traditional value as an efficient vessel for text, the paper book’s other qualities—from its role in literary history to its inimitable design possibilities to its potential for physical beauty—will take on more importance. The future is yet to be written, but a few possibilities for the fate of the paper book are already on display on bookshelves near you…

Abraham Lincoln Did Not Invent Facebook: How a Guy and His Blog Fooled the Whole Wide Internet by Megan Garber:

…He expected — and banked on — the web’s virality, he says; he didn’t anticipate, though, how eagerly that web’s self-defined news sources would pass along his “discovery.” And he assumed people would figure out the story’s hoaxiness much more quickly than they actually did — and, then, that the corrective powers of the social web would make that joke clear within the first hour or so after the story went live…

WWW inventor warns against call for comment sections to be placed under Data Rentention Act by Kristine Lowe:

…Berners-Lee said he was concerned about how increased demands for monitoring the web, both from governments looking for greater powers to track down terrorists and companies looking to trade our personal web data for commercial purposes, threatens the very infrastructure of the web.

He described his worry that people in the end will no longer trust and use the web for e.g. researching sensitive things like depression if they fear everything they do online is being monitored…

7 New Educational Startups Founded By Minorities in Tech by Wayne Sutton:

One of today’s most challenging yet promising markets is the educational system. If you want to see startups hungry to disrupt an industry, look no further. Founders are trying to solve the problems plaguing our education system: including reconciling student debt, providing students with the skills required to land a job both before and after graduation, and offering the best course material online regardless of age, location and educational level…

5 things med students can do to engage in social media and medicine by Josh Herigon:

One topic we neglected, however, was what current medical students can do right now to get their foot in the door and begin engaging in the social media and medicine conversation. I had hoped to get to this topic during my panel discussion, but there just weren’t enough hours to cover everything. Below is my attempt to remedy this omission. Here are a few simple things you can do:

Blinding us with science journals by Peter McKnight:

A competitive university culture that discourages the sharing of knowledge has led to the publication of many flawed and fraudulent studies…

The Arrogance of Publishers vs. Academic Culture – Why the Outcome Is Virtually Certain a scholarly kitchen metaphor by Mark Carrigan:

Imagine a situation where homes had no kitchens and utensils were unavailable. We would all be dependent on cafes and restaurants to eat and, it follows, our idea of what it is to prepare food would be exhausted by those working in such a capacity within these establishments. Now introduce kitchens into homes and affordable utensils into shops. Suddenly we can cook meals at home. Obviously the quality of the infrastructure is lower and there’s less expertise. For the sake of the thought-experiment, assume kitchens and utensils appeared suddenly, to an extent profoundly disruptive of established practices of going out for every meal. The meals cooked at home would be of poor quality, probably pragmatically orientated and often imitating (poorly) the meals available in restaurants and cafes.

The Science of Obituaries: Dead Pools, Obits in the Can and More by Arthur S. Brisbane:

Mr. McDonald said The Times currently has 1,500 advance obits in the can – “and we’re adding about 250 a year. Even if you subtract the number of those we’ll publish in a given year – say, 50 – the archive is growing significantly.”…

The Psychological Prerequisites of Punditry by Julian Sanchez (also see response by Andrew Sullivan):

….The nice way to say this is that selects for pundits who have a thick skin—or forces them to quickly develop one. The less nice way to say it is that it forces you to stop giving a shit what other people think. Maybe not universally——you’ll pick out a domain of people whose criticisms are allowed to slip through the armor—but by default….

Four perspectives on communicating your research, and then one more. #EB2012 by William Gunn:

…The most popular sentence of the whole session was “Don’t underestimate your audience’s intelligence, but do underestimate their vocabulary.” In other words, drop the jargon if you want the public to get what you’re saying. …

Filter-then-publish vs. publish-then-filter by Mike Taylor:

…In the face of such a flood of information, no-one can read everything that’s made it through the filters into all their favourite journals. So in practice what actually happens is that each of us filters again – finding relevant publications in a huge range of journals by the social web we’re in: mailing lists, blogs, Twitter, and so on. I believe some people even use FaceBook….

10 Commandments of Twitter for Academics by Katrina Gulliver:

…Twitter is what you make of it, and its flexibility is one of its greatest strengths. I’m going to explain why I have found it useful, professionally and personally, and lay out some guidelines for academics who don’t know where to start….

Fungible by Stijn Debrouwere:

A treatise on fungibility, or, a framework for understanding the mess the news industry is in and the opportunities that lie ahead.

Why Publishers Don’t Like Apps by Jason Pontin:

…But the real problem with apps was more profound. When people read news and features on electronic media, they expect stories to possess the linky-ness of the Web, but stories in apps didn’t really link. The apps were, in the jargon of information technology, “walled gardens,” and although sometimes beautiful, they were small, stifling gardens. For readers, none of that beauty overcame the weirdness and frustration of reading digital media closed off from other digital media. …

The brilliant Joe Weisenthal by Felix Salmon:

Appelbaum is absolutely right that Weisenthal stands apart by starting earlier, writing more, publishing faster. That’s who Joe is. But he’s absolutely wrong that there’s an “intensely competitive world of financial blogging, dominated by young men who work long hours and comment on every new development”. Go on — name a single other financial blogger who fits that description. I’m waiting. There’s the anonymous group blog ZeroHedge, perhaps. But the fact is that Henry Blodget, in hiring and promoting Joe, has succeeded in identifying and harnessing and leveraging a nervous energy which has been there all along. He didn’t start with some kind of inhuman job description and then hire Joe to fill it; he found Joe and then basked in the fruits of encouraging him to simply be his natural self.

River of News — FTW! by Dave Winer:

…I don’t think that fancy layout trumps newness. The name “news” tells you what’s important about news. Newness. So if you follow that clue, it leads you to the obvious conclusion that news should present first the newest bits we have. What’s next? The second newest bits. And third, fourth and so on. permalink
News is one of those things that is that simple. But it takes people a while to get there if they don’t allocate the time to take walks in the park and think about this stuff in an organized way….

Blogging and Kickstarter go together by Dave Winer:

…But once the users can communicate with each other, we will be able to pool our experience, and given enough time, smart users will learn the technology well enough to make the products that (key point here) they know there is demand for. Because they are the ones demanding it….

The Pernicious Myth That Slideshows Drive ‘Traffic’ by Alexis Madrigal:

…If you’re trying to juice page views, your staff will ineluctably be forced to make galleries. Where else can they get a 10x or 20x multiplier on their work? I can guarantee you that will not help you break the kinds of stories or do the kinds of analysis that will keep people coming back. Not only that, but it’s demoralizing to your best people, the ones who want to be out there producing their best work.

Worse, readers may click through your slideshow, but they’ll hate you a liiitttle bit more than they did when they got to the site. And I bet they’ll feel the same way about whatever advertiser was unlucky enough to get stuck on the page with some stupid thing that a reporter did with a little bit of hate in his heart and fingertips. ….

Clock Evolution

This post, originally published on January 16, 2005, was modified from one of my written prelims questions from early 2000.


“Circadian clocks allow organisms to predict, instead of merely react to, cyclic (predictable) changes in the environment”. A sentence similar to this one is the opening phrase of many a paper in the field of chronobiology. Besides becoming a truth by virtue of frequent repetition, such a statement appeals to common sense. It is difficult to imagine a universe in which it was not true. Yet, the data supporting the above statement are few and far-between. Believe it or not, the data are not always supporting it either.

This post will attempt to briefly review the literature on evolutionary and adaptive aspects of biological rhythmicity. Also, using the perspectives and the methodology of evolutionary physiology, I will try to suggest some ways to test the hypothesis stated in the first sentence above.


For outside observers of the field of chronobiology and its recent successes in molecular, neural and medical aspects of biological rhythmicity, it may come as a surprise that the field was founded by ecologists, ethologists and evolutionary biologists. When the statements about adaptive function of clocks were initially made, the authors were much more careful than is usually seen today. It was meant as a hypothesis to be tested, and elaborate reasoning was often offered to persuade the reader why it might be true (Daan 1981, Pittendrigh 1967,1993, Enright 1970).

One of the most common arguments that a clock must be adaptive (for one reason or another) was its ubiquity – all plants, fungi, protista, invertebrates and vertebrates (more recently cyanobacteria, too) tested by the pioneers in the field showed circadian rhythmicity. The way those rhythms behaved in the laboratory in various experimental treatments was surprisingly similar over all species. Thus, the reasoning goes, if a physiological mechanism is found in every living thing, and it seems to work in the same way in all of them, then it must have originated early due to natural selection and was preserved over eons due to natural selection.

Some of the earliest experimental work was designed to test the genetic basis of biological rhythmicity. Many generations of laboratory organisms were raised and spent all their lives in aperiodic environments, yet the rhythms persist (Sheeba et al. 1999). Period of the rhythm was species -specific, highly heritable, and very amenable to artificial selection. So, if it is in the genes, the clock must have evolved due to some kind of selective pressure.

When reviewing evolutionary literature on biological rhythms, it is often difficult to distinguish between hypotheses of current utility from hypotheses of origin. It was often assumed that same selective pressures which keep the clocks ticking all over biosphere today, are the pressures responsible for the initial discovery of timing mechanisms by early forms of life.

The current adaptive functions of biological rhythms are often divided into two, mutually not exclusive categories. The Internal Synchronization hypothesis stresses the need for temporal separation of incompatible biochemical and physiological processes within a body (or cell), and for temporal synchronization of processes which need to coincide. An example of the former would be temporal separation of photosynthesis from nitrogen fixation. For the latter, surge of a hormone and availability of its receptor need to be synchronized for the generation of the endocrine effect. Evolution of such timing control mechanisms would presumably alleviate energetic costs of constant production of enzymes and their substrates.

The External Synchronization hypothesis supposes existence of temporal niches. For instance it would be adaptive for an animal to forage at the time when food is available, to hide when the predators are hungry, and to find an individual of the opposite sex at the time conducive to mating. Notably, it was never explicitly stated that possession of a clock is adaptive only if everyone else has a clock, too. So, who had it first?

The two hypotheses are easily meshed. A bird will sleep instead of foraging while its body temperature is low. It will wake up, raise its temperature and corticosterone levels and start to forage when the conditions outside are most conducive to it – when it’s warm, light and worms are crawling around. The old adage about the early bird getting the worm is often invoked (and, as R.A.Heinlein once quipped, “it just goes to say that the worm should have stayed in bed”).

Coupled to the second hypothesis is also the notion that circadian clock is involved in temporal memory (Enright 1975, Biebach et al. 1991). Thus every event which is committed to memory will, along with information about “what” and “where”, also have a time-stamp given by the clock – the “when” of memory. If doing something at one time of day yesterday resulted in survival it might be prudent to do it again today at the exactly same time (Daan 1995).

One important distinction between the origin of the first clock and its current use is in the size and complexity of the organisms in question. The first clock presumably appeared in a unicellular organism. Most of the research today focuses on multicellular organisms.

In the first case, we are talking about a single-cell clock, in the second about the circadian system, which may be composed of many clocks of different properties, all interacting with each other, with the environment, and with other functions of the body. There is only so much a single cell can do. A complex clockshop which exists at a higher level of organization can evolve complex new functions, e.g., photoperiodic time measurement, time-compensated sun-compass orientation, tidal, lunar and circannual rhythms.

In the study of evolution of biological rhythms, are we talking about evolution of the cellular building blocks or evolution of higher-order systems?


The 2000 review of Evolutionary Physiology by Feder, Bennett and Huey currently serves as a manifesto of the field (Feder et al. 2000). In this section, I will follow the organization of their paper to explore how circadian physiology might fit into the framework of evolutionary physiology, as well as how evolutionary approaches may benefit the study of biological rhythms.

Evolutionary physiology is a relatively recent natural outgrowth of the field of comparative physiology, which, in turn, developed out of general mechanistic physiology. The evolutionary physiologists are direct intellectual (and often academic) descendants of traditional comparative physiologists, so the topics remain similar: scaling, symmorphosis, as well as studies of metabolism, respiration, osmoregulation, thermoregulation and locomotor performance. However, other aspects of physiology have been tackled by other groups of scientists, e.g., comparative endocrinology, neurobiology, sensory physiology, digestive physiology and reproductive physiology are vibrant fields of their own. Comparative chronobiology has a long tradition, too (Horton 2001). The importance of comparative studies to understanding of underlying mechanisms can be seen from examples of medically driven areas of physiology (e.g., sleep). Such areas fumbled in the dark for decades due to lack of basic understanding of what the process is all about, which in turn was due to lack of comparative studies of the phenomenon within an adaptive and evolutionary context.

It would be erroneous to state that evolutionary thinking was not a part of physiological thinking in the past, yet evolutionary physiology explicitly imports evolutionary theories, paradigms, concepts, models and techniques into the study of physiological adaptation. Feder et al. (2000) recognize four major developments which led to the rise of evolutionary physiology out of its general and comparative precursors.

First, the critique of adaptationist thinking (Gould and Lewontin1979) had an enormous ripple effect through all of biology, including physiology. The naive assumption that every trait is an adaptation forged by natural selection gave way to a more sophisticated view of evolution that includes non-adaptive forces like constraints and drift. Here, the ubiquity of biological clocks and the inability to imagine a clock-less universe led to the common view that not just the sheer existence of the clock, but every aspect of its mechanism must be an adaptation to the environment which evolved through the agency of natural selection. The non-adaptive evolutionary mechanisms are difficult to fathom in this context, and no explicit statements were made in the literature along these lines.

Second, new awareness of non-independence of species as analytical units for comparative biology has resulted in development of new analytical tools, new approaches to comparative studies, and, most importantly, in the shift in emphasis to ancestor-descendant relationships. Comparative studies of biological clocks were the foundation on which the whole field of chronobiology was built. Yet, these studies were not explicitly phylogenetic. The clocks are so widespread that comparisons were rarely made between closely related species. It was, and still is, more common to compare representatives of plants to fungi to insects to mammals. On those rare occasions when a phylogenetic tree appears in chronobiological literature, it is most likely to be the Tree of Life and not just a tiny piece of it. Thus, the non-independence of species is a problem that did not have much impact on comparative work to date, but is one that will have to be tackled in the future when more analyses of closely related species are performed.

Third, incorporation of tools of evolutionary biology into physiology allows research to state evolutionary hypotheses a priori, instead of post hoc. Using these tools, one is able to monitor evolution in progress and predict future evolutionary trajectories, instead of just registering the results of past evolution. In chronobiology, a few studies have recently been performed along these lines, more concerned with photoperiodic than circadian time-measurement, though (Ben Saad and Maurel 2001, Heideman et al. 1999, Heideman and Bronson 1991).

Fourth, use of most recent tools of molecular biology allows one to escape from standard genetic laboratory models to many other species of interest to physiologists. Comparative molecular analyses of genes involved in circadian rhythmicity have been performed in Diptera and Lepidoptera, and work on other organisms is sure to follow in the near future (Piccin et al. 2000, Peixoto et al. 1998, Costa and Kyriacou 1998, Kyriacou et al. 1996, Saleem et al. 2001).

Evolutionary biology aims to answer two kinds of questions: about the process (“how evolution works”) and the pattern (“what has evolution wrought so far in the history of life on this particular planet”). Evolutionary physiology, as its subset, is likewise interested in both process and pattern. After all, one informs the other and vice versa. In the same vein, mechanistic and evolutionary data inform each other and vice versa, too. While traditional comparative physiology explained mechanistically how the organisms adapt to their environments and added adaptive explanations post hoc, the modern evolutionary physiology starts with evolutionary predictions and tests them with comparative studies in the laboratory and in the field.

Of particular interest is the question of optimality – is there a close match between requirements of the environments and the physiological answers to these, or are safety margins and overdesign the rule. It would be difficult to define what would safety margins and overdesign mean in the field of circadian clocks. The clock is at the very core of physiological function of an organism. It acts as a relay station which controls practically every other aspect of biochemistry, physiology and behavior. It is not expected that the cellular clock at the core will be much affected by the environment, but the outputs of the clock, the signals from the clock to all the other functions, are much more likely to be the target of selection. Plasticity of the circadian system and of its coupling to downstream functions is a trait that can be expected to correlate to environmental parameters, e.g., stability vs. variability of the environment.


Several approaches to study of evolutionary pattern and process have been employed by students of biological rhythms. These include studies of variation in natural populations, including latitudinal clines (Skopik and Takeda 1987, Sawyer et al. 1997), tests of correlated traits, e.g., circadian vs. photoperiodic (Majoy and Heideman 2000) or circadian vs. developmental timing (Bloch et al. 2001), and studies of responses to artificial selection.

Comparative studies have been performed on levels from molecular to organismal. However, the choice of species is questionable. If relevant environmental parameter is the light-dark cycle, then most species studied so far occupied the same environmental niche – the earth surface in a temperate region. For a comparative study to be able to discriminate between ecological specialization and phylogenetic inertia, one needs to compare organisms occupying different environments. In the case of clocks, such environments would include polar regions (light-dark cycle of LD 6mo:6mo), equator (constant LD12h:12h), and life below the surface (constant darkness, DD). Although many species have been studied in such conditions in the lab, the study of organisms that live in such conditions in the wild is rare. Recent studies on subterranean and cave animals are a welcome change to the comparative work in chronobiology (Lee 1969, Hoenen and Gnaspini 1999, Riccio and Goldman 2000a, b, Avivi et al. 2001, Koilraj et al. 2000, Trajano and Menna-Barreto 2000).

Most recent data on adaptive function of circadian clocks employed measurements of fitness in altered light environments, as well as comparisons of fitness between genetic mutants of clock function. However, the only measure of fitness used is longevity (Pittendrigh and Minis 1972, Klarsfeld and Rouyer 1998, Hurd and Ralph 1998), and only two papers look at the trade-off between longevity and the lifetime reproductive output (Sheeba et al. 2000, Beaver et al. 2002).

Phenotypic engineering is the hallmark of studies by Patricia DeCoursey, one of the pioneers of the field (DeCoursey et al. 1997, 2000, DeCoursey and Krulas 1998). She measures survival of various species of rodents in the wild after she has removed their circadian pacemakers in the suprachiasmatic nuclei of the hypothalamus. The data are not as straightforward as one might expect – the survival is dependent on how bad was the year in regard to abundance of predators. Masking effects of light on behavior, i.e., burrowing during the day due to bright light, can protect clockless animals from predation in some cases, dependent on the species of rodent and the species of predator. There are two main problems with these kinds of studies. First, the effect of removal of the clock is observed in only one generation. If some clock-less individuals managed to survive and reproduce every year, and if it was engineered (genetically?) in such a way that the progeny were also clock-less, would such a population manage to establish itself in the wild? What alternative mechanisms it would evolve to decrease risk from predation? Would other correlated aspects of timing (e.g., photoperiodism, developmental timing, ultradian rhythms) additionally reduce their fitness? If we are removing a mechanism that was inherited for billions of years, why would we expect that an alternative mechanism would exist to protect the animals in the absence of the clock?


Earlier in this post I noted that most of the thinking about adaptive function of biological clocks concentrated on adaptation to physical environment – the daily rhythm of light and darkness. That is quite reasonable assumption when one is