Yearly Archives: 2007

Sleep News

Sleep Deprivation Affects Airport Baggage Screeners’ Ability To Detect Rare Targets:

A lack of sleep may affect the performance of airport employees, which can, in turn, compromise the safety of airline passengers. Sleep deprivation can impair the ability of airport baggage screeners to visually search for and detect infrequently occurring or low prevalence targets that may ultimately pose a threat to an airline and its passengers, according to new research.

Night Shift Nurses More Likely To Have Poor Sleep Habits:

Nurses who work the night shift are more likely to have poor sleep habits, a practice that can increase the likelihood of committing serious errors that can put the safety of themselves as well as their patients at risk, according to recent research.
Arlene Johnson, of the University of Alabama at Birmingham, surveyed 289 licensed nurses while they were working on the night shift in the hospital setting, and classified the subjects as either sleep deprived or not sleep deprived. The results showed that 56 percent of the sample was sleep deprived.

ClockQuotes

A minister has to be able to read a clock. At noon, it s time to go home and turn up the pot roast and get the peas out of the freezer.
– Garrison Keillor

Texans to drill for oil at the World Heritage Site in Sicily.

Skeptical Alchemist has the whole story.
Sign the petition to prevent the drilling.

Blogrolling for Today

Interprete

Biological Ramblings

A Passion For Nature

Life in the Bristolwood

Dragonfly Eye

Mary’s View

The Winding Path

Obligatory Reading of the Day – the Experimental Darwin

Darwin did not just sail on the Beagle and then settle down in his armchair and think for the rest of his life. He performed an amazing number of very creative experiments. Afarensis has been writing about them for a while now and I hope you are following his series every week.

Teaching tonight

Physiology: Coordinated Response
Blogging resumes later tonight….

My Picks From ScienceDaily

Ancient DNA Traces Woolly Mammoth’s Disappearance:

Some ancient-DNA evidence has offered new clues to a very cold case: the disappearance of the last woolly mammoths, one of the most iconic of all Ice Age giants, according to a recent article. DNA lifted from the bones, teeth, and tusks of the extinct mammoths revealed a “genetic signature” of a range expansion after the last interglacial period. After the mammoths’ migration, the population apparently leveled off, and one of two lineages died out.

For more, see this and this.
Scientists Propose The Kind Of Chemistry That Led To Life:

Before life emerged on earth, either a primitive kind of metabolism or an RNA-like duplicating machinery must have set the stage – so experts believe. But what preceded these pre-life steps? A pair of UCSF scientists has developed a model explaining how simple chemical and physical processes may have laid the foundation for life. Like all useful models, theirs can be tested, and they describe how this can be done. Their model is based on simple, well-known chemical and physical laws.

The Fisherman Is A Predator Like Any Other:

For Peru fishing is a prime source of foreign exchange, second only to mining. The country’s anchovy fishing fleet, which seeks the Peruvian anchovy Engraulis ringens, is the world’s largest single-species fishery, with an average of 8% of global landings. For safety and monitoring purposes, vessels have the statutory obligation to be equipped with satellite geopositioning indicators, seeing that industrial-scale fishing is prohibited within a band of 5 nautical miles (about 9 kilometres) from the coast. This satellite device, the vessel monitoring system (VMS), gives the real-time position of the vessels to an accuracy of 100 m, communicated to bodies responsible for vessel movement recording and scientific monitoring of fishing.

The Insect Vector Always Bites Twice:

The reality of the threat from vector-borne diseases has been recognized and the problem is prompting research scientists to take a strong interest. Most of these infections, classified as emerging or re-emerging diseases, are linked to ecosystem changes, climatic variations or pressure from human activities. Malaria, sleeping sickness and so on lead to the death of millions of people in the world. African countries are particularly strongly hit. The expansion of Dengue fever and the recent epidemics of Chikungunya and West Nile disease illustrate the trend.

ClockQuotes

I work until beer o’clock.
– Stephen King

Obligatory Reading of the Day – Sponges and Synapses

The best coverage of the paper so far:
Neurophilosophy
Pharyngula
Lab Notes
Dispatches from the Culture Wars

Science Blogging Conference

2008NCSBClogo200.pngI don’t have to remind you every day, but behind the scenes, we are busily working on the organization of the 2nd Science Blogging Conference. The organizing committee is meeting on Thursday and I’ll report on any news and updates then. The new wiki is almost all set up (and it will be updated on Thursday as well).
One of the pages we have not moved yet from the old to the new wiki is this one, a list of resources for finding science blogs, as well as a list of blogs that showcases the diversity of the scientific blogosphere and serves as an entry point into it without being too intimidatingly long and comprehensive. So yes, the list is totally subjective. I picked a number of blogs I know well that are as different from each other as possible so there is something there for everyone. The target audience are conference participants who are not familiar with science blogs, but are interested to find out more. So there is a small sampler for them.
I’ve been working on the list a little bit last night until I got tired and went to bed. Now, I’d like to ask you to help me, not by adding another gazillion science blogs, but by suggesting perhaps a dozen top medical blogs that are not already on the list. The medical blogosphere is rapidly expanding and I am not able to follow it as closely as I did before. I also am aware that several prominent medbloggers have recently stopped blogging (and perhaps restarted?). So, help me out, either in the comments here, or directly by editing that wiki page.
Also, did I miss any of the carnivals (bottom of the page), aggregators, or good articles about science blogging?
Finally, let me use this post for my monthly reminder to nominate posts, your own or other bloggers’, for the 2nd science blogging anthology. Use this online form. And go here to pick up the code that can help you spread the word about it.

The Iron Science Teacher

I love Iron Chef (on those rare occasions when I watch it, but I did more in the past), so I am excited about this spin-off – the Iron Science Teacher:

Parodying the syndicated, tongue-in-cheek, cult Japanese TV program, Iron Chef, the Exploratorium’s Iron Science Teacher competition showcases actual Bay Area science teachers as they build experiments around a given “secret ingredient” — an everyday item such as a paper-towel tube, a straw or a soda can. According to astrophysicist Dr. Linda Shore, Director of the Exploratorium Teacher Institute and host of the competition, “We try to show we can do science with anything. We show teachers how to use low-tech materials to illustrate classic principles of science and math.” As contestant Don Rathjen summed up, “This helps teachers teach the $10 million state science standards on a $10 budget.”
After building the gizmos, the teachers have a few minutes to explain what they are and the scientific principles they demonstrate. Judging is done on a less scientific basis, using what Dr. Shore refers to as “the clap-o-meter” — audience applause as measured by the human ear.
In one competition where the secret ingredient was a soda can, the diversity of science activities based on a simple object became clear. Using soda cans, a mathematician demonstrated the X, Y, and Z-axes of geometric shapes, a physicist illustrated the Bernoulli Effect (which affects such things as lift on an airplane’s wing), a biologist demonstrated that Classic Coke is denser than Diet Coke, and a chemist rigged up alcohol burners.
Given the popularity of the Iron Science Teacher competition, the Exploratorium is bringing science to teachers nationally via the World Wide Web.
The Exploratorium Teacher Institute provides teacher development for middle and high school science and mathematics teachers in the form of intensive summer long workshops and follow-up programs through the school year. There are currently 3000 alumni of the Teacher Institute, funded by the National Science Foundation, the State of California, the William and Flora Hewlett Foundation, the Noyce Foundation and the Eisenhower Program.

The event will take place on June 29, July 6, 13, and 20, and August 3, 10 in the Bay Area, so I may be able to go and watch two or three of those in person (and liveblog it!). For more information, check the Iron Science Teacher website and watch their Web Cams.

Obligatory Reading of the Day

All you need to know about Philosophy of Science (but were too afraid to ask) you can read in John Wilkins’ triptych:
Philosophy is to science, as ornithologists are to birds: 1. Introduction
Philosophy is to science, as ornithologists are to birds: 2. Two topics of philosophy of science
Philosophy is to science, as ornithologists are to birds: 3. Science is a Dynamic Process

Matt Bai on Poverty and Edwards

The article is here in the NYT Magazine (apparently free access to all!), but before you read it (and you SHOULD read it), read the analysis by DHinMI on Next Hurray, which points out the binary thinking, ignorance of US history, and the underlying Compulsive Centrist Disorder of Matt Bai, so characteristic of the inside-the-Beltway crowd that has never been exposed to the real world.

ClockQuotes

When late morning rolls around and you’re feeling a bit out of sorts, don’t worry; you’re probably just a little eleven o’clockish.
– Alan Alexander Milne

Blogrolling for Today

Research Remix

Academicsecret

Psychology and Crime News

Deep Grace of Theory

Hope for Pandora

Letters from a broad…

Pondering Pikaia

Sleep Expert

Average Professor

Thou Shall Not….

…miss the new edition of the Carnival of the Godless, up on Action Skeptics. But, since it is up early anyway, you can still have time to watch Belmont Stakes first.

Why are dinosaur fossils’ heads turned up and back?

OK, it’s been about 20 years since I was last in vet school and I have fogotten most of the stuff I learned there. But I remember a few things.
I clearly remember the Pathology class (and especially the lab!) and the Five Signs (or stages) of Death: pallor mortis (paleness), algor mortis (cooling), rigor mortis (stiffening), livor mortis (blood settling/red patches) and decomposition (rotting). The linked Wikipedia articles are pitifully anthropocentric, though, and there is much more cool stuff to learn when comparing various animals.
The most interesting of the five signs of death is Rigor Mortis. If you go back to the very basic physiology of muscle contraction, you may remember that ATP is needed for the cross-bridges to be released (i.e., to separate actin from myosin). After death, ATP breaks down and the muscles remain stiff for a period of time until decay and decomposition start breaking down muscle proteins. Exactly when rigor mortis sets in, and when the muscles start softening up again depends on a number of factors, including species, body size, proportional muscle mass, physical condition, physical activity prior to the time of death, age, cause of death, environmental temperature and humidity.
I also remember the word Opisthotonus, a backward arching of the head and neck caused by injury of the cerebellum, meningitis, and some types of poisoning (e.g., strychnine). Opisthotonus also occurs after death as a result of rigor mortis.
Back in vet school, all I was interested in was equine medicine (so I studied other species only as much as needed to pass the class), so I spent some time studying that all-important Ligamentum nuchae in the horse. If you ride and train horses, that is one of the most important pieces of equine anatomy, the biggest and strongest ligament (actually a fused composite of hyndreds of smaller ligaments) in the horse’s body, connecting the poll (top of the head, a ridge on the occipital bone), the top-line of the neck, withers, back, loins, rump and dock (the base of the tail).
I thought back then, that the contraction of the nuchal ligament was the cause of the occurence of opisthotonus after death. The ligament is so large and powerful, no groups of muscles are supposed to be able to counteract this movement. Particularly in later stages after death, as the muscles start decomposing, nothing would stop the ligament to pull the head and neck up.
Apparently, I was wrong:

Smith (1921) mentioned the function of the funicular ligamentum nuchae. He believed it assisted the muscles in keeping the head extended as, for example, when grazing. He also said that shortening of the ligament was responsible for the dorsiflexion (opisthotonus) of the head/neck after death. This is not the case since severing the ligament does not release such dorsiflexion; rigor mortis of the dorsal cervical muscles causes opisthotonus after death.

Now, Grrrl and Laelaps point to and discuss at length a new paper by a veterinarian, Cynthia Marshall Faux, and a famous dinosaur paleontologist Kevin Padian, who argue that the opishtotonus seen in many dinosaur fossils is not a result of rigor mortis, but a result of pre-death brain injury or poisoning. Contrary to the quote above, they did not observe opisthotonus in dead horses.
Apparently, Kevin Padian promised to come by Grrrl’s blog and answer questions in the near future. I’ll let you know when this happens. I am intrigued. Not persuaded yet, but open to changing my mind if their evidence is persuasive. Perhaps opisthotonus has different causes in different fossils, depending on the species and the individual case: some got poisoned or brain-injred, while others curved due to rigor mortis. After all, an Archaeopterix is not exactly built like a horse. What do you think?
Update: Kevin Padian responds.

My Picks From ScienceDaily

Origins Of Nervous System Found In Genes Of Sea Sponge:

Scientists at the University of California, Santa Barbara have discovered significant clues to the evolutionary origins of the nervous system by studying the genome of a sea sponge, a member of a group considered to be among the most ancient of all animals.

[PZ Myers explains it better]
Hives Ferment A Yeasty Brew, Attract Beetle Pest:

The honeybee’s alarm signal may not only bring help, but also attract the small hive beetle. Now, an international team of researchers has found that small hive beetles can detect some alarm pheromones at levels below that detected by honeybees.

‘Cultured’ Chimpanzees Pass On Novel Traditions:

The local customs that define human cultures in important ways also exist in the ape world, suggests a study reported online June 7th in Current Biology, a Cell Press publication. Indeed, captive chimpanzees, like people, can readily acquire new traditions, and those newly instituted “cultural practices” can spread to other troops.

Super Fruit Fly May Lead To Healthier Humans; Aging Slowed With Single Protein:

In a triumph for pests, scientists have figured out how to make the fruit fly live longer. But humans still may get something out of the deal. As reported online in Nature Chemical Biology, the discovery that a single protein can inhibit aging holds implications for human longevity and for treatment of some of the world’s most feared diseases.

Bigger Horns Equal Better Genes:

Size matters. At least, it does to an alpine ibex. According to a team of international researchers, mature, male alpine ibex demonstrate a correlation between horn growth and genetic diversity. Past research studies have shown that greater genetic diversity correlates with a greater chance of survival.

Caribbean Frogs Started With A Single, Ancient Voyage On A Raft From South America:

Nearly all of the 162 land-breeding frog species on Caribbean islands, including the coqui frogs of Puerto Rico, originated from a single frog species that rafted on a sea voyage from South America about 30-to-50-million years ago, according to DNA-sequence analyses led by a research group at Penn State, which will be published in the 12 June 2007 issue of the Proceedings of the National Academy of Sciences and posted in the journal’s online early edition this week. Similarly, the scientists found that the Central American relatives of these Caribbean frogs also arose from a single species that arrived by raft from South America.

The Bee That Would Be Queen:

A team of researchers from Arizona State University, Purdue University and the Norwegian University of Life Sciences has discovered evidence that honeybees have adopted a phylogenetically old molecular cascade — TOR (target of rapamycin), linked to nutrient and energy sensing — and put it to use in caste development. The findings, published in the June 6 edition of PLoS ONE, the online, open-access journal from the Public Library of Science, show that TOR is directly linked in the nutrient-induced development of female honeybees into either queens, the caste of large dominant egg-layers, or into workers, the caste of small helpers.

Organic Food Miles Take Toll On Environment:

Organic fruit and vegetables may be healthier for the dinner table, but not necessarily for the environment, a University of Alberta study shows. The study, conducted by a team of student researchers in the Department of Rural Economy at the University of Alberta in Edmonton, Canada, showed that the greenhouse gas emitted when the produce is transported from great distances mitigates the environmental benefits of growing the food organically.

ClockQuotes

Sleep, to the homeless thou art home; the friendless find in thee a friend.
– Ebenezer Elliott

Blogiversary

On this day a year ago, A Blog Around The Clock was born. Twenty-something other bloggers moved to the Scienceblogs.com empire on that same day. My old blogs are still up there, gathering cyberdust, slowly losing Google traffic and rankings, because all of the action is right here. During this year, I posted 2941 posts (that is about 8.12 posts per day) and received 5233 legitimate comments. While my new job is likely to somewhat change the tone of the blog (more science, less politics, most likely), I have no intention of slowing down. I hope you are all still here for the second anniversary next year.

Koufax Awards

So, it appears that Koufax Awards will happen. These are the most celebrated blog awards of them all (unless you are a wingnut). I am not exactly sure when all the lists of nominations will be finalized (or if any additions will be allowed at this date – these are 2006 awards, after all) and when the voting will begin.
But I found my blog nominated in several categories, including Best Blog (no chance in hell), Best Post (for this post, for which I have high hopes), Best Series (the BIO101 lecture notes), Best Consonant Level Blog, Best Expert Blog and Most Deserving of Wider Recognition. Check here for other categories. Lots of interesting blogs to check out.
But most importantly, once the voting is open, I’d like you all to vote for Scienceblogs.com for the Best Community.

Steeplejacking

Why didn’t I hear about this before? Why is it not in the media? On blogs?
Lindsay reports on the new book “Steeplejacking” that documents how the Religious Right, hand-in-hand with the hawkish conservative Democrats, systematically, over the past couple of decades, performed hostile take-overs of liberal churches. Whenever a pastor/priest/whatever preached peace (and tolerance, equality, need to fight the environmental problems and problems of poverty, etc), the “Institute on Religion and Democracy” would move in and, using various heavy-handed tactics, including lawsuits, remove such clergy and replace them with conservative warmongers. Read the entire post for details and links and spread the word! Lindsay concludes in the end:

Secular Democrats are often blamed for marginalizing the religious left. As I’m constantly trying to tell people, that blame is misplaced. It’s not secular Democrats who are driving liberal pastors out of their churches and replacing them with hardline Republican-friendly conservatives!
If the central claims of Steeplejacking are correct, it seems as if the main reason we don’t have a more powerful religious left in this country is because of sabotage by the religious right, not hostility from the secular left.

OK, this is something I am quite conflicted about: the whole Democratic Party “outreach” to the people of “faith”.
One part of me, the atheist part, wants to see religion completely left out of politics (and governing). If Religious Right takes over all of organized religion in the country – let them have it: that will just make religion more unpalatable to more people and marginalize religion even more.
The other part of me, the liberal part, is more pragmatic. Yes, the non-religious (under various names) are the fastest growing category according to many censuses and polls. But it is still not big enough number for the US to join the civilized world in its complacent ignoring of religion in politics altogether. I understand that running as openly atheist is a political suicide at any level, and particularly at the Presidential level. I am hopeful that this will change in the near future, but it will not just yet. And it is quite imperative that GOP gets booted out of governance ASAP, hopefully in 2008. Let them reform or disappear – I don’t care which, it’s up to them.
This means that I want to see a Dem elected to the White House as well as to see the Dems win a greater majority in both houses of Congress, more governorships, more state legislatures, more mayors of major cities. Once that happens, on the day after the election, the God-talk will miraculously stop as there is a lot of work to do, rolling back the immense damage that Repubs have inflicted on the country and the world over the last 27 (and especially the last 6) years. There will be just no time for faith-based platitudes.
I am also aware that many religious folks are liberal, keep their beliefs out of their pragmatic lives, and want to fight for equality, tolerance and peace and to fight the environmental problems and problems of poverty and such. I may not agree with their personal beliefs, but those beliefs are completely irrelevant to the bigger effort of changing the country and the world for the better. They are natural allies. In a political fight I don’t care or need to know what the religious views of my co-fighters are.
Thus, I understand why the Sojourners wanted to make a little TV spectacle of interviewing leading Democratic contenders. This was a way for them to start regaining the foothold in the popular view of religion, to try to snatch it back from the Religious Right, to try to sway some mid-grade religious voters to support Democrats by showcasing that the Dems are not anti-religion as the Right Wing noise machine keeps telling them.
So, why did they pick Soledad O’Brian to referee? She thinks only abortion and homosexuality are religious issues, although the Sojourners explicitely care about poverty and environment? Did she drink the Rightwing frames or what?
Anyway, as an atheist, I am perfectly OK with the idea of voting for a religious person (as well as anyone pretending to be so for political reasons). Otherwise, there would be nobody to vote for. But I want to be sure that the candidate’s personal faith has no play in his or her decision-making processes once in office. I want to see pragmatic decisions based on best available information.
Thus, watching the 10 GOP candidates crawl over each other trying to show off who is more pious (including the silly non-belief in evolution!) is such a disgusting experience. I don’t want their religious ideology guiding their decisions when in office. Just look at the Dominionist in the White House now to see how tragic such a mix can be.
But watching the Sojourners’ interview of the top three Dem candidates did not make me as sick as I expected (and hell I was surprised with that). Here is one of the detailed descriptions of the event.
First, as expected, all three had to speak about the way they were raised in church and how that affected them and how important that is for them, etc., etc., OK, I get it. But all three were equally quick to point out that their personal faith will have no negative effect on the pragmatism of their decisions in office. They were not afraid to say that evolution is good science and that alternatives have no place in public schools. And they addressed the issues that Sojourners (and not Soledad) thought were important: poverty and environment.
Mike links to an interesting discussion of the event and, as conflicted I am on this issue, I tended to agree with every commenter, one at a time. One of the participants, a rabbi, wrote:

One, it’s a good thing that, in response to the ascendancy of the Religious Right in American politics, the Progressive religious community is being heard now as well. Many of us religious leaders have been frustrated by the dominance of one religious voice in the public discourse and it’s refreshing to hear a greater diversity of expression in that regard.
However, as I listened to Edwards, Obama and Clinton articulate themselves quite clearly, I grew increasingly depressed. Because the truth of the matter is that I don’t care whether or not my president goes to church or synagogue on any given Saturday or Sunday. I want my president to execute their job with the best talent they can find, in the most efficient, caring, and ethical way in service to all citizens of the country–believers and non-believers alike.
It matters not to me what the President “believes.” I want a government that works, that cares for the disadvantaged, that defends us when we are under attack as a nation.

But, that is exactly what Edwards, Obama and Clinton were saying: their faith is personal and they are running for office because they think they can institute a government that works. Fine with me.
Of the three main candidates, Obama is the one who most uses God-talk in his speaches. But, what he says is so ambiguous that people of all religious persuasions equally agree with him:

Although Sen. Barack Obama (D-Ill.) is a Christian, he “embodies the basic ideals and values of most Hindus,” said Prianka S., a Hindu from Chicago.
Obama’s “love for Israel” is “evident not just in his work, but also in his heart,” said Rep. Robert Wexler (D-Fla.), an Orthodox Jew.
Obama “represents true faith,” said the Rev. Bertha Perkins, a Baptist minister in New Hampshire.

Well, that is how Obama talks about everything, not just religion, so everyone who likes Obama reads into his speeches whatever he/she wishes for it to mean anyway. He has not said anything specific that could possibly alienate anyone yet. But if he becomes the President, I am not afraid that his religion will take a precedence over smart governing. Actually, of the eight current Dem candidates, the only one who actually mixes religion (some kind of New Age crap) and politics in a way I dislike is Dennis Kucinich. As Markos noted:

Here’s the difference — Kucinich is using his “faith” as the basis of his “Department of Peace”. In other words, he’s trying to inject his faith into the public sphere.
And that’s not something I’m willing to tolerate, whether it comes from the Religious Right or from our side.
People are free to talk about the source of their values. But I believe strongly in the wall between church and state.

Chernobyl Area – a Wildlife Haven?

Ruchira Paul alerted me to this article about a scientific fight between Robert J. Baker of Texas Tech University (who I never heard of) who alleges that the evacuation of humans from the area allowed animals to come in and multiply with no apparent bad consequences from radiation, and Timothy Mousseau of the University of South Carolina (who I have met and read and greatly respect) who finds whopping numbers of bad mutations in the region and very low fertility rates. The first argues that the populations are growing, while the latter suggests that the area is a sink for animals who come in but are unable to sustain their populations once there.
I am not sure who is right, but the first thing I noticed in the article (and this may not be true in the real world, but article makes it seem so) is that all the work by Baker is on small mammals, while all the work by Mousseau is on birds. Perhaps mammals are better able to cope with radiation than birds? Any thoughts?

Medical Imaging of the Month

Radiology Grand Rounds XI are up on Sumer’s Radiology Site

Malaria and DDT

I often blog about malaria because it is a fascinating disease which has to be studied in a highly integrative manner, is a great teaching topic and I could tie it in with my own field.
If you share my fascination, than your Obligatory Reading Of The Day is this post by Bug Girl (via) about the truth about DDT, Rachael Carson, malaria and the wingnut lies about it. Follow the links within it as well for more information.

Friday Weird Sex Blogging!?

On some Fridays, I write about strange reproductive strategies and mating habits of various organisms, sometimes in excrutiating detail, though I have not done it very regularly lately (see the Friday Weird Sex Blogging archives).
But some people just collect them all in one place, in one post full of strangeness. You can read about 30 Strangest Animal Mating Habits on Neatorama. Or 11 Examples of Unusual Mating Habits on Canongate (both via Liberals in Exile).
Others have a regular feature on science and nature of sex, e.g., Insect Sex on What’s That Bug, the Sexy Beast category on the Primordial Blog and the Friday Flower Porn on Dr.Joan Bushwell’s Chimpanzee Refuge.
And there are sites and blogs entirely dedicated to the science of sex, ranging from scandalous, like The Illustrated Book of Sexual Records, through funny yet informative, like Secret Sex Lives of Animals and Physics of Sex, all the way to the “serious” stuff, e.g., Dr.Petra Boynton’s sexology blog and The Well-Timed Period (human reproductive physiology, health and associated politics).
How can one possibly compete in such a crowded field?

ClockQuotes

There is a time for some things, and a time for all things; a time for great things, and a time for small things.
– Miguel de Cervantes

It’s the World Oceans Day

So, it is fitting that Carnival of the Blue kicks off today. The first edition (already huge!) is up on Blogfish. Lots of great posts!

So, why did the mammoths REALLY go extinct?

A paper in press in Current Biology (press release here) looks at mitochondrial DNA of mammoths and advances a primarily environmental cause for the mammoth extinction. Razib explains why such a black-and-white dichotomy is unhealthy.
Looking at a different hypothesis, also environmental, for the mammoth extinction (comet impact), Archy places the black-and-white dichotomy in the historical context and tries to figure out why the environmental hypotheses are so popular nowadays, while extinction at the hands of human hunters is not a popular idea any more.

Invisibility Cloak

When I was a kid I swallowed science-fiction by the crates. And I was too young to be very discerning of quality – I liked everything. Good taste developed later, with age. But even at that tender age, there was one book that was so bad that not only did I realized it was bad, it really, really irked me. It was The Ayes of Texas (check the Amazon readers’ reviews!), a stupid 1982 Texas-secessionist fairy-tale in which a rich (and of course brilliant and smooth with ladies) conservative Texan, by throwing millions of dollars at scientists, gets all sorts of new gizmos and gadgets which he uses to win the Cold War by defeating both the Soviet and the US military, ending with Texas as the remaining standing military superpower. Hey, at that age I barely new where Texas was but the whole schtick was so sick, not to mention the stupid idea that scientific discovery can be bought just like that, with bags of money and few weeks of effort!
Anyway, since I doubt you’d care if I spoiled the plot of a book that you will not and should not read, the key weapon in the battle was an old WWII battleship armed with new types of weapons and, most importantly, made invisible by being plastered with panels made of a new material (which, if I remember correctly, break several laws of physics).
And while the invisibility panels as described in the book were impossible, that does not mean that nobody’s ever looked at the possibility of making materials that can make stuff more-or-less invisible. There was a report last year that saw a lot of press, and recently a new one came out, looking at chemicals called reflectins, coded by six genes unique to squid. Cephalopods rule, of course, and the distribution of reflectins in the skin is under the neural control of melanophores in cuttlefish and octopods.
Now, as MC explains very well, a new paper came out describing the properties of reflexins inserted into and expressed in E.coli. Then, reflexin synthetized by bacteria were coaxed into forming films on the surface of water and the light-reflecting properties were studies under varying conditions. You’ll have to read MC’s post for details.
Anyway, as MC notes, this is clearly of interest to the military, though I doubt they’ll ever use the synthetic reflexins to coat a WWII-era warship in order to defeat both the Soviet and the US armies in order to secede and form a Greater Texas.

Space Out!

The Carnival of Space #6 – ISDC Edition – is up on Music of the Spheres.

Gastropod Neuroscience

Bjoern Brembs is attending and liveblogging from the Gastropod Neuroscience meeting at Friday Harbor Laboratories and has posted about several talks already and will likely post more over the next couple of days.
Something struck me in his coverage of Dennis Willows’ talk about magnetoreception in Tritonia:

However, in 20 years of research, the researchers haven’t found the cells which sense the magnetic field and transmit the information to the neurons in the brain.

Well, Ken Lohmann, barely a mile or so from me, has already published several papers on Tritonia neurons sensitive to changes in the Earth’s geomagnetic field. Is there a controversy about this? I doubt Willows is unaware of Lohmann’s work, so why did he ignore it in his talk? Or did I misunderstand that remark?
Ronald Chase: snails slugs and sex adds more complexity to the story of penis fencing in molluscs than I was aware of previously.
More from the meeting so far:
Robert Meech: Why Mollusks behave the way they do
Richard Satterlie: Swimming Speed Changes in a Predatory Mollusk
Leonard Kaczmarek: Regulation of prolonged changes in neuronal excitability
Klaude Weiss: Dynamic reorganization of the feeding CPG of Aplysia (Aplysia used to be a biggie animal model in circadian field, but I don’t think there is anyone working on it any more)
Paul Katz: Nudibranchs, Neuromodulation, Neural circuits, & Neuromics
Unfortunately, no pretty pictures of Nudibranchs (or any gastropods for that matter – just people, people, people). For that, you have to visit Bouphonia on Fridays.

Skeptic’s Circle is up

It’s Thursday, so it’s that time of week for Thursday to host the Circle.

ClockQuotes

I am long on ideas, but short on time. I only expect to live about a hundred years.
– Thomas Alva Edison

Today’s carnivals

Tangled Bank #81 is up on Behavioral Biology Blog (darn, I forgot to send my entry this time).
Grand Rounds Vol 3., No. 37 are up on Inside Surgery.
Pediatric Grand Rounds 2:4 are up on Adventures of An Awesome (Sometimes) Mother.
Bio::Blogs #11 is up on Nodalpoint.
The Festival of the Trees 12 – Meditations – is up on Arboreality.

Blogrolling for Today

On Topp of the World

Liberals In Exile

Green Chameleon

Monkey Trials

Carnival of the Blue

Epidemix

PLoS 500

Yesterday, PLoS-ONE celebrated the publication of the 500th paper (and additional 13). Here are some quick stats:

1,411 submissions
513 published paper
360 member editorial board and growing
19 day average acceptance to publication
600+ post publication comments posted

I am assuming that the remaining 898 manuscripts are in various stages of the publication process: rejected, in review, in revision, or in the pipeline to appear on the site any day now.
The very first paper was published on December 20, 2006. The 500th paper is this one “Climate Change Cannot Explain the Upsurge of Tick-Borne Encephalitis in the Baltics”, which is quite an interesting read (and I wonder if global warming denialists will try to misuse it in the near future).
Since I got the job with PLoS-ONE I’ve been asked some questions about it (even though I’m just an egg: I will start working a month from now) which reveal some misunderstandings about this journal. So I looked around the site and I asked some PLoS people trying to find the right answers.
First, the word ONE in its title suggests that this is meant to become the flagship journal in the PLoS stable and a direct competitor to Science and Nature. Sure, but that does not mean that the format and the publishing philosophy is the same as those two journals. ONE refers more to being the first (and so far unique) journal using the 21st century model of publishing, rather than to the ambition to reach the #1 spot on the Citation Index.
The hardcopy journals are limited by the size of their journal – how many papers can appear each week? Being entirely online, PLoS has no such space constraints. So PLoS-ONE does not seek only spectacular papers or revolutionary (thus potentially wrong) papers on topics with potentially wide interest. Everything that is well done and well written and passes the peer-review, no matter how specialized or obscure the field, will be accepted. As Chris Surrige, the managing editor of PLoS-ONE explained to me:

ONE certainly isn’t meant to be Science or Nature. What we wanted with ONE was for it to be ONE place to contain all of science. Supremely broad and deep. We want to publish papers that could have been published in Science or Nature AND papers that would otherwise have been heading for the most specialist of specialist journals. PLoS ONE is supposed not to fit within the current hierachy of journals, it stands outside it as an alternative not to any journal in particular
but to ALL conventional journals.

This also means that papers from all areas of science are welcome (excepting, perhaps, meta-science papers, e.g., in history, sociology and philosophy of science). For now, most of the papers published so far are in the biology/genetics/medicine areas, which is understandable as the researchers in these areas are already familiar with the publishing philosophy of PLoS through its other journals. But PLoS-ONE is trying to expand its scope to all the other disciplines as well and is welcoming the brave, enterprenurial people who are willing to break the ice and submit the first manuscript in their area od study (and hopefully bring in other colleagues as well).
These and many other questions have already been discussed (and surely will be in the future) on the PLoS blog which should be your regular read (dig through the archives as well – there is some good and important stuff there). The instructions for submission of manuscripts are clear and detailed: it is fast and streamlined, but it is most definitely peer-review.
Anyway, my job will not be on the publication end of the process, but on the post-publication end – the post-publication peer-review of sorts. PLoS-ONE allows and encourages scientists and other educated readers to annotate the papers and to post comments/discussions on papers. You can read about those here and try it out in a neutral space (if you are still nervous about annotating/discussing a real paper) here. My goal, among others, will be to bring in more people to the site to discuss papers and to develop ways to make this activity worth people’s time and effort (on top of being fun to do, as we bloggers already know). In this effort, I will occasionally use you – my readers – as my own focus group, asking for your feedback on changes and innovations we will try to implement in the future. Stay tuned. I’ll explain more once I actually start working there.

Another job application on a blog

Jason aka Argonaut saw how I got the job and decided to try the same tactic. And, lo and behold, check the first comment on this post! I hope it works out for Jason as it did for me.

My Picks From ScienceDaily

What Did Dinosaurs Hear?:

What did dinosaurs hear? Probably a lot of low frequency sounds, like the heavy footsteps of another dinosaur, if University of Maryland professor Robert Dooling and his colleagues are right. What they likely couldn’t hear were the high pitched sounds that birds make.

Scientists Join Fight To Save Tasmanian Devil From Deadly Cancer:

CSIRO scientists have joined the battle to save Australia’s iconic Tasmanian devils from the deadly cancer currently devastating devil populations.

Stray Penguins Probably Reached Northern Waters By Fishing Boat:

Guy Demmert got quite a surprise when he hauled a fishing net into his boat off the coast of southeast Alaska in July 2002. There among the salmon, in living black and white, was a Humboldt penguin, thousands of miles from where any of its kind should have been.

Hormone Helps Mice ‘Hibernate,’ Survive Starvation:

A key hormone enables starving mice to alter their metabolism and “hibernate” to conserve energy, revealing a novel molecular target for drugs to treat human obesity and metabolic disorders, UT Southwestern Medical Center researchers have found. The starvation-fighting effects of the hormone, called fibroblast growth factor 21 (FGF21), are described for the first time in a study appearing online today in Cell Metabolism.

Climate Change And Deforestation Will Lead To Declines In Global Bird Diversity, Study Warns:

Global warming and the destruction of natural habitats will lead to significant declines and extinctions in the world’s 8,750 terrestrial bird species over the next century, according to a study conducted by biologists at the University of California, San Diego and Princeton University.

24 Species Believed New To Science Discovered In Suriname Rainforest:

Conservationists are in the northern Amazon nation of Suriname today calling for better environmental protections from illegal mining and other threats. To make the case for improved conservation practices, scientists from Conservation International (CI) and partner institutions are presenting a report to government officials that details eastern Suriname’s invaluable biodiversity. The report documents the results of a 2005 expedition and 2006 follow-up survey, led by CI’s Rapid Assessment Program (RAP), during which researchers found 24 species previously unknown to science.

EduBlogging of the week

The Carnival Of Education #122 is up on Educaton Wonks.
Carnival of Homeschooling #75 is up on HomeSchoolBuzz.

AnthroBlogging of the Week

15th edition of the Four Stone Hearth is up on Testimony of the spade

ClockQuotes

Time is the most valuable thing a man can spend.
– Theophrastus

This is what my wife gave to me today…

…and made me very, very happy:
Darwin%20puppet.jpg
(From here)

Carnival of the Liberals #40

Dr. Snedley, the Mr.Hyde to Dr.Biobrain’s Dr.Jeckyll (confused yet?) has taken over the blog and compiled the latest Carnival of the Liberals accompanied by his right-wing snark!

Open Notebook Science is more than just Open Access

As explained by Jean-Claude Bradley in this excellent interview: The Pursuit of Automation: Open Notebook Science:

The difference between Bradley’s idea and traditional open source projects is the clutter, i.e., all of the data collected from research. In a journal article, what the reader receives is a set of findings, published after peer review, along with the conclusions and basic data used to reach them. Bradley’s project allows the reader to see the process unfold, from hypothesis to conclusion, with all data, experiments and notes that are collected along the way. This inclusiveness allows other researchers to better assess their own ideas, because not only do they have the conclusion and data used to support it, but also they have access to every failed or incomplete subset of data to use in their equations.

Those on the Losing End are always the Loudest

And they also make themselves look silly in the process. This time, it is the dinosaurs of journalism, putting out all the old anti-Web canards. Perhaps we should compile an Index of Old-Journalist Claims similar to the Index of Creationist Claims (on TalkOrigins.org). Two examples this week:
First, (via Ed Cone) Jay Rosen rips into this article by Neil Henry:

My impression: we’re at the twilight of the curmudgeon class in newsrooms and J-schools. (Though they can still do a lot of damage.) You know they’re giving up when they no longer bother to inform themselves about what they themselves say is happening. And if their “who lost journalism?” call-for-justice op-ed disappears behind a pay wall so the search engines can’t find it, silencing that call online, the beautiful thing is they won’t know it happened, and they won’t understand why it matters because they never got how Google works in the first place.
It’s clown time for the curmudgeons because they’ve lost the smart people who can save the business the curmudgeons had tried to save by jeering at the stupids and their attempted changes.

Oh, and definitely read the rest and follow the excellent links within. It’s as beautiful a smackdown as anything anti-Creationists bloggers can write. Or perhaps even closer to that ideal is this marvelous fisking by Lessig of Andrew Keen’s new book “The Cult of the Amateur”:

And then it hit me: Keen is our generation’s greatest self-parodist. His book is not a criticism of the Internet. Like the article in Nature comparing Wikipedia and Britannica, the real argument of Keen’s book is that traditional media and publishing is just as bad as the worst of the Internet. Here’s a book — Keen’s — that has passed through all the rigor of modern American publishing, yet which is perhaps as reliable as your average blog post: No doubt interesting, sometimes well written, lots of times ridiculously over the top — but also riddled with errors. Keen’s obvious point is to show those with a blind faith in the traditional system that it can be just as bad as the worst of the Internet. Indeed, one might say even worse, since the Internet doesn’t primp itself with the pretense that its words are promised to be true.
So lighten up on poor Mr. Keen, folks. He is an ally. His work will help us all understand the limits in accuracy, taste, judgment, and understanding shot through all of our systems of knowledge. The lesson he teaches is one we should all learn — to read and think critically, whether reading the product of the “monkeys” (as Keen likens contributors to the Internet to be) or books published by presses such as Doubleday.

Ooooh, this hurts!
Or, as Ed does whenever asked about the problems of accuracy and trustworthiness of blogs, he has a two-word response: “Judith Miller”.

Hooray for Open Science

Social Science and Humanities bloggers have been doing it for quite a while, but natural scientists have largely been very reluctant to do this. Now, with approval of his PI, Attila Csordas will start posting parts of his Dissertation on his blog. Stem cell research – mmmm, nice! Sure, the actual data may never appear there, but this is a big move forward anyway.
Most useful is the view of Nature that he reprints on his blog on what actually constitutes ‘previously published’ work, i.e., what not to do if you want to have the paper published in their journal. I’d really like to see equivalent statements for some other popular journals as well.
And he also points to a student writing her chemistry Masters Thesis on a wiki.

My Picks From ScienceDaily

Duetting Birds With Rhythm Present A Greater Threat:

Birds that sing duets with incredible rhythmic precision present a greater threat to other members of their species than those that whistle a sloppier tune, according to a study of Australian magpie-larks reported in the June 5th issue of Current Biology, published by Cell Press.

Going Fishing? Only Some Catch And Release Methods Let The Fish Live:

NSW Department of Primary Industries (DPI) fisheries scientists are investigating ways to boost the survival rates of several more species of fish caught and then released by anglers. Some guidelines designed to improve fish survival were recently developed for released line-caught snapper, silver trevally, mulloway, sand whiting, yellowfin bream and dusky flathead.

New Animal Model Boosts Biodefense Research On Lassa Fever:

Scientists at the Southwest Foundation for Biomedical Research have developed a new tool in the battle against a potential biological weapon, Lassa fever, which kills several thousand people each year and leaves thousands more with disabilities such as deafness and liver damage. In an article in the June 2007 issue of the Journal of Virology (Vol. 81, Issue 12), SFBR scientists Jean Patterson and Ricardo Carrion Jr. and colleagues detail the development of a new animal model, the marmoset monkey, for use in Lassa fever research.

Male Mice Get A Longevity Boost From Compound Found In Creosote Bush:

Aspirin didn’t pan out. Neither did two other potential anti-aging agents. But a synthetic derivative of a pungent desert shrub is now a front-runner in ongoing animal experiments to find out if certain chemicals, known to inhibit inflammation, cancer and other destructive processes, can boost the odds of living longer.

Climate Change Linked To Origins Of Agriculture In Mexico:

New charcoal and plant microfossil evidence from Mexico’s Central Balsas valley links a pivotal cultural shift, crop domestication in the New World, to local and regional environmental history. Agriculture in the Balsas valley originated and diversified during the warm, wet, postglacial period following the much cooler and drier climate in the final phases of the last ice age. A significant dry period appears to have occurred at the same time as the major dry episode associated with the collapse of Mayan civilization, Smithsonian researchers and colleagues report in the Proceedings of the National Academy of Sciences online.

Furry-clawed Asian Crabs Found In Delaware And Chesapeake Bays:

Chinese mitten crabs, first reported in the Chesapeake Bay, are more widespread than initially thought. Four crabs have now been caught in Delaware Bay during the last week of May 2007, and may occur in other waters of the U.S. east coast.

The Scientist And The Contortionist:

Watching a ballet dancer or circus acrobat perform, who hasn’t winced at the thought of trying to replicate the impossible flexibility on display? Emilie Mackie ’07, a neuroscience major, wondered what exactly is happening to the brain during this type of visceral response to someone else’s physical state, so she cast about for a contortionist.

If the quizzmakers could only spell…

I could not resist this one, first seen here:


What Science are You?

You are Entymology. You are a conneseiur of the crawly. Bugs fascinate you. Let’s face it, they are cool. Most people will think you’re weird icky, but those of sophisticated taste will realize just how exquisit a roach can truly be.
Take this quiz!




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ClockQuotes

Under all speech that is good for anything there lies a silence that is better. Silence is deep as Eternity; speech is shallow as Time.
– Thomas Carlyle