My picks from ScienceDaily

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Clock Quotes

I sometimes think we expect too much of Christmas Day. We try to crowd into it the long arrears of kindliness and humanity of the whole year. As for me, I like to take my Christmas a little at a time, all through the year.
– David Grayson

Happy holidays

Belgrade and Serbia for tourists

A review of nightlife and some awesome pictures:
konji%20na%20Zlatiboru.jpg

Blogs – a means to finding people to do rhythmic things with?

I found this quite intriguing:

Those thinking that online social networking is a substitute for face-to-face interactions might want to think again. Recent research in psychology suggests there are some benefits to real-life socializing that the Internet just can’t provide; researchers at Stanford University have published a report in Psychological Science called “Synchrony and Cooperation” that indicates engaging in synchronous activities (e.g., marching, singing, dancing) strengthens social attachments and enables cooperation. As most of our online social networking to date is based on asynchronous communication and interaction, this could spell trouble for those that prefer to engage in relationships online rather than off.

Hmmm, isn’t this quite a leap? There is a difference between being in the same physical space and doing something rhythmic in it. There is also a difference between doing something together online vs. offline. I do not see how those things are comparable.

Scientists have theorized that synchronous activities lead to group cohesion ever since the 1970s, but Stanford’s Scott Wiltermuth and Chip Heath wanted to put some backing behind this notion. In one study, the researchers led 30 participants around campus in two different conditions: one walking in step (marching), the other walking normally. Afterwards, the participants were instructed to play an experimental economics game called the “Weak Link” in which productivity is a function of the lowest level of input. Wiltermuth and Heath found that participants that walked in step were initially more likely to cooperate as a team.
In a second study, participants were instructed to read or sing the Canadian National Anthem while performing a simple activity in tandem or separately. As you’d expect from the hypotheses, individuals that sang together or acted together showed a greater level of cooperation. A third study cemented these results.

OK, that’s fine. This is why people chant, sing, dance, march, etc. There are good reasons why simultaneous rhythmic activity fosters cooperation and closeness. Have you ever been to a political rally and chanted something in unison with thousands of others? That’s building a communal spirit:

Have you ever been to a soccer game in Europe:

The game started a couple hours later as it was getting dark. It gets dark here at 4:30pm. And that was around the time the crowd began to cheer for their team. It was amazing to listen to. Imagine an entire stadium cheering together… but not the kind of cheering that we know in the States. This was not the sound of random cheers… or the periodic screams that come with doing the wave… and at no time did I ever heard the word “fence”. No, the Serbian fans were singing. They were all singing together to support their team. And their voices in unison echoed through the chilly night and into our apartment. It was astonishing. I truly believe that everyone should have the great privilege of listen to European soccer fans. Then again… I have no idea what they were singing… honestly, it could have been about a fence… but I’m not going to focus on that.

It does not matter if you are playing for Milan, Borussia, Real-Madrid or Manchester United – you have to be a professional, an amazingly self-controlled person with nerves of steel in order not to be affected by the continuous chant of 100,000 Red Star fans when playing at their stadium. The players play in sync with the audience chants, and the audience alters the chant to match the rhythm of the play. It is absolutely amazing to watch. So yes, rhythmic synchronized behavior is a great way to ensure group cohesion which is needed for attaining the group goals, e.g., of scoring goals. Or winning elections.
But now we get to the argument that does not seem to have anything to do with rhythmic behavior:

The Internet is a great enabler of asynchronicity. Instead of phone conversations or face-to-face chats, for instance, occuring in real time, instant messaging allows all parties involved to think and react at their own paces. E-mail is handled at the recipient’s leisure. The pace of social networking is dictated by the participants. Is the nature of online communication- that is, a lack of synchronicity- potentially damaging for relationships? If it takes a certain sort of tandem activity to strengthen social connections, maybe the Web is missing out big-time.
As an aside, this might also suggest why individuals that are deep into the gaming scene (e.g., MMORPGs, first person shooters, etc.) often tend to find companionship online more easily than most: perhaps playing a game online is a cooperatively kinesthetic experience that satisfies this human need for synchronicity.

Hmmm, none of this is rhythmmic activity. It is social, communal and synchronous, but it is not rhythmic. Thus, the study noted above can’t really say anything about it. A lot of the stuff online happens synchronously, in real time – Skype, chat, fast-moving discussions on blogs and forums, etc. are just as synchronous as a real-life conversation. Here, the distinction is not between rhythmic and arrhythmic, but between online and offline.
Now, a lot of online activity is centered around finding like-minded people. When you find them, and, let’s say you read their blogs regularly, after a while you start wishing to meet them in person. What do you do? You connect with them on Facebook or Dopplr.com in order to track each other’s travel so you can meet up whenever you are in the same town. You organize a Blogger MeetUp to meet like-minded people in your area, or a BloggerCon if you want to broaden the scope geographically. That is how Science Blogging Conference originated – my wish to meet other science bloggers in person.
But when we meet in person, do we engage in rhythmic behaviors (no, I don’t want to know about that kind!)? Perhaps we may raise a glass of beer or wine in a completely synchronous and rhythmic manner, but that is rare. It is not about rhythmicity, it is about physical proximity. Even most of the Flash Mob activities (see this list for examples) are rarely rhythmic – I found only one example that is synchronously rhythmic.
This is also related to my obsession with the Death Of The Office, i.e., with the world of telecommuting and coworking. Instead of having the people picked for you by others – going to the office – you pick your own friends and, whenever possible, meet them in person. You actively choose to live in the place where you can combine all your needs for a particular climate and culture, with the proximity to a substantial number of people you like to see often, although you have first discovered each other online. Then you can go with them to a soccer match and chant in sync if you want, but that’s not the point.

Three perspectives on Santa Claus

The inner workings of the North Pole:

Of course, the elves are the backbone of Santa’s work force. It’s never clear to me that they are happy workers.
I hear occasional rumors that the elves have tried to organize a union, only to be thwarted by the man in red.
I’m not even sure Santa pays the elves, and they seem to live on site.
The North Pole is a company town. How jolly is that for those paid in Santa scrip?

If I Were Santa’s Public Relations Guy…:

For such a high-profile, influential figurehead, Santa’s PR could really use some work. I mean, the merchandising is pretty neat but there’s a lot more potential there.
So… here’s what I’d suggest if I were running Santa’s communications.

Santa Claus is for parents:

I’m not a parent, and it’s not my place to say one way or another if you choose to engage in what is a relatively harmless tradition. But I do think that I’d like the whole thing a lot more if people quit spinning self-serving tales about how Santa is there for the kiddies. I realize that parental sadism is not P.C., and so in order to engage in it, parents have to convince themselves and others that it’s for the kids’ own good. But I say fuck that. Parents wipe asses, give time-outs, worry about nutrition, lose sleep, and get kid germs. Parents deserve a little payback. Santa may not be great for kids, but it’s great for parents, and that’s reason enough in my eyes. Just so long as the parents admit it. Not everything in this world has to be for the children, and people who think that everything in the entire world should be sculpted around the raising of children to be good people are, at best, tedious bores and many of them run the risk of writing tedious letters to the FCC because Bono said “fuck” at the Grammys. Perhaps having a little fun with the kids at the expense of the child’s credulity isn’t the worst thing in the world. What’s bothersome to me is playing it off as something it’s not.

Blogger Of The Year

Eleven years ago, two or three guys with awesome programming skilllz sat down and almost simultaneously, and not knowing of each other at the time, wrote the first blogging software. Dave Winer was one of those guys and, like the rest of them, strongly dislikes the “who was the first blogger” frenzy that sometimes sweeps through the blogosphere. He was one of them, but nobody was “the first”.
If you read or write blogs, it is thanks to guys like Dave. If you are reading this post in an RSS feed reader, it’s because Dave invented and wrote the RSS. If you have ever been to an “unconference”, it’s probably because Dave pushed and popularized the format over the years. He can be maddeningly curmugeounly at times, but more often than not, he has profound insights and his blog is always worth reading – gives us all hope when we see that even after 11 years Dave’s blogging has not lost any of its steam.
Last year, Dave gave out his first Blogger Of The Year Award to Naked Jen. When Dave picks a winner, it is worth paying attention.
This year, Dave has announced his second Blogger Of The Year Award to Jay Rosen. And it’s a well deserved award. If you want to know how journalism works, how it is changing, where it is going and what role the blogs play in it, read the entire archives of Jay’s blog – I did.
Jay reserves his blog for longer, thoughtful pieces, so his blogging frequency is low. But he has recently started microblogging on Twitter and FriendFeed and took it by the storm (do yourself a service and start following him on those places).
Readers of my blog are probably familiar with Jay, as I tend to link to him often. On Twitter and FriendFeed he is the one I tend to pay attention the most of all:
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But now, thinking of all this in terms of science blogging community – who is the Science Blogger Of The Year? Do you need more than one category – perhaps separate Best Medical, Best Skeptical, Best Science-and-Politics, Best Lab Life, etc.?
My first nomination, in the category of The Best New Science Blogger (started writing in 2008) is SciCurious.
Nominate your favourites in the comments here.

Crime of Passion (video)

Naughty male Australian satin bower bird selectively steals blue items to decorate his nest. The female bower birds rate their partner by their home decor so they do a lot of stealing.

My picks from ScienceDaily

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Clock Quotes

Once upon a time – of all the good days in the year, on Christmas Eve – old Scrooge sat busy in his counting-house.
– Charles Dickens

VHS is dead

VHS era is winding down – “The last big supplier of the tapes is ditching the format, ending the long fade-out of a product that ushered in the home theater.”:

Pop culture is finally hitting the eject button on the VHS tape, the once-ubiquitous home-video format that will finish this month as a creaky ghost of Christmas past.
After three decades of steady if unspectacular service, the spinning wheels of the home-entertainment stalwart are slowing to a halt at retail outlets. On a crisp Friday morning in October, the final truckload of VHS tapes rolled out of a Palm Harbor, Fla., warehouse run by Ryan J. Kugler, the last major supplier of the tapes.
“It’s dead, this is it, this is the last Christmas, without a doubt,” said Kugler, 34, a Burbank businessman. “I was the last one buying VHS and the last one selling it, and I’m done. Anything left in warehouse we’ll just give away or throw away.”….

Read the rest, for some amusing examples of what sells and what doesn’t….

Hummingbird Nest Documentary (video)

Using science to make roads safer

Duke University’s John Staddon makes the case for less, and more effective, road signage in the U.S – using Durham roads and streets as examples:

ugh, WordPress does not like this format. You can see the video here or here.

From here, which I discovered here because I am fascinated by the science of traffic and driving. If only explaining the mathematical models of traffic flow and the cognitive psychology of driving to the traffic cop could get one out of a ticket….

Bizarre Squid Sex (no video)

In National Geographic:

A new investigation into the tangled sex lives of deep-sea squid has uncovered a range of bizarre mating techniques. The cephalopods’ intimate encounters include cutting holes into their partners for sex, swapping genders, and deploying flesh-burrowing sperm. These and other previously unknown reproductive strategies were documented in a survey of ten squid species living worldwide at depths of between 984 and 3,937 feet (300 and 1,200 meters). Study leader Henk-Jan Hoving, a Ph.D. student at the University of Groningen in the Netherlands, examined squid caught during research voyages as well as preserved museum specimens.

Of course, you can find many more examples of Weird Cephalopod Sex on Pharyngula….

5 Stages Of Twitter Acceptance

For people like this:
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From here

Talk of the Defense of Food of the Nation

Michael Pollan will be on NPR’s Talk of the Nation tomorrow to discuss his book Defense of Food.

This is your honeybee. And this is your honeybee on drugs.

A well-written press release on a very well done and exciting study:
Honey bees on cocaine dance more, changing ideas about the insect brain:

In a study published in 2007, Robinson and his colleagues reported that treatment with octopamine caused foraging honey bees to dance more often. This indicated that octopamine played a role in honey bee dance behavior. It also suggested a framework for understanding the evolution of altruistic behavior, Robinson said.
“The idea behind that study was that maybe this mechanism that structures selfish behavior – eating – was co-opted during social evolution to structure social behavior – that is, altruistic behavior,” he said. “So if you’re selfish and you’re jacked up on octopamine, you eat more, but if you’re altruistic you don’t eat more but you tell others about it so they can also eat.”
But it was not even known if insects have a bona fide reward system. That question led the researchers to study the effects of cocaine on honey bee behavior. Cocaine – a chemical used by the coca plant to defend itself from leaf-eating insects – interferes with octopamine transit in insect brains and has undeniable effects on reward systems in mammals, including humans. It does this by influencing the chemically related dopamine system.
Dopamine plays a role in the human ability to predict and respond to pleasure or reward. It is also important to motor function and modulates many other functions, including cognition, sleep, mood, attention and learning.
One aspect of reward in the human brain involves altruistic behavior, Robinson said. Thinking about or performing an altruistic act has been found to excite the pleasure centers of the human brain.
“There are various lines of thought that indicate that one way of structuring society is to have altruistic behavior be pleasurable,” he said.
Because cocaine causes honey bees to dance more – an altruistic behavior – the researchers believe their results support the idea that there is a reward system in the insect brain, something that has never before been shown.

To determine whether the cocaine was merely causing the bees to move more or to dance at inappropriate times or places, the researchers conducted a second set of experiments. These tests showed that non-foraging honey bees don’t dance, even when exposed to cocaine. They showed that foragers on cocaine do not move more than other bees (except when dancing), and that they do not dance at inappropriate times or in locations other than the dance floor.
The researchers also found that the bees on cocaine do not dance every time they go on a foraging excursion. And, most important, their dances are not distorted.
“It’s not like they’re gyrating wildly on the dance floor out of control,” Robinson said. “This is a patterned response. It gives distance information, location information. That information is intact.”
In a final experiment that also shows parallels to human behavior, the researchers found that honey bees on cocaine experience withdrawal symptoms when the drug is withheld.
“This study provides strong support for the idea that bees have a reward system, that it’s been co-opted and it’s now involved in a social behavior, which motivates them to tell their hive mates about the food that they’ve found,” Robinson said.

Read the whole thing….

New and Exciting in PLoS ONE

What a Christmas present – there are 32 new articles in PLoS ONE today and they are amazing! As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Norepinephrine Controls Both Torpor Initiation and Emergence via Distinct Mechanisms in the Mouse:

Some mammals, including laboratory mice, enter torpor in response to food deprivation, and leptin can attenuate these bouts of torpor. We previously showed that dopamine β-hydroxylase knockout (Dbh −/−) mice, which lack norepinephrine (NE), do not reduce circulating leptin upon fasting nor do they enter torpor. To test whether the onset of torpor in mice during a fast requires a NE-mediated reduction in circulating leptin, double mutant mice deficient in both leptin (ob/ob) and DBH (DBL MUT) were generated. Upon fasting, control and ob/ob mice entered torpor as assessed by telemetric core Tb acquisition. While fasting failed to induce torpor in Dbh −/− mice, leptin deficiency bypassed the requirement for NE, as DBL MUT mice readily entered torpor upon fasting. These data indicate that sympathetic activation of white fat and suppression of leptin is required for the onset of torpor in the mouse. Emergence from torpor was severely retarded in DBL MUT mice, revealing a novel, leptin-independent role for NE in torpor recovery. This phenotype was mimicked by administration of a β3 adrenergic receptor antagonist to control mice during a torpor bout. Hence, NE signaling via β3 adrenergic receptors presumably in brown fat is the first neurotransmitter-receptor system identified that is required for normal recovery from torpor.

Gaze Strategy in the Free Flying Zebra Finch (Taeniopygia guttata):

Fast moving animals depend on cues derived from the optic flow on their retina. Optic flow from translational locomotion includes information about the three-dimensional composition of the environment, while optic flow experienced during a rotational self motion does not. Thus, a saccadic gaze strategy that segregates rotations from translational movements during locomotion will facilitate extraction of spatial information from the visual input. We analysed whether birds use such a strategy by highspeed video recording zebra finches from two directions during an obstacle avoidance task. Each frame of the recording was examined to derive position and orientation of the beak in three-dimensional space. The data show that in all flights the head orientation was shifted in a saccadic fashion and was kept straight between saccades. Therefore, birds use a gaze strategy that actively stabilizes their gaze during translation to simplify optic flow based navigation. This is the first evidence of birds actively optimizing optic flow during flight.

Neanderthal Extinction by Competitive Exclusion:

Despite a long history of investigation, considerable debate revolves around whether Neanderthals became extinct because of climate change or competition with anatomically modern humans (AMH). We apply a new methodology integrating archaeological and chronological data with high-resolution paleoclimatic simulations to define eco-cultural niches associated with Neanderthal and AMH adaptive systems during alternating cold and mild phases of Marine Isotope Stage 3. Our results indicate that Neanderthals and AMH exploited similar niches, and may have continued to do so in the absence of contact. The southerly contraction of Neanderthal range in southwestern Europe during Greenland Interstadial 8 was not due to climate change or a change in adaptation, but rather concurrent AMH geographic expansion appears to have produced competition that led to Neanderthal extinction.

Male Weaponry in a Fighting Cricket:

Sexually selected male weaponry is widespread in nature. Despite being model systems for the study of male aggression in Western science and for cricket fights in Chinese culture, field crickets (Orthoptera, Gryllidae, Gryllinae) are not known to possess sexually dimorphic weaponry. In a wild population of the fall field cricket, Gryllus pennsylvanicus, we report sexual dimorphism in head size as well as the size of mouthparts, both of which are used when aggressive contests between males escalate to physical combat. Male G. pennsylvanicus have larger heads, maxillae and mandibles than females when controlling for pronotum length. We conducted two experiments to test the hypothesis that relatively larger weaponry conveys an advantage to males in aggressive contests. Pairs of males were selected for differences in head size and consequently were different in the size of maxillae and mandibles. In the first experiment, males were closely matched for body size (pronotum length), and in the second, they were matched for body mass. Males with proportionately larger weaponry won more fights and increasing differences in weaponry size between males increased the fighting success of the male with the larger weaponry. This was particularly true when contests escalated to grappling, the most intense level of aggression. However, neither contest duration nor intensity was related to weaponry size as predicted by models of contest settlement. These results are the first evidence that the size of the head capsule and mouthparts are under positive selection via male-male competition in field crickets, and validate 800-year-old Chinese traditional knowledge.

Wind, Waves, and Wing Loading: Morphological Specialization May Limit Range Expansion of Endangered Albatrosses:

Among the varied adaptations for avian flight, the morphological traits allowing large-bodied albatrosses to capitalize on wind and wave energy for efficient long-distance flight are unparalleled. Consequently, the biogeographic distribution of most albatrosses is limited to the windiest oceanic regions on earth; however, exceptions exist. Species breeding in the North and Central Pacific Ocean (Phoebastria spp.) inhabit regions of lower wind speed and wave height than southern hemisphere genera, and have large intrageneric variation in body size and aerodynamic performance. Here, we test the hypothesis that regional wind and wave regimes explain observed differences in Phoebastria albatross morphology and we compare their aerodynamic performance to representatives from the other three genera of this globally distributed avian family. In the North and Central Pacific, two species (short-tailed P. albatrus and waved P. irrorata) are markedly larger, yet have the smallest breeding ranges near highly productive coastal upwelling systems. Short-tailed albatrosses, however, have 60% higher wing loading (weight per area of lift) compared to waved albatrosses. Indeed, calculated aerodynamic performance of waved albatrosses, the only tropical albatross species, is more similar to those of their smaller congeners (black-footed P. nigripes and Laysan P. immutabilis), which have relatively low wing loading and much larger foraging ranges that include central oceanic gyres of relatively low productivity. Globally, the aerodynamic performance of short-tailed and waved albatrosses are most anomalous for their body sizes, yet consistent with wind regimes within their breeding season foraging ranges. Our results are the first to integrate global wind and wave patterns with albatross aerodynamics, thereby identifying morphological specialization that may explain limited breeding ranges of two endangered albatross species. These results are further relevant to understanding past and potentially predicting future distributional limits of albatrosses globally, particularly with respect to climate change effects on basin-scale and regional wind fields.

Lions and Prions and Deer Demise:

Contagious prion diseases – scrapie of sheep and chronic wasting disease of several species in the deer family – give rise to epidemics that seem capable of compromising host population viability. Despite this prospect, the ecological consequences of prion disease epidemics in natural populations have received little consideration. Using a cohort study design, we found that prion infection dramatically lowered survival of free-ranging adult (>2-year-old) mule deer (Odocoileus hemionus): estimated average life expectancy was 5.2 additional years for uninfected deer but only 1.6 additional years for infected deer. Prion infection also increased nearly fourfold the rate of mountain lions (Puma concolor) preying on deer, suggesting that epidemics may alter predator-prey dynamics by facilitating hunting success. Despite selective predation, about one fourth of the adult deer we sampled were infected. High prevalence and low survival of infected deer provided a plausible explanation for the marked decline in this deer population since the 1980s. Remarkably high infection rates sustained in the face of intense predation show that even seemingly complete ecosystems may offer little resistance to the spread and persistence of contagious prion diseases. Moreover, the depression of infected populations may lead to local imbalances in food webs and nutrient cycling in ecosystems in which deer are important herbivores.

Effectiveness of Action to Reduce Exposure of Free-Ranging California Condors in Arizona and Utah to Lead from Spent Ammunition:

California condors (Gymnogyps californianus) released into the wild in Arizona ranged widely in Arizona and Utah. Previous studies have shown that the blood lead concentrations of many of the birds rise because of ingestion of spent lead ammunition. Condors were routinely recaptured and treated to reduce their lead levels as necessary but, even so, several died from lead poisoning. We used tracking data from VHF and satellite tags, together with the results of routine testing of blood lead concentrations, to estimate daily changes in blood lead level in relation to the location of each bird. The mean daily increment in blood lead concentration depended upon both the location of the bird and the time of year. Birds that spent time during the deer hunting season in two areas in which deer were shot with lead ammunition (Kaibab Plateau (Arizona) and Zion (Utah)) were especially likely to have high blood lead levels. The influence upon blood lead level of presence in a particular area declined with time elapsed since the bird was last there. We estimated the daily blood lead level for each bird and its influence upon daily mortality rate from lead poisoning. Condors with high blood lead over a protracted period were much more likely to die than birds with low blood lead or short-term elevation. We simulated the effect of ending the existing lead exposure reduction measures at Kaibab Plateau, which encourage the voluntary use of non-lead ammunition and removal of gut piles of deer and elk killed using lead ammunition. The estimated mortality rate due to lead in the absence of this program was sufficiently high that the condor population would be expected to decline rapidly. The extension of the existing lead reduction program to cover Zion (Utah), as well as the Kaibab plateau, would be expected to reduce mortality caused by lead substantially and allow the condor population to increase.

Harmonic Allocation of Authorship Credit: Source-Level Correction of Bibliometric Bias Assures Accurate Publication and Citation Analysis:

Authorship credit for multi-authored scientific publications is routinely allocated either by issuing full publication credit repeatedly to all coauthors, or by dividing one credit equally among all coauthors. The ensuing inflationary and equalizing biases distort derived bibliometric measures of merit by systematically benefiting secondary authors at the expense of primary authors. Here I show how harmonic counting, which allocates credit according to authorship rank and the number of coauthors, provides simultaneous source-level correction for both biases as well as accommodating further decoding of byline information. I also demonstrate large and erratic effects of counting bias on the original h-index, and show how the harmonic version of the h-index provides unbiased bibliometric ranking of scientific merit while retaining the original’s essential simplicity, transparency and intended fairness. Harmonic decoding of byline information resolves the conundrum of authorship credit allocation by providing a simple recipe for source-level correction of inflationary and equalizing bias. Harmonic counting could also offer unrivalled accuracy in automated assessments of scientific productivity, impact and achievement.

Keep Your Options Open: An Information-Based Driving Principle for Sensorimotor Systems:

The central resource processed by the sensorimotor system of an organism is information. We propose an information-based quantity that allows one to characterize the efficiency of the perception-action loop of an abstract organism model. It measures the potential of the organism to imprint information on the environment via its actuators in a way that can be recaptured by its sensors, essentially quantifying the options available and visible to the organism. Various scenarios suggest that such a quantity could identify the preferred direction of evolution or adaptation of the sensorimotor loop of organisms.

Evidence of Repeated and Independent Saltational Evolution in a Peculiar Genus of Sphinx Moths (Proserpinus: Sphingidae):

Saltational evolution in which a particular lineage undergoes relatively rapid, significant, and unparalleled change as compared with its closest relatives is rarely invoked as an alternative model to the dominant paradigm of gradualistic evolution. Identifying saltational events is an important first-step in assessing the importance of this discontinuous model in generating evolutionary novelty. We offer evidence for three independent instances of saltational evolution in a charismatic moth genus with only eight species. Maximum parsimony, maximum likelihood and Bayesian search criteria offered congruent, well supported phylogenies based on 1,965 base pairs of DNA sequence using the mitochondrial gene cytochrome oxidase subunit I, and the nuclear genes elongation factor-1 alpha and wingless. Using a comparative methods approach, we examined three taxa exhibiting novelty in the form of Batesian mimicry, host plant shift, and dramatic physiological differences in light of the phylogenetic data. All three traits appear to have evolved relatively rapidly and independently in three different species of Proserpinus. Each saltational species exhibits a markedly different and discrete example of discontinuous trait evolution while remaining canalized for other typical traits shared by the rest of the genus. All three saltational taxa show insignificantly different levels of overall genetic change as compared with their congeners, implying that their divergence is targeted to particular traits and not genome-wide. Such rapid evolution of novel traits in individual species suggests that the pace of evolution can be quick, dramatic, and isolated–even on the species level. These results may be applicable to other groups in which specific taxa have generated pronounced evolutionary novelty. Genetic mechanisms and methods for assessing such relatively rapid changes are postulated.

Long-Term Cycles in the History of Life: Periodic Biodiversity in the Paleobiology Database:

Time series analysis of fossil biodiversity of marine invertebrates in the Paleobiology Database (PBDB) shows a significant periodicity at approximately 63 My, in agreement with previous analyses based on the Sepkoski database. I discuss how this result did not appear in a previous analysis of the PBDB. The existence of the 63 My periodicity, despite very different treatment of systematic error in both PBDB and Sepkoski databases strongly argues for consideration of its reality in the fossil record. Cross-spectral analysis of the two datasets finds that a 62 My periodicity coincides in phase by 1.6 My, equivalent to better than the errors in either measurement. Consequently, the two data sets not only contain the same strong periodicity, but its peaks and valleys closely correspond in time. Two other spectral peaks appear in the PBDB analysis, but appear to be artifacts associated with detrending and with the increased interval length. Sampling-standardization procedures implemented by the PBDB collaboration suggest that the signal is not an artifact of sampling bias. Further work should focus on finding the cause of the 62 My periodicity.

Looking for Myself: Current Multisensory Input Alters Self-Face Recognition:

How do I know the person I see in the mirror is really me? Is it because I know the person simply looks like me, or is it because the mirror reflection moves when I move, and I see it being touched when I feel touch myself? Studies of face-recognition suggest that visual recognition of stored visual features inform self-face recognition. In contrast, body-recognition studies conclude that multisensory integration is the main cue to selfhood. The present study investigates for the first time the specific contribution of current multisensory input for self-face recognition. Participants were stroked on their face while they were looking at a morphed face being touched in synchrony or asynchrony. Before and after the visuo-tactile stimulation participants performed a self-recognition task. The results show that multisensory signals have a significant effect on self-face recognition. Synchronous tactile stimulation while watching another person’s face being similarly touched produced a bias in recognizing one’s own face, in the direction of the other person included in the representation of one’s own face. Multisensory integration can update cognitive representations of one’s body, such as the sense of ownership. The present study extends this converging evidence by showing that the correlation of synchronous multisensory signals also updates the representation of one’s face. The face is a key feature of our identity, but at the same time is a source of rich multisensory experiences used to maintain or update self-representations.

…and many more. Enjoy the feast!

Yugo Transformers (video)

It’s hard to tell which one is the original, I think it’s this one, as YouTube is full of well-done parodies of the Citroen Tranformers commercial. Of course, I am partial to this one:

Today’s carnivals

Four Stone Hearth #26 is up on The Greenbelt
Carnival of Space Week #84 is up on Next Big Future
Grand Rounds 5.14 are up on Highlight HEALTH

My picks from ScienceDaily

Continue reading

Clock Quotes

The invention of the teenager was a mistake, in Miss Manners’ opinion…. Once you identify a period of life in which people have few restrictions and, at the same time, few responsibilities – they get to stay out late but don’t have to pay taxes – naturally, nobody wants to live any other way.
– Judith Martin

War on Christmas? Ho-ho-ho!

There is no clearer and better example of Artificial controversy than the War on Christmas, as Bill O’Reilly and Sean Hannity re-invent it every year in order to boost their tanking ratings. What War on Christmas? Just drive along a street and see all the lights on houses, go into a store and look at the merchandise while listening to the Christmas music, peer into people’s windows to see decorated Christmas trees and presents, or turn on any radio station – Christmas is everywhere.
But, believe it or not, there are people who are even stupider than O’Reilly and Hannity – people who really want to ban Christmas! Who? The Bosnian education authorities:

“Is Santa Clause a religious figure? He doesn’t wear anything religious (maybe only a funny hat like the Pope). He is dressed in red – probably a communist, in which case it’s safe to say he’s not that religious. He is fat and round just like Buddah, but I guess that’s probably the consequence of a reindeer meat diet and too much coke.
—————-
By banning the Santa, people from the Bosnian education authorities who did this proved that ultra-nationalists from all three sides in Bosnia – Croatian, Serbian and Bosniak, have two things in common – 1. they all really, really hate Santa, and 2. they are all really, really stupid. This ban would probably not last thanks to the outrage it caused among normal people in Bosnia and the decision will probably be reversed, just like after that Darwin ban situation in Serbia some time ago.”

New and Exciting in PLoS this week

Lots of cool new papers in PLoS Biology, PLoS Medicine and PLoS Neglected Tropical Diseases today. My picks are under the fold, but you look around and see what you are interested in:

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New and Exciting in PLoS ONE

There are 12 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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I’m Keeping Kosher for Christmas (video)


Hat-tip: Mom

Today’s carnivals

Encephalon #61: Brain & Mind Reading for the Holidays is up on SharpBrains
Friday Ark #222 is up on Modulator
159th edition of the Carnival of The Green is up on Lighter Footstep

My picks from ScienceDaily

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Clock Quotes

A little inaccuracy sometimes saves tons of explanation.
– Hector Hugh Munro (1870-1916)

The Shock Value of Science Blogs

There was a good reason why the form and format, as well as the rhetoric of the scientific paper were instituted the way they were back in the early days of scientific journals. Science was trying to come on its own and to differentiate itself from philosophy, theology and lay literature about nature. It was essential to develop a style of writing that is impersonal, precise, sharply separating data from speculations, and that lends itself to replication of experiments.
The form and format of a scientific paper has evolved towards a very precise and very universal state that makes scientist-to-scientist communication flawless. And that is how it should be, and at least some elements of style and form (if not format) will remain once the scientific paper breaks down spatially and temporally and becomes a dynamic ongoing communication – clarity and precision will always be important.
But that is strictly technical communication between scientists in the same research field. How about communication between scientists in far-away fields, between scientists and lay audience, or among the educated lay-people? How about communication between scientific colleagues outside of peer-reviewed papers? This is where we are seeing the biggest changes right now and not everyone’s happy. And the debate is reminiscent of the debate in mainstream journalism.
Until pretty recently, the informal communication between scientists was limited to Letters To The Editor of scientific journals, conferences and invited seminars. In all three of those venues, the formal rhetoric of science remained. Fine, but….
Part of training in the academia is training in rhetoric. As you go up the ladder of academic science, you are evaluated not just by the quality of your research (or teaching, in some places), but also in how well you mastered the formalized kabuki dance of the use of Scientese language. The mastery of Scientese makes one part of the Inside club. It makes one identifiable as the Member of this club. The Barbarians at the Gate are recognizable by their lack of such mastery – or by refusal to use it. And it is essential for the Inside Club to make sure that the Barbarians remain at the Gate and are never allowed inside.
Academic science is a very hierarchical structure in which one climbs up the ladder by following some very exact steps. Yes, you can come into it from the outside, class-wise, but you have to start from the bottom and follow those steps “to the T” if you are to succeed. But those formal steps were designed by Victorian gentlemen scientists, thus following those steps turns one into a present-time Victorian gentleman scientist. But not everyone can or wants to do this, yet some people who refuse are just as good as scientists as the folks inside the club. If you refuse to dance the kabuki, you will be forever kept outside the Gate.
The importance of mastery of kabuki in one’s rise through the hierarchy also means that some people get to the top due to their skills at glad-handling the superiors and putting down the competitors with formalized language, not the quality of their research or creativity of their thought. Those who rose to the top due to being good at playing the game know, deep inside, they do not deserve that high position on merit alone. And they will be the loudest defenders of the system as it has historically been – they know if the changes happen, and people get re-evaluated for merit again, they will be the first to fall. This is the case in every area (mainstream journalism, business, politics, etc.), not just academic science.
Insistence on using the formalized kabuki dance in science communication is the way to keep the power relations intact. Saying “don’t be angry” is the code for “use the rhetoric at which I excel so I can destroy you more easily and protect my own spot in the hierarchy”. It is an invitation to the formal turf, where those on the inside have power over those who cannot or will not use the kabuki dance. This has always been the way to keep women, minorities and people from developing countries outside the club, waiting outside the Gate. If, for reasons of your gender, race, nationality or class you are uncomfortable doing the kabuki dance, every time you enter the kabuki contest you will lose and the insider will win. The same applies outside science, e.g., to mainstream journalism and politics.
This is why some people in the academic community rant loudly against science bloggers. If they cannot control the rhetoric, they fear, often rightly, that they will lose. Outside their own turf, they feel vulnerable. And that is a Good Thing.
The debates about “proper” language exist on science blogs themselves. See this and this for recent examples (the very best discussion was on this post which is now mysteriously missing). In response I wrote:

We here at Sb are often accused of being cliquish and insular. But if you look at our 70+ blogs and dig through the archives, you will see that we rarely comment on each other’s blogs – most (99%?) of the comments come from outside readers. Also, most of our links point to outside of Sb. On the other hand, NN [Nature Network] is specifically designed to be a community (not a platform for independent players) and almost all of the comments there are from each other. Thus, it is easy for them to maintain a high level of politeness there (this is not a bad thing – this is how they designed it on purpose). It is much harder to harness the hordes of pharyngulites that spill over to all of our blogs – and I do not mind them at all, I think they make the debate spirited and in a way more honest by bypassing superficial niceness and going straight to the point. This may also have something to do with NN bloggers mainly being in the academia, while a large proportion of SciBlings are ex-academia, journalists, artists, etc. with a different rhetoric. The rhetoric of academia is a very formalized kabuki dance, while the rhetoric of the blogosphere has shed all formalities and is much more reminiscent to the regular everyday oral conversation.

Remember the Roosevelts on Toilets saga? The biggest point of contention was the suggestion by the authors of the paper to the bloggers to move the discussion away from blogs to a more formal arena of letters to the editor. We, the bloggers, fiercely resisted this, for the reasons I spelled above – in the letters to the editor, the Insiders have power over the Outsiders because it is their turf. No, if we want to have a non-kabuki, honest discussion, we will have it out here on the blogs, using our rhetoric, because the honest language of the modern Web places everyone on the even ground – it does not matter who you are, what degrees you have, or how well you’ve learned to dance the kabuki: it is what you say, the substance, that counts. This is why being pseudonymous online works, while academia requires full names and degrees. The Web evaluates you directly, by what you write. The academia uses “tags” – your name and degree – to evaluate you. The academia is in the business of issuing credentials, the stand-ins for quality. The credentials are rough approximations of quality – more often then not they work fine, but they are not 100% foolproof. And if one is insecure about one’s own quality, one would insist on using credentials instead of quality. The use of “proper” rhetoric is, as I said above, a good quick-and-dirty way to recognize credentials.
During the Roosevelt saga, I wrote this post very, very carefully, with a specific purpose in mind. First, I went to great effort to explain the science at length and as simply, clearly and conclusively as possible. This performed several functions for me: first, to establish my own credentials, second, to make my readers understand the science and thus be on “my side” in the comments, and third, to make sure I was as complete about science as possible so as to not have to talk about science at all in the comments. Apart from science, I also included several snarky comments about the authors which served as bait – I wanted them to come and post comments. And they bit. Go read the comment thread there to see what was happening. The author insisted on discussing science. I insisted on refusing to talk about science (to him, I did respond a little bit to some other commenters) and to talk about rhetoric instead.
But first, in a comment I posted even before the authors showed up, in order to set the stage for what I wanted, I wrote this:

In an earlier post, burried deep inside, is this thought of mine:

The division of scientists into two camps as to understanding of the Web is obvious in the commentary on PLoS ONE articles (which is my job to monitor closely). Some scientists, usually themselves bloggers, treat the commentary space as a virtual conference – a place where real-time oral communication is written down for the sake of historical record. Their comments are short, blunt and to the point. Others write long treatises with lists of references. Even if their conclusions are negative, they are very polite about it (and very sensitive when on the receiving end of criticism). The former regard the latter as dishonest and thin-skinned. The latter see the former as rude and untrustworthy (just like in journalism). In the future, the two styles will fuse – the conversation will speed up and the comments will get shorter, but will still retain the sense of mutual respect (i.e., unlike on political blogs, nobody will be called an ‘idiot’ routinely). It is important to educate the users that the commentary space on TOPAZ-based journals is not a place for op-eds, neither it is a blog, but a record of conversations that are likely to be happening in the hallways at conferences, at lab meetings and journal clubs, preserved for posterity for the edification of students, scientists and historians of the future.

What happened on Dr.Isis’ blog is very similar – a clash of two cultures. I think that the picture of the Teddy Bear on the potty was a clever and funny shorthand for your point. If you did it about something I published, I’d laugh my ass off. But I can see how the uptight strain of the scientists would balk at it. It is them, though, who need to get up to speed on the changed rhetoric of science. The straight-laced, uber-formal way of writing in science is on its way out.
The rhetoric, even after it completely modernizes, will still have four concentric circles: the paper itself will always be more formal, especially the Materials/Methods and Results sections due to the need for precision; the letters to the editor will remain pretty formal, but not as formal as they are now; the comments on the paper itself will be still less formal but still polite; the commentary on the trackbacked blogs will be freewheeling, funny and to-the-point, just like yours was, not mealy-mouthing with politeness on the surface and destructive hatred underneath, but honest and straightforward. So, if it is crap, what better way to say it than with a picture of a Teddy Bear on a potty – much more lighthearted and polite than saying it politely, and less devastating for the paper’s authors as it takes their mistake lightly instead of trying to destroy their reputation forever.
The point that both Dr.Isis and I made is that the paper is neat, experimental method sound, data are good, but the interpretation is crap. Now, having a couple of crappy paragraphs in an otherwise good paper is not the end of the world. A paper is not some kind of granite monument with The Truth writ in stone. It is becoming a living document (with comments on the paper and tracbacked blogs), and it has always been a part of a greater living document – the complete literature of a field. That is how science works.
It is hard to know which paper will persist and which one will perish in the future, what sentence will turn out to be a gem of prophetic wisdom, and which one is crap. People publish a lot of stuff, some better than other.
Making a mistake in one paper is not the end of one’s career. But many people perceive criticism as if they are just about to be sent out to join a leper colony. This is, in part, due to the formal rhetoric of science: outwardly polite, but underneath it is an attempt to destroy the person. In comparison, a light-hearted joke with a Teddy Bear acknowledges the failability of humans, allows for everyone to make a mistake and move on (we all shit, don’t we?). It is actually much more normal, and much less dangerous for one’s career to receive such a funny form of criticism than a formal-looking destruction of all our work and our personna.

In the next comment I did the one and only hat-tip to science, then moved onto the territory I wanted – rhetoric (many comments, so go and read them all now). As a result, Dr. Janszky grokked it – and we’ll probably see more of him in the blogosphere in the future. The reason he grokked it is because he is confident in his own qualities – he can change the rhetoric and tone and still not lose the debate because he knows what he’s talking about. Those who know they do not have the quality, would just have ranted harder and harder, complaining about the tone. Dr. Janszky adopted the bloggy tone in the comments right then and there. Which was a victory for everybody.
The informal rhetoric of blogs is a form of subversion – breaking the Gate and letting the Barbarians in (while not allowing quacks and Creationist to hitch a ride inside as well – which is why so many science bloggers focus on those potential free-riders and parasites). What we are doing is leveling the playing field, pointing out the inherent dishonesty of the formalized rhetoric, and calling a space a spade. This is a way to make sure that smart, thoughtful people get heard even if they did not have a traditional career trajectory, or refuse to play the Inside club games. If some of the insiders fall down in the process, that’s a good thing – they probably did not deserve to be up in the first place.
Different bloggers do this in different ways. We can use a brilliant, but snarky use of English (PZ Myers), or texting/LOLCat snark (Abbie), or awe and reverence for the great scientists of old (Mo), or sexual innuendo (SciCurious), or shoes (Dr.Isis), or a light-hearted sense of humor (Ed or Darren), or excessive use of profanity (PhysioProf). What we all do is write in unusual, informal ways. We want to shock. We feel there are many people out there who need a jolt, an injection of reality. We do it by using informal language. And this can be very powerful – just see how the dinosaurs squirm when they read some of our posts! But that’s the point. We are testing them: if, like Dr. Janszky, you “get it”, this means that you have the balls, which means you are confident about your own qualities independent from your credentials. If you keep ranting about “dirty, angry bloggers”….what are you so insecure about? Why are you so afraid of being shown a fraud if you are not? Or, are you?
Another point about blogs, which I alluded above already, is the time-frame. This is a very important point that is often forgotten in the scientists vs. bloggers “let’s be polite” debates. In the formal arenas (Letters, conferences, etc.), where formal language is used, the game some people play is to use an outwardly seemingly polite language to write or say something that is designed to destroy a career. Often in multiple places over a stretch of time. On blogs, when we snarkily attack you, our purpose is to teach a lesson (more to our readers than the scientists in question who may not even know the blog post was written). In other words, it is a one-time thing that is designed to correct a single error, not an attempt at destroying a career.
For good recent examples of the way scientists use the formal venues as well as formal language to destroy each other, see this and this (I have seen more on PLoS ONE, but don’t want to draw your attention to those right now, for professional reasons – keeping my job).
I post 8.2 posts per day on this blog, on a large variety of topics. Do you really think I have the time, energy and interest to study in great detail the life-time achievements of everyone who did something wrong on the Internet? Of course not. I see an article that says something stupid and I shoot a post that shows how stupid it is, so the readers, especially if the deconstruction of stupidity requires some expertise I may have and most people don’t, can see why that particular argument is wrong. Then I move on to the next post on some completely different topic. I have forgotten about your existence in about a nanosecond after publishing that post. I have no interest in destroying your career, but I understand that you are touchy – the life in academia, with its poisonous kabuki game, has trained you to defend yourself against every single little criticism because, underneath the veneer of civility is the career-damaging attack by someone powerful who is hell-bent on destroying you. We don’t do that on blogs. We don’t care enough to do that (unless you are a dangerous peddler of pseudoscience or medical quackery). We want to educate the lay audience and have fun doing it. I have no idea if everything else you have written before and after is brilliant and I don’t care – I think that this one stupid paragraph you wrote is good blogging material, amusing, edifying and useful to use to educate the lay audience. You are NOT the target personally. Your stupid argument is. And I don’t care if that was your one-off singular mistake in life, or an unusually bad moment for you. So, don’t take it personally. This is not academia. We are, actually, honest here on the intertubes, and you need to learn to trust us.
The attempts at character assassinations within academia, by using the formalized kabuki language by the powerful and forcing the powerless to adopt the same and thus be brought to slaughter, do not happen only in print. They also happen in person. Read this and this for a recent example of a senior researcher trying to publicly destroy a younger, female colleague at a meeting. And he was wrong. But he was powerful and intimidating. I wish the young woman responded by going outside of formal kabuki dance, shocking the audience in one way or another, giving all the present colleagues a jolt, making them listen and perhaps notice what is happening. Or, if she was shy, I wish some senior male colleague did the same for her and put the old geezer in his place. I wrote a comment:

“Tone it down” and “Why are you so angry?” are typical sleazy tactics used by a person in power over a person not in power. It was used against people of other races, against women, against gays, against atheists – this is the way to make their greivances silent and perpetuate the status quo, the power structure in which they are on the top of the pecking order. The entire formal, convoluted, Victorian-proper discourse one is supposed to use in science is geared towards protecting the current power structure and the system that perpetuates it. Keeping the dissenters down and out. Bur sometimes, anger, or snark, or direct insult, are the jolt that the system needs and it will have to come from the people outside the power structure, and it would have to occur often and intensely until they start paying attention.

And then, there is the area in between scientists and lay audience. The job of translating Scientese into English (or whatever is the local language) has traditionally been done by professional science journalists. Unfortunately, most science journalists (hats off to the rare and excellent exceptions) are absolutely awful about it. They have learned the journalistic tools, but have no background in science. They think they are educated, but they only really know how to use the language to appear they are educated. Fortunately for everyone, the Web is allowing scientists to speak directly to the public, bypassing, marginalizing and pushing into extinction the entire class of science “journalists” because, after all, most scientists are excellent communicators. And those who are, more and more are starting to use blogs as a platform for such communication.
The problem is, the professional science journalists also love to put down the blogs and use the paternalistic “tone it down” argument. But, unlike the political journalists who are incapable of seeing the obvious (stuck too far inside Cheney’s rectum to see what we all could see?), the science journalists have the added problem of not having the expertise for their job in the first place. In politics, everyone with the brain, not just journalists, could see that excuses for going to Iraq were lame. But in science journalism, there exist out there people with real expertise – the scientists themselves – who now have the tools and means to bypass you and make you obsolete because you cannot add any value any more.
To the list that includes MSM “journalists” aka curmudgeouns like Richard Cohen, Sarah Boxer, Andrew Keen, Lee Siegel, Michael Skube, Neil Henry and many others, we can now add curmudgeounly science journalists George Johnson and John Horgan as well – just listen to this!!!!! Yes go an listen before you come back. If you can stand it. But if I suffered through it, you can, too. I am a pretty calm kind of guy, but listening to that “dialogue” filled me with rage – I felt insulted, my intelligence insulted, and my friends insulted. Frankly, I’ve heard smarter science-related conversations from the drunks in rural Serbian bars.
I’ve been in this business (both science and science communication) for a long time, but I have never heard of George Johnson until today. From what I saw in that clip, I have not missed anything. Where does his smugness come from then? As for John Horgan, I’ve heard of him – he earned his infamy when he published – and was instantly skewered and laughed at by anyone with brains – his book “The End of Science”, arguably one of the worst and most misguided books about science (outside of Creationist screeds) ever. Where is his humbleness after such a disaster? Why is he not hiding in the closet, but instead shows up in public and appears – smug. Some people just have no self-awareness how stupid they appear when they behave as if they have authority yet they don’t and it’s obvious. What is it about professional journalists that makes them have illusions they are educated? “No, I am not a scholar but I play one on TV” turns into “Since I can transcribe and read smart stuff I must be really smart myself”.
Luckily, bloggers have no qualms about defending themselves – please read this gorgeous smack-down by Abbie, this older post by Ed in which he explains exactly what he meant, and perhaps this old post of mine which also, in a circuitous way, predicts the extinction of science journalistic dinosaurs.
But perhaps I shouldn’t be that nasty to Johnson and Horgan? After all, my blogging schtick is niceness. This makes it very easy for me to destroy someone – on those rare occasions when someone like me, renowned for endless patience, flies off the handle, people sit up and pay attention. If I use profanity to describe someone, that one probably richly deserves it. I know I have to use this power with prudence. If I attack someone full-blast, people will tend to believe me, as I rarely do that kind of stuff. And if you subsequently Google that name, my blogpost about him/her is likely to be the #1 hit on the search, or in the top ten.
Perhaps Johnson and Horgan are actually nice and smart guys. They may be nice to their wives and kids. Perhaps they wrote, 30 years ago, something really smart. But I have no interest in digging around for that. I want to finish this post and move on. And after watching this movie, I really have no motivation to search for anything else by these two guys as it appears to be a waste of my time. It does not appear to me like a bad-day, one-off mistake that everyone sometimes makes. It is 30 minutes of amazing ignorance and arrogance at display – probably sufficient material to make me doubt I’d ever find anything smart penned by them in the past, so why should I bother with them at all? I can probably evaluate their qualifications quite accurately from these 30 minutes and safely conclude they equal zero. Their “angry bloggers” shtick was the first give-away they know deep inside they are irrelevant and on their way out. Their subsequent chat about science was amateurish at best, no matter how smug their facial expressions at the time.
Perhaps if we remove those middle-men and have scientists and the public start talking to each other directly, then we will have the two groups start talking to each other openly, honestly and in an informal language that is non-threatening (and understood as such) by all. The two sides can engage and learn from each other. The people who write ignorant, over-hyping articles, the kinds we bloggers love to debunk (by being able to compare to the actual papers because we have the background) are just making the entire business of science communication muddled and wrong. Please step aside.
Update: Brian, Greg, Ed, Dr.Isis, Mike Brotherton, Hank and Larry chime in on this discussion as well. More: Alex, Chris Mooney, Mike, Chad, Eric Wolff, Stephanie and Tom Levenson, Sabine and Tom again.

Joan Baez – Diamonds and Rust

My picks from ScienceDaily

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Clock Quotes

Anytime I’ve gone to a movie for a first date, it’s been bad.
– Tom Everett Scott

Education 2.0

At the Western RCAC Symposium last week:
Rodd Lucier: Fertilizing the Grass Roots:

My personal suspicions are that most attendees will fail to make effective use of any of the many tools introduced today. Even with everyone recognizing that we have a long way to go: A significant knowing-doing gap will remain!

David Warlick: So Now What Do We Do?:

Then Rodd listed some comments that he overheard during the conference, that support his concern. I’m listing them here and will try to make some suggestions that may be useful. My suggestions are indented just a bit to better distinguish them from the overheard statements.

Doug Pete: How I Saw It:

David Warlick went first with his presentation “Our Students – Our Worlds”. Eyes were opened for many as David took us inside the minds and lives of today’s youth. His famous tentacles diagram affirmed that students aren’t “human” by a traditional view! It does drive home the message that they are indeed connected at levels that we suspect but don’t totally know. (at least until the texting bill comes in…) Rather than ask folks to turn off electronic devices, David let me know before the event that he would welcome a back channel through his presentation. Gulp! What to do?

Amber MacArthur: Talking about social media – A year on the road:

But what I’ve realized over time is that it’s critical for me to update my slides based on the audience that will sit in front of me. Sounds like a pretty obvious concept, one that becomes more apparent over time (also, in the web world, trends change too quickly to rely on one deck). Since I’ve spoken to such varied groups, from teams of probiotic scientists, oil engineers, and all-grades educators, I strive to find specific social media examples that will be relevant to each crowd. This usually means I spend a lot of time researching new Web 2.0 trends, videos, articles, and tips online.

Community, Collaboration & Conversation with Amber MacArthur – listen to the podcast.

I’m happy about this – science is back in the U.S. government

Because the truth is that promoting science isn’t just about providing resources–it’s about protecting free and open inquiry. It’s about ensuring that facts and evidence are never twisted or obscured by politics or ideology. It’s about listening to what our scientists have to say, even when it’s inconvenient–especially when it’s inconvenient. Because the highest purpose of science is the search for knowledge, truth and a greater understanding of the world around us. That will be my goal as President of the United States–and I could not have a better team to guide me in this work.

Read the entire text.

2008 EduBlog Awards winners have been announced

It is rare that I pick the winners in any contest, but this time I picked three! Congratulations to all the winners of the 2008 EduBlog Awards, but especially to my friend David Warlick who led the session on ‘blogs in science education’ at the last year’s Science Blogging Conference, and to Miss Baker’s students who will lead a ScienceOnline09 session on Science online – middle/high school perspective (or: ‘how the Facebook generation does it’?).

Einstein was smart, but Could He Play the Violin? – the winner of the synchroblogging contest

Happy Anniversary, PLoS ONE!
Today is PLoS ONE’s second anniversary and we’re celebrating by announcing that the winner of the second PLoS synchroblogging competition is SciCurious of the Neurotopia 2.0 blog.
“This fluent post captures the essence of the research and accurately communicates it in a style that resonates with both the scientific and lay community” – Liz Allen, PLoS.
Here is the winning entry, cross posted in its entirety:
====================
Einstein was smart, but Could He Play the Violin?
I already wrote one entry for PLoS ONE’s second birthday, but I’m feeling sparky today, and I think I like this paper better.
I don’t know about you guys, but when I was a sprog, my parents dragged me to music lessons. LOTS of music lessons. As of right now, I have been producing music of some type for the past 21 years straight. And I LOVE it.
Of course, I didn’t always love it. I remember my mother dragging me and my brother to lessons, making us sit down every day and practice (I was, and still am, no good with the practicing), and the fear and shakiness of recitals (heck, I still get that, and it’s been 21 years). In her time, Sci has actually “mastered” (it’s a debatable point), three different instruments (‘instruments’ is a loose term), and still uses one of them professionally on occasion. And if you can guess what they are, Sci will…do something cool. Like send you one of her favorite books. Or perhaps a tshirt with a molecule on it. Or perhaps some of her delicious cookies. Obviously, you can only guess if you don’t KNOW already (that means you, Dad). So there you go, contest open.
Anyway, years and years of music lessons. But the question is: did they do me any good? Does playing ‘Baby Mozart’ really do anything, and is anything achieved by starting your child on Suzuki when they are 2, other than the pain and misery of your child, and possibly an eventual love of music? Can it, perhaps, make me SMARTER?
ResearchBlogging.org Forgeard et al. “Practicing a musical instrument in childhood is associated with enhanced verbal ability and nonverbal reasoning” PLoS ONE, 2008.
And for the record, Einstein did play the violin. Apparently he was quite good.
There actually are several studies out there that show that techniques that you learn can “transfer” to other techniques, giving you a bit of an edge. This works best when you’re performing skills that are very similar to each other (like learning how to estimate the area of a square, and then learning how to estimate the area of a triangle). We know this happens for musicians in the development of fine motor skills. Once you’ve been playing the violin for a while, other things that require fine motor skills will come to you a bit easier (perhaps we should train all would-be surgeons on musical instruments, if you can master playing Rachmaninoff, brain surgery should be a piece of cake).
Of course, most of the studies that have been done are correlational in nature. Kids who play musical instruments have better motor skills. This could be due to the music, or the kids could play music because they have good motor skills. Good motor skills could be a development of things like the higher socio-economic class that often goes along with being taught music as a child, and thus parents are maybe able to put more effort to their development. The possibilities go on. Correlation is NOT causation.
The same thing goes for the correlation between musical learning and IQ. There was a modest correlation, but it could be just the effect of the extra lessons the kids were receiving, resulting in more time spent on focused attention and mastering a skill. Significant correlations have also been shown for music and verbal and language skills. Music lessons have been found to be correlated with increases in reading ability and phonetic comprehension. This actually leads me to a question: if language, reading, and phonetic comprehension are related to the pitch and tone of words, do children who are tone deaf have a harder time mastering reading and verbal skills? I think this might warrant a future PubMed search.
Unfortunately, all the previous tests tended to focus on the “transfer” of skills to not very related fields, like IQ. So in this study, the authors wanted to look at the effects of music learning on “near” transfers, skill closely related to music training: spatial reasoning, verbal abilities, nonverbal, and mathematical. They also looked for VERY closely related skills: fine motor control and auditory skill.
They grabbed a whole bunch of kids around 8-11 years old. Some played musical instruments, some didn’t (one of the problems with this study to me is that the control group is a good bit small than the instrumental group, 41 musicians vs 18 non). Kids were controlled for the socio-economic class of the parents. Average length of music training was close to five years. They also divided the kids up by whether or not they got Suzuki training, but ended up grouping them together, as Suzuki effects were no different from other instrumentalists.
Dang, they didn’t graph their data. Well, I shall fix. Because I can. People should be so grateful I do all their graphing…
graph1.png
There you go. So, as you can see from the graph (the pretty, pretty graph), musical kids scored a lot better on fine motor skills for left and right hand (the first two sets of bars). This is pretty expected, if you’re using fine motor skills a lot, presumably you’ll get better at them. The musical kids also did better when distinguishing tones and following melody lines, though interestingly, they didn’t show any improvements in rhythm. I wonder if this has anything to do with the kids of music the kids were studying. There wasn’t a single drummer in the bunch, it was all either piano or stringed instruments.
And finally, the kids with musical training scored a lot better (I know it doesn’t look like it, but the MANCOVA analysis uncovered a difference) on vocabulary testing. They outperformed their non-musical counterparts in both verbal ability (vocabulary) and non-verbal reasoning skills. They didn’t find any differences in math or spatial reasoning.
The authors hypothesize that music training may transfer skills to some other related domains. The other hypothesis is that music training doesn’t enhance a specific skill set, but rather your general intellectual ability. This would mean they would score higher on every test given. In fact, they DID score higher, but most of the time the scores didn’t reach significance.
Still, remember this is correlation, not causation. Families were of similar socio-ecoomic class and education, but that doesn’t mean they are all similar parents. Kids who take music lessons may have parents that are more involved in their intellectual development. Kids that persist in taking music lessons for a good chunk of time may have superior motivation. Correlation =/= causation.
But it’s still a cool paper, and no matter what, it’s quite clear that music lessons didn’t HURT. Time to tape your poor child to the piano bench!
Marie Forgeard, Ellen Winner, Andrea Norton, Gottfried Schlaug (2008). Practicing a Musical Instrument in Childhood is Associated with Enhanced Verbal Ability and Nonverbal Reasoning PLoS ONE, 3 (10) DOI: 10.1371/journal.pone.0003566

Undergraduate science research journals

I did not know there were so many of them:
Student science publishing: an exploratory study of undergraduate science research journals and popular science magazines in the US and Europe:

Science magazines have an important role in disseminating scientific knowledge into the public sphere and in discussing the broader scope affected by scientific research such as technology, ethics and politics. Student-run science magazines afford opportunities for future scientists, communicators, politicians and others to practice communicating science. The ability to translate ‘scientese’ into a jargon-free discussion is rarely easy: it requires practice, and student magazines may provide good practice ground for undergraduate and graduate science students wishing to improve their communication skills.

Clock Quotes

We’re a sentimental people. We like a few kind words better than millions of dollars given in a humiliating way. (Refusing economic aid from the West)
– Gamal Abdel Nasser

Online submission makes it easier for people in developing countries to submit their scientific manuscripts

Changes in publication statistics when electronic submission was introduced in an international applied science journal:

In a refereed journal in the food and agriculture sector, papers were tracked over a five-year period during the introduction of electronic submissions. Papers originated in the Americas and Pacific region and were processed in Canada. Acceptance times for revised papers were reduced (P < 0.001) to 59% of the original, from 156.5 ± 69.1 days to 92.8 ± 57.5 days. But the start of electronic submission coincided with a change in the geographical origin of papers, with papers from Anglophone countries changing from a 61% majority to a 42% minority. It is possible that submissions from non-Anglophone sources were facilitated, thus creating challenges to the traditional Anglophone reviewer population.

My picks from ScienceDaily

Continue reading

Scientific American – special evolution issue

January issue of Scientific American is devoted to Darwin’s 200th birthday and contains several excellent articles. Check out The Latest Face of Creationism in the Classroom by Glenn Branch and Eugenie C. Scott for starters.
But beware, there are other (and I would say better) ways of thinking about some of the issues in some of the articles, so check out what Larry has to say about Why Everyone Should Learn the Theory of Evolution and Testing Natural Selection. You may not agree 100%, but you need to think about it.

Pam Spaulding on Waynesutton.tv

Pam Spaulding and Wayne Sutton discuss blogs, election, Rick Warren and more:

Location: Carrboro Creative Coworking space. Who needs Silicon Valley when there are people and facilities like this right here in North Carolina?

ScienceOnline’09 – the Women’s Networking Event

scienceonline09.jpg
networking-event-flyer.jpgFrom WiSE (Women in Science and Engineering) of Duke:

WiSE is partnering with ScienceOnline’09, a national science blogging and communication conference, to host a Triangle-wide networking event for women scientists, engineers, educators, researchers, science writers, and students. This event also includes many of our local women’s groups and promises to be a networking extravaganza. Following a networking reception with free light eats and drinks, there will be a presentation by our guest speaker, Rebecca Skloot, a freelance science writer, contributing editor at Popular Science, and correspondent for PBS’s NOVA scienceNOW. Our goal in hosting this networking event is to bring together local women’s groups to support joint efforts in community outreach and to support communication of science information and ideas to the general public.

If you have already registered for ScienceOnline’09 and checked the “I will attend Friday events” box, you are already registered for this event as well. If you are not registered for ScienceOnline’09, but you live in the area and want to attend the WiSE event only, you can register for it here. And you don’t need to be a woman 😉
The program goes like this:
6:30 pm Doors open
7 – 8 pm Networking reception and informational booths with local women’s groups
8 – 9 pm Keynote talk by Rebecca Skloot: “Women, science, and storytelling: The immortal life of Henrietta Lacks (a.k.a. HeLa), and one woman’s journey from scientist to writer”
I hear there will be good wine served there as well….

Scarlett Johansson – Bioterrorist?

You may have heard the story that Scarlett Johansson had a cold when she appeared on Jay Leno’s show the other day. And you may have heard that she got the cold from her ‘The Spirit’ co-star Samuel L. Jackson. And you may have heard that she had to blow her nose into a tissue during the show. And you may have heard that this particular tissue is now up for sale on eBay. And you may have heard that all proceeds of this sale will benefit USA Harvest, the charity of Scarlett Johansson’s choice.
What you may not know is that, due to the content of the tissue being regarded as biohazard (or even bioterrorism), you may not be able to have it shipped to you if you live outside of United States.
Update: sold for $5,300

Best Pictures of 2008

From The Big Picture

2008 has been an eventful year to say the least – it is difficult to sum up the thousands of stories in just a handful of photographs. That said, I will try to do what I’ve done with other photo narratives here, and tell a story of 2008 in photographs. It’s not the story of 2008, it’s certainly not all stories, but as a collection it does show a good portion of what life has been like over the past 12 months. This is a multi-entry story, 120 photographs over three days:

Part 1
Part 2
Part 3
Those are some amazing pictures. Some are gory. Some are poignant. Some are tragic. Here are two of the more light-hearted ones from the collection – a woman cantering her horse alongside the Tour d’ France competitors, and the fans of Red Star Belgrade soccer team lighting up the red flares during a game:
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New and Exciting in PLoS ONE

There are 11 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Home Range Utilisation and Territorial Behaviour of Lions (Panthera leo) on Karongwe Game Reserve, South Africa:

Interventionist conservation management of territorial large carnivores has increased in recent years, especially in South Africa. Understanding of spatial ecology is an important component of predator conservation and management. Spatial patterns are influenced by many, often interacting, factors making elucidation of key drivers difficult. We had the opportunity to study a simplified system, a single pride of lions (Panthera leo) after reintroduction onto the 85 km2 Karongwe Game Reserve, from 1999-2005, using radio-telemetry. In 2002 one male was removed from the paired coalition which had been present for the first three years. A second pride and male were in a fenced reserve adjacent of them to the east. This made it possible to separate social and resource factors in both a coalition and single male scenario, and the driving factors these seem to have on spatial ecology. Male ranging behaviour was not affected by coalition size, being driven more by resource rather than social factors. The females responded to the lions on the adjacent reserve by avoiding the area closest to them, therefore females may be more driven by social factors. Home range size and the resource response to water are important factors to consider when reintroducing lions to a small reserve, and it is hoped that these findings lead to other similar studies which will contribute to sound decisions regarding the management of lions on small reserves.

A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes:

Inferring the intensity of positive selection in protein-coding genes is important since it is used to shed light on the process of adaptation. Recently, it has been reported that overlapping genes, which are ubiquitous in all domains of life, seem to exhibit inordinate degrees of positive selection. Here, we present a new method for the simultaneous estimation of selection intensities in overlapping genes. We show that the appearance of positive selection is caused by assuming that selection operates independently on each gene in an overlapping pair, thereby ignoring the unique evolutionary constraints on overlapping coding regions. Our method uses an exact evolutionary model, thereby voiding the need for approximation or intensive computation. We test the method by simulating the evolution of overlapping genes of different types as well as under diverse evolutionary scenarios. Our results indicate that the independent estimation approach leads to the false appearance of positive selection even though the gene is in reality subject to negative selection. Finally, we use our method to estimate selection in two influenza A genes for which positive selection was previously inferred. We find no evidence for positive selection in both cases.

Epidemiological Characteristics of Classical Scrapie Outbreaks in 30 Sheep Flocks in the United Kingdom:

Most previous analyses of scrapie outbreaks have focused on flocks run by research institutes, which may not reflect the field situation. Within this study, we attempt to rectify this deficit by describing the epidemiological characteristics of 30 sheep flocks naturally-infected with classical scrapie, and by exploring possible underlying causes of variation in the characteristics between flocks, including flock-level prion protein (PrP) genotype profile. In total, the study involved PrP genotype data for nearly 8600 animals and over 400 scrapie cases. We found that most scrapie cases were restricted to just two PrP genotypes (ARQ/VRQ and VRQ/VRQ), though two flocks had markedly different affected genotypes, despite having similar underlying genotype profiles to other flocks of the same breed; we identified differences amongst flocks in the age of cases of certain PrP genotypes; we found that the age-at-onset of clinical signs depended on peak incidence and flock type; we found evidence that purchasing infected animals is an important means of introducing scrapie to a flock; we found some evidence that flock-level PrP genotype profile and flock size account for variation in outbreak characteristics; identified seasonality in cases associated with lambing time in certain flocks; and we identified one case that was homozygous for phenylalanine at codon 141, a polymorphism associated with a very high risk of atypical scrapie, and 28 cases that were heterozygous at this codon. This paper presents the largest study to date on commercially-run sheep flocks naturally-infected with classical scrapie, involving 30 study flocks, more than 400 scrapie cases and over 8500 PrP genotypes. We show that some of the observed variation in epidemiological characteristics between farms is related to differences in their PrP genotype profile; although much remains unexplained and may instead be attributed to the stochastic nature of scrapie dynamics.

National Academy of Sciences Survey

I get mail:

The National Academies want to identify the topics in science, engineering, and medicine that matter most to the public and that people have the greatest interest in learning more about. Once the topics have been selected, we plan to create a suite of educational materials (in both print and web formats) about each subject, with the goal of offering objective, reliable resources about complex topics.
We developed a 2-minute survey that we’d like to distribute to our key audiences. Readers of your blog are one of those key audiences and we would love to hear what topics matter most to them. Please note that this survey is just one component of the research we are conducting to inform our selection process for the topics.

Sounds like a great idea to me. So, read this:

What topics in science, engineering, and medicine matter most to you? The National Academies are interested in developing useful and engaging print and web-based educational materials on the topics that you’d like to learn more about. They invite you to participate in a brief survey. You can find that survey here.
In the 2-minute survey you’ll be presented with a list of topics and asked to select the five that matter most to you. At the end, you can see how your answers compare with the results so far. And you can enter a drawing to receive a National Academies tote bag!
Let the National Academies know what topics you think they should focus on so they can be sure to provide you with materials that are informative and useful. Your participation is greatly appreciated.

Go do the survey.

PLoS ONE Second Birthday Synchroblogging Competition – final list of entries

The deadline for the PLoS ONE Second Birthday Synchroblogging Competition is now officially over. Here are all the posts written for the competition – 18 posts, written by 17 people, covering 22 PLoS ONE articles. Liz, Dave, Jason and I will be reading them today and will announce the winner as soon as we can:
Barn Owl of Guadalupe Storm-Petrel: DNA Repair During Spermatogenesis: Gimme a Break! about the article: Deletion of Genes Implicated in Protecting the Integrity of Male Germ Cells Has Differential Effects on the Incidence of DNA Breaks and Germ Cell Loss
Ed Yong of Not Exactly Rocket Science: Predatory slime mould freezes prey in large groups about the article: Exploitation of Other Social Amoebae by Dictyostelium caveatum
Scicurious of Neurotopia (version 2.0): Why Did the Dolphin Carry a Sponge? about the article: Why Do Dolphins Carry Sponges?
Scicurious of Neurotopia (version 2.0): Einstein was smart, but Could He Play the Violin? about the article: Practicing a Musical Instrument in Childhood is Associated with Enhanced Verbal Ability and Nonverbal Reasoning
Allyson of Systems Biology & Bioinformatics (Semantically Speaking) on One way for RDF to help a bioinformatician build a database: S3DB (also cross-posted on The mind wobbles: One way for RDF to help a bioinformatician build a database: S3DB) about the article: A Semantic Web Management Model for Integrative Biomedical Informatics
Simon Cockell of Fuzzier Logic: Contextual Specificity in Peptide-Mediated Protein Interactions about the article: Contextual Specificity in Peptide-Mediated Protein Interactions
Mike Haubrich of Tangled Up in Blue Guy : Small-Bodied Humans on Palau – A Disagreement about the articles: Small-Bodied Humans from Palau, Micronesia and Small Scattered Fragments Do Not a Dwarf Make: Biological and Archaeological Data Indicate that Prehistoric Inhabitants of Palau Were Normal Sized
Martin of The Lay Scientist : Catching Snowflakes: The Media and Public Perceptions of Disease about the article: Medicine in the Popular Press: The Influence of the Media on Perceptions of Disease
Nir London of Macromolecular Modeling Blog: Model for the Peptide-Free Conformation of Class II MHC Proteins about the article: Model for the Peptide-Free Conformation of Class II MHC Proteins
Greg Laden of Greg Laden’s blog: How to make an elephant turn invisible about the articles: Risk and Ethical Concerns of Hunting Male Elephant: Behavioural and Physiological Assays of the Remaining Elephants, Roadless Wilderness Area Determines Forest Elephant Movements in the Congo Basin, Elephant (Loxodonta africana) Home Ranges in Sabi Sand Reserve and Kruger National Park: A Five-Year Satellite Tracking Study and Population and Individual Elephant Response to a Catastrophic Fire in Pilanesberg National Park.
The Neurocritic of The Neurocritic blog: Can You Reread My Mind? about the article: Using fMRI Brain Activation to Identify Cognitive States Associated with Perception of Tools and Dwellings
Moneduloides of Moneduloides blog: A trypanosome and a tsetse walk into a bar… about the article: Factors Affecting Trypanosome Maturation in Tsetse Flies
El-Ho of Pas d’il y’on que nous: The Etiology of Fear about the article: Coupled Contagion Dynamics of Fear and Disease: Mathematical and Computational Explorations
Ian of Further thoughts: Evolution and conservation in Mexican dry forests about the article: Sources and Sinks of Diversification and Conservation Priorities for the Mexican Tropical Dry Forest
Alun Salt of Archaeoastronomy: If you put a snail shell to your ear can you hear the sound of your thoughts? about the article: Climate Change, Genetics or Human Choice: Why Were the Shells of Mankind’s Earliest Ornament Larger in the Pleistocene Than in the Holocene?
Michael Tobis of Only In It For The Gold: The Singularity about the article: Ecosystem Overfishing in the Ocean
PodBlack Cat of PodBlack blog: Pet Ownership – Maybe Not For Better Health, Perhaps Sense Of Humour? about the article: To Have or Not To Have a Pet for Better Health?
Juan Nunez-Iglesias of I Love Symposia!: Randomise your samples! about the article: Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results
Not in competition, because Dave Munger of Cognitive Daily is one of the judges: Make sure you get some sleep — or at least some caffeine — before that test about the article: Sleep Loss Produces False Memories

Darwin Day Trailer (video)

By Miss Baker: