Monthly Archives: May 2009

Why so few posts?

In the beginning, blogs were mainly collections of links. With the development of blogging platforms, many bloggers moved on to long-form writing. But blogs were still places for a lot of linkfests, or link-plus-one-liner posts as well. My blog has always been a mix of both styles. Thus, my average of 8.2 posts per day.
But recently, you may have noticed the most definite reduction in the number of posts per day. Why?
First, because I heard some complaints about my blog being a firehose of stuff that is “boring, just links” (although others said that my role as a trusted filter was appreciated).
Second, there are now much more appropriate platforms for such quick-link posts – and I have moved much of my quicky posts there.
If you are interested, i.e., if you appreciate my role of a ‘trusted filter’, then you can find those linkfests on my Twitter where I get some responses. My tweets (as well as links to blogposts) immediately show up on my FriendFeed stream where there are often additional comments, by a different set of people (you can also see what other stuff I like and comment on here). A few minutes later, that stream gets imported into my Facebook Wall where a completely different set of people may add their own comments. Thus, much of the conversation I participate in online has moved to those three social networks. Blog remains for the longer, more thoughtful posts that cannot be summarized in 140 characters, and also for posts that I think are the most important, e.g., news or announcements that I want to be seen by the greatest number of people (this blog still has more subscribers and visitors than my Twitter followers, FriendFeed subscribers and Facebook friends).
In other words, I am trying to adapt my online behavior to the current, new type of journalistic workflow. I hope you follow my experiment with me, in whichever of those four places you like and feel comfortable with.

Clock Quotes

The cat has too much spirit to have no heart.
– Ernest Menaul

Happy birthday, Milutin Milankovic

MilutinMilankovic.jpgToday is the 130th anniversary of the birth of Milutin Milankovic, a Serbian geophysicist best known for Milankovitch cycles that describe periodicities in Earth’s climate.
Vedran Vucic is in Dalj (near Vukovar, Croatia), Milankovic’s birthplace, today for the birthday celebrations. He says that the house in which Milankovic grew up has been renovated for the occasion. I am assuming it has been turned into a museum. As I will go to Serbia again this summer, perhaps Vedran and I can take a trip to Dalj, where a group of science popularizers are interested in hearing about Open Access publishing, science blogging and other developments in science communication.
[Image Source - Portrait of Milutin Milanković by Paja Jovanović (1859-1957)]

My picks from ScienceDaily

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Clock Quotes

Sometimes the questions are complicated and the answers are simple.
– Theodor Seuss Geisel

Total Eclipse of the Mullet with Flashlights!

From Arikia (The Millikan Daily) comes this LOL/LMAO/ROFL video of the day – Total Eclipse of the Heart: Literal Video Version:

XXVI International Association of Science Parks World Conference on Science & Technology Parks

I’ll be going to IASP next week, one of several people reporting from it for Science In The Triangle. We have organized our coverage strategically – I will be there for a couple of events on Tuesday and all day Wednesday. I’ll be posting here and on Twitter and Science In The Triangle will aggregate everyone’s posts in one place.
What is IASP?:

The International Association of Science Parks (IASP) is a worldwide network of science and technology parks. IASP connects science park professionals from across the globe and provides services that drive growth and effectiveness for members.
IASP members enhance the competitiveness of companies and entrepreneurs in their cities and regions, and contribute to global technology-led economic development through innovation, entrepreneurship, and the transfer of knowledge and technology.

What is the conference about?:

The future can be a daunting place. Regions and places around the world are looking at ways that they can be more prepared for the opportunities and challenges to come.
Places and regions that are fully integrated, viable, and use knowledge and its applications as the major driver in economic development will fair well in this new landscape. For the past fifty years, science and technology parks have led this model. The evolution of this industry’s growth will serve as a model for others.
Join us in Raleigh, NC, on June 1-4, 2009, to discuss what the elements of these future knowledge ecosystems might entail.

You can follow on Twitter (also here, or follow the #iasp hashtag) and Facebook:

This conference will focus on trends in technology-led economic development, the development and activities in science, research and technology parks including incubation, university relationships, corporate partnerships and workforce issues. It will also include discussions around intellectual property, venture capital and strategic partnerships.
In recent years, the International Association of Science Parks (IASP) has held this conference in Barcelona, Spain, and Johannesburg, South Africa, and future years will be hosted by Daejeon, Korea, and Copenhagen, Denmark. Take advantage of an international conference on a domestic ticket!

So, watch this space next week for my liveblogging of some of the events there.

My picks from ScienceDaily

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Clock Quotes

The finest workers in stone are not copper or steel tools, but the gentle touches of air and water working at their leisure with a liberal allowance of time.
– Henry David Thoreau

Science Online London 2009

You have proven your fitness, evolutionarily speaking, not when you have babies, but when your babies have babies. So I am very excited that my babies – the three science blogging conferences here in the Triangle so far – have spawned their own offspring. Not once, but twice. The London franchise will happen again this year. And just like we changed the name from Science Blogging Conference into ScienceOnline, so did they.
scienceonlinelondon logo.gifScience Online London 2009 will take place on Saturday August 22, 2009 at the Royal Institution of Great Britain in London, co-hosted by Nature Network, Mendeley and the Royal Institution of Great Britain. The organizers are Matt Brown (Nature Network), Martin Fenner (Hannover Medical School), Richard P. Grant (F1000), Victor Henning (Mendeley), Corie Lok (Nature Network) and Jan Reichelt (Mendeley).
To help build the program, suggest speakers/sessions, to register and organize your trip, or to participate virtually, you should join the Nature Network forum and the FriendFeed room. Follow @soloconf and the #soloconf_09 hashtag on Twitter.
There will probably be a registration fee to cover the costs, likely in the range of £10, so nothing really expensive. They are also looking for sponsors. And if anyone wants to sponsor my trip, I’ll go ;-)

If research papers had a comment section….

It appears that Jorge Cham has been reading some of these posts or associated FriendFeed threads, because today’s PhDcomics strip is this one:
phdcomic comments.gif
I am wondering how many of ‘weissberg’s’ comments have been removed by the moderators over the years.
Also, if duplicate comments are posted 14 years apart, is it because MoveableType stalled that long? Do they even count as duplicates any more?
And why did the reviewer take so long to post the review? And how does one get scooped by a 14-year old paper? Just the lack of habit of reading historical literature?
Task: identify the paper this is attached to (I see Miguel Nikolelis in the References, so it will be some kind of multi-electrode brain monitoring, most likely)?

New and Exciting in PLoS this week

Usually on Thursday nights I take a look at all seven PLoS journals to see what strikes my fancy. 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, Mendeley, 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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Yes, Archaea also have circadian clocks!

ResearchBlogging.orgIf you ever glanced at the circadian literature, you have probably encountered the statement that “circadian rhythms are ubiquitous in living systems”. In all of my formal and informal writing I qualified that statement somewhat, stating something along the lines of “most organisms living on or near the Earth’s surface have circadian rhythms”. Why?
In the earliest days of chronobiology, it made sense to do most of the work on readily available organisms: plants, insects, mammals and birds. During the 20th century, thousands of species of animals, fungi, protists and plants – all living on the planet’s surface – were tested for the possession of the circadian clock, and one was always found. Hence the “ubiquitous” statement seen in so many papers.
But, as it was later discovered, for some marine organisms moon cycles are more important than day-night cycles so they have evolved lunar clocks in addition or instead of circadian clocks (see sponges and cnidaria, for some examples). In the intertidal zone, the tides are more important for survival than the daily rhythms, so the organisms living there have evolved tidal clocks. Animals that live in caves have lost circadian rhythms, at least in behavioral output (a clock may still be operating underneath, driving metabolic or developmental rhythms). In the polar regions, rhythmicity may be seasonal. In subterranean animals, like Blind Naked mole-rats, most individuals are without rhythms, but young males that leave the colony in order to join another one develop rhythmicity during their adventurous journey. In social insects, only the individuals that go outside the hive to forage exhibit daily rhythms.
How does one figure out if an organism has a clock? You need to pick a good output and a way to continuously monitor it. Then you put the organism in constant conditions of light, temperature, air pressure, sound etc., and monitor the output for many days. If you do the statistics on the data at the end of the experiment and see that there is a periodicity in the data (for at least the first 2-3 days)that is reasonably close to 24 hours (between 16 and 32 hours is usually thought to be the limits), you know that your organism of choice has a circadian clock.
In a related experiment, you expose the organism to an environmental periodicity – usually a light-dark cycle, as it is usually the strongest cue, as the evolution of circadian clocks and light-detecting mechanisms is closely intertwined – to see if the rhythmicity of the organism can be synchronized (entrained) to the environmental cycle, indicating that it is a biological function and not the chance quirk in your data. Without these two experiments providing positive data it does not make sense to do any further investigations into mechanisms of entrainment, anatomical location of the clock or the cellular mechanism of the clock.
The trick is to find a good output to monitor. It is easy for rodents – they will run in running wheels (so will cockroaches). Songbirds will jump from perch to perch. Lizards will walk around the cage and tilt the floor from one side to another. And while behavioral output – the general locomotor activity – is not the most reliable (it is very prone to masking effects, so for instance mice will generally not run in wheels in bright light, while rats will), it is usually the easiest and cheapest to monitor and, in most cases (see an example where it failed, while monitoring body temperature worked) will be sufficient.
But what do you do when the organism does not have a measurable behavioral output, especially one that can be continuously monitored by machines? You start thinking very, very hard. And you come up with an alternative. You may be able to implant radiotransmitters and monitor body temperature. Or you may record vocalizations. Or you may take small blood samples several times per day and assay for something like melatonin.
The technological constrains limited our ability to discover circadian clocks in bacteria until the 1990s. Until then, the existence of such clocks was a mystery (one that everyone in the field was eager to see solved). I have written several posts about the discoveries of clocks in bacteria: Circadian Clocks in Microorganisms, Clocks in Bacteria I: Synechococcus elongatus, Clocks in Bacteria II: Adaptive Function of Clocks in Cyanobacteria, Clocks in Bacteria III: Evolution of Clocks in Cyanobacteria, Clocks in Bacteria IV: Clocks in other bacteria, Clocks in Bacteria V: How about E.coli? The understanding of the way bacterial clocks work (more like a relay or a switch than a clock) made us rethink the clock metaphor we have been using for almost a century.
So it appears that most Eukaryotes have clocks and at least some bacteria have them as well. But the other large group – the Third Domain: Archaea – eluded us thus far. After all, Archaea are notoriously difficult to culture in the laboratory and it took some time to figure out how to keep them alive outside of their natural extreme environments.
Do Archaea have clocks? We did not know. Until now. A couple of weeks ago, PLoS ONE published a paper that is the first to demonstrate the daily rhythms in an Archaeon: Diurnally Entrained Anticipatory Behavior in Archaea by Kenia Whitehead, Min Pan, Ken-ichi Masumura, Richard Bonneau and Nitin S. Baliga. Here is the text of the Abstract:

By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. Significantly, the diurnally entrained transcription was observed under constant darkness after removal of the LD stimulus (free-running rhythms). The memory of diurnal entrainment was also associated with the synchronization of oxic and anoxic physiologies to the LD cycle. Our results suggest that under nutrient limited conditions halophilic archaea take advantage of the causal influence of sunlight (via temperature) on O2 diffusivity in a closed hypersaline environment to streamline their physiology and operate oxically during nighttime and anoxically during daytime.

What does that mean? What did they do?
First, they picked a good candidate species – Halobacterium salinarum. Why is it a good candidate? Because it lives near the Earth’s surface, in salty lakes and ponds (like this one, in Africa):
salinarium in a lake.gif
Many Archaea live in places where no light ever penetrates: deep inside the rock or ice or the oceanic floor. Some Archaea are exposed to light in cyclical fashion but not a 24-hour cycle – I have written somewhere before that I expect the Archaea living in the waters of the Old Faithful geiser in Yellowstone National Park to have a 45-minute clock instead. But Halobacterium salinarum is exposed to the natural periodicity of the day-night cycle on the surface and is thus a good candidate for an Archaeon that may have evolved a circadian clock. This is how the Halobacterium salinarum look like under the microscope:
salinarium micrograph.gif
There is another reason this is a good candidate. The light-dark cycle has a potential adaptive consequence to the critter. Water that is saturated with salt will have a high variation of its oxygen content and this variation is dependent on the environmental temperature: when it is colder outside, oxygen can more readily disolve in the salty water. When it is warm, it cannot.
The environment where Halobacterium salinarum lives is cold during the night and hot during the day. But the temperature changes are much more gradual and slow than changes in illumination (as well as less dependable: there are colder and warmer days), so being in tune with the light is a better way to synchronize one’s activities than measuring temperature (or oxygen content) directly. By entraining to a ligh-dark cycle, these organisms can make switches in their oxygen-dependent metabolism in a more timely (and thus more energy-efficient) fashion: by predicting instead of reacting to the changes in temperature over the course of 24 hours.
So, Whitehead et al placed some Halobacterium salinarum in light-dark cycles and subsequently released them into constant darkness. But what did they measure? Archaea are known to be lousy wheel-runners!
In bacteria, much of the work is done by measuring bioluminescence coming from the expression of the luciferase gene inserted next to one of the clock gene promoters. But here, we don’t know which if any gene is a clock gene and we do not have the technology ready yet. But, these days microarrays are cheaper and easier to use then some years ago when I started grad school. And remember that Everything Important Cycles!
So they took samples of the organism six times per day and ran them on microarrays, comparing the expression of all the genes between the sampling times, both during entrainment to LD cycles and in the subsequent DD (constant dark) environment:
archaea microarrays.JPG
What they discovered is that about 12% of the genes cycle with the period of 24 hours in LD cycles and continue to cycle in DD with a circadian period of around 21.6 hours:
archaea periods.JPG
What is most interesting is that the genes that cycle are the genes that are involved in oxygen (or oxygen-dependent) metabolism – exactly the kinds of genes that are expected to cycle in this organism. Some of these genes are also know to be directly regulated by oxygen. Now we know they can also be regulated – directly and/or indirectly through a clock – by light, inducing expression in preparation for the changes in oxygen concentration, not just in direct response. In this way, the cell is ready to use oxygen a little bit ahead of time. No time wasted.
I am very excited about this finding. This opens up a whole avenue of future research, something that the authors also realize:

Indeed, further detailed experimentation is necessary to ascertain precise phasing, temperature compensation, adaptability to different periods of entrainment etc. to ascertain the mechanistic underpinnings of this diurnal entrainment and its physiological implications.

Once we know there is a clock in Archaea – and now we do due to this paper – we can start studying it in detail.
Furthermore, this finding has big implications for the study of the evolutionary origins of the circadian clock (and light-reception associated with it). The molecular mechanism of the clock is very different between Bacteria and Eukaryotes, leading the field to conclude that the clock evolved independently in these two groups (and perhaps more – some people think that protist, plant, fungal and animal clocks evolved independently of each other as well). Now we can try to figure out how Archaea measure time. Is their mechanism similar to that in Bacteria? Or in Eukaryotes? Or something completely different, indicating another independent evolutionary origin? Or something in-between Bacteria and Eukaryotes, containing some elements of both, suggesting that perhaps there was only one evolutionary origin for clocks in all the life on Earth. The authors note that this last scenario is a strong contender:

Finally, the discovery of diurnal entrainment of gene expression in an archaeon also raises important questions regarding the origin of light-responsive clock mechanisms. This is because archaeal information processing machinery is assembled from components that share ancestry with eukaryotic (general transcription factors and RNA polymerase) and bacterial (sequence-specific transcription regulators) counterparts [44]. Furthermore, components of both bacterial [45,46] and eukaryotic [47] clocks are encoded in its genome [6,32].

Of course, since this is an Open Access article, you can and should read it yourself to get more details. And post ratings, notes and comments while you are there.
Whitehead, K., Pan, M., Masumura, K., Bonneau, R., & Baliga, N. (2009). Diurnally Entrained Anticipatory Behavior in Archaea PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005485
Update: see comment thread for more. Unfortunately, scientists still at this day and age do not report everything and keep data secret. Apparently, this was the case in the question posed by this study. I hear from trusted sources that there is still not evidence for a clock in Archaea beyond the direct effects of light on gene expression and O2 metabolism.

My picks from ScienceDaily

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Today’s carnivals

I and the Bird #101 is up on Living the Scientific Life (Scientist, Interrupted)
The 104th edition of the Carnival of Space is up on Mang’s Bat Page
Change of Shift Vol 3 Number 24 is up on CodeBlog

Clock Quotes

None of us suddenly becomes something overnight. The preparations have been in the making for a lifetime.
– Gail Kathleen Godwin

Creative reuse of OA materials

Last week also demonstrated another benefit of Open Access. Not just that everyone could re-use the images from the Ida paper without wondering “is this too much for Fair Use principles?” (yes, I have seen people re-post every single image from the paper into their articles/posts, plus lengthy excerpts of text), but people could do fun stuff to them as well, and even use it for commercial endeavors.
And I am not talking just about the Google logo last Wednesday!
First to make a creative reuse of an article image was Ed Yong in his brilliant and hilariously funny post Darwinius changes everything in which Ida appears on toast:
Richard Carter was next, depicting Ida playing saxophone:
But then, there is also a way to use the hype to counteract hype…and make some money in the process. The first store I saw that is selling t-shirts and other merchandise with Ida on it was this one. You can get This Mug Which is Not Missing:
Darwinius mug.jpg
Or you can choose one of the t-shirts for which the proceeds go to a good cause, the Beagle Project, with a good message “There is no such thing as a missing link”:
Darwinius nomissinglink shirt.jpg
And you can find other t-shirt designs in this shop and this shop and this shop – perhaps walking around wearing one of these will be a conversation starter, or will get a kid to want to become a palaeontologist when s/he grows up, who knows.
Now, if I were a palaeontologist and got my hands on such a spectacular, one-in-a-lifetime fossil, I’d milk it for all it’s worth, too. I’d certainly not put all of the analysis in one paper – then what, retire? I’d also publish the description first, with a lot of fanfare if I could get it. Then I would spread all sorts of other analyses over several more papers – as it appears they are planning to do – including the cladistic analysis for those who think science without numbers is not scientific enough (forgetting the GIGO law and that every single thing input into the cladistic analysis programs is an assumption – I was astonished when I took a dinosaur class with Dale Russell some 10 years ago how the palaeontologists’ assumptions about traits – which are hard to evolve, thus likely to show up only once, and which are easy to evolve, thus could re-appear in independent lineages over and over again – differed dramatically from my thinking of developmental switches; who knows who was right about any trait – we both had our assumptions).
Now, I really hope they choose Open Access venues (perhaps PLoS ONE again) for the subsequent papers so the entrepreneurs in the future can print t-shirts with cladograms – imagine the street-fights inevitably breaking out between t-shirt wearing palaeontologists arguing the correctness of the depicted tree! Can’t do that if the journal holds the copyright to the images!

New and Exciting in PLoS ONE

There are 18 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, Mendeley, 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:
Mathematical Logic in the Human Brain: Syntax:

Theory predicts a close structural relation of formal languages with natural languages. Both share the aspect of an underlying grammar which either generates (hierarchically) structured expressions or allows us to decide whether a sentence is syntactically correct or not. The advantage of rule-based communication is commonly believed to be its efficiency and effectiveness. A particularly important class of formal languages are those underlying the mathematical syntax. Here we provide brain-imaging evidence that the syntactic processing of abstract mathematical formulae, written in a first order language, is, indeed efficient and effective as a rule-based generation and decision process. However, it is remarkable, that the neural network involved, consisting of intraparietal and prefrontal regions, only involves Broca’s area in a surprisingly selective way. This seems to imply that despite structural analogies of common and current formal languages, at the neural level, mathematics and natural language are processed differently, in principal.

Phylogeny and Biogeography of Hawkmoths (Lepidoptera: Sphingidae): Evidence from Five Nuclear Genes:

The 1400 species of hawkmoths (Lepidoptera: Sphingidae) comprise one of most conspicuous and well-studied groups of insects, and provide model systems for diverse biological disciplines. However, a robust phylogenetic framework for the family is currently lacking. Morphology is unable to confidently determine relationships among most groups. As a major step toward understanding relationships of this model group, we have undertaken the first large-scale molecular phylogenetic analysis of hawkmoths representing all subfamilies, tribes and subtribes. The data set consisted of 131 sphingid species and 6793 bp of sequence from five protein-coding nuclear genes. Maximum likelihood and parsimony analyses provided strong support for more than two-thirds of all nodes, including strong signal for or against nearly all of the fifteen current subfamily, tribal and sub-tribal groupings. Monophyly was strongly supported for some of these, including Macroglossinae, Sphinginae, Acherontiini, Ambulycini, Philampelini, Choerocampina, and Hemarina. Other groupings proved para- or polyphyletic, and will need significant redefinition; these include Smerinthinae, Smerinthini, Sphingini, Sphingulini, Dilophonotini, Dilophonotina, Macroglossini, and Macroglossina. The basal divergence, strongly supported, is between Macroglossinae and Smerinthinae+Sphinginae. All genes contribute significantly to the signal from the combined data set, and there is little conflict between genes. Ancestral state reconstruction reveals multiple separate origins of New World and Old World radiations. Our study provides the first comprehensive phylogeny of one of the most conspicuous and well-studied insects. The molecular phylogeny challenges current concepts of Sphingidae based on morphology, and provides a foundation for a new classification. While there are multiple independent origins of New World and Old World radiations, we conclude that broad-scale geographic distribution in hawkmoths is more phylogenetically conserved than previously postulated.

Migration of Whooper Swans and Outbreaks of Highly Pathogenic Avian Influenza H5N1 Virus in Eastern Asia:

Evaluating the potential involvement of wild avifauna in the emergence of highly pathogenic avian influenza H5N1 (hereafter H5N1) requires detailed analyses of temporal and spatial relationships between wild bird movements and disease emergence. The death of wild swans (Cygnus spp.) has been the first indicator of the presence of H5N1 in various Asian and European countries; however their role in the geographic spread of the disease remains poorly understood. We marked 10 whooper swans (Cygnus cygnus) with GPS transmitters in northeastern Mongolia during autumn 2006 and tracked their migratory movements in relation to H5N1 outbreaks. The prevalence of H5N1 outbreaks among poultry in eastern Asia during 2003-2007 peaked during winter, concurrent with whooper swan movements into regions of high poultry density. However outbreaks involving poultry were detected year round, indicating disease perpetuation independent of migratory waterbird presence. In contrast, H5N1 outbreaks involving whooper swans, as well as other migratory waterbirds that succumbed to the disease in eastern Asia, tended to occur during seasons (late spring and summer) and in habitats (areas of natural vegetation) where their potential for contact with poultry is very low to nonexistent. Given what is known about the susceptibility of swans to H5N1, and on the basis of the chronology and rates of whooper swan migration movements, we conclude that although there is broad spatial overlap between whooper swan distributions and H5N1 outbreak locations in eastern Asia, the likelihood of direct transmission between these groups is extremely low. Thus, our data support the hypothesis that swans are best viewed as sentinel species, and moreover, that in eastern Asia, it is most likely that their infections occurred through contact with asymptomatic migratory hosts (e.g., wild ducks) at or near their breeding grounds.

Article-Level Metrics (at PLoS and beyond)

Pete Binfield, the Managing Editor of PLoS ONE, presented a webinar about article-level metrics to NISO – see also the blog post about it:

3 Quarks Daily Announces The Quarks – blogging prizes

The First Award for Best Science Blogging Judged by Steven Pinker
Celebrating the best of blog-writing on the web, 3 Quarks Daily will award four annual prizes in the respective areas of Science, Arts & Literature, Politics, and Philosophy for the best blog post in those fields. This year, the winners of the 3QD Prize in Science will be selected from six finalists by Steven Pinker, who will also provide comments about each of the three winning entries.
Please nominate your favorite blog entry in the field of the Natural and Social Sciences by placing the URL for the blogpost in the comments section here. You may also add a brief comment describing the entry and saying why you think it should win.
The nominating process will end at midnight (Eastern Standard Time) June 1, 2009. So get those nominations in today!
* The editors of 3QD reserve the right to reject entries that we feel are not appropriate.
* The blog entry must have been written after May 24, 2008.
* You may nominate an entry from your own or a group blog.
* Guest columnists at 3 Quarks Daily are eligible to be nominated, and may nominate themselves.
VOTING ENDS midnight June 8, 2009 (Eastern Standard Time)
Winners will be announced June 21, 2009
About The Quarks
‘The Quarks’ will be awarded every year on the two solstices and the two equinoxes:
Science Prize: announced June 21
Arts & Literature Prize: announced September 22
Politics Prize: announced December 21
Philosophy Prize: March 20, 2010
About a month before the prize is awarded we will solicit nominations of blog entries from our readers. The nominating period will last one week. At the end of this time, we will open up the voting to our readers. The four main daily editors of 3 Quarks Daily (Abbas Raza, Robin Varghese, Morgan Meis, and Azra Raza) will take the top twenty voted-for nominees, and will select six finalists from these, plus a wildcard entry of their choosing. Finally, a well-known intellectual from the field will pick the three final winners from these, and write short comments on the winning entries to be published on 3 Quarks Daily.
The first place award will be called the “Top Quark,” and will include a cash prize of $1,000; the second place prize, the “Charm Quark,” will include a cash prize of $300; and the third place winner will get the honor of winning the “Strange Quark,” along with $200.
About the Science Category Judge, Steven Pinker
Steven Pinker is Harvard College Professor and Johnstone Family Professor in the Department of Psychology at Harvard University. Until 2003, he taught in the Department of Brain and Cognitive Sciences at MIT. He conducts research on language and cognition, writes for publications such as The New York Times, Time, and The New Republic, and is the author of seven books, including The Language Instinct, How the Mind Works, Words and Rules, The Blank Slate, and most recently, The Stuff of Thought: Language as a Window into Human Nature.
There’s a reason why leading intellectuals like Richard Dawkins have declared, “I have placed 3 Quarks Daily at the head of my list of web bookmarks.” There aren’t many places on the web to get the one-stop intellectual surfing experience 3 Quarks Daily provides. With the original writings of Monday Musings–penned by the editors as well as an international roster of critics, politicians, and intellectuals–and 3QD editors culling the most fascinating science, design, literature, current affairs, art, and criticism every day from all over the web, 3 Quarks Daily is more of an intellectual wonder cabinet than a filter blog.
please direct any press inquiries to

Technical problems

As you may know, is run on MoveableType 4 specially modified by SixApart for the site. The latest tweak was, apparently, a mistake, so the system was reverted to an older version (I have no idea what I am talking about, am I?) which makes posting and commenting painfully slow and likely to cause time-outs. The help is on the way, and the system should be fixed by the end of the week, so we hear.
If you post a comment and get a timeout, it is likely your comment has registered but will take a couple of minutes to show up. Save the text elsewhere (WordPad or such), click on Back, then Refresh the page a couple of times over a couple of minutes and, only if no comment appears, you should try posting it again. If I receive duplicates anyway, I will try to delete one of the copies.

Commenting on scientific papers

There have been quite a few posts over the last few days about commenting, in particular about posting comments, notes and ratings on scientific papers. But this also related to commenting on blogs and social networks, commenting on newspaper online articles, the question of moderation vs. non-moderation, and the question of anonymity vs. pseudonymity vs. RL identity.
You may want to re-visit this old thread first, for introduction on commenting on blogs.
How a 1995 court case kept the newspaper industry from competing online by Robert Niles goes back into history to explain why the comments on the newspaper sites tend to be so rowdy, rude and, frankly, idiotic. And why that is bad for the newspapers.
In Why comments suck (& ideas on un-sucking them), Dan Conover has some suggestions how to fix that problem.
Mr. Gunn, in Online Engagement of Scientists with the literature: anonymity vs. ResearcherID tries to systematize the issues in the discussion about commenting on scientific papers which has the opposite problem from newspapers: relatively few people post comments.
Christina Pikas responds in What happens when you cross the streams? and Dave Bacon adds more in Comments?…I Don’t Have to Show You Any Stinkin’ Comments!
You should now go back to the analysis of commenting on BMC journals and on PLoS ONE, both by Euan Adie.
Then go back to my own posts on everyONE blog: Why you should post comments, notes and ratings on PLoS ONE articles and Rating articles in PLoS ONE.
Then, follow the lead set by Steve Koch and post a comment – break the ice for yourself.
Or see why T. Michael Keesey posted a couple of comments.
You may want to play in the Sandbox first.
I am watching all the discussions on the blog posts (as well as on FriendFeed) with great professional interest, of course. So, what do you think? Who of the above is right/wrong and why? Is there something in Conover’s suggestions for newspapers that should be useful for commenting on scientific papers? What are your suggestions?

My picks from ScienceDaily

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Clock Quotes

We don’t love qualities, we love persons; sometimes by reason of their defects as well as of their qualities.
– Jacques Maritain (1882-1973)

Silly me, I thought it was the cool fossils…

From PhDcomics.

Why the anti-vaccine movement even exists? And how it got started?

An article that is likely to make the rounds of the science/medical blogosphere (and get the anti-vaccer trolls out of the woodwork):

Researchers long ago rejected the theory that vaccines cause autism, yet many parents don’t believe them. Can scientists bridge the gap between evidence and doubt?

Writes Liza Gross in the latest Feature article in PLoS Biology: A Broken Trust: Lessons from the Vaccine-Autism Wars:

Until the summer of 2005, Sharon Kaufman had never paid much attention to the shifting theories blaming vaccines for a surge in reported cases of autism. Kaufman, a medical anthropologist at the University of California, San Francisco, knew that the leading health institutions in the United States had reviewed the body of evidence, and that they found no reason to think vaccines had anything to do with autism. But when she read that scientists and public officials who commented on the studies routinely endured malevolent emails, abusive phone calls, and even death threats, she took notice.
“Hecklers were issuing death threats to spokespeople,” Kaufman exclaims, “people who simply related the scientists’ findings.” To a researcher with a keen eye for detecting major cultural shifts, these unsettling events signaled a deeper trend. “What happens when the facts of bioscience are relayed to the public and there is disbelief, lack of trust?” Kaufman wondered. “Where does that lead us?”
Struck by how the idea of a vaccine-autism link continued to gain cultural currency even as science dismissed it, Kaufman took a 26-month hiatus from her life’s work on aging and longevity to investigate the forces fueling this growing divide between scientists and citizens (see Figure 1). She wanted to understand how parents thought about risk and experts, how these attitudes shaped parents’ decisions about vaccination, and what the vaccine wars might teach us about the long-term erosion of public trust in science….

Read the whole thing

New and Exciting in PLoS ONE

There are 24 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, Mendeley, 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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My interviews with Radio Belgrade

Last year in May, when I visited Belgrade, I gave interviews with Radio Belgrade, talking about science publishing, Open Access, science communication and science blogging. The podcasts of these interviews – yes, they are in Serbian! – are now up:
Part 1
Part 2
I know that this blog has some ex-Yugoslavs in its regular audience, people who can understand the language. I hope you enjoy the interviews and spread the word if you like them.

Open Lab 2009 submission bookmarklet

Sometimes, you read a blog post on a science blog and think to yourself “Hmmm, perhaps I should submit this one for Open Lab 09″, then fumble to find a blog with a submission button and end up giving up. Not any more!
Bill Hooker was bothered by this enough that he decided to something about it. So, he built a little bookmarklet.
All you need to do is drag this link to your browser’s toolbar:
Open Lab
and click on it next time you have the urge to submit an entry to the anthology. A new window with open, with the submission form in it, ready to be filled out.
Thanks, Bill!

My picks from ScienceDaily

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Clock Quotes

The human brain is like a TV set. When it goes blank, it’s time to turn off the sound.
– Pat Elphinstone

Only a few days left…

…until I pronounce the Blog Post Of The Month for May. Make sure your post is aggregated on There are 33 entries there so far – make sure yours shows up there by May 31st at midnight EST.

Today’s carnivals

Encephalon #71: Big Night – is up on Neuroanthropology
Friday Ark #244 is up on Modulator
Carnival of the Green #181 is up on Green Phone Booth
Praxis is dead (it takes a few months of hand-holding and arm-twisting for a carnival to get its own life,….)
Call for Submissions for the Diversity in Science Carnival is on Urban Science Adventures! The next edition will be on The Oyster’s Garter.

North Carolina science/nature/medical blogs

I am trying to put together a list of science, nature and medical blogs based in North Carolina, mainly in order to update the Blogroll/aggregator on the Science In The Triangle media page. I tried to put together, out of my own memory, the names and URLs of blogs based in NC, but I need your help to make the list better.
These are either personal, or news, or institutional blogs based in the state. In some cases, these are blogs of people who I know are coming to live in NC very soon. Some of these are group blogs in which one or more co-bloggers are living here. And one is a large group blog with the server based here.
So, if one of these is yours, but you have moved out of NC, or moved the URL elsewhere, let me know. If your blog, based in NC, is not listed, let me know. If you are aware of a science/nature/medicine blog in NC that I forgot, let me know in the comments.
Blogs in the Triangle:
The Panda’s Thumb
De Rerum Natura
A Blog Around The Clock
Terra Sigillata
The Intersection
Deep Sea News
CogSci Librarian
The Drinking Bird
Bonobo Handshake
Lemur health & conservation
Biochemical Soul
Fishtown University
Wild Muse
Trisha Saha’s blog
ChemSpider Blog
MLS Animal Department Blog
Science Café Raleigh
Duke Research
CIT Blog
Morehead Planetarium blog
Science Education blog
Real Oceans
The Green Grok
From the Trenches
Duke Research Advantage
The Pimm Group
High Touch
Forth Go
B4 – The blood-brain barrier blog
Scripted Spontaneity
UNC Health Care’s Weblog
Science On Tap
Dr. Tom Linden’s Health Blog
JMP® Blog
NC Conservation Network Blog
Brain Blog
Blogs in the rest of North Carolina: Blog
Cognitive Daily
Pondering Pikaia
Endless Forms
Southern Fried Science
Skulls in the Stars
Island of Doubt
Watershed Hydrogeology Blog
The Other 95%
Crowded Head, Cozy Bed
Carpenter Library News
Greensboro Birds
Our Backyard Life
Mary’s View

My picks from ScienceDaily

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Clock Quotes

Every normal man must be tempted at times to spit on his hands, hoist the black flag, and begin slitting throats.
– Henry Lewis Mencken

Identify Mystery Mammal


Clock Quotes

Although you may remain somewhere for a long time,
It is certain that you will have to leave;
Whatever may be the manner of parting,
The actual going cannot be avoided.

– Nagarjuna

Night, night, Ida…

Some 47 million years ago, Ida suffocated in the volcanic ashes. I feel the same way at the end of this week – I need to get some air. And some sleep.
But watching the media and blog coverage of the fossil around the clock for a few days was actually quite interesting, almost exhilarating – and there are probably not as many people out there who, like me, read pretty much everything anyone said about it this week. Interestingly, my own feel of the coverage was different if I assumed an angle of a scientist, an angle of an interested student of the changes in the media ecosystem, and an angle of a PLoS employee. It is far too early to have any clear thoughts on it at this point.
But if you want to catch up with me, I have put together a sampling of the blog and media coverage over on the everyONE blog.

Welcome the newest SciBling!

Go say Hello to Christina Pikas at Christina’s LIS Rant – yes, we got another librarian! w00t! You can check the archives of her old blog here.

My picks from ScienceDaily

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Clock Quotes

There was a definite process by which one made people into friends, and it involved talking to them and listening to them for hours at a time.
– Rebecca West

The Open Laboratory 2009 – the submissions so far

OpenLab logo.jpg
Here are the submissions for OpenLab 2009 to date. As we have surpassed 130 entries, all of them, as well as the “submit” buttons and codes, are under the fold. You can buy the 2006, 2007 and 2008 editions at Please use the submission form to add more of your and other people’s posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):

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‘Special for Bora’

Earlier today I went up the street to Town Hall Grill and saw their white-board where they write the descriptions of Dinner Specials….and there is a new one today with the name “Special for Bora”! Wow! The perks of being a regular customer!
Well, of course I got one, brought it home, re-arranged it on one of my plates and took a picture:
special for Bora.jpg
Deliciously tender fried chicken, corn on the cob and fresh (probably locally grown) vegetables: carrots, squash. onions and broccoli. A very summery, light and delicious meal! Yum!

New and Exciting in PLoS this week

Just in case you missed them, there were other papers published in seven PLoS Journals this week besides Ida ;-)
Here are my own picks for the week – you go and look for your own favourites. As always, and for the first time this applies to all seven journals, 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, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click.
Effects of Nocturnal Light on (Clock) Gene Expression in Peripheral Organs: A Role for the Autonomic Innervation of the Liver:

The biological clock, located in the hypothalamic suprachiasmatic nucleus (SCN), controls the daily rhythms in physiology and behavior. Early studies demonstrated that light exposure not only affects the phase of the SCN but also the functional activity of peripheral organs. More recently it was shown that the same light stimulus induces immediate changes in clock gene expression in the pineal and adrenal, suggesting a role of peripheral clocks in the organ-specific output. In the present study, we further investigated the immediate effect of nocturnal light exposure on clock genes and metabolism-related genes in different organs of the rat. In addition, we investigated the role of the autonomic nervous system as a possible output pathway of the SCN to modify the activity of the liver after light exposure. First, we demonstrated that light, applied at different circadian times, affects clock gene expression in a different manner, depending on the time of day and the organ. However, the changes in clock gene expression did not correlate in a consistent manner with those of the output genes (i.e., genes involved in the functional output of an organ). Then, by selectively removing the autonomic innervation to the liver, we demonstrated that light affects liver gene expression not only via the hormonal pathway but also via the autonomic input. Nocturnal light immediately affects peripheral clock gene expression but without a clear correlation with organ-specific output genes, raising the question whether the peripheral clock plays a “decisive” role in the immediate (functional) response of an organ to nocturnal light exposure. Interestingly, the autonomic innervation of the liver is essential to transmit the light information from the SCN, indicating that the autonomic nervous system is an important gateway for the SCN to cause an immediate resetting of peripheral physiology after phase-shift inducing light exposures.

When Art, Science, and Culture Commingle:

The history of modern science is punctuated by moments when the fruits of science captivate the public imagination. Traces of these impressions can be found in works of art; for instance, one sees the influence of 17th century astronomy on poetry in Paradise Lost, as when Satan stops by the sun to ask for directions to the earth, Milton alludes to Galileo’s discovery of sunspots: “There lands the Fiend, a spot like which perhaps/Astronomer in the Sun’s lucent Orbe/Through his glaz’d Optic Tube yet never saw” and in the sudden emergence of the ellipse in baroque architecture [1]. More recently, scholars have argued for the influence of relativity theory on the development of cubist painting [2] and of both relativity and quantum mechanics on the poetry of T.S. Eliot [3]. (“What might have been is an abstraction/Remaining a perpetual possibility/Only in a world of speculation.”)

Paleogenomics in a Temperate Environment: Shotgun Sequencing from an Extinct Mediterranean Caprine:

Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations. A DNA extraction of a ~6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous. A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.

How to Get the Most out of Your Curation Effort:

Data annotation (manual data curation) tasks are at the very heart of modern biology. Experts performing curation obviously differ in their efficiency, attitude, and precision, but directly measuring their performance is not easy. We propose an experimental design schema and associated mathematical models with which to estimate annotator-specific correctness in large multi-annotator efforts. With these, we can compute confidence in every annotation, facilitating the effective use of all annotated data, even when annotations are conflicting. Our approach retains all annotations with computed confidence values, and provides more comprehensive training data for machine learning algorithms than approaches where only perfect-agreement annotations are used. We provide results of independent testing that demonstrate that our methodology works. We believe these models can be applied to and improve upon a wide variety of annotation tasks that involve multiple annotators.

Female Meiotic Sex Chromosome Inactivation in Chicken:

Meiosis is a sequence of two specialized cell divisions during which haploid gametes are generated. During meiotic prophase, homologous chromosomes pair and recombine to allow proper separation of chromosomes during the first meiotic division. The pairing mechanism is challenged by the presence of the largely nonhomologous sex chromosomes in spermatocytes of male mammals, since X and Y pair only in the short regions of homology. The unpaired nonhomologous regions are recognized and transcriptionally silenced, which leads to the formation of the so-called XY body. In mammalian females, which carry two homologous X chromosomes, no such structure is formed and the sex chromosomes are both active in oocytes. We asked whether meiotic silencing of sex chromosomes also occurs during gametogenesis in chickens. In this species, males carry two Z chromosomes, and females are ZW. We show that Z and W fully pair in oocytes, despite the overall lack of sequence homology. Surprisingly, the ZW pair is transcriptionally silenced during meiotic prophase and remains inactive until the two chromosomes have largely separated. Reactivation of Z at this stage may be necessary to allow expression of genes that are required for further oocyte development. These data show that meiotic sex chromosome silencing occurs also in species with female heterogamety.

XY and ZW: Is Meiotic Sex Chromosome Inactivation the Rule in Evolution?:

The sex chromosomes are among the most rapidly evolving and most diverse genetic systems in all of biology. Students of model organisms may, however, have the false impression that there is only one chromosomal mechanism of specifying sex. Among the best-studied metazoans, the XY system is indeed the rule, with inheritance of two X’s determining the female sex (XX), and inheritance of an X and a Y specifying the male sex (XY) [1]. In this system, females produce only one type of oocyte (X), whereas males produce two types of sperm (X and Y). However, sex is not always determined this way. Throughout evolution, the XY system has co-existed alongside the lesser known ZW system, a scheme exemplified by members of the avian clade who diverged from Mammalia 300 million years ago (Figure 1) [2],[3]. In birds, females are the heterogametic sex, as females have one Z and one W chromosome (ZW) and can therefore produce two types of gametes (Z or W oocytes). By contrast, males are ZZ and can produce only one type of gamete (homogametic)–the Z-bearing sperm. In XY and ZW systems, the homologous sex chromosomes are genetically unequal due to suppression of homologous recombination and accumulation of deleterious mutations on one chromosome of the heterogametic sex [1]. In the XY system, it is the Y that genetically degenerates; in the ZW system, it is the W. Today, the mammalian X carries over three times more genes than the Y does, whereas the chicken Z carries over ten times more than the W.

Policy Coherence in US Tobacco Control: Beyond FDA Regulation:

As the Obama administration moves to enact meaningful and comprehensive health care reform in the United States, tobacco control must be elevated as a public health priority [1]. Though tobacco control efforts have been recognized as a top public health achievement of the 20th century [2], tobacco use continues to be the leading preventable cause of death in the US [3]. As Box 1 shows, the US bears a heavy burden from the health and fiscal effects of smoking. Thus, continued progress in preventing tobacco use and promoting smoking cessation must be a leading priority for health care reform under the new administration. This policy paper gives the current status of tobacco control policies, initiatives, and legislative action at the time of going to press.

Today’s carnivals

Four Stone Hearth #67 is up on Sorting Out Science
Grand Rounds Vol. 5 No. 35 are up on Healthcare Technology news
The 111th Meeting of the Skeptics Circle is up on Action Skeptics
Carnival of the Liberals, Number #91 is up on Crowded Head, Cozy Bed

My picks from ScienceDaily

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Clock Quotes

Despite the warnings of the ancient Greeks – nothing in excess – there are a few things in the world that you just can’t have too much of. In addition to currency, I would mention, in no particular order, health, warm weather, ice-cream flavors, free time, second chances, and good taste.
– Joe McGarvey, Inter@ctive Week

Librarian vs. Stereotype

Now that we have a real librarian on board, perhaps this is the perfect timing to post these two videos:

Hat-tip to CogSci Librarian who is right now live-tweeting her drive down to North Carolina.

Wow! Check

…and you’ll see this:
ida google.JPG