This morning on the radio – podcast is now online!

Podcast of this morning’s radio show is now up – you can listen to it here.
We covered ScienceOnline09, including its history, several individual sessions and underlying themes, the changes in science communication and journalism and more. A brief plug for PLoS at the beginning. Answered a couple of e-mailed questions, including one from Greg Laden (who almost stumped me – had to think quickly on my feet!).
Thanks to Stephanie and Mike for inviting me on.

Circadian Rhythm of Aggression in Crayfish

ResearchBlogging.orgLong-time readers of this blog remember that, some years ago, I did a nifty little study on the Influence of Light Cycle on Dominance Status and Aggression in Crayfish. The department has moved to a new building, the crayfish lab is gone, I am out of science, so chances of following up on that study are very low. And what we did was too small even for a Least Publishable Unit, so, in order to have the scientific community aware of our results, I posted them (with agreement from my co-authors) on my blog. So, although I myself am unlikely to continue studying the relationship between the circadian system and the aggressive behavior in crayfish, I am hoping others will.
And a paper just came out on exactly this topic – Circadian Regulation of Agonistic Behavior in Groups of Parthenogenetic Marbled Crayfish, Procambarus sp. by Abud J. Farca Luna, Joaquin I. Hurtado-Zavala, Thomas Reischig and Ralf Heinrich from the Institute for Zoology, University of Gottingen, Germany:

Crustaceans have frequently been used to study the neuroethology of both agonistic behavior and circadian rhythms, but whether their highly stereotyped and quantifiable agonistic activity is controlled by circadian pacemakers has, so far, not been investigated. Isolated marbled crayfish (Procambarus spec.) displayed rhythmic locomotor activity under 12-h light:12-h darkness (LD12:12) and rhythmicity persisted after switching to constant darkness (DD) for 8 days, suggesting the presence of endogenous circadian pacemakers. Isogenetic females of parthenogenetic marbled crayfish displayed all behavioral elements known from agonistic interactions of previously studied decapod species including the formation of hierarchies. Groups of marbled crafish displayed high frequencies of agonistic encounters during the 1st hour of their cohabitation, but with the formation of hierarchies agonistic activities were subsequently reduced to low levels. Group agonistic activity was entrained to periods of exactly 24 h under LD12:12, and peaks of agonistic activity coincided with light-to-dark and dark-to-light transitions. After switching to DD, enhanced agonistic activity was dispersed over periods of 8-to 10-h duration that were centered around the times corresponding with light-to-dark transitions during the preceding 3 days in LD12:12. During 4 days under DD agonistic activity remained rhythmic with an average circadian period of 24.83 ± 1.22 h in all crayfish groups tested. Only the most dominant crayfish that participated in more than half of all agonistic encounters within the group revealed clear endogenous rhythmicity in their agonistic behavior, whereas subordinate individuals, depending on their social rank, initiated only between 19.4% and 0.03% of all encounters in constant darkness and displayed no statistically significant rhythmicity. The results indicate that both locomotion and agonistic social interactions are rhythmic behaviors of marbled crayfish that are controlled by light-entrained endogenous pacemakers.

I think the best way for me to explain what they did in this study is to do a head-to-head comparison between our study and their study – it is striking how the two are complementary! On one hand, there is no overlap in methods at all (so no instance of scooping for sure), yet on the other, both studies came up with similar results, thus strengthening each other’s findings. You may want to read my post for the introduction to the topic, as I explain there why studying aggression in crayfish is important and insightful, what was done to date, and what it all means, as well as the standard methodology in the field. So, let’s see how the two studies are similar and how the two differ:
1) We were sure we used the Procambarus clarkii species. They are probably not exactly sure what species they had, so they denoted it as Procambarus sp., noting in the Discussion that it was certainly NOT the Procambarus clarkii, which makes sense as our animals were wild-caught in the USA and theirs in Germany. As both studies got similar results, this indicates that this is not a single-species phenomenon, but can be generalizable at least to other crayfish, if not broader to other crustaceans, arhtropods or all invertebrates.
2) We used only males in our study. They used only females. In crayfish, both sexes fight. It is nice, thus, to note that other aspects of the behavior are similar between sexes.
3) We used the term ‘aggression’. They use the term ‘agonistic behavior’, which is scientese for ‘aggression’, invented to erase any hints of anthropomorphism. Not a bad strategy, generally, as assumed aggression in some other species has been later shown to be something else (e.g., homosexual behavior), but in crayfish it is most certainly aggression: they meet, they display, they fight, and if there is no place to escape, one often kills the other – there is no ‘loving’ going on there, for sure.
4) The sizes of animals were an order of magnitude different between the two studies. Their crayfish weighed around 1-2g while ours were 20-40g in body mass. This may be due to species differences, but is more likely due to age – they used juveniles while we used adults. Again, it is nice to see that results in different age groups are comparable.
5) We did not measure general locomotor activity of our animals in isolation. We, with proper caveats, used aggressive behavior of paired animals as a proxy for general locomotor activity, and were straightforward about it – we measured aggressive behavior alone in a highly un-natural setup. As Page and Larimer (1972) have done these studies before, we did not feel the need to replicate those with our animals.
The new study, however, did monitor gross locomotor activity of isolated crayfish. Their results, confirming what Page and Larimer found out, demonstrate once again that activity rhythms are a poor marker of the underlying circadian pacemaker (which is why Terry Page later focused on the rhythm of electrical activity of the eye, electroretinogram – ERR – in subsequent studies) in crayfish. Powerful statistics tease out rhythmicity in most individuals, but this is not a rhythm I would use if I wanted to do more complex studies, e.g., analysis of entrainment to exotic LD cycles or to build and interpret a PhaseResponse Curve. Just look at their representative example (and you know this is their best):
crayfish image 1.JPG
You can barely make out the rhythm even in the light-dark cycle (white-gray portion of the actograph) and the rhythms in constant darkness (solid gray) are even less well defined – thus only statistical analysis (bottom) can discover rhythms in such records. The stats reveal a peak of activity in the early night and a smaller peak of activity at dawn, similarly to what Page and Larimer found in their study, and similar to what we saw during our experiments.
6) They used an arena of a much larger size than ours. We did it on purpose – we wanted to ‘force’ the animals to fight as much as possible by putting them in tight quarters where they cannot avoid each other, as we were interested in physiology and wanted it intensified so we could get clearly measurable (if exaggerated) results. Their study is, thus, more ecologically relevant, but one always has to deal with pros and cons in such decisions: more realistic vs. more powerful. They chose realism, we chose power. Together, the two approaches reinforce and complement each other.
7) As I explained in my old post – there are two methodological approaches in this line of research:

Two standard experimental practices are used in the study of aggression in crustaceans. In one, two or more individuals are placed together in an aquarium and left there for a long period of time (days to weeks). After the initial aggressive encounters, the social status of an individual can be deduced from its control of resources, like food, shelter and mates.
In the other paradigm, two individuals are allowed to fight for a brief period of time (less than an hour), after which they are isolated again and re-tested the next day at the same time of day.

They used the first method. We modified the second one (testing repeatedly, every 3 hours over 24 hours, instead of just once a day).
What they did was place 6 individuals in the aquarium, a couple of hours before lights-off, then monitor their aggressive behavior over several days. What they found, similar to us, is that the most intense fights resulting in a stable social hierarchy occur in the early portion of the night:
crayfish image 2.JPG
Once the social hierarchy is established on that first night, the levels of aggression drop significantly, and occasional bouts of fights happen at all times, with perhaps a slight increase at the times of light switches: both off and on. Released into constant darkness, the pattern continues, with the most dominant individual initiating aggressive encounters a little more often during light-transitions then between them. The other five animals had no remaining rhythm of agonistic behavior: they just responded to attacks by the Numero Uno when necessary.
In our study we tried to artificially elevate the levels of aggression by repeatedly re-isolating and re-meeting two animals at a time. And even with that protocol, we saw the most intense fights at early night, and most conclusive fights, i.e., those that resulted in stable social hierarchy, also occuring at early nights, while the activity at other time of the day or night were much lower.
8) The goals of two studies differed as well, i.e., we asked somewhat different questions.
Our study was designed to provide some background answers that would tell us if a particular hypothesis is worth testing: winning a fight elevates serotonin in the nervous system; elevated serotonin correlated with the hightened aggression in subsequent fights, more likely leading to subsequent victories; crayfish signal dominance status to each other via urine; melatonin is a metabolic product of serotonin; melatonin is produced only during the night with a very sharp and high peak at the beginning of the night; if there is more serotonin in the nervous system, there should be more melatonin in the urine; perhaps melatonin may be the signature molecule in the urine indicating social status.
In order to see if this line of thinking is worth pursuing, we needed to see, first, if the most aggressive bouts happen in the early night and if the most decisive fights (those that lead to stable hiararchy) happen in the early night. This is what we found, indicating that our hypothesis is worth testing in the future.
They asked a different set of questions:
Is there a circadian rhythm of locomotor activity? They found: Yes.
Is there a circadian rhythm of aggression? They found: Yes.
Do the patterns of general activity and aggressive activity correlate with each other? They found: Yes.
Does the aggression rhythm persist in constant darkness conditions? They found: Yes.
Do all individuals show circadian rhythm of aggression? They found: No. Only the most dominant individual does. The others just defend themselves when attacked.
Is there social entrainment in crayfish, i.e., do they entrain their rhythms to each other in constant conditions? They found: No. All of them just keep following their own inherent circadian periods and drift apart after a while.
Is there a pattern of temporal competitive exclusion, i.e., do submissive individuals shift their activity patterns so as not to have to meet The Badassest One? They found: No. All of them just keep following their own inherent circadian periods.
So, a nice study overall, the first publication I know of that attempts to connect the literature on circadian rhythms in crayfish to the literature on aggressive behavior in crayfish.
Except….

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Brand spankin’ new carnivals!

Carnival of the Arid #1 is up on Coyote Crossing. Get all your deserted bloggy goodness all in one place.
A new carnival is in the making – Diversity in Science – covering the minorities in science and engineering. February being the Black History Month, the inaugural edition of the carnival will have a special focus on African American experience in the world of science. Deadline is Friday, February 20th. DNLee will host the first edition on Tuesday, February 24.

Denis Dutton on Colbert Show (video)

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My picks from ScienceDaily

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Clock Quotes

The police are the public and the public are the police; the police being only members of the public who are paid to give full time attention to duties which are incumbent on every citizen in the interests of community welfare and existence.
– Robert Peel

Look what came in the mail today:

Emerging Model Organisms:
emerging animal models cover.jpg
All exciting, but of course, I got it for the chapter on Japanese Quail. The protocol desribes how to make a transgenic quail. It sounds easy on paper. A few years back I took a graduate class and we spent the entire semester going through all the steps needed to make a transgenic bird. Nice to see this species getting a serious look once again. Will keep watching….

Nature Network Hubs

Hubs on Nature Network are multiplying. First, there was a Boston hub, then a London hub, and now a brand new New York City hub. Toronto and Berlin are itching to be the next.
On the other hand, the Research Triangle group is still pretty small. I think it’s due to a different geography. Boston, London and NYC are huge cities with lots of people, including many scientists and bloggers. The areas outside of those cities – the ‘countryside’ – are really not that relevant to the sizes of those hubs – add a few people here or there.
On the other hand, North Carolina is a large state, in area and population, but there is no humongous city in it – all the scientists and bloggers are spread all over the state. Why would people from Asheville, or Charlotte, Greensboro, Winston-Salem or Wilmington join the Triangle hub when they don’t live there? I think we should expand the Triangle list to include the entire state and rename the group ‘North Carolina’ people. After all, no state has more bloggers on scienceblogs.com than NC, not even close, yet no NC city can come close to one of the Big Cities elsewhere.
In the meantime, if you are in NC, no matter where in it, please join the Triangle location and increase our numbers, so we can compete for a Hub in the future.

You can laugh now….

…but some people knew waaay back then that news will, one day, move from expensive paper to cheap internet:

From here

TechCrunch surfaced this look at a story that ran back in 1981 that covered
how internet news would someday be delivered. At least watch the last 30 seconds. The reporter remarks it would take more than 2 hours to deliver the digital text needed to read the “online newspaper.” She added the per minute (i think) charge was around $5 and comments about the difficulty the new approach would have when competing with the .20 cent daily.
What’s in store for us over the next 30 years?

Look what came in the mail yesterday:

Evolution vs. Creationism: An Introduction by Eugenie C. Scott.
genie scott book cover.jpg
Written at this time.

ScienceOnline’09 – Saturday 3:15pm – Blog carnivals

scienceonline09.jpg
The very first blog carnival was conceived right here, in Chapel Hill, some four-five years ago or so. Since then, the idea took off and there are now thousands of blog carnivals, some generalist, some regional, but most are topical with topics ranging from food to sports to politics. But, probably due to the funny name, new bloggers and observers are often baffled at the concept. I thought it would be a good idea to have a session that explains the concept of the carnival, specifically how the carnivals related to science, nature and medicine are somewhat different from other kinds of carnivals, and why they are Good For You.
Well, there are two people who have spent a lot of time studying and writing about science-related carnivals. I am one of them (read this for the latest, as well as for the links to older material) but as an organizer I did not want to tie myself down with actually leading the session. The other one is Mike Bergin, so he was the obvious choice to invite to lead this session – Blog carnivals: why you should participate.
Mike has written probably the most comprehensive guide to blog carnivals ever – a must read if you intend to participate in, host or start a carnival. So, in his session, he delivered – a good explanation of what a carnival is, how to approach it as a new blogger (or an old blogger for that matter) and why carnivals are an important aspect of the blogosphere.
Science-related carnivals are similar to popular science magazines, or, in some cases, even to lightly peer-reviewed journals. A well-maintained archive of a carnival is like a human-managed search engine on the topic: you can use it to start your search of a topic and how science blogosphere covered it at the moment it was hot news. This function will become more and more important in the future, as blogosphere becomes older.
Sure, you can go to Google or Technorati and search blogs for a topic, but what you’ll get are millions of hits, most of them simple links or copy+paste jobs – useless waste of time. A carnival will contain the best examples of blog coverage of the topic and the included posts will often also contain links to other worthwhile coverage of the same topic – thus a good start for a smart, targeted search. Not to mention how much more fun it is to read stuff with a human touch and an editorial hand as compared to just using an automated, soulless application.
But carnivals have several other functions. And I was happy to see some of them mentioned in other sessions at the conference.
For instance, many bloggers use carnivals for self-discipline in their blogging. Yes, you post LOLcats and YouTube videos most of the time, but once every week or two you make yourself sit down and do some research and write a serious, carnival-worthy post, just so you can submit it to your favourite carnival.
Furthermore, the existence of a particular carnival may make a blogger get outside of regular topics and explore something different. For instance, The Giant’s Shoulders has provoked many science bloggers to start digging into the history of science and writing posts about classical papers or historical concepts in science. This was, I understand, stressed strongly in the ‘History of Science’ session that day.
One function of carnivals that many appreciate the most is the community building it enables. For intance, in her analysis of the connectivity of science blogs, Christina Pikas discovered an unusually tight cluster of female scientist blogs. Several of those bloggers were present at the conference and, in a few sessions, all credited Scientiae carnival as one of the key community-building tools.
We could also see (and hear, oh did we ever!) that marine bloggers are also a tightly-knit community. In another session (on blogging networks, for instance) they mentioned that Carnival of the Blue is a key tool for building their community, discovering and introducing new marine biology bloggers, introducing each other and organizing events (even if it’s The Invertebrate War – a wonderful community-building tool in itself).
I And The Bird was mentioned as an important tool for building communities in the ‘Nature blogging’ session as well. A carnival similar to Scientiae but focused on minorities in science may come out of discussions at the conference as well.
Finally, usually around Christmas when everyone is either busy or offline, some carnivals suffer gaps or start appearing dead – managing them takes work! The discussions at the conference led to appeals to rescue some of those, with immediate results – Circus of the Spineless has a new manager and will re-start publishing on Monday. Likewise, Tangled Bank (the carnival equivalent of Nature) is about to stage a comeback.
I hope that Mike’s session has informed new people about the importance of carnivals and spurred others to revive old or start new ones.
More coverage of this session:
10000birds: Talking Blog Carnivals at ScienceOnline09
Nature Blog Network: What is a Blog Carnival?
Deep Thoughts and Silliness: Semi-live Blogging Scienceonline09: Day 1
Living the Scientific Life: What Happened to Tangled Bank?
Living the Scientific Life: Science Blog Carnivals: Another Endangered Species
Other sessions in this time-slot that I missed:
Open Notebook Science:
bjoern.brembs.net: ScienceOnline09: Open Notebook Science
Highly Allochthonous: ScienceOnline Day 1: generalised ramblings
Science in the open: The integrated lab record – or the web native lab notebook
Art and science — online and offline:
The Flying Trilobite: ScienceOnline09 – Art & Science afterword
Ideonexus: ScienceOnline09: Science and Art
Bioephemera: Art vs. Science, Part One: Semiconductor
The Flying Trilobite: Art & Science at ScienceOnline ’09 discussion continues…
Expression Patterns: ScienceOnline09 – Day 2
Nobel Intent: ScienceOnline 09: History, art, and science
Anonymity, Pseudonymity – building reputation online:
HASTAC blogs: Liveblogging ScienceOnline ’09: Anonymity and Pseudonymity – Building Reputation Online
Knowledge Sharing: ScienceOnline’09: Anonymity, Pseudonymity
Confessions of a Science Librarian: ScienceOnline ’09: Saturday summary
Christina’s LIS Rant: Science Online ’09: Saturday PM
Extreme Biology: Anna’s Favorite Moment from Science Online ’09
The blog/media coverage linkfest is growing fast (perhaps start at the bottom and work your way up, posting comments on the way and saying Hello to your new friends), there are ongoing discussions on FriendFeed and new pictures on Flickr. Also, if you were there, please fill up this short form to give us feedback, so we can make next year’s meeting even better.

Circus of the Spineless – call for submissions

Circus of the Spineless is back! Under the new management of Kevin Zelnio, this lovely carnival will re-start this month.
The next edition will be this Monday, February 2nd, on The Other 95% so send in your entries (kzelnio at gmail dot com) on all things invertebrate, anything carnival-worthy that you have written since August 2008!

Blogroll Amnesty Day

BAD2-2-1.jpg
skippy and Jonn Swift and Blue Gal are spearheading the Blogroll Amnesty Day (read the detailed instructions in there) again this year.
This weekend, a long weekend starting today and lasting four days, you are supposed to use the above logo, link to the Blogroll Amnesty Day post and link to five blogs that have either smaller traffic or narrower reach than you, or at least are new and unknown to your readers. Then e-mail your permalink to skippy.
Let’s promote the new and smaller voices that you think should be known by a wider audience!
I could, of course, list 50 or 500, but I’ll stick to the rules and, after agonizing for a long time, suggest these five blogs for you to check out:
Urban Science Adventures!
FYI: Science!
Endless Forms
Dara Sosulski’s blog
The Extrovert Scientist

Today’s carnivals

Berry Go Round #13 is up on Watching the World Wake Up

My picks from ScienceDaily

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Clock Quotes

I want to talk to these people because they stay in power and you change all the time.
– Nikita Sergeyevich Khrushchev

Periodic System of Elements

Check out Element Displays, including The Element Collection and Interactive Installations. Each page is also interactive – keep clicking for more information.

Don’t forget….

…to tune in in the morning.

Randolph Nesse on Darwinian Medicine (video)

New and Exciting in PLoS ONE

There are 14 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:
Forest Structure and Roe Deer Abundance Predict Tick-Borne Encephalitis Risk in Italy:

The Western Tick-borne encephalitis (TBE) virus often causes devastating or lethal disease. In Europe, the number of human TBE cases has increased dramatically over the last decade, risk areas are expanding and new foci are being discovered every year. The early localisation of new TBE foci and the identification of the main risk factors associated with disease emergence represent a priority for the public health community. Although a number of socio-economic parameters have been suggested to explain TBE upsurges in eastern Europe, the principal driving factors in relatively stable western European countries have not been identified. In this paper, we analyse the correlation between the upsurge of TBE in 17 alpine provinces in northern Italy from 1992 to 2006 with climatic variables, forest structure (as a proxy for small mammal reservoir host abundance), and abundance of the principal large vertebrate tick host (roe deer), using datasets available for the last 40 years. No significant differences between the pattern of changes in climatic variables in provinces where TBE has emerged compared to provinces were no clinical TBE cases have been observed to date. Instead, the best model for explaining the increase in TBE incidence in humans in this area include changes in forest structure, in particular the ratio of coppice to high stand forest, and the density of roe deer. Substantial changes in vegetation structure that improve habitat suitability for the main TBE reservoir hosts (small mammals), as well as an increase in roe deer abundance due to changes in land and wildlife management practices, are likely to be among the most crucial factors affecting the circulation potential of Western TBE virus and, consequently, the risk of TBE emergence in humans in western Europe. We believe our approach will be useful in predicting TBE risk on a wider scale.

The Effect of Transposable Element Insertions on Gene Expression Evolution in Rodents:

Many genomes contain a substantial number of transposable elements (TEs), a few of which are known to be involved in regulating gene expression. However, recent observations suggest that TEs may have played a very important role in the evolution of gene expression because many conserved non-genic sequences, some of which are know to be involved in gene regulation, resemble TEs. Here we investigate whether new TE insertions affect gene expression profiles by testing whether gene expression divergence between mouse and rat is correlated to the numbers of new transposable elements inserted near genes. We show that expression divergence is significantly correlated to the number of new LTR and SINE elements, but not to the numbers of LINEs. We also show that expression divergence is not significantly correlated to the numbers of ancestral TEs in most cases, which suggests that the correlations between expression divergence and the numbers of new TEs are causal in nature. We quantify the effect and estimate that TE insertion has accounted for ~20% (95% confidence interval: 12% to 26%) of all expression profile divergence in rodents. We conclude that TE insertions may have had a major impact on the evolution of gene expression levels in rodents.

Nitric Oxide Administration Using an Oxygen Hood: A Pilot Trial:

We have shown earlier that inhaled nitric oxide (iNO) administered by oxygen hood reduces pulmonary hypertension in an animal model (J Perinatol 2002; 22:50-6). Our objective in this study was to determine feasibility of iNO by oxygen hood in neonates with elevated alveolar-arterial oxygen gradients (A-aDO2). Masked randomized controlled pilot trial. Inclusion criteria were: gestation≥34 weeks, age100 torr, while oxygenation was unchanged in the controls. Methemoglobinemia and other adverse effects were not noted in any infant. Environmental levels of NO and NO2 were minimal (0.3 m from the hood. Administration of iNO by oxygen hood is feasible. Larger randomized controlled trials are required to measure the efficacy and determine an appropriate target population for this technique.

On the Evolution of the Standard Genetic Code: Vestiges of Critical Scale Invariance from the RNA World in Current Prokaryote Genomes:

Herein two genetic codes from which the primeval RNA code could have originated the standard genetic code (SGC) are derived. One of them, called extended RNA code type I, consists of all codons of the type RNY (purine-any base-pyrimidine) plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. In order to test if putative nucleotide sequences in the RNA World and in both extended RNA codes, share the same scaling and statistical properties to those encountered in current prokaryotes, we used the genomes of four Eubacteria and three Archaeas. For each prokaryote, we obtained their respective genomes obeying the RNA code or the extended RNA codes types I and II. In each case, we estimated the scaling properties of triplet sequences via a renormalization group approach, and we calculated the frequency distributions of distances for each codon. Remarkably, the scaling properties of the distance series of some codons from the RNA code and most codons from both extended RNA codes turned out to be identical or very close to the scaling properties of codons of the SGC. To test for the robustness of these results, we show, via computer simulation experiments, that random mutations of current genomes, at the rates of 10−10 per site per year during three billions of years, were not enough for destroying the observed patterns. Therefore, we conclude that most current prokaryotes may still contain relics of the primeval RNA World and that both extended RNA codes may well represent two plausible evolutionary paths between the RNA code and the current SGC.

Confusion and Conflict in Assessing the Physical Activity Status of Middle-Aged Men:

hysical activity (including exercise) is prescribed for health and there are various recommendations that can be used to gauge physical activity status. The objective of the current study was to determine whether twelve commonly-used physical activity recommendations similarly classified middle-aged men as sufficiently active for general health. We examined the commonality in the classification of physical activity status between twelve variations of physical activity recommendations for general health in ninety men aged 45-64 years. Physical activity was assessed using synchronised accelerometry and heart rate. Using different guidelines but the same raw data, the proportion of men defined as active ranged from to 11% to 98% for individual recommendations (median 73%, IQR 30% to 87%). There was very poor absolute agreement between the recommendations, with an intraclass correlation coefficient (A,1) of 0.24 (95% CI, 0.15 to 0.34). Only 8% of men met all 12 recommendations and would therefore be unanimously classified as active and only one man failed to meet every recommendation and would therefore be unanimously classified as not sufficiently active. The wide variability in physical activity classification was explained by ostensibly subtle differences between the 12 recommendations for thresholds related to activity volume (time or energy), distribution (e.g., number of days of the week), moderate intensity cut-point (e.g., 3 vs. 4 metabolic equivalents or METs), and duration (including bout length). Physical activity status varies enormously depending on the physical activity recommendation that is applied and even ostensibly small differences have a major impact. Approximately nine out of every ten men in the present study could be variably described as either active or not sufficiently active. Either the effective dose or prescription that underlies each physical activity recommendation is different or each recommendation is seeking the same prescriptive outcome but with variable success.

Skewed views of science (video)

Today’s carnivals

Carnival of Evolution #8 is up on Biochemicalsoul
The fifty-ninth Four Stone Hearth is up on A Very Remote Period Indeed
Friday Ark #228 is up on Modulator

Attenborough makes sense (video)

Darwin Day talk by Carl Zimmer in Raleigh

From NESCENT:

Carl Zimmer
“Darwin and Beyond: How Evolution Is Evolving”
February 12, 2009
6:30 pm – 7:30 pm
Talk Overview: Charles Darwin launched the modern science of evolution, but he hardly had the last word. In fact, today scientists are discovering that evolution works in ways Darwin himself could not have imagined. In my talk I will celebrate Darwin’s achievements by looking at the newest discoveries about evolution, from the emergence of life to the dawn of humanity.
Please join us for a Darwin Day presentation by Carl Zimmer. Mr. Zimmer is well known for his popular science writing, particularly his work on evolution. He has published several books including Soul Made Flesh, a history of the brain, Evolution: The Triumph of an Idea, At the Water’s Edge, a book about major transitions in the history of life, The Smithsonian Intimate Guide to Human Origins; and his latest book Microcosm: E. coli and the New Science of Life. Mr. Zimmer contributes to the New York Times, National Geographic, Discover, Scientific American, Science, and Popular Science. He also maintains an award winning blog The Loom.
Location:
North Carolina Museum of Natural Sciences
11 W. Jones St.
Raleigh, NC 27601-1029

More info to come. I’ll try to grab Carl and take him to some cool local undisclosed location for a beer. I’ll have more when the time gets closer and we have something planned….

My picks from ScienceDaily

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Clock Quotes

We live in a time of such rapid change and growth of knowledge that only he who is in a fundamental sense a scholar – that is, a person who continues to learn and inquire – can hope to keep pace, let alone play the role of guide.
– Nathan M. Pusey

New and Exciting in PLoS this week

So, let’s see what’s new in PLoS Genetics, PLoS Computational Biology, PLoS Pathogens and PLoS ONE this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:
Microblogging the ISMB: A New Approach to Conference Reporting:

The International Conference on Intelligent Systems for Molecular Biology (ISMB) has become an important communication hub for bioinformaticians, and the core element of the Conference–presentations of peer-reviewed papers–is now only one of many activities. Presentation of timely journal publications (the Highlights sessions), Special Sessions organized by experts in the respective fields, Tutorials, and Special Interest Group meetings should attract attendees who might otherwise prefer smaller, more focused meetings. In addition to these formal activities, an important aspect is the informal communication between participants. This year, about 1,600 participants attended the meeting in the conference center under the CN Tower in Toronto. ISMB 2008 also left a footprint on the Web, via a Web service named FriendFeed (http://friendfeed.com/), to capture highlights from the Conference in near real time. FriendFeed allows users to share items, either directly or by importing their latest content from any Web site that generates an RSS feed, leading to a continuous stream of information around which communities build (Figure 1). In addition, and of most relevance to ISMB, FriendFeed acts as a microblogging platform: Users post short, typically single-sentence messages which generate conversations in the ensuing comment threads. Microblogging, best exemplified by the Twitter service (http://twitter.com/), is popular in the IT/tech sector, but little used by life scientists. It may be thought of as the fusion of instant messaging and traditional blogs: Anyone can follow or join a conversation, and conversations are archived. We recommend an article by Cameron Neylon entitled FriendFeed for Scientists: What, Why, and How? (http://blog.openwetware.org/scienceintheopen/2008/06/12/friendfeed-for-scientists-what-why-and-how/) for an introduction.

The Sicker Sex

Arguments about the weaker sex notwithstanding, there is no contest about the identity of the sicker sex–it is males, almost every time. Everyone knows that old age homes have more widows than widowers, but the disparity extends far beyond the elderly. Fewer women than men died in the 1917-1918 influenza epidemic; the differential mortality was not related to World War I, as originally thought, but was global and widespread among ages. Kruger and Nesse [1] compared men’s and women’s mortality rates for 11 causes of death in men and women from 20 countries, including accidents and homicide as well as infectious and non-infectious diseases, and found that men virtually always die earlier. They concluded, “Being male is now the single largest demographic risk factor for early mortality in developed countries”. Furthermore, in many free-living mammals, males are more likely than females to harbor parasites or to suffer more intensely from their effects. During the mid-20th century, a virtual cottage industry developed in which investigators experimentally infested laboratory rodents with parasites and documented any resulting sex differences in the prevalence or intensity of the infection that developed [2]. Males usually developed higher parasitemia, with castration removing the sex difference. The persistence of these patterns in the laboratory suggests that the sex difference is not merely due to differences in exposure to parasites, with males and females behaving differently in the field and hence incurring different risks of infection, but to an inherent sex difference in vulnerability.

And check out the first of PLoS ONE CollectionsStress-Induced Depression and Comorbidities: From Bench to Bedside:

This collection of articles represents the output of a group of international research institutions (informally referred to as EUMOOD) who collaborated around the causal link between stress exposure and depression vulnerability.
Within the collection, preclinical and clinical research papers present an integrated experimental effort, employing a variety of methods and concepts from different disciplines such as biological psychiatry, neuroscience, and neuroendocrinology.
Editorial oversight, and coordination of the peer-review, was provided by Bernhard Baune, PLoS ONE Section Editor for Neuroscience and Psychiatry.

A very nice article about ScienceOnline09 in BioTechniques

By Colleen M. Smith: NEWS: ScienceOnline’09 explores the evolution of science on the web:

Research Triangle Park, NC, Jan. 16–The third annual science communication conference, ScienceOnline’09, took place at the Sigma Xi Center last weekend. The event was open to all scientists, bloggers, educators, students, journalists, and others interested in exploring science and ways to communicate it on the web….

Today’s carnivals

104th Skeptics’ Circle: The Skepticism Review and Education Program Edition…..is up on Space City Skeptics
Carnival of the Liberals #83: Obacalypse Edition is up on And Doctor Biobrain’s Response Is…

Transforming Learning Through Computational Thinking

From SCONC:

Tuesday, Feb. 10
7 p.m.
Science Cafe Durham: Transforming Learning Through Computational Thinking
Bob Panoff of the Shodor Foundation tells Periodic Tables why he left academics to create an organization devoted to hands-on learning projects.
Broad Street Café, 1116 Broad Street, Durham, NC 27705.
More – http://www.ncmls.org/periodictables#transforming

My picks from ScienceDaily

Continue reading

Clock Quotes

I do not think there is any thrill that can go through the human heart like that felt by the inventor as he sees some creation of the brain unfolding to success…. Such emotions make a man forget food, sleep, friends, love, everything.
– Nikola Tesla

Teaser…..

Coming soon:
openlab08cover.JPG

Thank them – they made ScienceOnline’09 possible

scienceonline09.jpg

ScienceOnline’09, the third annual science communication conference (successor to the 2007 and 2008 North Carolina Science Blogging Conferences), was another unqualified success wifi issues notwithstanding. Around 215 scientists, educators, students, journalists and bloggers gathered for three days of activities, meals, sessions and hallway conversations to explore ways to use online tools to promote the public understanding of, and engagement in, science.

Find a comprehensive listing of links to the many blog entries and video clips posted before, during and after the conference to learn about the conversations and networking at the conference.

Like our first two conferences, ScienceOnline’09 was a collective activity many organizations, companies and individuals pitched in, in ways large and small, to keep this conference free, attendees fed and the discussion lively. Please join us in thanking them read below, and click through to their websites to show your interest in what they do. (We thanked the sponsors of the second event here and the first event here.)

So, a huge Thank you to our sponsors for helping us to keep this event free:

Our host
Sigma Xi once again hosted the ScienceOnline’09 conference, as well as the WiSE networking event for free in their beautiful center. Meg Murphy kindly facilitated this – she’s the unsung hero of the conference! and Mike was on hand for tech support. Sigma Xi was founded in 1886 to honor excellence in scientific investigation and encourage a sense of companionship and cooperation among researchers in all fields of science and engineering.

Our institutional partner
The NC Museum of Life and Science, which last year arranged for the awesome grab bags, this year stepped up to be our institutional partner (to handle our funds). Debbie May, VP for Administration/CFO, was a delight to work with, and Troy Livingston, VP for Innovation Learning, continues to be one of our biggest boosters. The museum exists to create a place of lifelong learning where people, from young child to senior citizen, embrace science as a way of knowing about themselves, their community, and their world.

Our sponsors
Burroughs Wellcome Fund once again gave us a substantial grant to support the conference. Russ Campbell, communications officer, helped to make sure this funding was available to us. BWFund is an independent private foundation dedicated to advancing the biomedical sciences by supporting research and other scientific and educational activities.

The North Carolina Biotechnology Center repeated its support with a biotechnology event sponsorship grant; Ginny DeLuca and Chris Brodie there are our supporters. NCBiotech seeks to provide longterm economic and societal benefits to North Carolina by supporting biotechnology research, business and education statewide.

We used the grants from BWFund and NCBiotech to give small travel stipends to our many session discussion leaders.

JMP Software, for the third year in a row, provided a cash grant to help pay for our delicious lunch. JMP is a division of SAS, the leader in business intelligence and analytics – they’ve also donated a copy of their JMP 8 software (worth $1500), which we’ll have as a drawing prize on Saturday (you need to fill the feedback form to enter the drawing).

Science In the Triangle was a new sponsor this year. This site is an evolving experiment in community science journalism and scientific community organizing. If you are based here in the Triangle, think about how you might collaborate with the site to spread news of your organization or research – Anton and I are looking forward to getting involved with the effort.

Research Triangle Foundation helped us even our accounts with a last-minute grant. The Foundation just celebrated the 50th anniversary of Research Triangle Park, and will host the XXVI International Association of Science Parks World Conference June 14, 2009.

Blogads has sponsored many of our BlogTogether events over the last four years, and once again Henry Copeland and his crew made a donation to this conference. They pioneered blog advertising in 2002 and trailblaze today.

We used the donations from JMP, Science In the Triangle, Research Triangle Foundation and Blogads to feed everyone, with good coffee in the morning and delicious sandwiches and Mediterranean salads at lunch.

Our donors
Enrico Maria Balli, Kim Gainer, Ryan Somma and Russ Campbell made personal cash donations, and David Kroll, our coorganizer, dipped into his own pocket to help make the conference unique.

Grab bag of science swag
This year, IBM provided recycled reusable bags. Other organizations, companies and individuals donated materials, including: Howard Hughes Medical Institute, Seed Magazine, Public Library of Science, COPUS Year of Science, Harper Collins, JMP Software, NC Sea Grant, National Evolutionary Synthesis Center and others to be named later.

Friday events
Counter Culture Coffee invited us to attend their weekly coffee cupping. Mark Overbay, marketing communications manager, facilitated our group of 25 and gave a tour of the coffee roasting operation.

Afternoon lab tours were hosted by NCCU‘s Biomanufacturing Research Institute and Technology Enterprise (David Kroll, director), Duke’s Lemur Center and Smart Home (Karl Bates arranged these), and the NC Museum of Natural Sciences (Roy Campbell was host and tour leader).

Rebecca Skloot couldn’t join us last year, but with her book finally drafted and off to her publisher, she was game to come to RTP this year to attend ScienceOnline’09 and keynote the Women in Science and Engineering networking event Friday night at Sigma Xi. Erica Tsai, Phoebe Lee, Ana Sanchez, Amrika Deonarine and Rachel Witek put together a fantastic event, and Skloot’s talk about the immortal contribution of Henrietta Lacks to science was riveting. (Abel Pharmboy hosted a rousing wine tasting, too.)

Our discussion leaders
ScienceOnline’09 was an unconference in which all attendees were encouraged to participate and share alike; we asked 77 of them to serve as session discussion leaders, to provide their experiences or perspectives as a way to spark the session conversations. See the conference agenda to find out who facilitated which session.

Our volunteers
Elle Cayabyab Gitlin and Risha Zuckerman demanded the opportunity to spend the conference sitting at our welcome/registration table -; they were awesome! Larry Boles and Bill Hooker stuck around to help clean up. Lots of others helped out throughout the weekend, offering rides, organizing the swag table, keeping us on track and much more. Kevin Zelnio designed awesome name badges that in the end, couldn’t be completed due to some technical difficulties with our printer. Thank you to you all.

The Food
Meals were catered or ordered from Fetzko Coffees, Weaver Street Market, Saladelia Cafe, and Mediterranean Deli. The Thursday Early Bird Dinner was held at Town Hall Grill. Many local attendees brought fruit to share.

The organizers
Finally, big thanks to Anton Zuiker and Abel Pharmboy for making this all possible, by patiently putting together all the pieces of the conference throughout the entire year of planning. See you all next year!

Again, a huge ‘thank you’ to all the individuals and organizations supporting our free, publicunderstandingofscience conference.

New and Exciting in PLoS ONE

There are 10 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:
Rhythmicity in Mice Selected for Extremes in Stress Reactivity: Behavioural, Endocrine and Sleep Changes Resembling Endophenotypes of Major Depression:

Dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis, including hyper- or hypo-activity of the stress hormone system, plays a critical role in the pathophysiology of mood disorders such as major depression (MD). Further biological hallmarks of MD are disturbances in circadian rhythms and sleep architecture. Applying a translational approach, an animal model has recently been developed, focusing on the deviation in sensitivity to stressful encounters. This so-called ‘stress reactivity’ (SR) mouse model consists of three separate breeding lines selected for either high (HR), intermediate (IR), or low (LR) corticosterone increase in response to stressors. In order to contribute to the validation of the SR mouse model, our study combined the analysis of behavioural and HPA axis rhythmicity with sleep-EEG recordings in the HR/IR/LR mouse lines. We found that hyper-responsiveness to stressors was associated with psychomotor alterations (increased locomotor activity and exploration towards the end of the resting period), resembling symptoms like restlessness, sleep continuity disturbances and early awakenings that are commonly observed in melancholic depression. Additionally, HR mice also showed neuroendocrine abnormalities similar to symptoms of MD patients such as reduced amplitude of the circadian glucocorticoid rhythm and elevated trough levels. The sleep-EEG analyses, furthermore, revealed changes in rapid eye movement (REM) and non-REM sleep as well as slow wave activity, indicative of reduced sleep efficacy and REM sleep disinhibition in HR mice. Thus, we could show that by selectively breeding mice for extremes in stress reactivity, clinically relevant endophenotypes of MD can be modelled. Given the importance of rhythmicity and sleep disturbances as biomarkers of MD, both animal and clinical studies on the interaction of behavioural, neuroendocrine and sleep parameters may reveal molecular pathways that ultimately lead to the discovery of new targets for antidepressant drugs tailored to match specific pathologies within MD.

Opposite Effects of Early Maternal Deprivation on Neurogenesis in Male versus Female Rats:

Major depression is more prevalent in women than in men. The underlying neurobiological mechanisms are not well understood, but recent data shows that hippocampal volume reductions in depressed women occur only when depression is preceded by an early life stressor. This underlines the potential importance of early life stress, at least in women, for the vulnerability to develop depression. Perinatal stress exposure in rodents affects critical periods of brain development that persistently alter structural, emotional and neuroendocrine parameters in adult offspring. Moreover, stress inhibits adult hippocampal neurogenesis, a form of structural plasticity that has been implicated a.o. in antidepressant action and is highly abundant early postnatally. We here tested the hypothesis that early life stress differentially affects hippocampal structural plasticity in female versus male offspring. We show that 24 h of maternal deprivation (MD) at PND3 affects hippocampal structural plasticity at PND21 in a sex-dependent manner. Neurogenesis was significantly increased in male but decreased in female offspring after MD. Since no other structural changes were found in granule cell layer volume, newborn cell survival or proliferation rate, astrocyte number or gliogenesis, this indicates that MD elicits specific changes in subsets of differentiating cells and differentially affects immature neurons. The MD induced sex-specific effects on neurogenesis cannot be explained by differences in maternal care. Our data shows that early environment has a critical influence on establishing sex differences in neural plasticity and supports the concept that the setpoint for neurogenesis may be determined during perinatal life. It is tempting to speculate that a reduced level of neurogenesis, secondary to early stress exposure, may contribute to maladaptation of the HPA axis and possibly to the increased vulnerability of women to stress-related disorders.

Crohn’s Disease and Early Exposure to Domestic Refrigeration:

Environmental risk factors playing a causative role in Crohn’s Disease (CD) remain largely unknown. Recently, it has been suggested that refrigerated food could be involved in disease development. We thus conducted a pilot case control study to explore the association of CD with the exposure to domestic refrigeration in childhood. Using a standard questionnaire we interviewed 199 CD cases and 207 age-matched patients with irritable bowel syndrome (IBS) as controls. Cases and controls were followed by the same gastroenterologists of tertiary referral clinics in Tehran, Iran. The questionnaire focused on the date of the first acquisition of home refrigerator and freezer. Data were analysed by a multivariate logistic model. The current age was in average 34 years in CD cases and the percentage of females in the case and control groups were respectively 48.3% and 63.7%. Patients were exposed earlier than controls to the refrigerator (X2 = 9.9, df = 3, P = 0.04) and refrigerator exposure at birth was found to be a risk factor for CD (OR = 2.08 (95% CI: 1.01-4.29), P = 0.05). Comparable results were obtained looking for the exposure to freezer at home. Finally, among the other recorded items reflecting the hygiene and comfort at home, we also found personal television, car and washing machine associated with CD. This study supports the opinion that CD is associated with exposure to domestic refrigeration, among other household factors, during childhood.

New microbiology aggregator

New microbiology aggregator just went live in Belgrade, built (as always) by Vedran Vucic.

Tear Down This Myth

Tear Down This Myth.jpgWill Bunch of Attytood recently published an interesting and important book – Tear Down This Myth: How the Reagan Legacy Has Distorted Our Politics and Haunts Our Future.
On his blog, Will provides an excerpt and commentary:

Twenty years gone – but Reagan still matters. About this time one year ago, unceasing Reagan idolatry hijacked the race for the White House. Sometimes it was voiced in the name of policies on immigration or toward Iran that were the exact opposite of what really happened a generation ago. The power of this political fantasy – expressed mainly, of course, on the GOP side but occasionally even spilling over to the Democrats – caused me to begin work on a book about the Ronald Reagan myth. The result – “Tear Down This Myth: How the Reagan Legacy Has Distorted Our Politics and Haunts Our Future” – is coming out now from Simon & Schuster’s Free Press.
———————————-
OK – but you may ask whether the Reagan myth matters as much now that George W. Bush is back at the ranch and President Obama in the White House. I would argue that it does. Increasingly, the GOP minority in Washington, including 41 senators with just enough votes to derail the administration’s proposals, is going to invoke the Reagan myth to continue to justify a tax system that harms the middle class and policies that ignore the scientific consensus on climate change. Look at the first major policy debate of the Obama presidency, over the proposed $825 billion economic stimulus. Democrats are under enormous political pressure to weight the plan toward tax cuts, and away from spending programs, which Republicans quickly branded as much pork – despite evidence that jobs programs stimulate the economy at twice the rate of tax reductions. “I remain concerned about wasteful spending that might be attached to the tax relief,” House GOP leader John Boehner said – and right-wing talk radio was a lot less restrained. Ironically, the spending sought by the Democrats seek to undo the crumbling of America’s infrastructure and the failure to create “green-collar” jobs that dates back to the Reagan era.
And here’s another reason the Reagan myth still matters, and that’s because there’s a pundit class inside the Beltway that cuts its teeth in the 1980s and remains firmly convinced that America is a “center-right” nation, despite massive evidence to the contrary. These pundits will urge Obama to enact an economic recovery package in the Gipper’s image, ignoring the long-term harmed caused by Reagan’s brand of “trickle-down economics.
Unless we don’t let them – and tear down this myth.

On a crusade to save us from bad statistical errors

From SCONC:

Wednesday, Feb. 4
5:30 p.m.
SCONC reception at NISS
National Institute of Statistical Sciences in RTP (click here for directions) has invited the SCONCs over for our usual socializing/networking/eating/drinking and a talk with Dr. Stan Young, Assistant Director for Bioinformatics at NISS. Stan is a one-man army fighting multiple testing/false positive reports that abound in most observational studies. He’s on a crusade to save us from bad statistical errors. Please RSVP to NISS Communications Director Jamie Nunnelly (Nunnelly@niss.org) by close of business on Monday, February 2. Address: 19 TW Alexander, RTP.

Triangle science blogging battalion gets reinforcements

Stephanie Willen Brown, aka CogSci Librarian is moving to Chapel Hill!
Blogger meetup!

ScienceOnline’09 on Minnesota Atheist Radio

Science is moving onto the internet. Collection of data, collaboration between researchers, communication and critique of results, teaching and learning–all are increasingly being done online. ScienceOnline, held January 16 – 18 in 2009, is a conference dedicated to discussing the intersection of science and online technologies. Bora Zivkovic, one of the founders and organizers of ScienceOnline will join Atheists Talk Sunday, February 1, to talk about the purpose of the conference, the results of this year’s sessions, and why it’s important to meet your online colleagues in person.
Produced by Minnesota Atheists. Directed and hosted by Mike Haubrich. Interview by Stephanie Zvan.

Podcast Coming Soon!
SUBSCRIBE TO THE iTunes PODCAST
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Write a review of Atheists Talk
Listen to AM 950 KTNF on Sunday at 9AM Central to hear Atheists Talk produced by Minnesota Atheists. Stream live online. Call the studio at 952-946-6205 or email us at radio@mnatheists.org.

My picks from ScienceDaily

Continue reading

Clock Quotes

Let your life lightly dance on the edges of time like dew on the tip of a leaf.
– Rabindranath Tagore

Today’s carnivals

Grand Rounds, totally Babelicious! Vol. 5 No. 19, are up on ChronicBabe
Carnival of the Green # 164! is up on GetWithGreen
The 161st Carnival of Homeschooling is up on Life on the Road

Carrboro Creative Coworking on NPR

Brian Russell was on NPR Marketplace this morning, talking about Carrboro Creative Coworking. Worth a listen:

New and Exciting in PLoS ONE

There are 13 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 (wow! two circadian papers, plus dinosaurs and honeybees and heterochrony! – what a week!) – you go and look for your own favourites:
Evidence of Combat in Triceratops:

The horns and frill of Triceratops and other ceratopsids (horned dinosaurs) are interpreted variously as display structures or as weapons against conspecifics and predators. Lesions (in the form of periosteal reactive bone, healing fractures, and alleged punctures) on Triceratops skulls have been used as anecdotal support of intraspecific combat similar to that in modern horned and antlered animals. If ceratopsids with different cranial morphologies used their horns in such combat, this should be reflected in the rates of lesion occurrence across the skull. We used a G-test of independence to compare incidence rates of lesions in Triceratops (which possesses two large brow horns and a smaller nasal horn) and the related ceratopsid Centrosaurus (with a large nasal horn and small brow horns), for the nasal, jugal, squamosal, and parietal bones of the skull. The two taxa differ significantly in the occurrence of lesions on the squamosal bone of the frill (P = 0.002), but not in other cranial bones (P>0.20). This pattern is consistent with Triceratops using its horns in combat and the frill being adapted as a protective structure for this taxon. Lower pathology rates in Centrosaurus may indicate visual rather than physical use of cranial ornamentation in this genus, or a form of combat focused on the body rather than the head.

Already blogged about by one of the authors, Andy Farke and by Ed Yong.
Number-Based Visual Generalisation in the Honeybee:

Although the numerical abilities of many vertebrate species have been investigated in the scientific literature, there are few convincing accounts of invertebrate numerical competence. Honeybees, Apis mellifera, by virtue of their other impressive cognitive feats, are a prime candidate for investigations of this nature. We therefore used the well-established delayed match-to-sample paradigm, to test the limits of honeybees’ ability to match two visual patterns solely on the basis of the shared number of elements in the two patterns. Using a y-maze, we found that bees can not only differentiate between patterns containing two and three elements, but can also use this prior knowledge to differentiate three from four, without any additional training. However, bees trained on the two versus three task could not distinguish between higher numbers, such as four versus five, four versus six, or five versus six. Control experiments confirmed that the bees were not using cues such as the colour of the exact configuration of the visual elements, the combined area or edge length of the elements, or illusory contours formed by the elements. To our knowledge, this is the first report of number-based visual generalisation by an invertebrate.

Circadian Control of Dendrite Morphology in the Visual System of Drosophila melanogaster:

In the first optic neuropil (lamina) of the fly’s visual system, monopolar cells L1 and L2 and glia show circadian rhythms in morphological plasticity. They change their size and shape during the day and night. The most pronounced changes have been detected in circadian size of the L2 axons. Looking for a functional significance of the circadian plasticity observed in axons, we examined the morphological plasticity of the L2 dendrites. They extend from axons and harbor postsynaptic sites of tetrad synaptic contacts from the photoreceptor terminals. The plasticity of L2 dendrites was evaluated by measuring an outline of the L2 dendritic trees. These were from confocal images of cross sections of L2 cells labeled with GFP. They were in wild-type and clock mutant flies held under different light conditions and sacrified at different time points. We found that the L2 dendrites are longest at the beginning of the day in both males and females. This rhythm observed under a day/night regime (LD) was maintained in constant darkness (DD) but not in continuous light (LL). This rhythm was not present in the arrhythmic per01 mutant in LD or in DD. In the clock photoreceptor cryb mutant the rhythm was maintained but its pattern was different than that observed in wild-type flies. The results obtained showed that the L2 dendrites exhibit circadian structural plasticity. Their morphology is controlled by the per gene-dependent circadian clock. The L2 dendrites are longest at the beginning of the day when the daytime tetrad presynaptic sites are most numerous and L2 axons are swollen. The presence of the rhythm, but with a different pattern in cryb mutants in LD and DD indicates a new role of cry in the visual system. The new role is in maintaining the circadian pattern of changes of the L2 dendrite length and shape.

Genetic and Molecular Analysis of Wild-Derived Arrhythmic Mice:

A new circadian variant was isolated by screening the intercross offspring of wild-caught mice (Mus musculus castaneus). This variant was characterized by an initial maintenance of damped oscillations and subsequent loss of rhythmicity after being transferred from light-dark (LD) cycles to constant darkness (DD). To map the genes responsible for the persistence of rhythmicity (circadian ratio) and the length of free-running period (τ), quantitative trait locus (QTL) analysis was performed using F2 mice obtained from an F1 cross between the circadian variant and C57BL/6J mice. As a result, a significant QTL with a main effect for circadian ratio (Arrhythmicity; Arrh-1) was mapped on Chromosome (Chr) 8. For τ, four significant QTLs, Short free-running period (Sfp-1) (Chr 1), Sfp-2 (Chr 6), Sfp-3 (Chr 8), Sfp-4 (Chr 11) were determined. An epistatic interaction was detected between Chr 3 (Arrh-2) and Chr 5 (Arrh-3). An in situ hybridization study of clock genes and mouse Period1::luciferase (mPer1::luc) real-time monitoring analysis in the suprachiasmatic nucleus (SCN) suggested that arrhythmicity in this variant might not be attributed to core circadian mechanisms in the SCN neurons. Our strategy using wild-derived variant mice may provide a novel opportunity to evaluate circadian and its related disorders in human that arise from the interaction between multiple variant genes.

Heterochrony and Cross-Species Intersensory Matching by Infant Vervet Monkeys:

Understanding the evolutionary origins of a phenotype requires understanding the relationship between ontogenetic and phylogenetic processes. Human infants have been shown to undergo a process of perceptual narrowing during their first year of life, whereby their intersensory ability to match the faces and voices of another species declines as they get older. We investigated the evolutionary origins of this behavioral phenotype by examining whether or not this developmental process occurs in non-human primates as well. We tested the ability of infant vervet monkeys (Cercopithecus aethiops), ranging in age from 23 to 65 weeks, to match the faces and voices of another non-human primate species (the rhesus monkey, Macaca mulatta). Even though the vervets had no prior exposure to rhesus monkey faces and vocalizations, our findings show that infant vervets can, in fact, recognize the correspondence between rhesus monkey faces and voices (but indicate that they do so by looking at the non-matching face for a greater proportion of overall looking time), and can do so well beyond the age of perceptual narrowing in human infants. Our results further suggest that the pattern of matching by vervet monkeys is influenced by the emotional saliency of the Face+Voice combination. That is, although they looked at the non-matching screen for Face+Voice combinations, they switched to looking at the matching screen when the Voice was replaced with a complex tone of equal duration. Furthermore, an analysis of pupillary responses revealed that their pupils showed greater dilation when looking at the matching natural face/voice combination versus the face/tone combination. Because the infant vervets in the current study exhibited cross-species intersensory matching far later in development than do human infants, our findings suggest either that intersensory perceptual narrowing does not occur in Old World monkeys or that it occurs later in development. We argue that these findings reflect the faster rate of neural development in monkeys relative to humans and the resulting differential interaction of this factor with the effects of early experience.

ScienceOnline’09 – Saturday 2pm, and on the organization of an Unconference

scienceonline09.jpg
About a month ago we had a spirited debate on Twitter if ScienceOnline09 is an Unconference or not. I think the problem stems from two distinct meanings of the term.
See what Wikipedia, the Unconference Blog and this article say about the concept.
On one hand, people in the tech industry who like to attend various BarCamps and FooCamps (like SciFoo) really like the idea that the program is set entirely by participants ahead of the coference, either on a wiki, or on a big white poster board on the morning of the conference, and thus take it that this is the defining aspect of an Unconference. It is fun to do it this way, it sounds democratic and in the spirit of the “wisdom of the crowds” but it has serious drawbacks we wanted to avoid – on that later, keep reading.
On the other hand, the term Unconference also applies to the way sessions are run, regardless of who picked the topics. It is probably the best to quote Dave Winer on this:

The sum of the expertise of the people in the audience is greater than the sum of expertise of the people on stage.

Thus, if the person on the podium is talking and the audience is jotting notes, you are doing it Wrong. The unconferenc-ey session is highly participatory, with the person behind the lectern serving, pretty much, only as a moderator, breaking the ice and defining the topic at the beginning, making sure nobody hijacks the discussion, and making sure that the discussion does not veer off on crazy tangents without ever coming back to the topic.
In a perfect world, every conference and every session would be an Unconference in both senses of the term, but in the real world, it does not work that way. Why? Here is my experience from organizing three conferences to date, and why we chose a hybrid model.
First, for the 1st Science Blogging Conference, we did it the full Unconference way – the Program was set by the participants on the wiki beforehand. It worked pretty well, actually. But there was also something that bothered me at the time, and even more when we opened for the suggestions for the 2nd conference: the Program (just as it happened at SciFoo) was quickly populated by sessions suggested by A-type, self-promoting, middle-aged, white males – people just like me. The women, minorities, the very young, the very old, the tech non-savvy, the n00bs, the marginalized, the shy, the always-silenced… they got silenced again. And we wanted to hear their voices. Especially their voices.
Second, many of the suggestions were for sessions that are blogging universals, e.g., how to deal with trolls, which don’t have much to do with science. Most of the suggestions were about blogging in general. But, blogging is not the only thing in science online. There are online scientific journals, magazines, books, social networks, virtual words, various repositories, applications, video, reference software, etc. and that’s just the technical side, not to mention the social aspects of it all. The blogs are just one part of that ecosystem, perhaps the glue that binds those all together, and we wanted to have more than just blogging sessions – we wanted to explore how all those aspects relate to each other and how the Web is changing the way science is done. This is the motivation, also, for the name-change of the conference to make this point clear: instead of Science Blogging Conference, now it is called ScienceOnline.
Third, ScienceOnline is an evolving conference and we are trying to have year-to-year continuity, a year-to-year improvement, and yet having each conference having its own coherence and its own “stamp”. Discussions starting in one year continue the next year, perhaps with an entire year of events and technical inventions in-between to report on, perhaps becoming more focused or more derived, or splitting into two or three more specific sessions. They should be providing something new to repeat participants, yet are not completely out of context for the first-time guests either.
A general “science education online” session in 2007 became a “using online technologies in the classroom” session in 2008, which became three sessions in 2009: online science for kids/parents, use of online technologies in middle/high schools from students’ perspective, and using online technology in college teaching. The ‘gender and race’ session last year provided so much fodder, it turned into four sessions this year (gender in science, race in science, blogging through transitions, and anonymity/pseudonymity session).
This is a tough balance to provide, and the “wisdom of the crowds” does not work well with fine-tuning the sessions in this way. If we continued to let the participants set the Program on the wiki by themselves, every year we would have the same conference: a bunch of white, middle-age geeks leading sessions about beating the trolls on blogs. It would get old pretty fast.
So, we decided to have a much bigger say on what the Program will be, picking among the suggestions that arrive on the wiki, working with moderators on building and defining their sessions, and actively pursuing interesting people to talk about interesting topics, in order to have exciting, novel, fresh and coherent program every year.
In other words, the pre-conference crowd-planning may work for one-off conferences, but not for a series of annual conferences. Also, as the meeting gets bigger and bigger each year, a proper balance and diversity is harder to attain: this year 31 out of 77 presenters/moderators/panelists were women, which is actually not as good a ratio as we had last year, when the conference was smaller, but some changes always happen at the last moment and are out of our control. On the other hand, the diversity in race, ethnicity and age was greater this year than before.
Fourth, not every topic lends itself well to the unconference format. First, there are demos – 15 minute show-and-tell sessions where someone shows their site or software to the potentially interested users. There is not enough time for a long discussion beyond a brief Q&A. Then, there are workshops where it is obviously intended to have an expert in front and the audience coming in with a specific goal to learn something new – Blogging 101, Blogging 102 and ‘Paint your own blog images’ sessions fall into this category.
Then, there are sessions where the person on the podium clearly has greater expertise than all or most in the room, but once the audience learns something, a discussion may ensue, thus, having about half the time for a presentation and half the time for discussion is perfectly OK – examples: Semantic Web session, GeneWiki session, Rhetorics session, Carnivals session, Online resources for kids and parents session.
Some sessions are introductory (Open Access), some highly derived (Impact Factor, Open Notebook Science). On the other hand, some sessions were quite possible to open up to the audience right off the bat, even as easily as the moderator starting with a question “the topic is X, what do you want to talk about?”.
And then, there are the panels (three this year) which are an entirely different animal….
Interestingly, in the feedback form (90 respondents so far – if you are not one of them, please take a couple of minutes to fill it – we will analyze the data and use it to make the next conference better), most people really liked the free-flowing feel of the participatory sessions. Some like the unconference feel so much they actively disliked when a session was any less than 100% participatory. And then, there are always a couple who are uneasy with the format and would prefer more top-down control and formalized lecture-like sessions (no, we are not going that way!). I think a hybrid model, with each session’s format geared towards it’s topic and audience, is the way to go, perhaps erring on the side of free-flow when in doubt.
So, while we were planning this year’s program, I wanted to combine several of the things I mentioned above and do an experiment. I wanted to see if we could still have a free-flowing participatory discussion if we had a huge panel with a lot of panelists, each panelist being kind of a blogging superstar, and each having unique experiences that others in the room don’t have. Can we pull that off?
So, in the spirit of sessions evolving out of previous year’s sessions, I thought that expanding the “blogging on the ocean” session of 2008 could be expanded into a “blogging from various exotic and weird places” panel this year. So, I put the feelers out to see if there was any interest in this. And – oh yes! – there was interest, was there ever!
In the end, we had quite a large and delicious set of people on the panel: Karen James, Talia Page, Anne-Marie Hodge, Meredith Barrett, Kevin Zelnio, Vanessa Woods and Rick McPhearson, all participating in the session on Blogging adventure: how to post from strange locations (it could have been even bigger, as I also tried to lure in Samantha Larson (who liveblogged her ascent to the top of Mt.Everest), John McKay (who liveblogged a mammoth dig), Laura Hendrix (who blogs from rural places in the developing world) and perhaps some of the Antartctica bloggers, but they either could not come or could not be reached in time).
weird places 1.jpg
And, even with such a large panel, and each panelist having a story to tell, it worked wonderfully! First, they started off by engaging the audience – asking us to liveblog the session while they were going around the room and making it physically and mentally difficult to do – lights going on and off, strange noises, chairs shaking, pens falling out of our hands, weird insects falling into our hair…hey, it wasn’t easy!
Getting the taste of what it feels like to try to blog outside the comfort of our pajamas in our basements, we were eager to hear about the real challenges they experiences while blogging from strange places. Rick and Kevin are marine biologists and they do their field work on ships, submarines and while diving. When you are out at sea, there is a lot of water around you, and that water contains a lot of salt. Neither water nor salt are good for your laptops! But more importantly, there is no time – a month at sea is all one has to collect a year-worth of data. Thus data-collecting takes precedence. They work 24/7 on their research, do not even sleep enough, and there is just no time for sitting down and writing.
weird places 2.jpg
The time constraints were also the biggest problem for Anne-Marie, Vanessa and Meredith, who do ecological/conservation field-work in the tropics. Anne-Marie blogged from Belize last summer, Vanessa studies bonobos in Kenya, and Meredith studies lemurs on Madagascar. In such places, electricity is another limiting factor – it is unreliable, or rationed. Likewise for internet access.
Anne-Marie also realized that poachers do not like cameras that they set up to take pictures of animals in the rainforest – when they triggered the light-beams and got pictures taken off, they just smashed and broke the expensive equipment.
Finally, having diarrhea-inducing tropical diseases, like Ghiardia, is not just all-around bad news for you, but also a special impediment to blogging. While in India, Talia had to use an Internet cafe to write her blog. First time the nasty bug sent her running to the bathroom someone stole her notes from the computer desk. She diligently immediately copied them from memory, but then had to run to the bathroom again. But this time, there was no toilet paper. Oh, look, what’s that in my hand? Notes? I am so glad I took them with me so they do not get stolen again. And notes are on paper – a very useful material in this situation. You know how that story ended….
Next year, Talia will report on blogging from South American countryside, and in 2012 she will blog from space – a Virgin Atlantic space flight. By that time, as technology progresses, she probably will not need to have a laptop with her – we will be able to instantly see what she sees, hear what she hears, and read what she says. I hope.
A number of people in the room added their stories, and a number of technical suggestions were made (see the wiki page of the session and the blog coverage of this session). Sending datasets to one’s advisor back home is one problem – requires time and bandwidth and reliable internet.
On the other hand, blogging requires time and energy – something most people in the field do not have. Thus, long essays on a blog are unlikely to become common. But Twittering, or using audio (something you can do while walking and talking, or while finally resting in the hammock with a cold beer in the evening) may catch on as the favourite method for communicating the wonders of doing science in the field.
Other coverage of this session:
Highly Allochthonous: Liveblogging from ScienceOnline…
Pondering Pikaia: ScienceOnline09 Conference Update
Space Cadet Girl: For a Good Time, Check out Science Online 09
TalkingScience: For A Good Time, Check out Bloggers from Science Online 09
Deep Sea News: Science Online ’09: Blogging Adventure
Sessions in this timeslot I missed:
Web and the History of Science (which I really, really wanted to see, but we messed up the schedule when we printed the program, swapping some sessions in comparison to the program we had on the wiki):
Skulls in the Stars: ScienceOnline ’09: Web and the History of Science
Ideonexus: ScienceOnline09: The Web and the History of Science
Knowledge Sharing: ScienceOnline’09: Web and the History of Science
Christina’s LIS Rant: Science Online ’09: Saturday PM
Nobel Intent: ScienceOnline 09: History, art, and science
Race in science – online and offline:
HASTAC blogs: Liveblogging ScienceOnline ’09: Race in Science Online and Offline
Adventures in Ethics and Science: ScienceOnline’09: Diversity in science, online and off
Almost Diamonds: Whither Allies
Thesis – with Children: On Not Quite Passing
Alternative careers: how to become a journal editor
Confessions of a Science Librarian: ScienceOnline ’09: Saturday summary
Deep Thoughts and Silliness: Semi-live Blogging Scienceonline09: Day 1
Expression Patterns: ScienceOnline09 – Day 2
The blog/media coverage linkfest is growing fast (perhaps start at the bottom and work your way up, posting comments on the way and saying Hello to your new friends), there are ongoing discussions on FriendFeed and new pictures on Flickr. Also, if you were there, please fill up this short form to give us feedback, so we can make next year’s meeting even better.

Chris Mooney on Colbert Report

My SciBling Chris was on Colbert Report last night. If you missed it, watch now:
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New year – everyone wants new banners

I think that my banner is the best banner ever and it’s not going anywhere. But perhaps you can help Miriam or Scicurious and Evil Monkey if you feel artistic and are good with Photoshop….

Science Cafe Raleigh – Supernova: The Violent Death of a Star

Hosted by Museum of Natural Sciences:

Supernova: The Violent Death of a Star
Massive stars end their lives in spectacular supernova explosions, visible across the Universe, that blast material into space that contributes to future generations of stars, produces cosmic rays, and stirs up interstellar gases. Many heavy elements, including the calcium in our bones and trace amounts of copper and zinc in our bodies, are formed only in supernovae; we are quite literally made of star stuff. Some supernovae can even be used to gauge distances to remote galaxies; from these we have learned the astonishing fact that the expansion of our Universe is actually picking up speed. Join us as we discuss ongoing work on supernovae, their remnants and related astronomical work.
About the Speaker:
Dr. Stephen Reynolds, professor of physics at NC State University, has been studying supernova remnants for almost 30 years. Reynolds’ research focuses on the generation of cosmic rays by supernova remnants, involving theoretical work and observations with national radio-astronomical facilities and orbiting X-ray observing satellites. Reynolds and his colleagues recently made international headlines when they discovered the youngest-known remnant of a supernova in the Milky Way.
Wednesday January 28, 2009
6:30-8:30 pm, discussion beginning at 7 pm followed by Q&A
Location: Tir Na Nog 218 South Blount Street, Raleigh, 833-7795

My picks from ScienceDaily

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