Today’s carnivals

June Scientiae is up on Sciencewomen
Four Stone Hearth #68 is up on remote central
Friday Ark #246 is up on Modulator

Clock Quotes

Perfection of planning is a symptom of decay. During a period of exciting discovery or progress, there is no time to plan the perfect headquarters.
– C. Northcote Parkinson

Science & Technology Parks – what next?

As you may have noticed if you saw this or you follow me on Twitter/FriendFeed/Facebook, I spent half of Tuesday and all of Wednesday at the XXVI International Association of Science Parks World Conference on Science & Technology Parks in Raleigh. The meeting was actually longer (starting on Sunday and ending today), but I was part of a team and we divided up our online coverage the best we could do.
IASP2009 001.jpgChristopher Perrien assembled a team (including his son) to present (and represent) Science In The Triangle, the new local initiative. They manned a booth at which they not only showcased the website, but also had a big screen with TweetDeck showing the livetweeting of the conference by a few of us (e.g., @maninranks, @mistersugar, @IASP2009 and myself), gave out flyers explaining step-by-step how to start using Twitter, and gave hands-on instruction helping people get on Twitter and see what it can do for them.
You can look at the coverage by seaching Twitter for IASP or #IASP or #IASP2009 (in some of my first tweets I misspelled it as IESP). You can search FriendFeed for all the same keywords as well, as most of the tweets got imported there.
IASP2009 002.jpgScience In The Triangle is an online portal for news (and stories about news) about scientific research happening in the Triangle region of North Carolina. This is a way to keep the researchers in the Triangle informed about each other’s work and local science-related events, as well as a way to highlight the local research efforts for the outside audience. It is in its early stages but we’ll work on developing it more. It will be interesting to compare it to other similar portals, like NSF Science Nation and The X-Change Files (neither one of which is regional in character).
Apart from that, what was I doing at this kind of conference? Frankly, I never really thought about science/technology parks much until now. I have spent the last 18 or so years inside the sphere of influence of the Research Triangle Park and was blissfully unaware of the existence of any others. I did not know that there were dozens, perhaps hundreds of such parks around the world (including – and I should have known about it – the Technology Park Ljubljana in Slovenia). I did not know they had an official international association. I did not know that there are specified criteria as to what makes a park a park. Or that, for instance, the NCSU Centennial Campus is considered a science/technology park and is itself a member of the Association, outside of its proximity to RTP. Just learning these things was enlightening in itself, besides the actual susbtance of the talks.
IASP2009 003.jpgThis was also an interesting cultural experience for me. For the past several years, my conference experiences were mainly unconferences or very laid back and friendly science conferences. This was not it. This was a formal, old-style business conference with about a thousands businessmen (and very few women) wearing business suits. Even I felt compelled to wear a coat and tie and uncomfortable shoes to fit in. I also forgot that the program itself was bound to be much more formal. A session called a “panel” does not mean that 3-4 people on the stage will vigorously discuss a topic between themselves and with the vocal audience, but that 3-4 people will give PowerPoint presentations in rapid succession.
But I am not complaining – I know that the business world is even slower to evolve than the science world and that the tech world is light years ahead – as some of those talks were quite interesting and enlightening (see all the Tweets from the various sessions), and some of the people I met (and I knew almost nobody there in the beginning) were interesting as well. For example, Will Hearn prospects the sites for potential corporate (or industrial park) development around the world, from Peru to Macedonia. He runs Site Dynamics and has developed software – SiteXcellerator – that provides important information about the population, education and economics of any place on earth the company may be interested in moving into.
So, what is a science/technology/industrial park? It is a place. Seriously, and importantly, it is a place, in a geographical sense. It is a piece of land which houses a collection of science, technology, business and industrial companies and organizations, all placed together because they can potentially collaborate.
IASP2009 004.jpgThe location of the Park is chosen for being conducive to business (nice tax breaks by the state, for instance) and for containing well-educated and skilled workforce in abundance (thus usually close to a big university). In some cases, the companies go where the skilled potential employees already are. In other cases, the Park members build educational institutions needed to produce skilled workforce out of the local population (so, for example, if biotech moves into a place abandoned by the textile industry, a college needs to be built to re-train the local workers for the new and more high-tech jobs). Some parks are focused on a single industry (e.g., pharmaceutical, or even defense in some places) or even a single product (e.g., solar panels), while other parks are drawing together a variety of different fields.
More than 20 Parks received silver medals last night for existing 25 or more years. So this is not a new fad in any way. Research Triangle Park got a gold medal as it celebrated 50 years of existence this year. It is the largest and the oldest of the science/technology parks in the world, at least among the members of the Association.
But I had a nagging thought in the back of my head. Is RTP really the oldest?
IASP2009 005.jpgSo last night when I got home I went online and started searching for “science cities” or Naukograds of the old Soviet Union. The most famous is Akademgorodok which is possibly a couple of years older than RTP as the Wikipedia page states “in the 1950s” (RTP was founded in 1959) and this NYTimes article from 1996 says “four decades ago” which places its foundation at around 1956.
By the way, that NYTimes article (I actually remember reading it at the time – the heady old days of reading newspapers on paper!) is quite interesting. But take it with a big grain of salt – remember the source and the time: the New York Times in the 1990s was essentially Clinton’s Pravda, especially in the area of foreign politics, so any article about a foreign country is automatically suspicious. I’d love to see a blog post on the topic by a respected Russian blogger, either as an antidote or as a confirmation of that NYTimes article.
I would love to see someone cover the history and evolution of Naukograds, their strengths and weeknesses, ups and downs, during the Soviet era, during Perestroika, and in modern Russia, as well as the science cities that are now located in other countries that gained independence from USSR during the 1990s. That would be quite a teaching moment for everyone involved, I’m sure. If I am reading it correctly, these science cities conform to the criteria of being science/technology parks as the Association of Science Parks defines them. I wonder if any one of them actually became members of the Association since then?
IASP2009 006.jpgBack to the RTP now. Plenary talk by the Duke University President Richard Brodhead confirmed some of the history and some thoughts I had about the importance of RTP in North Carolina history (I missed the talk by Andrew Witty, but Anton blogged it and it appears to have been along similar lines).
UNC-Chapel Hill is the oldest state university in the country. NCSU and Duke are also very old. There are a couple of dozen smaller universities and colleges (and a couple of amazing high schools for kids with math and science talent) in the Triangle. And other science-related organizations. Then, there are many more schools around the state. From what I gather, each one of those schools was on its own, pretty isolated from each other. Researchers at one school were not aware of the researchers at another.
Then, some enlightened people in the state decided that with all those schools churning out all those educated graduates, the jobs for those graduates should also be in North Carolina. Why teach them here, just to see them leave for the greener pastures? And thus the RTP was born.
IASP2009 007.jpgIt took a while for the park to grow, but it attracted or spawned some powerful and creative organizations, from RTI and Glaxo and NIEHS, through IBM and SAS, to Sigma Xi and NESCENT and Lulu.com. Instead of educated people leaving the state in search of jobs, the companies started bringing jobs to where the educated people are – and there was one place to move to: the Research Triangle Park or as close to it as possible.
But that was not the end of the story. All those companies and organizations started collaborating with (or hiring) the researchers from local universities and….this brought people from different Universities together! People from NCSU and Duke and UNC and other schools got introduced to each other this way and started collaborative research with each other. Soon formal and informal collaborations between schools and departments were put in place. As a result, science in the state boomed. Instead of isolated nodes, there was now a network.
And I still think this network is pretty unique in the USA. In other places known for top-level science all of it is concentrated in one big city (e.g., New York City, Boston, Atlanta, or San Francisco) while the countryside of the state has nothing of the sort. And if one adds the historical rivalries between those old Universities in these cities, there is not much network effect there. Much more competitive than collaborative. But in North Carolina there are long-term ongoing collaborations between researchers, departments and schools all across the state, from Wilmington and Greenville, to Triangle, Winston-Salem and Greensboro, to Charlotte, Davidson, Cullowhee, Boone and Asheville (which is why I argued that the Nature Network Triangle Group should be renamed North Carolina Group which you should join if you are in NC and interested in science). Just look at how geographically dispersed the NC science bloggers are, if that is any indication.
IASP2009 008.jpgThus RTP, besides bringing together researchers and industry (which some of us purist scientists may not like that much) also inadvertently spurred on the advancement of pure, basic research. RTP provided the central place that connected all the schools and then people in those schools could make their own connections and do whatever kind of research they liked, even the most basic kind that does not have an obvious and immediate application (of course, long-term, all that basic knowledge ends up being applied to something, it is just impossible to predict at the time what the application could be).
There are other effects of this rise in science and technology in the state. Instead of graduates leaving the state, people from other places started coming in (look at licence plates on cars on I-40, or parked on campuses – you can see everything from Ohio and Michigan and Georgia to New York and California and Alaska), further increasing the concentration of highly educated people. The knowledge and education and expertise are regarded quite highly. Thus, the reality-based party has been in charge of state politics for a long time and last year even the national offices were deemed important enough for locals to vote out the anti-science party.
But that was last 50 years. That is 20th century world. How about today and tomorrow, now that everything about the world is changing: economics, communication, environmental awareness, even the mindset of the new generations?
You know that the rapid changes in the workplace are one of my ‘hot’ topics here. How will the information revolution affect parks (and the domino effect downstream from parks – universities, jobs, infrastructure)?
This is the moment to introduce the most interesting presentation at the meeting, by Anthony Townsend. Anthony is the Research Director at The Institute for the Future, focusing on Science In Action as well as coworking. I tried to get him in touch with Brian Russell of Carrboro Creative Coworking (and if you are in the Triangle area, but Carrboro is too far for you, fill out this survey about the potential need for coworking spaces in other parts of the Triangle), but I am not sure if they found time to meet this week. For this meeting, Anthony wrote a booklet – Future Knowledge Ecosystems: The Next Twenty Years of Technology-Led Economic Development – which you can download as a PDF for free, and I think you should.
His talk was a firehose – I tried live-tweeting it, but even the speed of Twitter was not fast enough for that. I am sure happy that he mentioned PLoS (and showed the homepage of PLoS Genetics on one of his slides) as an example of the new global, instantenuous mechanism of dissemination of scientific information. But I digress…
The main take-home message I got from his talk is that the world has fundamentaly changed over the past decade or so and that science/technology parks, old or new, need to adapt to the new world or die. He provided three possible scenarios. In the first scenario, parks evolve gradually, adapting, with some delay, to fast but predictable changes. In the second scenario, the physical space of the park becomes obsolete as research and connections move online – the park dies. In the third scenario, the parks are forced to adapt quickly and non-incrementally – inventing whole new ways of doing research combining physical and virtual worlds.
A traditional Park is a place where different companies occupy different buildings. The interaction is at the company-to-company level.
A new Park may become a giant coworking space, where the interactions are at the individual-to-individual level. Anthony actually showed a slide of a Park in Finland where a building (or a large floor of a large building) was completely re-done and turned into a coworking space.
As more and more people are turning to telecommuting and coworking, the institution of a physical office is becoming obsolete. What does that mean?
Employees are happy because they can live where they like. They get to collaborate with who they find interesting and useful, not who their corporation also decided to employ. They don’t have to see their bosses or coworkers every day (or ever). Everything else can be done in cyberspace.
What does the company gain from it? Happy productive employees. No echo-chamber effect stemming from employees only talking to each other. Ability to hire employees who are the best in what they do and, knowing that, unwilling to move from the place on Earth they like to live in. Employees who are always up to the latest trends and industry gossip due to constant mingling with the others. Free PR wherever the employees are located – they all meet the locals and answer the inevitable question “What do you do?”
The phenomenon of company loyalty is quickly fading. Most people do not expect to work for a single employer all their lives. They will work several jobs at a time, changing jobs as needed, sometimes jumping from project to project. Getting together with other people in order to get a particular job done, then moving on.
This will actually weaken the corporation – making everyone but controlling CEOs and CFOs happy. Corporations will have to become fluid, somewhat ad hoc, very flexible and adaptable, as their people will be constantly circulating in and out.
In such a world, a sci/tech Park will have to be where the people want to live – a nice place, with nice climate, nice culture, good school systems, safe, etc.
In such a world, single-payer health-care system that is not disbursed via the employer will become a necessity.
Sure, there is the production part of companies that actually produce ‘stuff’ and they will also be in such Parks so their own (and other’s) blue-collar and white-collar employees can routinely interact (Anthony showed a slide of a production line literally weaving through the offices, forcing workers, bureacrats and R&D personel to get to know each other and watch each other at work, thus coming to creative solutions together).
As for science itself, a Park may be something like a Science Motel, a place where both affiliated and freelance scientists can come together, exchange ideas and information, work together, use common facilities and equipment, regardless of who their official employers are and where those are located geographically.
Sounds like something out of science fiction? That kind of future is right around the corner.
The interaction at the organization-to-organization level, the cornerstone of Parks and the local economic growth in the 20th century, has been discussed quite a lot at the meeting, as expected. Especially collaboration between Universities and industry (and sometimes government).
The park-to-park level of interaction, essential in the global economy, and the reason the Association of Science Parks exists, was discussed quite a lot, of course.
IASP2009 009.jpgBut I did not get the vibe that the level of individual-to-individual was on many people’s minds. The idea that the corporation will have to get less coherent and/or hiererchical because the new generations will insist on the individual-to-individual collaboration did not get much air play. The time when people realize that information wants to be free and that, with current technology, it can be set free, is a challenge to corporations, especially for keeping trade secrets. Perhaps there will be less trade secrets as the new mindset sets in – a network can do more and better than competing units.
This was brought splendidly to us all last night, at the end of the Gala (no, not the amazing Tri-chocolate mousse dessert!), by theCarolina Ballet dancers, each bringing his or her own individual skills and talent (and it was visible that they all differ – some are more athletic, some more elegant, the #1 ballerina is top-world-class) and working together to produce a collective piece of beauty.

New and Exciting in PLoS this week

Here are some titles, from all seven PLoS journals, that caught my attention this week. 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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Today’s carnivals

Special, one-time carnival “Uncovering Ida” is up on Laelaps
Skeptic’s Circle #112 is up on Cheshire

Caryn Shechtman: A Blogger Success Story (an interview with Yours Truly)

You may have noticed a couple of days ago that Caryn Shechtman posted an interview with me on the New York blog on Nature Network. Then, Caryn and Erin and I thought it might be a good idea to have the entire interview reposted here, for those who missed it. So, proceed under the fold:

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My picks from ScienceDaily

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Clock Quotes

One way to make sure everyone gets to work on time would be to have 95 parking spaces for every 100 employees.
– Michael Iapoce

Duke Univ pres Richard Brodhead RTP, Local Synergy

Anthony Townsend & Future Knowledge Ecosystems, IASP 2009

My picks from ScienceDaily

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Clock Quotes

Do not think of your faults, still less of others’ faults; look for what is good and strong, and try to imitate it. Your faults will drop off, like dead leaves, when their time comes.
– John Ruskin

Mister Sugar, Science Blogger, on IASP2009

This is Anton Zuiker, the other day:

New and Exciting in PLoS ONE

There are 23 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 day – you go and look for your own favourites:
The Emergence of Predators in Early Life: There was No Garden of Eden:

Eukaryote cells are suggested to arise somewhere between 0.85~2.7 billion years ago. However, in the present world of unicellular organisms, cells that derive their food and metabolic energy from larger cells engulfing smaller cells (phagocytosis) are almost exclusively eukaryotic. Combining these propositions, that eukaryotes were the first phagocytotic predators and that they arose only 0.85~2.7 billion years ago, leads to an unexpected prediction of a long period (~1-3 billion years) with no phagocytotes – a veritable Garden of Eden. We test whether such a long period is reasonable by simulating a population of very simple unicellular organisms – given only basic physical, biological and ecological principles. Under a wide range of initial conditions, cellular specialization occurs early in evolution; we find a range of cell types from small specialized primary producers to larger opportunistic or specialized predators. Both strategies, specialized smaller cells and phagocytotic larger cells are apparently fundamental biological strategies that are expected to arise early in cellular evolution. Such early predators could have been ‘prokaryotes’, but if the earliest cells on the eukaryote lineage were predators then this explains most of their characteristic features.

Effects of Global Warming on Ancient Mammalian Communities and Their Environments:

Current global warming affects the composition and dynamics of mammalian communities and can increase extinction risk; however, long-term effects of warming on mammals are less understood. Dietary reconstructions inferred from stable isotopes of fossil herbivorous mammalian tooth enamel document environmental and climatic changes in ancient ecosystems, including C3/C4 transitions and relative seasonality. Here, we use stable carbon and oxygen isotopes preserved in fossil teeth to document the magnitude of mammalian dietary shifts and ancient floral change during geologically documented glacial and interglacial periods during the Pliocene (~1.9 million years ago) and Pleistocene (~1.3 million years ago) in Florida. Stable isotope data demonstrate increased aridity, increased C4 grass consumption, inter-faunal dietary partitioning, increased isotopic niche breadth of mixed feeders, niche partitioning of phylogenetically similar taxa, and differences in relative seasonality with warming. Our data show that global warming resulted in dramatic vegetation and dietary changes even at lower latitudes (~28°N). Our results also question the use of models that predict the long term decline and extinction of species based on the assumption that niches are conserved over time. These findings have immediate relevance to clarifying possible biotic responses to current global warming in modern ecosystems.

Coping with Commitment: Projected Thermal Stress on Coral Reefs under Different Future Scenarios:

Periods of anomalously warm ocean temperatures can lead to mass coral bleaching. Past studies have concluded that anthropogenic climate change may rapidly increase the frequency of these thermal stress events, leading to declines in coral cover, shifts in the composition of corals and other reef-dwelling organisms, and stress on the human populations who depend on coral reef ecosystems for food, income and shoreline protection. The ability of greenhouse gas mitigation to alter the near-term forecast for coral reefs is limited by the time lag between greenhouse gas emissions and the physical climate response. This study uses observed sea surface temperatures and the results of global climate model forced with five different future emissions scenarios to evaluate the “committed warming” for coral reefs worldwide. The results show that the physical warming commitment from current accumulation of greenhouse gases in the atmosphere could cause over half of the world’s coral reefs to experience harmfully frequent (p≥0.2 year−1) thermal stress by 2080. An additional “societal” warming commitment, caused by the time required to shift from a business-as-usual emissions trajectory to a 550 ppm CO2 stabilization trajectory, may cause over 80% of the world’s coral reefs to experience harmfully frequent events by 2030. Thermal adaptation of 1.5°C would delay the thermal stress forecast by 50-80 years. The results suggest that adaptation – via biological mechanisms, coral community shifts and/or management interventions – could provide time to change the trajectory of greenhouse gas emissions and possibly avoid the recurrence of harmfully frequent events at the majority (97%) of the world’s coral reefs this century. Without any thermal adaptation, atmospheric CO2 concentrations may need to be stabilized below current levels to avoid the degradation of coral reef ecosystems from frequent thermal stress events.

The Alliance Hypothesis for Human Friendship:

Exploration of the cognitive systems underlying human friendship will be advanced by identifying the evolved functions these systems perform. Here we propose that human friendship is caused, in part, by cognitive mechanisms designed to assemble support groups for potential conflicts. We use game theory to identify computations about friends that can increase performance in multi-agent conflicts. This analysis suggests that people would benefit from: 1) ranking friends, 2) hiding friend-ranking, and 3) ranking friends according to their own position in partners’ rankings. These possible tactics motivate the hypotheses that people possess egocentric and allocentric representations of the social world, that people are motivated to conceal this information, and that egocentric friend-ranking is determined by allocentric representations of partners’ friend-rankings (more than others’ traits). We report results from three studies that confirm predictions derived from the alliance hypothesis. Our main empirical finding, replicated in three studies, was that people’s rankings of their ten closest friends were predicted by their own perceived rank among their partners’ other friends. This relationship remained strong after controlling for a variety of factors such as perceived similarity, familiarity, and benefits. Our results suggest that the alliance hypothesis merits further attention as a candidate explanation for human friendship.

Trophic Garnishes: Cat-Rat Interactions in an Urban Environment:

Community interactions can produce complex dynamics with counterintuitive responses. Synanthropic community members are of increasing practical interest for their effects on biodiversity and public health. Most studies incorporating introduced species have been performed on islands where they may pose a risk to the native fauna. Few have examined their interactions in urban environments where they represent the majority of species. We characterized house cat (Felis catus) predation on wild Norway rats (Rattus norvegicus), and its population effects in an urban area as a model system. Three aspects of predation likely to influence population dynamics were examined; the stratum of the prey population killed by predators, the intensity of the predation, and the size of the predator population. Predation pressure was estimated from the sizes of the rat and cat populations, and the characteristics of rats killed in 20 alleys. Short and long term responses of rat population to perturbations were examined by removal trapping. Perturbations removed an average of 56% of the rats/alley but had no negative long-term impact on the size of the rat population (49.6±12.5 rats/alley and 123.8±42.2 rats/alley over two years). The sizes of the cat population during two years (3.5 animals/alley and 2.7 animals/alley) also were unaffected by rat population perturbations. Predation by cats occurred in 9/20 alleys. Predated rats were predominantly juveniles and significantly smaller (144.6 g±17.8 g) than the trapped rats (385.0 g±135.6 g). Cats rarely preyed on the larger, older portion of the rat population. The rat population appears resilient to perturbation from even substantial population reduction using targeted removal. In this area there is a relatively low population density of cats and they only occasionally prey on the rat population. This occasional predation primarily removes the juvenile proportion of the rat population. The top predator in this urban ecosystem appears to have little impact on the size of the prey population, and similarly, reduction in rat populations doesn’t impact the size of the cat population. However, the selected targeting of small rats may locally influence the size structure of the population which may have consequences for patterns of pathogen transmission.

Explaining the Evolution of Warning Coloration: Secreted Secondary Defence Chemicals May Facilitate the Evolution of Visual Aposematic Signals:

Several pathways have been postulated to explain the evolution of warning coloration, which is a perplexing phenomenon. Many of these attempt to circumvent the problem of naïve predators by inferring kin selection or neophobia. Through a stochastic model, we show that a secreted secondary defence chemical can provide selective pressure, on the individual level, towards developing warning coloration. Our fundamental assumption is that increased conspicuousness will result in longer assessment periods and divergence from the predators’ searching image, thus reducing the probability of a predator making mistakes. We conclude that strong olfactory signaling by means of chemical secretions can lead to the evolution of warning coloration.

Paleo-Immunology: Evidence Consistent with Insertion of a Primordial Herpes Virus-Like Element in the Origins of Acquired Immunity:

The RAG encoded proteins, RAG-1 and RAG-2 regulate site-specific recombination events in somatic immune B- and T-lymphocytes to generate the acquired immune repertoire. Catalytic activities of the RAG proteins are related to the recombinase functions of a pre-existing mobile DNA element in the DDE recombinase/RNAse H family, sometimes termed the “RAG transposon”. Novel to this work is the suggestion that the DDE recombinase responsible for the origins of acquired immunity was encoded by a primordial herpes virus, rather than a “RAG transposon.” A subsequent “arms race” between immunity to herpes infection and the immune system obscured primary amino acid similarities between herpes and immune system proteins but preserved regulatory, structural and functional similarities between the respective recombinase proteins. In support of this hypothesis, evidence is reviewed from previous published data that a modern herpes virus protein family with properties of a viral recombinase is co-regulated with both RAG-1 and RAG-2 by closely linked cis-acting co-regulatory sequences. Structural and functional similarity is also reviewed between the putative herpes recombinase and both DDE site of the RAG-1 protein and another DDE/RNAse H family nuclease, the Argonaute protein component of RISC (RNA induced silencing complex). A “co-regulatory” model of the origins of V(D)J recombination and the acquired immune system can account for the observed linked genomic structure of RAG-1 and RAG-2 in non-vertebrate organisms such as the sea urchin that lack an acquired immune system and V(D)J recombination. Initially the regulated expression of a viral recombinase in immune cells may have been positively selected by its ability to stimulate innate immunity to herpes virus infection rather than V(D)J recombination Unlike the “RAG-transposon” hypothesis, the proposed model can be readily tested by comparative functional analysis of herpes virus replication and V(D)J recombination.

Virtual Partner Interaction (VPI): Exploring Novel Behaviors via Coordination Dynamics:

Inspired by the dynamic clamp of cellular neuroscience, this paper introduces VPI–Virtual Partner Interaction–a coupled dynamical system for studying real time interaction between a human and a machine. In this proof of concept study, human subjects coordinate hand movements with a virtual partner, an avatar of a hand whose movements are driven by a computerized version of the Haken-Kelso-Bunz (HKB) equations that have been shown to govern basic forms of human coordination. As a surrogate system for human social coordination, VPI allows one to examine regions of the parameter space not typically explored during live interactions. A number of novel behaviors never previously observed are uncovered and accounted for. Having its basis in an empirically derived theory of human coordination, VPI offers a principled approach to human-machine interaction and opens up new ways to understand how humans interact with human-like machines including identification of underlying neural mechanisms.

Science Cafe Raleigh – The Science of Chocolate

The Science of Chocolate
Tuesday, June 16, 2009
6:30-8:30 pm with discussion beginning at 7:00 followed by Q&A
Location: The Irregardless Café, 901 W. Morgan Street, Raleigh 833-8898

From drinks to desserts, chocolate is a favorite that is loved by cultures worldwide. Can a food as delicious as chocolate also be good for your health? Join us to learn about the history of chocolate from ancient times to modern day manufacturing, and find out what current research is telling us about the science of this special food.
About the Speaker:
Dr. Gabriel Keith Harris is an Assistant Professor of Food Science at North Carolina State University. His research interests involve the functional properties of plant foods. His specific interests include the antioxidant and anti-inflammatory effects of flavonoids and related compounds.

Interview at Nature Network

Caryn Shechtman, one of the two bloggers at the New York blog and manager of the New York City Hub at Nature Network, called me up last week and interviewed me for the blog. The interview – on a range of topics, but mostly about blogging – is now published and you can read it here.

My picks from ScienceDaily

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Today’s carnivals

Carnival of Evolution #12 is up on Deep Sea News
Carnival of the Green #182 is up on Green Building Elements
Grand Rounds Vol. 5 No. 37 are up on Health Blawg

Clock Quotes

Walk softly and carry a big magnifying glass.
– Richard Lacayo

2009 3QuarksDaily Blogging Prize in Science – voting has started

The entries are listed and linked here. Go and vote here.
If you are interested in voting for me (but there are many other good choices, of course), know that to date the Archaea post got 0 votes, the Shock-Value got 2 and the others got 1 vote each. Perhaps we can do better (it appears impossible to vote more than once, so choose wisely).

New and Exciting in PLoS ONE – the farm animal edition

There are 13 new articles in PLoS ONE today, as well as 12 articles published Friday night. 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:
The Multifaceted Origin of Taurine Cattle Reflected by the Mitochondrial Genome:

A Neolithic domestication of taurine cattle in the Fertile Crescent from local aurochsen (Bos primigenius) is generally accepted, but a genetic contribution from European aurochsen has been proposed. Here we performed a survey of a large number of taurine cattle mitochondrial DNA (mtDNA) control regions from numerous European breeds confirming the overall clustering within haplogroups (T1, T2 and T3) of Near Eastern ancestry, but also identifying eight mtDNAs (1.3%) that did not fit in haplogroup T. Sequencing of the entire mitochondrial genome showed that four mtDNAs formed a novel branch (haplogroup R) which, after the deep bifurcation that gave rise to the taurine and zebuine lineages, constitutes the earliest known split in the mtDNA phylogeny of B. primigenius. The remaining four mtDNAs were members of the recently discovered haplogroup Q. Phylogeographic data indicate that R mtDNAs were derived from female European aurochsen, possibly in the Italian Peninsula, and sporadically included in domestic herds. In contrast, the available data suggest that Q mtDNAs and T subclades were involved in the same Neolithic event of domestication in the Near East. Thus, the existence of novel (and rare) taurine haplogroups highlights a multifaceted genetic legacy from distinct B. primigenius populations. Taking into account that the maternally transmitted mtDNA tends to underestimate the extent of gene flow from European aurochsen, the detection of the R mtDNAs in autochthonous breeds, some of which are endangered, identifies an unexpected reservoir of genetic variation that should be carefully preserved.

A Genome Scan for Positive Selection in Thoroughbred Horses:

Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed a genome scan using 394 autosomal and X chromosome microsatellite loci and identified positively selected loci in the extreme tail-ends of the empirical distributions for (1) deviations from expected heterozygosity (Ewens-Watterson test) in Thoroughbred (n = 112) and (2) global differentiation among four geographically diverse horse populations (FST). We found positively selected genomic regions in Thoroughbred enriched for phosphoinositide-mediated signalling (3.2-fold enrichment; P<0.01), insulin receptor signalling (5.0-fold enrichment; P<0.01) and lipid transport (2.2-fold enrichment; P<0.05) genes. We found a significant overrepresentation of sarcoglycan complex (11.1-fold enrichment; P<0.05) and focal adhesion pathway (1.9-fold enrichment; P<0.01) genes highlighting the role for muscle strength and integrity in the Thoroughbred athletic phenotype. We report for the first time candidate athletic-performance genes within regions targeted by selection in Thoroughbred horses that are principally responsible for fatty acid oxidation, increased insulin sensitivity and muscle strength: ACSS1 (acyl-CoA synthetase short-chain family member 1), ACTA1 (actin, alpha 1, skeletal muscle), ACTN2 (actinin, alpha 2), ADHFE1 (alcohol dehydrogenase, iron containing, 1), MTFR1 (mitochondrial fission regulator 1), PDK4 (pyruvate dehydrogenase kinase, isozyme 4) and TNC (tenascin C). Understanding the genetic basis for exercise adaptation will be crucial for the identification of genes within the complex molecular networks underlying obesity and its consequential pathologies, such as type 2 diabetes. Therefore, we propose Thoroughbred as a novel in vivo large animal model for understanding molecular protection against metabolic disease.

Today’s carnivals

First June Scientia Pro Publica is up on Pro-science
Circus of the Spineless #39 is up on Bug Girl’s Blog
Berry Go Round #17 is up on Gravity’s Rainbow
Festival of the Trees – Edition 36 is up on Roundrock Journal
The 105th Carnival of Space is up on Space Disco
Friday Ark #245 is up on Modulator

The Open Laboratory 2009 – the submissions so far

OpenLab logo.jpg
Here are the submissions for OpenLab 2009 to date. As we have surpassed 150 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 Lulu.com. 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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Speaking of Medicine

If you read this blog even superficially, you are probably aware of everyONE, the community blog of PLoS ONE. The blog has been so successful, that our colleagues at PLoS Medicine have decided to follow our example and start their own community blog.
And, today they are ready to reveal – Speaking of Medicine. Go check it out – click on all the tabs on top for all the additional information. Bookmark and subscribed. Spread the word about it. And come back often and use it – and post comments.

The May Blog Pick Of The Month at PLoS ONE is….

…to be found on the everyONE blog.

SILENCE IS THE ENEMY

About a week ago, Nicholas Kristof wrote an eye-opening op-ed in NYTimes – After Wars, Mass Rapes Persist. In Liberia, and probably in some other places, the end of war does not automatically mean the end of rape:

Of course, children are raped everywhere, but what is happening in Liberia is different. The war seems to have shattered norms and trained some men to think that when they want sex, they need simply to overpower a girl. Or at school, girls sometimes find that to get good grades, they must have sex with their teachers.

The war, and the use of rape as a weapon of war, changes the culture in a way that permits the rape to continue in a civilian society, as a means of asserting power, nursing one’s wounded sense of masculinity and keeping the women under control. Kristof writes:

The evidence is overwhelming that the best way to deal with rape — whether in Darfur or Liberia, or even in the United States — is to demystify it, dismantle the taboos, and address it directly. That is happening.
The United Nations Security Council held a formal session last year on sexual violence, and the International Criminal Court in The Hague issued its arrest warrant for Sudan’s president in part because of mass rapes. Senators Barbara Boxer and Russ Feingold chaired subcommittee hearings on rape just this month, focused on Congo and Sudan, where the brutality is particularly appalling. But the lesson of Liberia is equally sad: that even when wars end, mass rape continues by inertia.

In a related article, Eve Ensler focuses on similar issues in the Congo:

Nothing I have heard or seen compares with what is going on in the Democratic Republic of Congo, where corporate greed, fueled by capitalist consumption, and the rape of women have merged into a single nightmare. Femicide, the systematic and planned destruction of the female population, is being used as a tactic of war to clear villages, pillage mines and destroy the fabric of Congolese society.
In 12 years, there have been 6 million dead men and women in Congo and 1.4 million people displaced. Hundreds and thousands of women and girls have been raped and tortured. Babies as young as 6 months, women as old as 80, their insides torn apart. What I witnessed in Congo has shattered and changed me forever. I will never be the same. None of us should ever be the same.

Ensler is also the founder of V-Day, a global movement to end violence against women and girls.
Sheril Kirshenbaum is leading a very important blogospheric initiative called SILENCE IS THE ENEMY starting today, June 1st to help a generation of young women half a world away. She says:

An International Rescue Committee survey suggests 12 percent of girls aged 17 and under acknowledged having been sexually abused in some way in the previous 18 months. Further, of the 275 new sexual violence cases treated Jan-April by Doctors Without Borders, 28 percent involve children aged 4 or younger, and 33 percent involve children aged 5 through 12. That’s 61% age 12 or under. We read about their plight and see the figures, but it’s so easy to feel helpless to act in isolation. But these are not statistics, they are girls. Together we can do more.

Today, on June 1 at 9am, ‘SILENCE IS THE ENEMY’ begins – so named because we will not be (also lyrics of a rising Top 30 song, and therefore memorable).
What can you do?
Post about this. Send the URL of your post to Sheril (see the details and instructions in her post) so she can add it to the ‘SILENCE IS THE ENEMY’ homepage. And make sure you include the links to the Doctors Without Borders Donation Page and ask for donations, as well as to the Congressional Directory so readers can contact their representatives. Sheril will also post a static letter to Congress on the sidebar of her blog, so that readers can copy it and include it in their letters to Congressmen.
And spread the word using all the online and offline tools you have.

The World Science: a virtual Science Cafe

The World is a radio show co-produced by WGBH Boston, Public Radio International and BBC. You can probably hear it on your local NPR station – if not, you can find all the shows recorded on the website.
You may remember that I went to Boston a couple of months ago, as part of a team of people helping the show do something special: use the NSF grant they recently received to expand their science coverage and, in collaboration with Sigma Xi and NOVA, tie their radio science coverage to their online offerings.
The result is The World: Science website, a series of weekly science podcasts with Elsa Youngsteadt and David Kohn (subscribe to the RSS feed) and, starting this week, something new.
First, the radio show will have a brief segment on a science topic that includes an interview with a science-related person. A longer version of that story/interview will be on the website as a podcast, with additional links to outside sources. And, most exciting, the person who was interviewed for the show will come by the online forum for a week after the show and answer readers/listeners’ questions. Like an online version of a Science Cafe.
So, on the last Friday’s radio show, there was a segment about the science of decision-making featuring Jonah Lehrer (also my SciBling on The Frontal Cortex blog). The longer version of the story is online as a podcast and the forum discussion is ongoing until next Friday. Since we did not promote it (except for a brief mention on the radio show itself) on Friday, the discussion has just begun. We hope that, with all of you checking in and spreading the word, the discussion will grow. And get bigger every time – hopefully becoming a weekly event.
You should also follow the news about this endeavor on Twitter, in the FriendFeed room and a Facebook page. Join, friend, follow, subscribe. And come back next week and next and next. And don’t feel shy to give feedback as this is just in the early stages of development and we are open to suggestions.

Trip to Germany and Serbia

Later this month, I’ll be attending the 59th Meeting of Nobel Laureates in Lindau, Germany. The list of Nobel Laureates (about 20 of them) and the list of about 600 young researchers from 66 countries are very impressive. Of course, not being a chemist, I’ll have to do some homework before I go, learning what these people did to get the prizes.
The program certainly looks interesting – there is a lot of “meta” stuff beyond pure chemistry, so I will always find interesting sessions to attend and blog from. Yes, I am going to be there as a blog-reporter. I understand that PZ will also be there in the same capacity.
The meeting is from June 28th to July 3rd, after which I’ll fly to Belgrade for a few days, to visit my Mom and meet some friends (especially those I missed last year). Ana, Vedran and some others are already trying to organize for me to give lectures and interviews while there.
If you’ll be either at the Lindau meeting or in Belgrade at the above dates, let me know. I’ll be flying through London, but will not have much or any time to stop and do any socializing there this time around.

The Best of May

I posted only 128 posts in May – the reason for this reduction in numbers I explained here. Traffic has suffered only a little bit so far, I’ll keep an eye. Looking back at the month, I noticed how many videos I have posted: about half are very informative and thought-provoking, the other half are hilariously funny. Take a look. So, what did I actually blog about last month?
There was some serious science on this blog last month, e.g., Why social insects do not suffer from ill effects of rotating and night shift work? and Yes, Archaea also have circadian clocks!
I celebrated my birthday and got an iPhone!
I wrote a longish post praising (deservedly) the Undergraduate science summer camp at Petnica Science Center.
Work-related, I announced the April Blog Pick Of The Month and posted about Trackbacks – the hows and the whys – on PLoS journals’ articles.
The big story of the month was Ida, of course. I mostly kept my mouth shut about it, but could not avoid introducing the paper in Introducing Ida – the great-great-great-great-grandmother (or aunt), then following up with Wow! Check Google.com, Night, night, Ida… and Creative reuse of OA materials.
I posted the links to Columbia Scholarly Communication Program Speaker Series Videos and the two one-hour interviews (in Serbian) I gave to Radio Belgrade last year about science communication, blogs and OA.
I posted announcements of the inauguration of The Clade and Cognitive Monthly. Science Online London 2009 and XXVI International Association of Science Parks World Conference on Science & Technology Parks also needed to be announced.
I went to the Triangle Tweetup and met some interesting people there. I asked my readers to help me compile a collection of all North Carolina science/nature/medical blogs. And I recommended three bizarre, morbid and strange new blogs I discovered.
I posted a not-so-well-thought-out question – A Radical Transparency society is difficult to describe in a SF novel – where my commenters set me straight and produced a lot of thought-provoking material. There was a lot of discussion about commenting on scientific papers. Then I pointed out two great examples of Open Science.
Then I found a poem – The Evolution of Peeps and some pictures of mating slugs and a turtle. And celebrated the birthday of the originator of Milankovitch cycles.

Clock Quotes

The events of our lives happen in a sequence of time, but in their significance to ourselves, they find their own order.
– Eudora Welty

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:
Darwinius-on-toast.jpg
Richard Carter was next, depicting Ida playing saxophone:
darwinius-sax.jpg
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!
CONTEST RULES
* 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.
ABOUT 3 QUARKS DAILY
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.
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