Saturday, September 27, 2008

Body Language and Politics

When I watched the McCain-Obama debate last night, I wasn't so much interested in what they had to say, but rather how they said it. I was wondering who would be the dominant male. What struck me most was McCain's awkwardness, a stiffness in the way he postured towards Obama. It seemed as if McCain was going out of his way to avoid looking Obama in the eyes. The full significance of this never hit me, but Franz de Waal saw it clearly. Blogging at the Huffington Post, de Waal writes,

"I read the body language between McCain and Obama as that between a senior male being challenged by a remarkably confident junior one. The senior didn't know exactly what to do. He avoided eye contact and body orientation, probably realizing that a direct confrontation might not go his way.

If McCain was an alpha male, it was an incredibly insecure one."

Thursday, September 25, 2008

More on Obama's Science Policy

One of the knocks on Senator Obama during the primary campaign was that he was all style and no substance. Back then, it was a fair charge; Obama's campaign did not offer up many specifics as to his policies. No more. Obama has offered up one of the most comprehensive policy plans for science that I have witnessed. I won't go into many specifics here, but Obama aims " to double funding for major science agencies over the next decade."

The Boston Globe reports that 62 Nobel Laureates have endorsed Obama. You can read the endorsement and see the signee's here.

"We have watched Senator Obama's approach to these issues with admiration. We especially applaud his emphasis during the campaign on the power of science and technology to enhance our nation's competitiveness. In particular, we support the measures he plans to take – through new initiatives in education and training, expanded research funding, an unbiased process for obtaining scientific advice, and an appropriate balance of basic and applied research – to meet the nation's and the world's most urgent needs."

Poster by Scott Hansen.

Wednesday, September 24, 2008

Questioning the Candidates

Previously I posted on the science policies of the US presidential candidates and Senator Obama's announcement of his science advisors, and have an update here. The science journal Nature has released an election special issue, and in it I see first mention of Senator McCain's science advisors.
The most obvious difference between the teams is that Obama's team consists of actual scientists. Another distinguishing factor is that Obama accepted Nature’s invitation to answer 18 science-related questions in writing whereas McCain declined.

As an evilutionary biologist, I found Obama's statement on creationism to be particularly heartening, "I believe in evolution, and I support the strong consensus of the scientific community that evolution is scientifically validated. I do not believe it is helpful to our students to cloud discussions of science with non-scientific theories like intelligent design that are not subject to experimental scrutiny."

I don't really know what McCain stands for. Nature reports, "McCain said last year, in a Republican primary debate: “I believe in evolution. But I also believe, when I hike the Grand Canyon and see it at sunset, that the hand of God is there also. In 2005, he told the Arizona Daily Star that he thought “all points of view” should be available to students studying the origins of humanity. But the next year a Colorado paper reported him saying that such viewpoints should not be taught in science class."

Nature's editors teams note, "The most worrying thing about a McCain presidency is not so
much a President McCain as a Vice-President Palin. Sarah Palin, Alaska’s governor and McCain’s running mate, opposes all research into human embryonic stem cells. She is a creationist. And until lately, at least, she has been a skeptic of human-created climate change — a disquieting thought."

Monday, September 22, 2008

Advancing Science Thru Blogging

In an article published in PLoS Biology, Shelly Batts, Nick Anthis and Tara Smith write about blogging as a means of science communication.

Batts et al. write "Scientific discovery occurs in the lab one experiment at a time, but science itself moves forward based on a series of ongoing conversations, from a Nobel Prize winner's acceptance speech to collegial chats at a pub. When these conversations flow into the mainstream, they nurture the development of an informed public who understand the value of funding basic research and making evidence-based voting decisions. It is in the interests of scientists and academic institutions alike to bring these conversations into the public sphere....Because many science bloggers are practicing scientists or experts in their field, they can provide a unique educational bridge between academia and the public and distill important experimental findings into an accessible, interactive format."

Starting a science blog was a fairly random impulse for me. If the learning curve was steep or posting complicated, I probably would have abandoned the effort early, but Blogger's tool made posting effortless. In retrospect, blogging has been one of the best academic decisions I have ever made as it has facilitated communication with my peers and opened many doors for me.

Author Nick Anthis also blogs about his paper here. In it he writes that many other bloggers have had similar experiences to mine. After informally polling bloggers, Anthis and his coauthors found that, "Across the blogosphere, scientists had started new collaborations, enhanced their scientific work, advanced their careers, been able to communicate science as never before, and had been offered a whole array of new and unique experiences and opportunities in part or in full due to their blogs. In fact, the stories we heard were so compelling that instead of just communicating them we asked ourselves another question: why has this phenomenon gone so underreported and unappreciated within academic circles? And, more pointedly, how can we most effectively communicate this potential to an academic audience--in hopes of catalyzing even more of these wonderful successes?"

I think the scientific community is beginning to recognize the benefits of blogging. Every time I log on, there are more and more science blogs entering the blogosphere. Folks that don't blog definitely seem to read them. As with any new technology, it takes some time to get used to the idea. It may be that, in the future, blogs will be as much as part of the scientific discourse as scientific journals. Remember back in 1994, hardly any labs had a web page, but now its seems obligatory. Maybe research blogs will be ubitquitous in 2018.

Shelley A. Batts, Nicholas J. Anthis, Tara C. Smith (2008). Advancing Science through Conversations: Bridging the Gap between Blogs and the Academy PLoS Biology, 6 (9) DOI: 10.1371/journal.pbio.0060240

Figure from the Next Hurrah.

Update: Nick respond to comments here.

Friday, September 19, 2008


The Citizendium Project is gearing up for Biology Week and has released this press release.

Wiki Encyclopedia Invites Biologists to a Weeklong Open House

International Cyberspace - September 19 - Biology Week, an online "open
house" for biologists, biology students, and anyone else interested, begins
September 22 on Citizendium (, the
next-generation wiki encyclopedia started by Wikipedia co-founder Larry

During the week, biologists and anyone interested in the topic are invited
test out the Citizendium system. Editors and authors from the project's
Biology Workgroup will be on hand to meet and greet new people on the wiki.

Biology is one of the more active areas in the Citizendium, with nearly
1,000 articles in progress. Unlike the Encyclopedia of Life, the project is
a wiki and benefits from strong collaboration; for an example of the success
of the system, biologists might want to see the article "Life"

Dr. Gareth Leng, Professor of Experimental Physiology at the University of
Edinburgh, and Citizendium author and editor, described the project: "Our
role will not be to tell readers what opinions they should hold, but to give
them the means to decide, rationally, for themselves. The role of experts is
critical-not to impose opinions, but to support accuracy in reporting and
citing information."

The Citizendium, or "citizens' compendium," uses the same software as
Wikipedia. It is a successful public-expert hybrid project to produce a
general reference resource. The community encourages general public
participation, but makes a low-key, guiding role for experts. It also
requires real names and asks contributors to sign a "social contract."

As a result, the project is vandalism-free and, despite its youth (its
public launch was just 18 months ago), has steadily added over 8,000
articles, many of them of fine quality.


Citizendium website:
Biology Week homepage:
"Life" (sample article):

Thursday, September 18, 2008

Obama Campaign Reveals Science Advisors

I wrote a terse email to Senator Barack Obama a few months ago, chastising him for not taking a stronger stance on critical science issues and for declining to participate in a Science Debate. Recently Obama has turned a page; he has come out strongly on science issues. A few days ago Obama (as well as Senator John McCain) submitted responses to 14 science questions. Today Obama revealed his science advisors: Nobelist and former head of NIH Harold Varmus, former head of AAAS Gilbert Omenn, Nobelist Peter Agre, astrophysicist Don Lamb and former Stanford dean Sharon Long.

McCain on the other hand has selected as running mate Governor Sarah Palin, a young-earther, cretinist and global warming denialist.

Asilomar '75

For those of you who have access, Nature has an interesting essay from Nobelist Paul Berg on the Asilomar Conference back in '75.

Berg originally organized the Asilomar Conference on Recombinant DNA to discuss the potential biohazards and regulation of biotechnology. "At that gathering [of scientists]... it was agreed that the research should continue but under stringent guidelines. The conference marked the beginning of an exceptional era for science and for the public discussion of science policy." Jim Watson, who was at the meeting, was adamantly opposed to any regulation, but was soundly overruled.

The fears of many scientists turned out to be unfounded:

"In the 33 years since Asilomar, researchers around the world have carried out countless experiments with recombinant DNA without reported incident. Many of these experiments were inconceivable in 1975, yet as far as we know, none has been a hazard to public health. Moreover, the fear among scientists that artificially moving DNA among species would have profound effects on natural processes has substantially disappeared with the discovery that such exchanges occur in nature."

That was pretty much Jim Watson's opinion back in '75, but not many listened to him then. Watson later described Asilomar as "the worst week of my life".

Berg wonders, "Could an Asilomar-type conference help resolve some of the controversies now confronting scientists and the public — such as over fetal tissue, embryonic stem-cell research, somatic and germ-line gene therapy and the genetic modification of food crops?"

I disagree. I see no need for such regulation as the dangers posed by these technologies are excessively dramatized yet insufficiently documented. Moreover, unlike Asilomar, it is likely that any such conference today would be hijacked by ideological interests.

Photo: (left to right) Maxine Singer, Norton Zinder, Sydney Brenner, and Paul Berg were among the participants at the Asilomar Conference. From: National Academy of Sciences.

Wednesday, September 17, 2008

Phage in the News

Science Daily reports on a new paper in Biophysical Journal from Joshua Weitz and team. I met Joshua last winter at the Viral Paradigms Workshop. It was clear then that he was doing some exciting work.

"The researchers modeled the complex gene regulatory dynamics of the lysis-lysogeny switch for lambda phage.... The decision circuit is a race between two pathways and in the case of a single virus, the outcome is biased toward lysis," explained Weitz. "In our model, when multiple viruses infect a given cell, the overall production of regulatory proteins increases. This transient increase is reinforced by a positive feedback loop in the latency pathway, permitting even higher production of lysogenic proteins, and ultimately the latent outcome."

The central idea in the model proposed by Weitz and collaborators is that increases in the overall amount of viral proteins produced from multiple viral genomes can have a dramatic effect on the nonlinear gene networks that control cell fate."

I've previously written about the lysis-lysogeny decision in phage.

I've just downloaded the paper and look forward to reading it closely.

Photo: Phage lambda electron-micrograph. Notice it lacks tail-fibers which is typical of laboratory reared lambda. Wild lambda have tail fibers.

Tuesday, September 16, 2008

The Flawed Premise of the HapMap

There's an interesting exchange afoot regarding the study of genetic variation among human populations. First, Nick Wade of the NYT wrote a piece on Duke geneticist David Goldstein whom I had the opportunity to hear speak earlier this year at the Yale Symposia on Health and Disease. Goldstein's talk then was on Pharmacogenetics, but now he has a few things to say on the $3 billion effort to decode the human genome. The major premise of the human genome project was that it would enable the discovery of the variant genes that predispose people to common diseases like cancer and Alzheimer’s.

“It’s an astounding thing,” Dr. Goldstein said, “that we have cracked open the human genome and can look at the entire complement of common genetic variants, and what do we find? Almost nothing. That is absolutely beyond belief.”

John Hawks points out, yeah that's exactly what we evilutionary biologists expected! Hawks writes "Of the variants that have been found in these genome-wide association studies, for Alzheimer's, Type 2 diabetes, schizophrenia -- a significant number appear to have been recently selected. So even these few that have been found wouldn't have been predicted under the "common variant" model. But most variants that cause senescence must be rare. That's Medawar's theory. Or they may be balances. That's Williams' theory. This is a case where modern evolutionary theory gives very clear predictions, which have now been confirmed at enormous cost."

Hawks refers to evolutionary icons Peter Medawar and George Williams, whose work on the evolution of senescence in the 50's seems to have been overlooked.

Oh well, the physicists got their LHC to look for the (probably) mythical boson; we got 3 billion to catalog the (almost) infinitely diverse human genome. Hawks says it best, "Recent human evolution is not progress toward a pinnacle. The human population is a snowdrift where ten thousand trade-offs have blown together, mostly by the luck of mutations."

Larry Moran, Daniel MacArthur, Dieneke, Razib and Jonathan Eisen also comment in their respective blogs.

Giant Shoulders 3rd Edition

The third edition of the Giant's Shoulders is up. Editions 1 and 2 are also available.

If I have seen a little further it is by standing on the shoulders of Giants.” - Isaac Newton, in a letter to Robert Hooke, 1676. (Though the metaphor goes back much further.)

“The Giant’s Shoulders” is a monthly science blogging event, in which authors are invited to submit posts on “classic” scientific papers. Submissions are due on the fifteenth of each month, and entries will be aggregated and linked to on the host blog of the month. Links to entries should be sent to that month’s host blog.

What defines a “classic” paper? This depends upon the field in question, but one expects that the work should have somewhat stood the test of time: we suggest perhaps 10 years old, or more. Contributors should not only describe the research involved but also put it in a broader historical/scientific context: why is the work in question important/groundbreaking/revolutionary/nifty?

Friday, September 12, 2008

This Week's Citation Classic

This week's citation classic is:

Dayton, PK (1971). Competition, Disturbance, and Community Organization: The Provision and Subsequent Utilization of Space in a Rocky Intertidal Community Ecological Monographs, 41 (4), 351-389

Paul Dayton once wrote, "Ecology often seems dominated by theoretical bandwagons driven by charismatic mathematicians; lost to many is the realization that good ecology rests on a foundation of solid natural history and progresses by use of proper scientific methods."

True to his words, Dayton gets out there in the middle of it. The present paper was only possible thru untold hours in the field. Lest anyone get the wrong impressions, field research is difficult. Your ability to work is dictated by the life history of the organisms you study and the elements, rain, snow, blazing sun and biting cold. All your tools need to be carried with you, and the beasties you study are famously uncooperative, often favoring niches far from prying eyes.

Despite these challenges, Dayton presents a wonderful monograph about competition for space among sessile intertidal organisms: barnacles, limpets, algae, and anemones. Most ecological research at the time discounted the effects of the physical environment on competition between species, but Dayton was able to show that physical disturbances e.g. waves, driftwood logs, exposure to the air modulates interspecific competition.

"The major conclusion of the present study is that although there are clear competitive dominants, this intertidal community is characterized by continuous physical and biological disturbance including the effects of carnivores and herbivores, an abundance of the potentially limiting spatial resource, and a large number of species which utilize this same resource."

Dayton has had a fabulous career since finishing the dissertation he presents here. He is on the faculty of the Scripps Institition of Oceanography and has recieved the Margalef Prize and the E. O. Wilson Naturalists Award.

And he clearly LOVES his work!

Photo: Dr. Paul Dayton deploying a cage experiment on the seafloor in McMurdo Sound in 1967. Notice his diving gear - he is using a double hose regulator (in use in the USAP until 1988) and a WETSUIT, in water that is -1.8° C (29° F)!

Thursday, September 11, 2008

Science Blogging in TREE

I don't know how I missed this because I am a regular reader of TREE, but John Wilkins of Evolving Thoughts has published an article on scientific blogging in the August issue.

One of the excellent points the paper makes is, "Blogging is also a way to demythologize science. Unlike laws and sausages, the public should see science during its manufacture, but the lay public is generally ill-equipped to interpret what they see, and science bloggers play a crucial role here. Bloggers with a deeper knowledge of the topic, or of science in general, can place studies in a context of prior work, thereby correcting or avoiding the myths and pigeonholes of science journalism."

I agree completely. Part of my reasoning for starting this blog was to connect with folks who would otherwise not hear about my work or work that I think is important.

The article ends by saying, "The academic research and teaching communities for science and related fields need to see blogging as more than a casual hobby, as core outreach for their science. It is an effective way for scientists to counter the misunderstandings, deliberate and otherwise, of popular culture. Not only graduate students, but more tenured professionals, need to engage in this to ensure that their science, and the science of others, is in the public eye."

I would love it if my colleagues all had active blogs, as I could see what they are up to, what issues they are struggling with and what they are thinking about at any given time.

Wednesday, September 10, 2008


Today Daniel Bunker, now at New Jersey Institute of Technology, presented at our departmental colloquium. While his talk on invasive species, ecosystem dynamics and climate change was excellent, what really captured my imagination was TraitNet, a collaboration with Shatid Naeem (Ecology With No Apology) of Columbia University.

I cannot count the number of times I've spoken with someone about some species, only to hear the remark "Well what we really need is some basic data on x!" The trouble is, determining the average weight of, say, newts in, say, the Cascades isn't really work that will get you published in Nature so there is a reluctance to embark on studies to collect such basic trait data.

Enter TraitNet!

The mission of TraitNet is:

  1. Identify key questions and Core Hypotheses in trait-based research.
  2. Identify data gaps that hinder the advancement of intra- and inter-disciplinary trait-based research.
  3. Coordinate the standardization of collection and curation of trait data.
  4. Build a model database to test explicit Core Hypotheses developed through TraitNet workshops.
  5. Facilitate the development of cross-disciplinary computational tools for merging, disseminating, and sharing trait data.
TraitNet will coordinate trait-based evolutionary and ecological research. Traits are biological properties of species that influence individual fitness and govern how species interact with their biotic and abiotic environment. Traits are used across a broad spectrum of disciplines, including niche theory, community assembly, metabolic ecological theory, phylogenetics, conservation, and ecological stoichiometry. While each discipline has developed its own operational definitions, protocols, and databases, there is little coordination across disciplines. TraitNet will advance syntheses and analyses by coordinating integration among disciplines.

I think TraitNet is an excellent idea who's time has come. We have Genbank, Tree of Life,
RCSB PD etc. Why no trait database?

Tuesday, September 9, 2008

The Amazing Randi

Uber-skeptic and MacArthur Award winner James Randi will be making a New York area appearance at Rockefeller University next month. Randi is being hosted by New York City Skeptics. This event is free and open to the public.

Friday, September 5, 2008

Heading to Dayton, TN

In stunning news, a Darwin-shaped wall stain has been reported at the former site of the Scopes Trial. The image has driven evolutionists into a scientific fervor.

"I have never felt closer to Darwin's ideas," said zoologist Fred Granger, who waited in line for 16 hours to view the stain. "May his name be praised and his theories on natural selection echo in all the halls of naturalistic observation forever."

I've abandoned my plans for the weekend, and am driving down to Dayton as soon as possible.

This Week's Citation Classic: Genetic Engineering

Genetic engineering is ubiquitous in biology labs today, and a popular whipping boy among a society that little recognizes the benefits it provides. But where did it all begin?

Over hot pastrami sandwiches in Waikiki.

This week's citation classic is: Cohen SN, Chang ACY, Boyer HW and Helling RB. 1973. Construction of Biologically Functional Bacterial Plasmids In Vitro. PNAS USA 70: 3240-3244.

In 1972, Herb Boyer, a biochemist at the University of California at San Francisco, and Stan Cohen, an associate professor of medicine at Stanford University, were presenting at a conference on bacterial plasmids in Hawaii when they noticed the complementary nature of their work. Following the conference, they met at a deli to hash out the details of the following experiment.

Cohen had previously determined how to make E. coli take in foreign DNA (a citation classic worthy feat in itself) when he transformed E. coli with a plasmid known as pSC101, that conferred resistance to the antibiotic tetracycline.

Boyer on the other hand had discovered EcoRI, a restriction enzyme that could snip open pSC101 while leaving "sticky ends".

Like chocolate and peanut butter, the combination was unbeatable. Cohen and Boyer realized they could combine their techniques to create a new plasmid containing foreign DNA.

First they digested the African clawed toad, Xenopus laevis, DNA with EcoRI to isolate the rRNA gene. Then they cleaved pSC101 with EcoRI. Since pSC101 has only a single restriction site, the plasmid was linearized. Because of the sticky ends, the plasmid and the Xenopus DNA joined together when placed in the same test tube, thus creating a recombinant plasmid. Using Cohen's technique, the plasmid containing the foreign DNA could then be transformed into E. coli where it would now be expressed. Genetic engineering was born!

Thursday, September 4, 2008

Henry Stewart Talks: Evolution and Medicine

Usually I hate unsolicited email, but I received one today that I was very glad to have received. The email directed me to this website where a series of talks on Evolution and Medicine are available. Henry Stewart Talks are advertised as Online Seminars By Leading World Experts. From the one's I have observed, the series basically consists of slide show with voice-over narration. Despite this, I found them totally engrossing and I am looking forward to viewing them all.

Some of the topics include:

Evolution and Medicine: From the Perspective of an Evolutionary Biologist
Prof. Stephen Stearns - Yale University, USA

Bacteria and Virus Evolution: A Model for the Study of Natural Selection
Dr. Paul Turner - Yale University, USA

Infection and Chronic Disease
Prof. Paul Ewald - University of Louisville, USA

The Original Human Diet: What was it and should it be a Model for Contemporary Nutrition?
Prof. S. Boyd Eaton - Emory University, USA

Why we Cook with Spices: Preventative Darwinian Medicine
Prof. Paul Sherman - Cornell University, USA

Genetic Conflicts in Human Pregnancy
Prof. David Haig - Harvard University, USA

Mental Disorders in the Light of Evolutionary Biology
Prof. Randolph Nesse - University of Michigan, USA

A Darwinian Eye View of Cancer
Prof. Mel Greaves - Institute of Cancer Research, UK

These are just the talks about Evolutionary Medicine. There are 800 other talks on other aspects of biology including stem cells, RNAi, gene regulation, epigenetics etc etc.