Unidentified Biological Organism

A diver named Jay Garbose videotaped this "creature" off the coast of Juno Beach, Florida. The creature has been tentatively identified by the Smithsonian as an unknown species of Nemertean Worm. They said he could name it if he found it again... ha ha. Nonetheless it looks pretty freaking cool. I'm amazed that anything of that size could have escaped notice for so long, especially off the busy coast of Florida.

Garbose says, "At first I thought it was a sea cucumber although no one's ever seen one stretched 7 to 10 feet the way this one was. It's sort of grey and putty-like and very smooth and taffy-like in the way it stretches. Some of my friends and I have sort of dubbed it the living intestine."

There's a video here.

I am Convinced that It is the Light and the Way

This comment on natural selection is the last sentence of Adaptation and Natural Selection, George Williams' masterpiece about evolution. An evolutionary biologist I know (who shall remain anonymous to spare him/her public shaming) claimed not to know who was George Williams. I was/still am aghast. This anonymous evolutionary biologist is the inspiration for this post, indeed for this series of citation classics. Williams is a professor emeritus at SUNY: Stony Brook, author of numerous influential books, and recipient of the 1999 Crawfoord Prize. In the words of no less a luminary than Stephen Pinker, "George Williams was instrumental in making natural selection an intellectually rigorous theory".

Today's citation classic is Williams, G.C. 1957. Pleiotropy, natural selection, and the evolution of senescence. Evolution, 11: 398-411. It was Williams' first significant paper and considered by many to be a cornerstone of modern evolutionary theory. At the time, aging was a major problem in biology (actually, it still is). In 1956, Alex Comfort wrote in The Biology of Senescence*, "In almost any other biological field, it is possible to ... show a steady progression from a large number of speculative, to one or two highly probable, main hypotheses. In the case of senescence this cannot profitably be done."

At the time of publication of Williams' Evolution of Senescence, many biologists considered aging an evolutionary adaptation. In an article in Science, Carl Zimmer (The Loom) wrote, "Williams recalls a lecture he heard by Alfred Emerson, a zoologist at the University of Chicago, about why people age and die. 'He said growing old and dying is a good thing,' Williams says. 'We’ve evolved to do it so we get out of the way, so the young people can go on maintaining the species. I thought it was absolute nonsense,' says Williams."

Williams' Evolution of Senescence paper was his opening salvo in his war against this "nonsense", this fuzzy-headed, group selectionist thinking. Views such as those held by Emerson were common. They culminated in V.C. Wynne-Edwards' book, Animal Dispersion in Relation to Social Behavior, where it was argued, for example, that many animals formed groups so that they could assess population density, and regulate their own numbers to avoid overpopulation. Balderdash! Humans, even with all our intellectual gifts, can't regulate our own population. Most adaptations benefit the individual, or more correctly, the gene producing the trait, not the group or any other higher level of biological organization. W.D. Hamilton later wrote "Geometry for the selfish herd" (a classic in its own right) to show that animals often grouped to reduce their own risks of being preyed upon.

In "Pleiotropy, natural selection, and the evolution of senescence", Williams argued that senescence was not an adaptation to remove old-folks to make room for young'uns. Rather senescence was the result of an evolutionary trade-off. Selection favored genes that enhanced reproduction in youth even though they were deleterious in old age. In Williams' words,

"So natural selection will frequently maximize vigor in youth at the expense of vigor later on and thereby produce a declining vigor (senescence) during adult life.... The rate of senescence shown by any species will reflect the balance between this direct, adverse selection of senescence as an unfavorable character, and indirect, favorable selection through age-related bias in the selection of pleiotropic genes."

In other words, genes for vigor late, as opposed to early, in life aren't favored because one's reproductive probability is at its maximum at reproductive maturity and subsequently declines as the cumulative probability of death increases. Less formally, better hurry up and reproduce, kid, before you get hit by a bus or something.

There is no biological law that says the body must wear out, that we must age, that we must die. Hypothetically, it should be easy enough to live forever as the energy expenditure for maintaining the present structure pales in comparison to the expenditure required to make a new body from scratch. What we observe as senescence, then, is just the consequence of genes selected for the reproductive advantages they provide during youth. As Zimmer writes, "Ironically, cancer, declining stamina, deteriorating vision and various diseases of old age could all be the result of natural selection". The possible genes producing these phenotypes simply have to make you more fecund at reproductive maturity.

Frans Roes interviews Williams here and touches on the above themes.

Williams recounts some of his adventures here at the Edge.

*During the George Williams symposium at SUNY: Stony Brook, I happened, as is my wont, to visit a local bookstore, and was delighted to find a 1st Edition copy of Comfort's The Biology of Senescence with Williams' stamp inside and annotated by Williams himself.

Take Action to Save the Savannah River Ecology Laboratory

The DOE is shutting down the Savannah River Ecology Laboratory. I suspect the current anti-science administration in Washington is behind the decision. Here's what you can do to help: SREL Action letter.

Other Blogs on this Issue

1. The Austringer: War On Science Continues: Savannah River Ecology Laboratory on Chopping Block
2. Thoughts From Kansas: Save the SREL
3. blustrydaz: This is really not good! (my graduate research is here!) If you get the chance, pls write a letter!
4. evolgen: DOE to Cut Funding to Major Environmental Research Laboratory
5. De Rerum Natura: Savannah River Ecology Laboratory in Jeopardy.

Peer Review Revisited

Madhusudan Katti over at Reconciliation Ecology picked up the thread about the issue of slow peer review. He makes some interesting comments, particularly regarding the time constraints at teaching-orientated institutions. I've thought a bit more about the issue and have a few more points to make regarding possible solutions.

What are the alternatives?

1. Do nothing.
-Is there really a problem? One could argue that time-to-publication times are faster now than ever, particularly with internet submissions. Being relatively new to the science publication business, I don't have any insight into what it was like back in the day. Perhaps some old-timers senior researchers could chime in on this.

2. Financial incentives
-Some have suggested paying reviewers. I think this is a non-starter. Most scientific societies are already strapped for cash. Besides it just introduces a whole new layer of potential conflicts of interest. Besides aren't we all getting paid already by our institutional salaries?

3. Service Counts
-Madhu suggests increasing the impact of service (and peer review) in the tenure review process. Great idea. However, someone (a tenured faculty who had served on many review committees) once said that tenure counts for ~10% of the decision. Someone else said that service counts for nothing! Whatever the impact of service, it is part of an institution's culture, and institutions are notoriously slow to change.

4. Penalties
-The original PLoS article suggested time penalties for late reviews. This is probably unworkable as well. Slow does not equate poor quality. James Crow wrote a Perspective in Genetics about peer review.

"Sewall Wright was a particularly thorough reviewer. When he received a manuscript for review, he typically dropped other activities and went over the copy in great detail. Usually this involved his redoing all the calculations and reanalyzing the data. Alex and I were convinced that he was spending too much time on other people's data, at the price of not getting his own more important work done. For that reason, we employed him sparingly, only where his unique insights were essential.

A review that stands out in my mind involved a study of quantitative traits in rodents. As usual, Wright reanalyzed all the data. He suggested a large number of changes, the most significant of which was to suggest a scale transformation of the data, which not only greatly simplified the interpretation, but also led to the opposite conclusion. The author made almost all of the suggested alterations and obligingly reversed the conclusion."

I suppose by Hauser and Fehr's standards, Wright's papers would never be published.

5. An interesting suggestion by Gavin Sherlock of Stanford is to match reviewers.

"An alternative system, which doesn't require holding articles in editorial limbo (which seems not to be in the editorial spirit) is to choose the reviewers of the article based on the length of time those reviewers typically take, and the length of time that the author usually takes, matching them up. Thus, if you usually take 6 weeks on average to review a manuscript, your manuscripts will be sent to reviewers that usually take that long too. On the other hand, if you normally review within a few days, you manuscripts will be matched up with suitably rapid reviewers."

This is an interesting option that deserves consideration, but it might turn out unworkable in the long run as it requires extensive databases on reviewer habits.

6. Greater Editorial Action
-Perhaps editors could be more responsible for review timing. I don't think this really has merit. Editors are thinly stretched as is, and chasing reviewers is one of the worst aspects of the job.

7. Open Access Reviews
-Nature attempted an experiment in Open Peer Review. While it was not an unqualified success, perhaps it takes time to change the inertia of the peer review culture. Of all the ideas I've heard, I think this one probably has the most merit. It would increase the democratization of science as well as make the review process a bit more transparent.

Can a Penn State center predict and prevent the next pandemic?

One of the hottest new research centers in the US is the Center for Infectious Disease Dynamics at Penn State. This month's The Scientist contains an article on the new center, highlighting the fact that the center has been particularly successful at attracting new faculty.

"Daniel Falush, an evolutionary geneticist at Oxford University, describes one effect CIDD has had in the United Kingdom: 'There was a great sucking sound because these famous British scientists were disappearing to Penn State.'"

CIDD's mission is to investigate infectious diseases both from theoretical and applied standpoints.

"Investigation of key biological questions Our research addresses issues of fundamental importance in biology. For instance:

• Many disease agents have a sufficiently short generation time that ecological and evolutionary dynamics operate on similar timescales. Consequently, host-parasite relationships provide a tractable system for investigating key questions in population and evolutionary biology.
• Though their interactions with host immunity are complex, some disease agents have small enough genomes that we can begin to dissect the molecular basis of important large-scale phenomena such as species barriers to transmission and herd immunity.

By collaborating across different disciplines, CIDD researchers cast important biological problems and processes in useful new lights. Application to disease management and control Infectious diseases have an immense impact on human health, agriculture and conservation. CIDD research has considerable relevance to management and control of pressing disease issues such as disease emergence, bio- and agro-terrorism and epidemic control strategies."

I've got a personal connection to CIDD. One of my former labmates, Siobain Duffy, is now a postdoctoral researcher in Eddie Holmes' Lab. Duffy is an amazing scientist and I can't wait to see what she discovers in her new position.

The photo, courtesy of the National Institute of Allergy and Infectious Diseases, shows HIV daughter viruses being shed from a T-cell.

Support Open Access

"Shortly after a large-scale clinical trial in 1955, the first inactivated polio vaccine was being injected into tens of millions of people around the world - possibly the most successful pharmaceutical product launch in history. Asked why he had not obtained a patent on the phenomenally successful vaccine, Jonas Salk reportedly replied, "That would be like patenting the sun." A few decades later, this view seemed laughably quaint." Alan Dove, When science rides the MTA, J. Clin Invest. 110:425-427 (2002)

Science Commons: Science Commons serves the advancement of science by removing unnecessary legal and technical barriers to scientific collaboration and innovation.

Built on the promise of Open Access to scholarly literature and data, Science Commons identifies and eases key barriers to the movement of information, tools and data through the scientific research cycle.

Our long term vision is to provide more than just useful contracts. We will combine our publishing, data, and licensing approaches to develop solutions for a truly integrated and streamlined research process.

See also: Scientific Commons: aims to provide the most comprehensive and freely available access to scientific knowledge on the internet.

The Great Science Publication Scam

I'm a big fan of open access publication. However, I haven't quite seen the point driven home like a recent opinion piece in the Harvard Crimson. Thanks to Jonathan Eisen at Tree of Life for pointing it out.

A passage from the article:

"Our professors do the research. They write the papers and proofread them. They even do the peer review. Then they sign the copyright over to publishers, who don’t pay them a dime—they’re paid by grants and salary, our taxes, and tuition. Harvard then pays again for the journals—many of them over $10,000 each—and most of us feel personally the bite each term when we buy our sourcebooks. Many of these cost upwards of $100 not because they’re on paper rather than online (printing costs pennies a page), but because of the fees charged by publishers like Elsevier (1,387 journals ranging across academia) and Wiley (348 journals), some higher than $1 per page. That’s three ways we pay for the same research, writing, proofreading, and peer review. Even Harvard has found the cost too high, and has cut down on its subscriptions."