Friday, December 19, 2008

This Week's Citation Classic: Red-Nosed Reindeer

This week's citation classic comes is Halvorsen, O. 1986. Epidemiology of reindeer parasites, Parasitology Today 2: 334-339.

Odd Halvorsen asks "Every Christmas we sing about Rudolph the red-nosed Reindeer, but do we give much thought to why his nose is red?"

Not to my knowledge. Halvorsen has identified a key question with significant bearing on reindeer population dynamics. What are the causes and consequences of red noses in reindeer? Is it indicative of illness as Halvorsen suggests "The general consensus is that Rudolf has caught a cold". Perhaps it is a rare mutant phenotype that is destined to undergo a selective sweep thru reindeer populations via sexual selection (female reindeer find red noses sexy, right?) or via reducing reindeer mortality on foggy Christmas nights.

Nay, claims Halvorsen. "Rudolf is suffering from a parasitic infection of his respiratory system. To some this may seem a bit far-fetched as one would not expect an animal living with Santa Claus at the North Pole to be plagued by parasites, but I shall show otherwise."

Indeed Halvorsen goes on to show that reindeer, despite being residents of the North Pole (or at least the Svalbard archipelago at 80 degrees N) are liberally populated by parasites of all types, including at least 25 types of nematodes.

Notably these parasites have larval stages highly tolerant of freezing. They may have accompanied reindeer on their initial dispersal northwards, then adapted to the colder climes alongside of reindeer. In fact, Svalbard reindeer often have greater parasite loads than their mainland counterparts!

Halvorsen ends by writing, "So far we have not been able to quantify the combined effects of these parasites, but it is no wonder that poor Rudolph, burdened as he is by parasites, gets a red nose when he is forced to pull along an extra burden like Santa Claus."

Happy Holidays from the Evilutionary Biologist

Thursday, December 18, 2008

Giant's Shoulders

The latest edition of The Giant's Shoulders is up at Rigorous Trivialities.

About “The Giant’s Shoulders”

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?

Lab Full of Vultures?

An article about my former advisor, Paul Turner, has appeared in this month's The Scientist1. I, for one, am quite happy that Dr. Turner did not follow thru on his "strange appreciation for carrion birds". Luckily for Dr. Turner's current and future students, his advisor Rich Lenski, "pointed out to Paul some of the scientific challenges of studying that sort of system."

I went thru a similar experience in graduate school when I realized my previous study organisms, pronghorn, were somewhat unamenable to experimental research. Nor was funding for behavioral ecology readily apparent. During this period, I was confronted with the question, Are you doing science because you want to learn more about some charismatic mammal or do you want to address fundamental questions about evolutionary ecology?

Thus commenced my trip down the hierarchy of biological complexity: pronghorn > mosquitoes > C. elegans > bacteriophages. I'm happy where I ended up and I owe that to Dr. Turner for introducing me to the wild world of phages.

As the article points out, microbes are excellent organisms to use to decipher the underlying rules of biology. Dr. Turner has used them to great effect to study sex, game theory, and cheating.

Dr. Turner will be speaking at a Darwin Day celebration at my own school on February 13, 2009.

1 I confess to being rather startled when I turned the page in my hard copy of the December issue to see a closeup of Dr. Turner staring back at me.

Friday, December 12, 2008

This Week's Citation Classic

The general goal of science is to find general laws that explain patterns observed in nature. An excellent example of this is found in this week's citation classic: James H. Brown. 1984. On the Relationship between Abundance and Distribution of Species. The American Naturalist, Vol. 124, No. 2. (Aug., 1984), pp. 255-279.

We are all aware that some species are common in some areas, but absent in others. Zebras are not naturally found in upstate New York, nor are polar bears found in Africa. But where a species is found, how is it distributed across is range? Are they distributed evenly? Patchily? More in the center than at the edges?

Until Brown's paper, few scientists systematically studied the relationship between an organism's abundance across its range. Brown synthesized distribution and abundance data from taxa as diverse as vascular plants, intertidal invertebrates, terrestrial arthropods, planktonic crustaceans, and terrestrial vertebrates to provide a general theory to explain species' biogeography.

Using this data, Brown observes that populations of most species show the highest density at the center of their range with density decreasing as you approach the perimeter.

"I now propose a single general explanation for both of these patterns: the relatively symmetrical, monotonic decrease in abundance from the center of the distribution toward all boundaries, and the positive correlation between local population density and extent of spatial distribution among similar species."

This general theory stems from three assumptions:

First, the abundance and distribution of each species are limited by the combination of physical and biotic environmental variables that determines the multidimensional niche. Second, spatial variation in these environmental variables is somewhat stochastic but autocorrelated, so that nearby sites tend to have more similar environmental conditions than more distant ones. Third, closely related, ecologically similar species differ in no more than a very few niche dimensions.

Thus Brown was able to look at the distributions and densities of just a few organisms and predict the distribution/density relationship for all of them. Naturally there are some exceptions (Brown predicts them too), but, generally speaking, Brown's theory has been confirmed over the intervening two decades.

James H. Brown is one of the founders of the emerging field of Macroecology, the study of the ecological phenomena at large spatial scales, and the editor of the excellent text: Scaling in Biology. He was elected to the National Academy of Sciences in 2005.

Thursday, December 4, 2008

This Week's Citation Classic

This week's citation classic is A.S Sarabhai, A. O. W. Stretton, S. Brenner and A. Bolle. 1964. Colinearity of the gene with the polypeptide chain. Nature 4914:13-17.

Following Crick and Watson's big breakthrough, the biology world sparkled with new hypotheses regarding the nature of the gene and the genetic code. The DNA molecule's structure implied a number of these hypotheses, but without empirical confirmation, they were nothing but speculation. One of these hypotheses was that the linear sequence of bases in a DNA strand coded for a complementary linear sequence of amino acids constituting the protein product of that gene. While this is the most obvious and parsimonious hypothesis, one need not think hard to imagine other possibilities.

Sidney Brenner was not reluctant to give his students difficult thesis problems. His graduate student, Anand Sarabhai was given the task of demonstrating colinearity of gene and polypeptide chain. For a graduate student to be given such a fundamental, but risky, problem is quite exceptional. Luckily Sarabhai was up to the task. He obtained phage T4 nonsense mutants from Dick Epstein of Geneva. Epstein called his mutants amber mutants, after the mother of Harris Bernstein, a Caltech grad student. German speakers will identify the connection; bernstein is the German word for Amber.

Sarabhai writes: "These mutants (it was believed) did not make a full polypeptide in a normal cell but did so in a suppressor-positive cell. What was not known was whether the amber mutations kept terminating and releasing the synthesized peptide or simply got jammed at the amber site. I told Dick that I could test this in Cambridge quickly. What I found was that the amber mutants kept terminating and releasing the polypeptide, so that you got large amount of fragments of polypeptide of lengths dictated by the position of the amber mutations in the gene. This broke open the co-linearity problem." J. Biosci. 2003, Vol. 28, p. 668.

Analysis of the broken fragments allowed Sarabhai to define 8 segments of the polypeptide chain that are in the same order as the segments on a defined genetic map. Thus Sarabhai, a graduate student, made a fundamental contribution to biology. DNA sequence = amino acid sequence.

Sunday, November 16, 2008

A Day for Darwin

Next February 12th will be the 150th anniversary of the publication of the Origin of Species and the 200th anniversary of Darwin's Birthday. Queens College will be celebrating the occasion with a symposium and panel discussion on Friday February 13th in the LeFrak Concert Hall beginning at 9AM.

This event is free and open to the public. If you are in the New York area, swing on by!

Speakers include:

Susan Foster
Dr. Foster is a Professor of Biology and the Warren Litsky Endowed Chair in Biology at
Clark University, the President-Elect of the Animal Behavior Society, and editor of the books The Evolutionary Biology of the Threespine Stickleback (with Michael Bell) and Geographic Variation in Behavior: Perspectives on Evolutionary Mechanisms (with John Endler). Dr. Foster's research focuses the evolution of reproductive and antipredator behavior, color, morphology, and life history following the post-glacial adaptive radiation of the threespine stickleback fish.

Jeffrey Schwartz
Dr. Schwartz is a Professor of Biological Anthropology at the University of Pittsburgh and President of the World Academy of Art and Science. Dr. Schwartz's books include The Red Ape: Orangutans and Human Origins, What the Bones Tell Us, and Sudden Origins: Fossils, Genes, and the Emergence of Species. As a systematist working with skeletal biology and dentition, Dr. Schwartz is interested in the research and theory underpinning our understanding of the origin and significance of morphological novelty.

Paul Turner
Dr. Turner is an Associate Professor of Ecology and Evolutionary Biology at Yale University and Chair of the American Society for Microbiology’s Division R. Dr. Turner is the recipient of the Top Ten Emerging Scholars Award from Diverse Issues in Higher Education and a Career Enhancement Fellowship for Junior Faculty from the Woodrow Wilson National Fellowship Foundation. He is interested in the ecology and evolution of infectious diseases and the use of laboratory populations of microbes as models to address these topics.

Patricia Wittkopp
Dr. Wittkopp is an Assistant Professor of Ecology and Evolutionary Biology at the University of Michigan and a recipient of an Alfred P. Sloan Research Fellowship, a March of Dimes Basil O’Connor Starter Scholar Research Award, and a Damon Runyon Cancer Research Foundation Postdoctoral Fellowship. She is interested in understanding the genetic basis of development, evolution and disease, with an emphasis on the molecular mechanisms controlling gene expression. Her laboratory uses the Drosophila pigmentation as a model system for understanding the genetic basis of phenotypic evolution.

The Giant's Shoulders

The latest edition of The Giant's Shoulders is up at Podblack Cat blog. Check out this months collection of classic science papers.

Monday, November 10, 2008

She's Gone

Sarah at the Badlands

First time I met Sarah in the spring of 1995, she jumped away from me and sprinted out a half open door. I finally caught up with her in a neighbor's backyard a few houses away. Since that moment, she's been my near constant companion and friend, showing an uncommon loyalty and dedication I've never before have witnessed.

Our first big adventure was a cross country trip to Idaho late that same summer. In no particular hurry, we took to the back roads, sleeping at natural forest campgrounds and even out under the stars in empty cow pastures. Despite being August, the nights in the mountains were chilly, and Sarah would climb into my sleeping bag and settle down by my feet. I worried she would suffocate so I would open the bag just a bit at its far end, and she would poke her head out. I found it comical the idea of a two-headed sleeping bag.

That fall, I took Sarah backpacking at the Selway River with some other graduate students from my department. At one spot, an enormous boulder loomed 3 meters above the churning whitewater. We took turns jumping off the rock and into the river. On my second go, I surfaced to see my friend's frantically gesticulating towards the water where to my shock, I saw Sarah furiously dog paddling towards me. She had leapt off a 3 meter rock into furious whitewater to follow me. I grabbed her by the collar and swam hard for the shore before we could be swept over a series of rapids downstream. On shore, and breathless, I hugged her and whispered to her "You crazy, crazy dog. You are amazing!" I knew she was something special.

The rock from which Sarah leapt

A few years later I was waterskiing at Squam Lake in New Hampshire. As the boat towed me by our dock on Cotton Cove, I saw Sarah's head bobbing in the water at least 100 meters from the shore. She had swum out to follow me while I was waterskiing. I quickly dropped the tow rope and swam over to her. That was Sarah. She could not bear to be apart from me. She always insisted on being next to me on the couch, on the bed and at my feet in the office.

Sarah in the Virgin River

So at least two times she had risked her life to be with me, but she would also save me from risking mine. One spring break, we drove to southern Utah to backpack up the Pariah River. Early in the evening, after I had set up camp, and we hiked up one of the side canyons to the mesa top. There was no trail, just a series of jutting red sandstone ledges haphazardly staggered along the canyon wall. Frequently I had to carry Sarah up a ledge, but within an hour we made it to the top. From there we enjoyed a marvelous view of the Pariah river sweeping down the canyon, as the sun set over the canyon rim to the west.

At the mesa top

However darkness threatened and I did not relish the thought of stumbling down a slot canyon at night. We started making our way down, but I quickly became confused and lost the "trail' we had come up. At one point Sarah refused to continue. I stood at the base of a ledge pleading with her to come so I could lower her to the next level. Increasingly frustrated and anxious about the approaching darkness, I cursed aloud and yelled at her vociferously. But she would not budge. Finally I scrambled back up the ledge and tried to grab her, but she darted out of reach. She continued back up the path we took, ever staying just out of reach, as I cursed her furiously. Suddenly I recognized an odd rock formation and realized I had come the wrong way. I continued to follow Sarah and to my amazement she led us down the correct trail and back to camp. I've often thought that, had continued down the wrong trail, I would have stumbled off a cliff in the night.

The portal thru which Sarah found our way back

So it was, she followed me in the mountains of the Rockies, on the streets of New York, in the woods of New Hampshire, and the deserts of the Southwest. She shared with me all that is beautiful in this world. And when things were rough, she was there to comfort me.

In Death Valley

Thirteen and a half years after we first met, Sarah finally succumbed to cancer. For two years and two courses of chemo, she battled valiantly. Our oncologist would marvel at her resiliency, saying Sarah was "amazing" and that she was a "wonderdog". In the end, the cancer could not be stopped. I had hoped for a good death, but I don't know if there is such a thing. Some must be better than others, but in the end, this was harder than anything I've ever done. She lost her appetite, and even steak would not entice her to eat. Soon she was unable to stand on her own, but the hardest part was that she was still lucid and, I imagined, happy to be here. I held her up to drink from her bowl and she wagged her tail vigorously. I knew we needed to say goodbye, but I couldn't let her go.

The next morning at the vet I told her I was sorry.

And now she's gone.

Such a long, long time to be gone and a short time to be here.

Sarah, I miss you terribly.

Sunday, November 9, 2008

Get out and Vote!

For the 2008 Blogging Scholarships...

My vote is for Brian Switek who writes the most excellent blog, Laelaps.

Switek is an ecology and evolutionary biology student at Rutger's University. He writes, "I am proud to say I'm in the running for $10,000 that will help finance my last semesters and pay down the debt I have accrued over the last few years."

Let's give him a hand!

The current leader writes about the Mariners baseball team. You know what to do!

Friday, October 24, 2008

This Week's Citation Classic: Human Natural Selection

R.A. Fisher, Julian Huxley, and E.B Ford were members of a small clique British and American scholars who were the driving forces behind the "New Synthesis", the refinement and spread of Darwin's theory of evolution during the 1930's and 40's.

They can together also be counted as publishing the first ever test of the effects of natural selection on humans.

This week's citation classic is FISHER, R. A., E. B. FORD and J. HUXLEY, 1939 Taste-testing the anthropoid apes. Nature 144: 750.

You probably remember phenylthiocarbamide or PTC from Intro Biology or Genetics class. Those little strips of paper which, depending on your genotype, was either bitter or tasteless. Bitter for me.

PTC's unique attributes was first discovered by Arthur Fox in 1932 when he was pouring some of the powder and it flew into the air (aahh the days before the Lab Safety Officers). His co-worker C.A. Noller complained that the powder was bitter, yet Fox could taste nothing. Fox set about testing a large group of people and found that indeed they could be divided into tasters and non-tasters.

Fisher, Ford and Huxley realized that this could be a great opportunity to test theories regarding the origins of balanced polymorphisms and whether natural selection has acted upon human genes.

Fisher et al. wrote "in the course of discussions on the possibility that the blood-group frequencies found in man were determined by a balance of selective influences, it occurred to one of the authors that evidence on the parallel possibility for taste could be obtained by testing the anthropoid apes."

In what must have been an almost comic series of experiments, the three tested whether apes could taste PTC. One of the apes took a strong dislike to Fisher and "and spat at him and even tried to grab him". But the trio succeeded in measuring PTC sensitivity for all apes, "excepting one chimpanzee, which was too shy".

The results were remarkable. Mendelian expectation for dominant and recessive genes suggests tasters should represent 3/4ths of the population and nontasters 1/4th. Of the 27 individuals tested, 20 were tasters and 7 were nontasters, implying allele frequencies of 49 and 51% for the taster and nontaster alleles, almost precisely as expected.

Fisher et al. write "Without the conditions of stable equilibrium it is scarcely conceivable that the gene - ratio should have remained the same over the million or more generations which have elapsed since the separation of the anthropoid and hominid stocks. The remarkable inference follows that over this period the heterozygotes for this apparently valueless character have enjoyed a selective advantage over both the homozygotes, and this, both in the lineage of the evolving chimpanzees and in that of evolving man. Wherein the selective advantages lie, it would at present be useless to conjecture, but of the existence of a stably balanced and enduring dimorphism determined by this gene there can be no room for doubt."

Fig. Hypotheses for the origin of PTC taster and nontaster alleles. (Left) FISHER et al.'s (1939) "Single Origin" hypothesis. Under this hypothesis, the taster (T) and nontaster (t) alleles diverged prior to the human–chimpanzee species divergence. Then both alleles were maintained separately in each species up to the present time. The maintenance of both alleles for such an extended period [FISHER (1939b) thought that it must be ~1 million generations, or 20–30 million years] is unlikely if balancing selection has not been active because one allele or the other would be expected to go to fixation. (Right) WOODING et al.'s (2006) "Separate Origin" hypothesis. Under this hypothesis, nontaster alleles were derived from taster alleles twice—once in each species—after the human–chimpanzee species divergence. Arrows indicate divergence events.

The biological significance of the polymorphism was not clear to Fisher et al. nor was it identified until quite recently. Long story short is that the non-taster allele is not non-functional. On the contrary it appears to provide the non-PTC taster with the ability to taste other compounds that the PTC taster cannot taste.

Evidence that the TAS2R38 nontaster allele is functional suggests an immediate mechanism through which heterozygote advantage might arise at this locus. If the taster allele confers sensitivity to PTC and its chemical relatives, and the nontaster allele confers sensitivity to some other set of compounds, then heterozygotes should be able to taste both sets of compounds. Thus, they might garner a fitness advantage by being able to regulate the intake of a greater diversity of bitter compounds than can homozygotes. Wooding 2006.

A final point is that the parsimonious hypothesis that the PTC allele arose once has been refuted.

Taken together, the findings of WOODING et al. (2006) support FISHER et al.'s (1939) finding that both humans and chimpanzees harbor taster and nontaster alleles and that these alleles are found at similar frequencies in each species; however, they reject the hypothesis that these alleles were derived once, prior to the human–chimpanzee divergence. Rather, the nontaster alleles, which confer their phenotypic effects through entirely different molecular mechanisms, appear to have twice evolved independently. The details of the selective pressures underlying this more complex process remain a matter of conjecture. Wooding 2006.

This post was largely derived from Wooding 2006.

Photo: (Left to right) R. A. Fisher, E. B. Ford, and Julian Huxley. Portraits are from YATES and MATHER (1963), CLARKE (1995), and BAKER (1976).

Thursday, October 23, 2008

Small World Winners Announced.

The Small World Photomicrography contest winners have been announced. This year's top prize went to Michael Stringer for the above image.

Though Mr. Stringer is not a microscopist by trade, he has been interested in diatoms for over 60 years. When he retired from his work as an Ophthalmic Nurse Practitioner, he decided to emulate English Botanist and Diatomist Dr. C. L. Odam and collect diatoms from tributaries. Stringer now works on Two Tree Island amassing information and collecting diatoms.

This image was one of a series Mr. Stringer created to illustrate a talk to a camera club on “Photography through the microscope.” His objective was to display diatoms in a modern way using super contrast and careful application of color. Rather than showing all the details, or warts and wrinkles as Mr. Stringer likes to call them, he dressed up the diatoms by manipulating the image and creating this beautiful photomicrograph.

Wednesday, October 22, 2008

Book Review: Myth of the Oil Crisis

I was pretty skeptical when I received Robin Mills Myth of the Oil Crisis because Peak Oil makes intuitive sense. Oil is a finite resource, demand is skyrocketing and there is no doubt that, at some point, demand will outstrip supply. However, Mills, a geologist and economist, makes a convincing case that Peak Oil is not imminent. If true, this finding has important implications for the global economy and environment.

In brief, Mills argues:

  1. supply is greater than we think
  2. supply and demand responsive to prices
  3. current high prices result of underinvestment due to oil glut of 80s-90s
  4. gas, unconventional, and alternative fuels can make up balance
  5. peak oil reasoning will lead us into bad decisions
I agree with many of Mills' claims. Peak oil scenarios of economic chaos and the collapse of civilization are overly dramatic. There probably is more oil (conventional and unconventional) than peak oil proponents believe. Economics will drive the switch to alternative fuels and products, and make no mistake, alternatives are available. The transition will not occur overnight but rather over many decades.

If Mills is correct, then some of the assumptions regarding global climate change need to be reconsidered. Many carbon scenarios suggest that a major decline in hydrocarbon availability will force carbon reductions by default. Governments will not need to make painful choices now because "the invisible hand" will make those choices for them. If hydrocarbon supply is not at risk, then we will need government manipulations of oil supply and demand to alleviate human induced climate change.

Some of Mills' arguments, however, ring false. The contention that supply is underestimated because large unconventional reserves (off-limits oil, coal, oil sands, gas) will seamlessly replace conventional oil is demonstratively false. Some unconventional reserves will have a much greater negative environmental impact and should be taken "off the table". For example, a recent report by David Israelson of the University of Toronto claims that developing the Alberta Oil Sands will devastate the Great Lakes basin.

"Difficult to extract and dirty to process, tar sands oil is coming to the Great Lakes via a planned network of pipelines and refinery expansions. Currently disclosed project costs show that pipeline companies and U.S. refiners plan to invest more than U.S. $31 billion between now and 2015 to upgrade, export, and refine tar sands oil. This expansion promises to bring with it an exponential increase in pollution – discharges into waterways including the Great Lakes, destruction of wetlands, toxic air emissions, acid rain, and huge increases in greenhouse gas emissions. All of this comes before anyone even uses a drop of this oil in their cars and trucks and factories, before the oil is even processed in these expanded refineries. If the great challenge of the 21st century is to figure out how to wean society off oil, this is the diametric opposite of the way to go about it."

The one thing we must not do is sacrifice our ecological future for our present comfort. Mills does make some concessions to this need in his final chapter on "Green Oil". However his willingness to advocate environmentally disastrous sources of energy make me queasy. Ultimately, while I subscribe to much of what Mills says, I think Peak Oil is probably closer than Mills believes, not because oil is running out, but rather the consequences of oil use is making it unsustainable. Despite these failings, I thought Mills' book was eminently readable, thought provoking and a worthy contribution to the Energy Debate.

In research for this post, I came across this great poster.

Saturday, October 11, 2008

This Week's Citation Classic: GFP

This week's citation classic is M Chalfie, Y Tu, G Euskirchen, WW Ward, and DC Prasher.
Green fluorescent protein as a marker for gene expression. Science 11 February 1994:
Vol. 263. no. 5148, pp. 802 - 805. DOI: 10.1126/science.8303295.

Martin Chalfie has just been awarded a Nobel Prize for his work relating to the development of one biology's most ubiquitous tools: green fluorescent protein. In one of Chalfie's first experiments, he marked six individual C. elegans cells in the with the aid of GFP.

GFP allows "the monitoring in time and space of an ever-increasing number
of phenomena in living cells and organisms like gene expression, protein localization and
dynamics, protein-protein interactions, cell division, chromosome replication and organization,intracellular transport pathways, organelle inheritance and biogenesis, to name but a few" [].

Chalfie first found out about GFP in 1988 during a seminar on bioluminescent organisms by Paul Brehm. Brehm's seminar reported that GFP, a protein found in the jellyfish, Aequoria victoria, fluoresces green in the presence of blue light.

Chalfie thought to himself, "What an absolutely wonderful, wonderful compound this would be. I would love to put it into C. elegans and look at gene expression. In fact I imagined a really large number of things I would like to do if I had such a way of marking gene expression and protein localization in living cells. I got very excited and didn’t listen to another word of the seminar."

Chalfie contacted Doug Prasher at Woods Hole who was attempting to clone the GFP cDNA. Chalfie and Prasher agreed to get in touch when Prasher succeeded with the cloning, but due to missed connections, four years passed before Chalfie saw the published sequence in Gene.

Chalfie contacted Prasher and asked "What happened to our collaboration? Do you still want to do this?". Prasher was unable to get the GFP to fluoresce but sent the protein to Chalfie anyway. Chalfie then gave it to his grad student Ghia Euschirken. Two weeks later, Euschirken had something to show Chalfie: green fluorescent E. coli.

Chalfie describes why he was able to get GFP to fluoresce while others failed:

I was very concerned that we only use the coding sequence and no flanking DNA in our construct. We used PCR to obtain just the coding sequence and that worked terrifically. But the others who tried to use GFP simply cut the original lambda cDNA clone with restriction enzymes, and got additional bases associated with each end. These extra sequences turned out to be quite detrimental; expression wouldn’t occur. So we were fortunate in the way we designed the experiment.

Chalfie and Euschirken eventually cloned GFP into worms as a promoter driven construct, and the rest is history.

On a sad note, Prasher no longer works in science. He is now driving a courtesy shuttle for a car dealership in Huntsville, Ala.

An interview with Chalfie is available here.

Friday, October 3, 2008

Noble Foundation

Today I am blogging from the 5th Virus Evolution workshop at the Samuel Roberts Noble Foundation in Ardmore OK. Also present is fellow blogger Abbie Smith of ERV. The talks have been excellent, the accommodations sumptuous and the grounds striking. This is clearly a high class outfit. In fact the Noble Foundation is Oklahoma's largest foundation and one of the 60 largest private charitable foundations in the United States. Apparently the Noble Foundation has an almost 1 billion dollar endowment . Where did this money come from? I've heard an interesting story. Apparently the Noble Family owned farm implements company. They sold farming tools to farmers on credit. Unfortunately for the farmers, disaster struck in the 1930s. The region was stricken by the catastrophic drought later known as the Dust Bowl. Unable to grow crops, many of the farmers defaulted on their debt and the Noble's came into possession of a large amount of Oklahoma's land. Lloyd Noble, who was a major player in the oil business, later started the foundation in honor of his father and dedicated the foundation to the betterment of the lives of Oklahomans. Today, the foundation provides ~60 million a year in grants for scientific research as well as hosting a campus devoted to the study of forage improvement, plant biology and agriculture. I'm not sure how true the story is since I've been unable to find corroboratory evidence but it is pretty interesting nonetheless.

Wednesday, October 1, 2008

Science Blogs Book Club: Autism's False Prophets

The latest edition of Science Blogs Book Club is up. This time the selected book is "Autism's False Prophets" by Dr. Paul Offit. The discussion panel includes Paul Offit, Kristina Chew, Kev Leitch, Orac and Bob Park.

I posed some questions for the panel:

In my microbiology class, I've fended questions from students regarding whether vaccines were "safe". Most students, although educated and worldly, were unaware of the studies showing no relationship between vaccines and autism for example.

The most disturbing issues for me (highlighted in Ch. 9 of the book) is the tendency of the media 1) to report only "sexy" stories 2) seek unwarranted "balance".

It is clear that the media attention given to reports that vaccines were unsafe far outweighed reports that vaccines are safe.

Moreover, reports of the safety of vaccines were often accompanied by contradictory opinions in the interests of "balance". I liken this to the Intelligent Design controversy where some believe educators should present "all sides" of the evolution "controversy".

So, my questions to the panel are "What do we do about it?" Can we create a media whose primary objective is to inform rather than to entertain, and, if so, how can we get people to pay attention to it?

I look forward to exciting discussions.

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?