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.