Friday, June 27, 2008

Tree of Life

Apparently there is a movie coming out called "The Tree of Life". It shares the same name as the web phylogeny project, "The Tree of Life". The site is one of my favorites, a very well done catalog of all of life's tribes.

The Tree of Life Web Project is a collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. Its goal is to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct. Connections between Tree of Life web pages follow phylogenetic branching patterns between groups of organisms, so visitors can browse the hierarchy of life and learn about phylogeny and evolution as well as the characteristics of individual groups.

Jonathan Eisen of The Tree of Life blog points out that the term "tree of life" is now endangered as a search term because google will put the most linked to sites first. He calls on all biologists to link to the Tree of Life page, and help keep "tree of life" reserved for evilutionary biology.

Tree of Life at wikipedia.

Monday, June 23, 2008

Earworms: What's up with songs that get stuck in your head

There's a new blog meme going around:

"List seven songs you are into right now. No matter what the genre, whether they have words, or even if they’re not any good, but they must be songs you’re really enjoying now, shaping your spring summer. Post these instructions in your blog along with your seven songs. Then tag seven other people to see what they’re listening to."

This got me thinking about all those songs that get stuck in your head. They're called Earworms. Supposedly, they are songs or tunes that become stuck in the phonological loop, the part of the brain that rehearses verbal information in Baddeley's model of working memory (so says wikipedia), and are the object of scientific study. I've caught a few lately, but fortunately they haven't been totally annoying like that umbrella ella ella eh eh eh song.

Fire It Up--Modest Mouse
Things Are What You Make of Them--Bishop Allen
Window--Fiona Apple
New Soul--Yael Naim
Last Living Souls--Gorillaz

Hat tip: Post doc ergo propter doc

Sunday, June 22, 2008

Darwin and Wallace: On the Origins of the Origins of Species

Alfred Russel Wallace isn't a household name, but he is generally credited with independently deriving the theory of natural selection. Today's Observer contains an excellent article on Wallace's and Darwin's discoveries.

Wallace apparently came up with his theory while confined to bed with malaria during an expedition to the Malay Archipelago. His first instinct was to publish. Although Darwin had been thinking on the problem for considerably longer, it was only the upstart Wallace's push that spurred Darwin to write his masterpiece.

And Wallace was impetuous. While Darwin fully understood the implications of his theory, holding back publication because he knew he would upset believers, including his wife, Wallace plunged in, happy to upset society. He didn't give a damn, said Jonathan Rosen, in an essay on Wallace in the New Yorker last year. 'This utter independence from public opinion is one of several reasons that he has all but vanished from popular consciousness.'

While Wallace did hit upon the right idea, it was Darwin's work with its voluminous evidences that captured the public interest. 'Natural selection was a brilliant idea but it was the weight of evidence, provided by Darwin, that made it credible. That is why we remember Darwin as its principal author.' On his round-the-world voyage on the Beagle, between 1831 and 1836, he had filled countless notebooks with observations, particularly those of the closely related animals he saw on the different islands of the Galapagos. And then, in his vast garden at Downe, Darwin had crossbred orchids, grown passionflowers and on one occasion played a bassoon to earthworms to test their response to vibrations. He collected masses of data about plant and animal breeding to support his arguments in The Origin of Species. Wallace could provide nothing like this.

Photo: Alfred Russel Wallace from Wikipedia

Thursday, June 19, 2008

This Week's Citation Classic

This week's citation classic is "The Molecular Biology of Bacterial Viruses" in honor of Gunther Stent, who recently passed away. Stent was one of the unsung heroes of the molecular biology revolution and member of the "phage group" and the RNA Tie Club. Although he was not credited with any major discoveries in molecular biology, "Gunther was part of the intellectual glue that kept this small band of pioneers together".

As one of Max Delbruck's students, he was asked "'Do you want to work on phage?' 'Yes sir,' Stent replied, 'that’s exactly what I want to work on, but could you refresh my memory as to just what phage is actually all about?'"

His classic text on bacteriophages is still frequently consulted in my laboratory and has been a standard reference for phage workers since the 60's.

Stent was remarkably diverse. After receiving his PhD in physical chemistry, he switched to phage biology. Then as the 60's came to a close, Stent became "bored with molecular biology". He switched to studying neurobiology with leeches as model organisms. Later Stent focused on the history and philosophy of science, publishing important works such as "Paradoxes of Free Will".

Stent explained his frequent career changes, "The problem is that I get bored. I see something new, and it becomes exciting for me, so I move on."

His autobiography is "Nazis, Women and Molecular Biology: Memoirs of a Lucky Self-Hater."

Wednesday, June 18, 2008

Science Made Stupid

I recently stumbled upon this website. It's pretty funny :)

Thursday, June 12, 2008

This Week's Citation Classic: The World is Green

This week's citation classic contains no data, no figures, no tables, no methods, i.e. none of the traditional trappings of the "Scientific Paper". Yet, judging by its 1,145 citations, its influence has been incalculable. The paper is commonly known as "the world is green paper" or "HSS 1960.

Hairston, N.G., Smith, F.E. and Slobodkin L. 1960. Community structure, population control and competition. American Naturalist 94:421-5, 1960.

Using simple logic, HSS take a simple observation (the world is green) and deduce that predators limit herbivore abundance, allowing plants to flourish. HSS summarize their deductions here:

In summary, then, our general conclusions are: (1) Populations of producers, carnivores, and decomposers are limited by their respective resources in the classical density-dependent fashion. (2) Interspecific competition must necessarily exist among the members of each of these three trophic levels. (3) Herbivores are seldom food-limited, appear most often to be predator-limited, and therefore are not likely to compete for common resources.

The paper was bold and controversial. Most ecologists either love it or hate it. (Personally I fall into the former category). It was not intended to be a be-all, end-all monograph, but rather as a starting point to synthesize ecological theory. Of course its points are simplistic, but the simplicity, brevity and generality are, to me, positive rather than negative aspects.

The paper was also one of the first to introduce Ecologists to the concept of the three terrestrial trophic levels: primary producers, herbivores and predators. It can also be seen as one of the progenitors of the food web concept. And if nothing else, it has spurred its detractors to experiments.

Monday, June 2, 2008

SMBE '08

I'll be attending the Society for Molecular Biology and Evolution's annual meeting in Barcelona, Spain. (Is anyone else attending?) At the meeting, I'll be presenting results from a sequencing study I did of bacteriophage populations that were evolved under sexual or asexual conditions. Surprisingly the asexual populations were more genetically diverse than sexual ones.

The study was motivated by the idea that sex generates genetic diversity.

The idea that sex functions to provide variation for natural selection to act upon was first advocated by August Weismann and it has dominated much discussion on the evolution of sex and recombination since then.” A. Burt, Evolution, 2000

Sex in phages is a function of the multiplicity of infection (MOI). When multiple phi6 phages infect the same host cell, they can reassort segments of their genomes.

Previously Dr. Paul Turner evolved populations of phi6 at either high or low MOI for 300 generations. The results were published in Genetics.
I hypothesized that sex increased diversity among phages. To test this hypothesis, I sequenced parts of the phi6 genome for ten clones of each of the six evolved populations. The results indicated that the asexual populations had more genetic diversity than the sexual populations.
I interpreted these results as indicative of the purifying selection of sex. Asexual populations are prone to clonal interference, i.e. multiple beneficial alleles compete with each other, but cannot be integrated into the same genotype as sex permits. So, the genetic diversity of the asexual populations remain high, while the sexual populations quickly fix the best available genotype.

The results will be submitted for publication later this year with my co-authors Siobain Duffy, Aashish Jethra, Kara O'Keefe, Scott Edwards, and Paul Turner.

Book Review: Blood Matters by Masha Gessen

What will you do when it is feasible to obtain your own genotype? Will you take advantage of the possibility to discover as much about yourself as possible? Or do you not want to know? Is ignorance truly bliss?

Masha Gessen, author of Blood Matters, gives us a glimpse of the future that awaits us when human genomic sequencing becomes ubiquitous. As an Ashkenazi Jew, Gessen is prone to genetic diseases such as breast/ovarian cancer, Cystic Fibrosis and Tay Sachs. It is believed that a combination of founder effect and inbreeding has burdened the gene pool of the Ashkenazi population with these autosomal recessive disorders.

Eleven years after her mother died of breast/ovarian cancer, Gessen had her own genes tested to see if she, too, risked breast cancer. The results revealed that she was a BRCA1 carrier. As such, she suffered an 85 percent chance of breast cancer and a 50 percent chance of ovarian cancer.)

Gessen then had to make the unenviable decision whether to have her ovaries and breasts preemptively removed. It's hard for me to imagine such a decision, but it must have been terrifying. Her genetic counselors advised the oophorectomy on the basis that breast cancer is easier to detect and treat.

But Gessen balked. Oophorectomies are associated with cognitive issues, depression, osteoporosis, and heart disease. “I politely suggested I could just shoot myself tomorrow: That would prevent my death from cancer with a 100 percent probability,” she writes.

Gessen's book does a wonderful job of illuminating the issues we face when we learn more about ourselves and our genes. She points out that the moral, medical, ethical, educational, personal foundations for dealing with this new knowledge are not yet in place.

My only complaint is that Gessen tries to do too much. The book wanders off topic frequently, and the potency of the book is diluted. What could have been a sharp, vivid exposition on a horrible personal choice is wasted on meanderings on Jewish matchmaking, Dr. Holmes Morton and other digressions.

What, then, should one do when faced with the possibility of obtaining your genetic predispositions? I am of the opinion that Knowledge is Power. Gessen is now, if she wasn't already, hyperaware of the chance of cancer and can take preemptive action or alter her behavior.

The first chapter is available at the NY Times. The book was developed from a series of articles at Slate.