Saturday, January 17, 2009

Giant Shoulders VII

The latest edition of Giant Shoulders is up at The Questionable Authority.

“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? It should go without saying by the use of the word “classic”, but papers should be in an accepted, established scientific field: contributions promoting non-traditional science and pseudo-scientific ideas are inappropriate. Why restrict yourself to “classic” papers? Entries profiling an important person or concept in the history of science are also acceptable.

Wednesday, January 14, 2009

Burning Man

This year's Burning Man art theme is Evolution.

The process of trial and error that has made this possible is called Natural Selection. Genetically encoded traits that aid survival tend to spread throughout entire populations. Living entities that bear these genes endure and reproduce, but maladaptive traits are not passed on. This causes species to evolve to better fit the world in which they live. However, this rigorous weeding out of 'unfit' individuals has gradually ceased to occur within our species. Medicine and mutual aid assure that nearly anyone is able to survive and reproduce.

At bottom every man knows well enough that he is a unique being, only once on this earth; and by no extraordinary chance will such a marvelously picturesque piece of diversity in unity as he is, ever be put together a second time.
— Frederick Nietzsche

Now adrift in our own gene pool, we have encountered a new phase of evolution. We've become a conscious breed of culture-bearing animals. Black Rock City is a kind of Petri dish, and Burning Man is an experiment in generating culture. We've learned that culture's a spontaneous phenomenon. It thrives as a result of numberless and unplanned interactions. All that's really needed is a fitting social vessel to sustain it. This happens best within communities that harbor many different modes of self-expression. We've also learned that cultures effloresce when human beings feel free to offer up their gifts.

Our theme this year prompts three related questions: What are we as human beings, where have we come from, and how may we adapt to meet an ever-changing world?

You can apply for a grant to create an evolutionary piece of art here. I'm looking forward to seeing what the creative types come up with.

Stanley Falkow in Annual Reviews

This is the time of year when the new Annual Reviews are published. Annual Reviews are among my favorite journals because of the timely content, excellent reviews and occasional historical and/or autobiographical papers.

The current edition of the Annual Review of Microbiology contains an excellent autobiographical account by Stanley Falkow.

Stanley Falkow is microbiologist and a professor of microbiology and immunology at Stanford University School of Medicine. He has published prolifically on the pathogenesis of microbial diseases. In 2008, Falkow received the Lasker Prize for being one of the all-time great microbe hunters.

I particularly like how Falkow closes his account,

"Finally, I realized a number of years ago that in life you never get to have as many dogs as you want or to find out how it all turns out. As you get older and are asked to be a keynote speaker or get an award of some kind, you also realize you are being given credit for things you never did and for attributes you never possessed."

Monday, January 12, 2009

This Week's Citation Classic

This Week's Citation Classic is Henry J. Vogel. 1964. Distribution of Lysine Pathways Among Fungi: Evolutionary Implications. The American Naturalist, Vol. 98, No. 903.

Francois Jacob and Jacques Monod are frequently credited with discovering "repressors" of gene expression. While they did come up with the operon model of gene regulation, it's not precisely true that they were the first to consider "repression" as a means of gene regulation.

In fact, the first repressor, the arginine repressor, was independently discovered by Henry Vogel and Werner Maas (see Maas 1994). This is enough to give any man lasting fame. However, in my estimation, this is not the greatest of Vogel's accomplishments. Even more worthy is the study described in The American Naturalist, Distribution of Lysine Pathways Among Fungi: Evolutionary Implications.

This study was one of the first attempts to resolve the phylogenetic relationships of organisms based on knowledge their metabolic pathways.

Vogel was the first to discover that there were two alternative pathways to synthesize lysine. One route starts from a-aminoadipic acid (AAA) while the other uses diaminopimelic acid (DAP) as a precursor. These lysine biosynthesis pathways are mutually exclusive in their occurrence.

"The two paths of lysine synthesis seem to be quite unusual in the consistency of their dichotomous distribution over a broad range of biological forms. This consistency suggests that these paths did not arise sporadically, and that their distribution pattern was not disturbed by genetic exchange. It appears probable that neither path emerged in an organism possessing the other, since a partial appearance of either path in the presence of the other may well have been selected against, and an appearance in toto is thought unlikely in view of the number of enzymes involved in each path. It is thus assumed that the two lysine paths arose individually in organisms incapable of lysine synthesis."

Vogel realized that, like any phenotype, these alternative forms could be used to dissect the evolutionary history of the fungi. Using C14 tracers, Vogel could determine which fungus used which lysine pathway.

"The general procedure consisted in allowing the organisms to utilize selected C14-labeled compounds, and measuring the relative specific radioactivity of the lysine, threonine, and aspartic acid from the protein of the cultures obtained, The radiocarbon tracers used were 3- and 4-labeled aspartic acids, 1-labeled alanine, and 2-labeled acetate. With these tracers, the mode of lysine synthesis is revealed through characteristic labeling patterns (cf. Vogel, 1959)."

Vogel found that,
"The labeling pattern corresponding to the a-aminoadipic acid-lysine path was given by all basidiomycetes and ascomycetes and by those phycomycetes which produce non-flagellate or posteriorly uniflagellate spores. The pattern characteristic of the a-e diiaminopimelic acid-lysine path was shown by those phycomycetes which produce anteriorly uniflagellate or biflagellate spores."

Vogel concluded his paper by writing,
"A common evolutionary precursor of organisms having the a-aminoadipic acid path is postulated; these organisms include euglenids as the only non-fungal forms known to have this path. The inferred common precursor is viewed as a lysine-non-producing, animal-like organism in an evolutionary line that had branched off the main stream of evolution of the plant kingdom.

Naturally today we would infer evolutionary relationships from genetic sequences, but back in the day, comparative morphology was the rule. Vogel's study was groundbreaking in that he expanded the purview of the phylogeneticists to include biochemistry and metabolism as an additional means to tease out the evolutionary history of organisms. For the most part, his phylogenetic conclusions have withstood the test of time. Quite clever indeed.

Saturday, January 10, 2009

The Year of Darwin

2009 is the 150th anniversary of the publication of Charles Darwin's On the Origin of Species and the 200th anniversary of the author's birth. The two top science journals in the world, Science and Nature, are gearing up to provide a year's worth of content.

Science has an online collection of Origins' related material, including a blog and an essay from Carl Zimmer. (Carl also provides a podcast on his essay here).

Nature has a special collection of Darwinania including 15 gems of natural selection.

Phage Genomics Research Initiative

My school has been selected to participate in the Howard Hughes Medical Institite's Science Education Alliance.

"The SEA’s first project is the National Genomics Research Initiative, a two-part, year-long research course offered by colleges and universities selected through a national competition. The course is aimed exclusively at beginning college students, who make real discoveries by doing research on bacterial viruses, called phage. In the first term, the students isolate colonies of phage from locally collected soil samples. Given the diversity of phage, each one is almost certain to be unique, so the students get to name their newly identified life form. They then spend the rest of the term purifying and characterizing their phage and extracting its DNA.

Between terms, the purified DNA is sent to the Joint Genome Institute-Los Alamos National Laboratory in New Mexico, where it is sequenced. In the second term, the students receive files containing their phage’s DNA sequence. The students then use bioinformatics tools to analyze and annotate the DNA from their phage."

I'll be offering this course to Queens College freshmen next year. It will be real exciting to see what new phages we can isolate from the Long Island soil. Part of the process involves visualizing phage thru electron microscopy (phage are too small to be seen thru ordinary light microscopy).
I've never done this before and am looking forward to seeing phage for the first time. Other professors report that this was the highlight of the course for their students.

"The students told professors teaching the SEA course that the most exciting moment came when they saw a picture of their phage for the first time....As the image of the phage emerged on the computer screen, many students pointed and jumped up and down. One student from Hope College in Michigan called her mom from lab when she saw her phage for the first time. In Findley’s class, the students later had the equivalent of a phage fashion show, and they “oohed” and “aahed” over the phage with the longest tail or darkest head.

The students’ excitement and creativity was also reflected in the names they gave their viruses. The quirky names aren’t the normal staid acronyms often seen in the scientific literature. For example, some students named their phage after the Comedy Central duo of “Colbert” and “Jon Stewart.” Other groups chose “Peaches” and “LRRHood” for Little Red Riding Hood. A student at Spelman College named her phage “Hope” the day after Barack Obama was elected President of the United States."

The hope is that this initiative will encourage college freshmen to consider science as a career.