Saturday, September 22, 2012

The Logic of Chance by Eugene Koonin (continuation)

Published by FT Press

In the first part of this post, I insisted on living organisms (viruses, bacteria, eukaryotes) and their evolutionary history. 

Here I want to look at what Koonin writes about the mechanism of evolution.

What drives evolution?

One central idea in Koonin’s book, I think, is to propose an evolutionary outlook that is based on an analogy with the physical world. Central, for instance, is stochasticity, as a force shaping the genomic evolution. Equally important, in Koonin’s view, are the statistical principles that govern the interactions between all genes within a genome (he likens the collection of all genes in a genome to the ideal gas model in physics). Thus, genes are influenced by a number of statistical rules. On this line, even though it is apparently not possible to define “laws of genomics”, certain regularities can be identified, such as the proportion of different functional classes of genes within a given prokaryotic genome.

Koonin writes, p. 405:

“it is remarkable that the advances of genomics and systems biology, while revealing an extremely complex, multifaceted picture of evolution, at the same time allow us to derive powerful and simplifying generalizations. It is tempting to offer yet another version of the famous phrase: Nothing in evolutionand in population geneticsmakes sense except in light of statistical physics.”

Sunday, September 16, 2012

The Logic of Chance by Eugene Koonin

Published by FT Press
About fifteen years ago, a revolution started in the biological sciences, which goes by the name whole genome sequencing. I don’t have memories of the announcement of the first bacterial genome in 1995 (I was in high school and not really following biology news…), but at the time of the human genome project I was a biology student at the University and I remember very well when the paper describing the human genome came out in 2001 (we had to read it in class!).

Until recently, my feeling about whole genome sequencing was that it was a technical revolution, not a conceptual one. After all, I thought, the sequence information revolution already took place in the seventies, when Carl Woese pioneered the use of 16S ribosomal RNA to construct phylogeny. 

I revised this feeling, thanks in part to the excellent book of Eugene Koonin, The Logic of Chance (2011)subtitled the nature and origin of biological evolution—and published by Financial Times Press (yes, they do have a science catalog!).

Sunday, September 09, 2012

Something scientists should consider about nature

Here, for a change, I want to wander into philosophical territory. I should first admit that I am rather ignorant of it, since I never studied philosophy past the high school level. But my interest remained vivid and I read philosophical books regularly. More important, I believe that every scientist has to keep an eye – even if it is half-open – on philosophy. Isn’t science the daughter of philosophy? (After all, science used to be “natural philosophy”.) And ironically, aren’t I a doctor in philosophy (Ph.D.)?

One year ago I was talking about philosophy with a colleague in the lab (although I can’t remember how the discussion drifted to this topic!). At some point my colleague said that he couldn’t find any use in philosophy, and this baffled me. I mentioned the philosophy of science and Karl Popper as a counter example, but retrospectively I didn’t need to be so specific. Philosophy is important per se if it has practical applications for scientists it is a good thing but not its final goal. 

Nonetheless, I started thinking about examples of philosophical inquiries that have repercussions in the day-to-day life of scientists, and I realized there’s plenty. Here I would like to share one which I think is essential: the reflection on nature and natural phenomena.