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.”



Natural selection comes on top of that, of course, but Koonin insists on the prominent role of non-adaptive evolution, exemplified by the neutral theory of Kimura. Partly because of this random evolution, the path towards more complex organisms might be far from optimized (we have to abandon the idea of a “progressive” evolution, in Koonin’s view). Thus, genomes of higher organisms (animals, plants,…), that are often considered more complex than the microbial ones, actually possess a lower information density, are less organized and contain much more junk DNA.

The author goes further in discussing the evolutionary processes. He considers the view of the modern synthesis, which focuses on variation and selection, too simplistic.  Hence he proposes to adopt a multifactorial view, and to recognize three modalities of evolution, so-called Darwinian (random mutation and selection), Lamarckian (directed mutation) and Wrightian (random mutation and random fixation), the latter from Sewall Wright, one of the founders of population genetics. As an example of Lamarckian modality, Koonin mentions the CRISPR system in bacteria, where ‘acquired’ modifications are transmitted in the genome (Koonin & Wolf, 2009). 

Now here, if I’m not mistaken, we enter territories devoid of consensus among evolutionary biologists. (I’m not an evolutionary biologist, and I admit that the subtleties of the debate often escape me.)  For instance Patrick Forterre, from the Institut Pasteur, is very critical of what he calls “the false come back of Lamarck” (Forterre, 2012). He considers the CRISPR example as misleading, and that in essence this is a Darwinian phenomenon. 

Personally I’m totally convinced by Forterre’s criticism! The new discoveries such as CRISPR are fascinating, but I don’t think that they represent a “paradigm shift” such as emphasized by Koonin (Koonin & Wolf, 2012). Another controversial idea is the “evolution of evolvability”, or the change of evolutionary processes during a species’ history (Koonin & Wolf, 2012).

Postmodern evolutionary biology

In the last chapter, the author insists on his view that evolutionary biology has now moved from the modern synthesis to a “postmodern” era, where adaptation is only one among several forces shaping evolution. This is debatable, of course, and that’s what makes Koonin’s book appealing to me: it stimulates reflection and discussion.

He proposes the following definition (p.397):

The evolution of life is largely a stochastic process based on historical contingency, substantially constrained by various requirements for the maintenance of basic biological organization, and modulated by adaptation.”

This is a little bit disappointing, since, in my opinion, it does not fundamentally differ from what Monod wrote in Chance and necessity (with its great opening line taken from Democritus:  Everything existing in the universe is the fruit of chance and necessity”), and to some extent to what Darwin proposed himself (variation and natural selection). 

Undoubtedly, there has been a great amount of refinements in evolutionary biology, and Koonin does a wonderful job at describing them. But as far as I can tell, refinement is not synonymous to revolution (or paradigm shift, or whatever name you want to give it). 

Is there a need for a “postmodern synthesis”, as Koonin hints at? Whatever is your take on this (I don’t see a need), it’s exciting to think and debate about it. So thank you Dr. Koonin!

References:
Koonin E. V. (2011) The Logic of Chance: The Nature and Origin of Biological Evolution. FT Press Science Series. 516 pages.
Koonin E. V. & Y. I. Wolf (2009). Is evolution Darwinian or/and Lamarckian? Biology Direct 4:42.
Koonin E. V. & Y. I. Wolf (2012). Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front. Cell. Inf. Microbio. 2:119
Forterre P. (2012). Darwin’s goldmine is still open: variation and selection run the world. Front. Cell. Inf. Microbio. 2:106.


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