Notes from the biomass

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life is the kind of paper that you would want for breakfast. Eugene Koonin combines a few back-of-the-envelope calculations on the absurdly low probabilities of the emergence of ribonucleotides/proteins capable of natural selection with a multiverse view of cosmology to explain why the existence of life as we know it is not unlikely.

The essay touches on the anthropic principle and I won’t be surprised if the anticreationists science blogs will have a word with him on fueling the intelligent design debate, although he states that their is no room for such quakery in this view of the world. Much of it sounds like I have heard it before; the novel elements are the numbers and the break point in evolution after the RNA world-protein world transition.
The article appears in Biology Direct, still my favorite journal for its open peer review. Again, the reviews are quite critical, including questioning Koonin’s background in philosophy. Then again, how many philosophers have his expertise in the RNA world?

If you haven’t had the time to follow up on ENCODE, you’re probably not alone. From what I have perceived so far, it looks a lot more interesting than the publication of the human genome back in 2000, which was much hyped but had hardly novel findings so that everyone had to elaborate on the “lower than expected” number of genes. I am still yawing but that’s because it’s 7am.

My day had started with one of the Genome Research publications accompanying the major ENCODE publication in Nature, the working definition of a gene by Mark Gerstein et al. It contains a review of the many concepts that we’ve had for the unit of heredity (remember “one gene, one enzyme”?). Their notion of gene has become very operational and reads:

The gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products.

In particular, the aspect of regulation has been removed, there is no single hard structure like a start codon and the focus is on products, irrespective of intermediate transcripts. It does not differ from the view of most bioinformaticians who always focused on a representative gene product for analyses, albeit typically ignoring ncRNAs. One should watch this space, even I it do not see much disagreement with my previous concepts on the matter, different opinions exist, particular the elimination of transcripts might find difficulties in acceptance.

Given that the paper describes a single sentence definition for gene, its conclusion seems fairly weak: The next big thing, the notion of function of a gene product, can hardly be summarized as elegantly ever in my opinion as the complexity of the organism is reflected in the functional definition - besides, Gene Ontology already has a fairly good grasp on the different aspects of it.

Anyway, could someone please update the Wikipedia article for Gene. I got to work.