Abstract.
``We calculate the optimality score of a doublet precursor to the canonical genetic code with respect to mitigating the effects of point mutations and compare our results to corresponding ones for the canonical genetic code. We find that the proposed precursor is much less optimal than that of the canonical code. Our results render unlikely the notion that the doublet precursor was an intermediate state in the evolution of the canonical genetic code. These findings support the notion that code optimality reflects evolutionary dynamics, and that if such a doublet code originally had a biochemical significance, it arose before the emergence of translation.''
First paragraph.
``It is now well established that the canonical genetic code is not a frozen accident, but exhibits a pattern of amino acid-codon correspondences that has the effect of making the code insensitive to certain classes of point mutation or translation error. A variety of schemes including one invoking evolutionary dynamics and stereochemistry, have been put forward to explain this pattern and others in the genetic code. Additionally, it has been shown recently that the genetic code has extreme error-minimizing optimality, being more optimal (resistant to the effects of point mutations) than all but one or two random codes generated in sets of ten million. It is important to stress that while the code exhibits some optimality with respect to several measures, such as hydrophobicity, the code exhibits extreme optimality with respect to only one particular class of amino acide attributes, related to the free amino acid polar requirement, and this suggests the code is a very ancient part of the cell's machinery, functioning either in its present role of translation, or in some earlier unknown function. This result lends strong support to the suggestion that the code's evolutionary dynamics was dominated by collective mechanisms arising from horizontal gene transfer. Computational evidence shows that core chemical affinities in the genetic code are fully compatible with, and independent from, evolutionary dynamics that lead to error minimizing optimality, suggesting that error-minimizing optimality is not a byproduct of chemistry but arises from the evolutionary dynamics...''
(Butler T, Goldenfied N, Optimality properties of a proposed precursor to the genetic code, Physical Review E 80, 032901, 2009)
Thanks to Les Schaffer for forwarding this article.
``This result lends strong support to the suggestion that the code's evolutionary dynamics was dominated by collective mechanisms arising from horizontal gene transfer...''
I remembered that HGT was the mechanism bacteria spread antibiotic resistance, but never thought about the evolutionary significance. Looking up the wiki for horizontal gene transfer:
As Woese has written, 'the ancestor cannot have been a particular organism, a single organismal lineage. It was communal, a loosely knit, diverse conglomeration of primitive cells that evolved as a unit, and it eventually developed to a stage where it broke into several distinct communities, which in their turn became the three primary lines of descent (bacteria, archaea and eukaryotes)' In other words, early cells, each having relatively few genes, differed in many ways. By swapping genes freely, they shared various of their talents with their contemporaries. Eventually this collection of eclectic and changeable cells coalesced into the three basic domains known today. These domains become recognisable because much (though by no means all) of the gene transfer that occurs these days goes on within domains."[22]
With regard to how horizontal gene transfer affects evolutionary theory (common descent, universal phylogenetic tree) Carl Woese writes:
"What elevated common descent to doctrinal status almost certainly was the much later discovery of the universality of biochemistry, which was seemingly impossible to explain otherwise. But that was before horizontal gene transfer (HGT), which could offer an alternative explanation for the universality of biochemistry, was recognized as a major part of the evolutionary dynamic. In questioning the doctrine of common descent, one necessarily questions the universal phylogenetic tree. That compelling tree image resides deep in our representation of biology. But the tree is no more than a graphical device; it is not some a priori form that nature imposes upon the evolutionary process. It is not a matter of whether your data are consistent with a tree, but whether tree topology is a useful way to represent your data. Ordinarily it is, of course, but the universal tree is no ordinary tree, and its root no ordinary root. Under conditions of extreme HGT, there is no (organismal) "tree." Evolution is basically reticulate."[23]
Woese is an interesting guy. So to answer Carrol's question, what's the big deal? I think the big deal is this, ``the ancestor cannot have been a particular organism, a single organismal lineage. It was communal, a loosely knit, diverse conglomeration of primitive cells that evolved as a unit,''
Evolved from what. An RNA world:
``My work over the last 5 years has centered on genomic analysis, with an emphasis on understanding the evolutionary significance of the phenomenon of horizontal gene transfer (HGT). This has involved in particular an in detail analysis of the phylogenies of the aminoacyl-tRNA synthetases and the effect HGT has had upon the distribution of these key enzymes. The ultimate goal is to construct a model (theory) of how the primary cell types (the archaeal, eubacterial, and eukaryotic) have evolved, from some ancestral state in the RNA-world''
http://mcb.illinois.edu/faculty/profile/1204
Here is something from his recent abstracts:
``Biology today is at a crossroads. The molecular paradigm, which so successfully guided the discipline throughout most of the 20th century, is no longer a reliable guide. Its vision of biology now realized, the molecular paradigm has run its course. Biology, therefore, has a choice to make, between the comfortable path of continuing to follow molecular biology's lead or the more invigorating one of seeking a new and inspiring vision of the living world, one that addresses the major problems in biology that 20th century biology, molecular biology, could not handle and, so, avoided. The former course, though highly productive, is certain to turn biology into an engineering discipline. The latter holds the promise of making biology an even more fundamental science, one that, along with physics, probes and defines the nature of reality. This is a choice between a biology that solely does society's bidding and a biology that is society's teacher.''
http://www.ncbi.nlm.nih.gov/pubmed/15187180?dopt=Abstract