The Singapore team noted, "Of the ASC base pairs, 99.7% were noncoding, suggesting that novel anthropoid functional elements were overwhelmingly cis-regulatory." The importance of reguatory changes is already well-known, but this high fraction is still surprising.

They also observed, "Unexpectedly, transposable elements (TEs) contributed to >56% of ASCs...." We are not surprised by this, because, in cosmic ancestry, genetic elements that are imported, multiplied, relocated and tested, like TEs, are essential for evolutionary advances.

The most interesting part, to us however, goes unremarked by the Singapore research team. Consider the regulatory ASCs that enable the major advances, in anthropoid vision and nervous systems, for example. Many of them are present in non-primates as well. But there they are unconstrained — not in use. Why is programming for those anthropoid-specific features there at all?

Genetic programs that are available before they are deployed confound strict darwinism and confirm cosmic ancestry.

10 September 2014

What'sNEW about HGT |

Given that the great majority (typically, around 90%) of nucleotide substitutions in evolving microbial genomes are silent and even among those that affect protein sequences, many are effectively neutral, it seems indisputable that the rapid gene flux is the most important route of change in prokaryotic evolution. Notably, the present results show substantially greater rates of gene family loss and gain compared to family contraction and expansion rates. Thus, the gene flux is not only rapid and extensive but often leads to qualitative changes in the gene repertoires. In general terms, these results emphasize that prokaryotic evolution is largely driven not by small variations, such as single nucleotide substitutions, but by much more dramatic changes brought about by HGT and gene loss.

These words come from a new article by five recognized experts at NIH who conducted a comprehensive analysis of the genome dynamics in 35 groups ...of closely related microbial genomes. To us these observations reaffirm the case for a complete paradigm shift in the theory of evolution — for prokaryotes. No longer is the neo-darwinian process of mutation-and-selection expected to account for much: ...Extreme divergence of duplicated genes that could lead to the appearance of a new family is highly unlikely on the short evolutionary scale of an ATGC [Alignable Tight Genome Cluster]. Clearly, the mainstream account of new genetic programs among prokaryotes is awash. The apparent new source is HGT. But this paradigm shift is not getting the attention it deserves.

We expect a corresponding paradigm shift — for evolution among eukaryotes — also to emerge. There, too, the evidence favoring HGT is overwhelming and the paucity of evidence for neo-darwinan creation of new genes is scandalous. Meanwhile, in cosmic ancestry, HGT is the expected source for new genes.

12 August 2014

CORRECTION, 18 Aug

...Our in silico results suggest that the known underground repertoire of E. coli enzymes can substantially increase the range of utilizable carbon sources available to this organism.... We speculate that the contribution of underground metabolism to adaptation to new environments might be even more pronounced in eukaryotes, where metabolic network expansion by means of horizontal gene transfer has a less prevalent role compared with bacteria.

The analysts are puzzled to note that the studied "underground reactions" apparently have not been exploited so far. They guess that the environments where the reactions might be helpful have simply not been encountered. And they found "no evidence" that the unexploited reactions might be harmful, lest that might be supressing their expression. They do not ask how the helpful catalysts might have evolved by darwinian trial-and-error if there were no trials. But for several hundred, only-beneficial catalysts, isn't that an obvious question?

In cosmic ancestry, all genetic programs are very old, and they must be installed, virtually complete, before they can be activated for testing and, if deployed, optimization. We think this analysis of underground reactions supports our view.

7 July 2014

What'sNEW about HGT |

These words come from a 2010 essay, by Nigel Goldenfeld (pictured) and Carl Woese, that argues for a new, physics-based perspective on biology. We think their dissatisfaction with the Modern Synthesis — its very foundation is questionable — is not overstated. We note that one problem they highlight, the speed of evolution, is easily solved with horizontal gene transfer (HGT).