16 Oct 2014

What'sNEW about HGT |

Lateral edges indicate 2,264 bacterial acquisitions in archaea. The number of acquisitions per group is indicated in parentheses, the number of times the bacterial taxon appeared within the inferred donor clade is colour coded (scale bar at right).

A paradigm shift for prokaryotic evolution seems to have arrived: new genetic programs are not invented by point mutations. Many are installed by HGT. For eukaryotes as well — in addition to the prokaryotic genes that came with mitichondria and chloroplasts — there are countless examples of genetic programs acquired by various means of HGT. (If any were composed by the strictly darwinian method, the evidence therefor is unconvincing.)

The "Yes, urgently" authors want to supplant standard evolutionary theory (SET) with an extended evolutionary synthesis (EES) that features their topics of interest: In our view, this 'gene-centric' focus fails to capture the full gamut of processes that direct evolution. Missing pieces include how physical development influences the generation of variation (developmental bias); how the environment directly shapes organisms' traits (plasticity); how organisms modify environments (niche construction); and how organisms transmit more than genes across generations (extra-genetic inheritance).

The "No, all is well" writers counter, The evolutionary phenomena championed by Laland and colleagues are already well integrated into evolutionary biology, where they have long provided useful insights.

We have read the two articles closely. Both sides discuss adaptation, speciation, modification and variation at length. And neither mentions innovation nor sustainable evolutionary progress — the most interesting and challenging aspects of evolution. Somehow, the general public has come to believe that these latter phenomena are also well-explained by mainstream science. They aren't.

Evolutionary progress on Earth is characterized by a long series of innovations, each of which requires new genetic programming. Where new genetic programming comes from is the big unanswered question. Nether side in this debate has anything to say about it. To us, the controversy looks like a tempest in a teapot.

Limited evidence indicates that there may be more pervasive de novo gene origination than currently appreciated. YE Zhang, M Long, "New genes contribute to genetic and phenotypic novelties in human evolution" [abstract | pdf], doi:10.1016/j.gde.2014.08.013, p 90-96 v 29, Current Opinion in Genetics & Development, Dec 2014.

De novo genes are genes that come from pre-existing DNA sequences that were not previously translated. In this study, a human-specific de novo gene was defined as a gene without intact orthologous ORF in multiple out-group species including chimpanzee, orangutan, rhesus macaque, mouse, dog and so on. The details of the process whereby they become translated genes is just nowadays being worked out, but the importance of de novo genes for evolutionary advances is well-documented.

These 24 were selected in a comparative transcriptome study. In rhesus macaque or chimpanzee, the untranslated orthologs are transcribed as polyadenylated non-coding RNAs. They are smaller than average human genes, with a median translated length of 150.5 amino-acids, compared with 416 a-as in the human genome. Alu elements contributed to eight exons ...and to three splicing junction sites..., further supporting the previous observation that repeat elements might be involved in the origination of some de novo genes.

Even a human-specific protein of only 150 amino acids, encoded by previously untranslated DNA, is something to wonder about. How did it acquire its programming? The chance that some or all of the DNA sequence was already transcribed for non-coding RNA would not explain the protein that it encodes. That protein appeared without having undergone natural selection, so the phenomenon is confounding for darwinism. But the phenomenon is consistent with cosmic ancestry, in which genetic programming comes first.