These processes plainly show that the genome is not a Read Only Memory (ROM) storage medium as traditional darwinism supposes, but a dynamic Read-Write (RW) system. He calls the collection of various processes that act on genomes Natural Genetic Engineering. The theory of evolution needs to incorporate these insights, he believes. We agree. Natural Genetic Engineering even sounds a lot like the software management systems that we think genomes must possess.

James A. Shapiro, Evolution: A View from the 21st Century, FT Press Science, [

The controversy started with Nicholas Wade's NYT article of two weeks ago. For suggesting a cease-fire with creationists, Wade was promptly ridiculed by arch-darwinist blogger Jerry Coyne. One of Coyne's respondents asked for any example that "defies explanation within the modern Darwinian framework." On his own blog Shapiro aswered with four, the first being the horizontal transfer of resistance plasmids among bacteria. A firestorm ensued.

Shapiro's calm exposition of the problems revealed by the new information from genomics is countered by catcalls from the defenders of strict, pre-genomics darwinism. We are encouraged that a serious, mainstream evolutionary biologist like Shapiro is upholding the importance of HGT and not ignoring the numerous phenomena that strict darwinism does not explain. We wish the arch-darwinists would actually listen.

The acquisition of new genetic material by HGT may account for over 1,000 genes in modern choanoflagellates. These genes originated from bacteria, algae, diatoms, and other prey species.... The potential impact of HGT on speciation in these organisms is nicely illustrated by the acquisition of entire enzymatic pathways from algae, with individual components that were able to replace or supplement pre-existing choanoflagellate genes, and by the evolution of novel transmembrane proteins like teneurins. [The figure below illustrates Teneurin orthologs in vertebrates and choanoflagellates.]

The regulatory sequences are micro RNAs (miRNA), short (20–24 nucleotide) single-stranded RNAs. In mammals, they form stable hairpin structures. These can, with the participation of special enzymes, control the expression of other genes, with profound effects.

This team searched eleven species for orthologs of all known human miRNAs, finding that 99% of them have at least one functional precursor. But ten human miRNAs had no detectable orthologs in any of the other species. Twelve more were activated from formerly silent sequences after humans and chimpanzees diverged. They wrote:

miRNAs are powerful gene expression regulators... Although some of these gene expression changes might be beneficial, most would be expected to be deleterious.... With time most novel miRNAs disappear, few being incorporated into regulatory networks and gradually increasing their expression level. This trend can be also clearly observed in our data with one notable exception of miR-941.

Although miR-941 precursor sequence has evolved after separation of the human and the chimpanzee lineages that took place as recently as 6–7 million years ago, expression level of miR-941 in the human brain is high and comparable to expression levels of functional miRNAs conserved in mammals.

...Human-specific effects of miR-941 regulation are detectable in the human brain and affect genes involved in neurotransmitter signaling. Deletion of the genomic region containing pre-miR-941 results in disruption of human-specific cognitive functions including language and speech. Taken together, the unusual features of miR-941 evolution, as well as its potential association with functions linked to human longevity and cognition, suggest roles of miR-941 in the evolution of human-specific phenotypes.

We see confirmations here.
The ten miRNAs without identifiable precursors illustrate the phenomenon of eukaryotic genes that "seem to have come from nowhere," in W. Ford Dolittle's words. Darwinism has no account for them. In cosmic ancestry, all genetic programs are old, but they must be installed, usually by HGT. Until then, they are nowhere in the phylogeny.
Once they are installed, genes may persist as silent DNA until all requirements for their fruitful expression are met. This would account for the twelve silent miRNAs recently activated. Darwinism does not explain how silent sequences happen to contain executable programs or subroutines.
Finally, in cosmic ancestry, newly activated genetic programs would be subject to immediate testing, possibly under positive selection. Most would fail, but a few would prove timely and beneficial, like miR-941.

This study uses a fuller dataset than previous studies, and concludes that "only three duplications and no deletions are necessary to explain opsin evolution." The research shows that genes for opsins and melatonin receptors in metazoans can be traced to a "last opsin common ancestor (LOCA)" that apparently existed more than 700 million years ago. This LOCA subsequently underwent duplications and mutations, including an important amino acid substitution that eventually produced vision in animals.

Orthologous genes are present even in the genomes of placozoans — microscopic eukaryotes of only about a thousand cells, with no differentiated tissues or organs of any kind. "...These opsin subfamilies must have evolved ...earlier than currently accepted. ...Our results are compatible with the view that the last common neuralian ancestor might have been more complex than generally assumed."

In our reading, no "origin" of vision is revealed here. Instead, a "last opsin common ancestor" is hypothesized to have existed already, more than 700 million years ago. The subsequent duplications, specializations and optimizations that it undewent — consistent with both cosmic ancestry and strict darwinism — are noteworthy, certainly. And the careful research uncovering the story is commendable. But how LOCA originated is not discussed. Instead, darwinism should be baffled by the early existence of the genetic programming for vision, even in primitive form, before selection pressure could affect it.

In cosmic ancestry this order of events is expected.

"The bacteria carried a gene involved in making the amino acid histidine that had a secondary, weak ability to contribute to the synthesis of another amino acid, tryptophan. In their study, they removed the main tryptophan-synthesis gene from the bacteria.... After growing the bacteria for 3,000 generations on a culture medium without tryptophan, ...[w]hat emerged was a tryptophan-synthesizing activity provided by a duplicated copy of the original gene."

That gene came under ongoing selective pressure after the removal of another gene previously doing the job. The experimenters reason that this immediate pressure prevented random mutations from disabling the needed function, and instead, optimized it. This team is another one doing experiments in quarantined biological systems, which experiments we wholly endorse.

The research does not discover a "new" function but an existing, previously silent function. This example adds to many others in which an existing program sits unused within a genome, ready and waiting for circumstances and selective pressure to promote it into service. These examples are surprising for darwinism, but they confirm a basic prediction of cosmic ancestry.