• Orthologous genes between the humans and chimps are very similar; 29% encode proteins that are identical.
• Aligned sequences differ by single nucleotide substitutions at a rate of 1.23%. Some of these must reflect within-species polymorphisms, but the majority, an estimated 1.06%, represent fixed divergences between the species.
• The median number of non-synonymous and synonymous nucleotide substitutions per gene are two and three, respectively.
• Positive selection is most noticeable in genes related to immunity and host defense, reproduction and olefaction.
• Another study shows relaxed constraint in hominids' gene promoter regions versus those of murids.
• Purifying selection appears to primarily affect genes pertaining to intracellular signalling, metabolism, neurogenesis and synaptic transmission, but even some silent sequences seem especially well-conserved.
• Insertions or deletions of polynucleotide sequences (indels) are rarer than single-nucleotide substitutions, but by their wholesale nature, they account for more of the total dfference between the human and chimp genomes, 1.5%.
• Certain transposable elements have been more active in humans.
• Chimps have acquired two new families of retroviral elements since the two species diverged.
• Processed pseudogenes appear to have arisen at a rate of ~50 per million years since the species diverged.
• Two chromosomes in chimps are fused into one in humans.
• At least seventeen human genes contain exons missing in chimps.

Brief comments: Two non-synonymous nucleotide substitutions per gene are clearly too few to have composed any new genes in the standard, gradual darwinian manner. Insertions and deletions per gene are even rarer, and could explore only the tiniest fraction of genome sequence space by the random search method. But if the search is not random, the data may be made rational. For nucleotide substitutions, perhaps genome operating systems have the capability to vary only the right few nucleotides necessary for optimizing a gene within its given range. For insertions and deletions of larger blocks of nucleotides, perhaps other subsystems are able to recognize compatible strands and their exact junction points. With randomness thus reduced, evolution could explore only the fruitful parts of genome sequence space.

In our philosophy, macroevolutionary advances depend on new genetic programs that must be acquired by gene transfer. The transfer may happen in stages, and generations of natural selection would be needed to sort and deploy acquired sequences. For turning on the new programs, relaxed constraint in their regulatory regions might be important.

The seventeen human genes with exons missing in chimps would support our contention that new evolutionary programs are supplied by gene transfer. Beyond them, the current sequence comparison suggests to us that recent human evolution comprised lots of post-transfer genomic activity.

• Nevertheless, the prediction of an open pan-genome is not surprising if we consider that sequencing a few hundred liters of water from the Sargasso Sea identified 1.2 million unknown genes from 1,800 predicted genomic species.
• If we consider that there are 10^31 bacteriophages on earth..., which infect 10^24 bacteria per second, we can imagine that a continuous flow of genetic material occurs between bacteria sharing the same environments.
• These results suggest that the environmental gene pool available for inclusion by mechanisms such as horizontal transfer, transposition, and transformation is much larger than previously estimated.
• It has been shown that the horizontal transfer of as little as one gene between two GBS serotypes can lead to [an important phenotypic change].
• These findings have implications for... evolution.

30 July 2005
Gene transfer in fungi accounts best for the acquisition of certain genetic programming controlling mating, Canadian and US botanists conclude. Asking how Stemphylia are able to reproduce asexually when their close relatives cannot, the team first identified the specific genes that account for this difference. Then they conducted phylogenetic analyses of the genes. "We had expected that ...self-fertility would have originated in different species by independent mating-type gene fusions. Instead, we found evidence for a single fusion that was transferred across lineages." They even add, "No other evolutionary event could have caused the discontinuous distribution of the fused MAT regions in the Stemphylium species phylogeny."

Lateral transfer and rearrangement of genes or substantial portions of them, as implicated here, are components of a newly appreciated way for eukaryotes to acquire genetic programs. It is different from the standard darwinian mechanism of gradual mutation. For bacterial evolution the paradigm shift toward lateral gene transfer is already well advanced. Now, evolutionary examples like this one are becoming noticed among eukaryotes as well.

14 July 2005
The World Summit on Evolution in the Galapagos Islands, 8-12 June, was attended by 210 scientists, students and journalists. "It was a veritable Who's Who of evolutionary theory, including William Calvin, Daniel Dennett, Niles Eldredge, Douglas Futuyma, Peter and Rosemary Grant, Antonio Lazcano, Lynn Margulis, William Provine, William Schopf, Frank Sulloway, Timothy White and others," writes Michael Shermer in Scientific American. The conference addressed many of the live issues within darwinism, including the definition of species, the target of selection (from genes to cells and individuals to species and communities), and just when Darwin became a darwinist. Lynn Margulis even distinguished between darwinism (good) and neo-darwinism (bad). But Shermer considers these disagreements healthy and he concludes, "the theory of evolution has never been stronger."

In his own lecture in the Galapagos he had bolstered this conclusion by deconstructing at length the tenets of creationism or Intelligent Design. Apparently, no other criticism of darwinism was even addressed at the conference, although Shermer's article once mentions "other outsiders."

Shermer explains, "Creationists and Intelligent Design theorists like to inquire how information can increase in a world filled with entropy and the decay of information. Symbiogenesis is one answer--incorporating the genome of other organisms." If there are other answers, he doesn't list them. Of course, symbiogenesis is a form of gene transfer — a wholesale one to be sure. Gene transfer adds information to the acquiring species, but not to the world. Shermer appears to have reasoned hastily and badly here. As Founding Publisher of Skeptic magazine and the Director of the Skeptics Society, he could do better.

We ask related questions: Can new genetic programs be acquired without gene transfer? Is evolutionary progress in a closed system possible? We wish darwinists like Shermer would carefully consider these questions and the evidence related to them.