23 June 2006
Viruses' staggering diversity and genetic promiscuity could make them the most creative force in evolution — Nature, 8 June 2006.

By shuttling genes into and out of their hosts, viruses seem to be a major driving force in the evolution of higher organisms.
Many viruses carry and use a long list of genes formerly thought to be useful only in cells, such as those needed for photosynthesis.
Plant virologist James Van Etten has cultured an algae-infecting virus that carries a gene for hyaluronic acid, a molecule used by vertebrates as a joint lubricant, as well as viruses that make chitin, the protein used as a building block in insect exoskeletons.
Viral diversity is just way different from anything else. Every time we sequence it, most of everything we run into is unknown — microbiologist Forest Rohwer.
In total there are now thought to be some 10^31 viral particles on the planet. One researcher estimates that these viral genes laid end to end would reach 250 million light years.
Some researchers now believe that viruses have been instrumental in assembling the various molecular components that define the cell types associated with life's three domains — bacteria, archaea and eukaryotes.

Garry Hamilton, "The Gene Weavers" [

20 June 2006
Bats and horses are closely related, according to a genomic study using retroposon (L1) analysis. Trees of life based on genomics often look different from ones based on morphology, and they may even look different from each other depending on the genes compared and the method used. In this study three biologists in Japan compared the presence or absence of specific retroposon alleles to draw their tree. They decide that bats and horses are so closely related that they belong together in a newly identified clade called Pegasoferae, because Pegasus refers to the flying horse. By their method, bats, horses, dogs and cats look much more closely related than, for example, common shrews, tree shrews, and elephant shrews. The big differences between bats and horses exist because of incomplete lineage sorting ...followed by rapid divergence into the extant orders over an evolutionarily short period.

A mammalian phylogeny reconstructed by retroposon insertion analysis. Arrows denote insertions of retroposons into each lineage. © The National Academy of Sciences, 2006

We wonder, could a species lacking a given retroposon allele have simply lost it? This team thinks not, because to date, no mechanism has been described for the reversal of retroposon integration. And we think that dissimilar species which carry closely related retroposon alleles might have acquired them separately, independently. Again, this biology team thinks not. It is highly unlikely that the same type of retroposon would integrate into the same genomic locus independently in different lineages.

But it is well known that whole introns, in whch the studied L1 sequences reside, can be precisely inserted; the process is sometimes called "homing." Could a software management capability like that also enable these retroposon sequences to home in on their destinations? Could the whole intron be a recent insertion? In sum, we think this study would have reached a more plausible conclusion if Nishihara et al. had recognized a bigger role for the gain and loss of introns, exons, and a variety of other large blocks of DNA in the course of evolution.

13 June 2006
Early life on Earth was already diverse. Australian and Canadian biologists conclude that the variety of stromatolites in Australia's Strelley Pool Chert was created by a rich marine ecosystem similar to ones that flourish on tidal platforms even now. But this formation can be reliably dated to 3.43 billion years ago, when such environments were new and rare. If life on Earth could have achieved this much diversity so quickly, could it have done the same on, say, Mars? People are asking.

9 June 2006

Faint red galaxies of the XMMXCS 2215-1738 galaxy cluster in the center, with the X-ray glow of hot intergalactic gas shown in blue. Credit: European Southern Observatory Imaging Survey; NOAO.

Galaxies theoretically young look old. "Almost ten billion light years distant, galaxy cluster XMMXCS 2215-1738 is seen in what should be its earliest stages of formation. Yet this distant cluster appears to be full of old galaxies," discovery team member Adam Stanford noted with amazement.... The total mass of the cluster is enough to contain 500 trillion stars comparable in mass to our Sun. That's a surprising stellar mass for a galaxy cluster to have achieved at such an early era in the evolution of the universe, said Stanford, a researcher at the University of California, Davis, and at Lawrence Livermore National Laboratory.

This result was announced at the 208th meeting of the American Astronomical Society in Calgary this week. This observation reminds us that the big bang theory still meets too many surprises for it to serve as the foundation for the rest of science. A recent article by Johns Hopkins astronomer Charles Bennett reinforces our opinion. He writes, We have not yet demonstrated that inflation actually happened, nor do we know the identity of the inflation field or the functional form of its effective potential.... We have no compelling model for the recent epoch of accelerated expansion."

9 May 2006
The structure of a bacterial enzyme that inserts mobile gene cassettes has been resolved by biochemists and geneticists in France. These ubiquitous gene cassettes provide antibiotic resistance, virulence factors and other traits to bacteria, and are among the major vehicles of bacterial gene exchange. How they are captured, inserted into their genomic arrays and subsequently regulated is worth knowing. The new research shows, among other things, that the enzyme's ability to recognize its target site depends on DNA bases that are "flipped out" of their normal double helix alignment. In another surprise, the enzyme complex (illustrated at right) installs the cassette as an unpaired (single) strand. In general, the process is quite complicated and the research raises several new questions.

9 May 2006
Organic matter in meteorites is extraterrestrial and ancient. Scientists at the Carnegie Institution's Department of Terrestrial Magnetism reached this conclusion after measuring the relative amounts of different isotopes of hydrogen and nitrogen associated with particles of organic matter in seven carbonaceous meteorites. Forty years ago, this finding would have been astonishing, because organic matter was thought to be only biotic or post-biotic. Now we know the stuff is out there. Now mainstream science welcomes it as pre-biotic, potential starting ingredients for life on Earth and other planets.

4 May 2006
A gene captured from a mobile element fused with another gene to make a new primate gene. Four biologists in Louisiana and Texas have used extensive sequence data to reconstruct the history of this gene, called SETMAR. Its assembly apparently occurred within a time window of 18 million years.

A simplified chronology of the divergence time of the species examined relative to hominoid primates (left) and the structure of the SETMAR locus (right) are shown. Starting at the bottom, pink boxes represent the two SET exons, which are separated by a single long intron (interrupted black line) and form a "SET-only" gene whose structure is conserved in all nonanthropoid species examined and terminated with a stop codon (*) located at an homologous position (except in cow...). The Hsmar1 transposon (#1) is inserted in the primate lineage, after the split between tarsier and anthropoids, but before the divergence of extant anthropoid lineages. The transposon is shown here with its TIRs (black triangles) and transposase coding sequence (red box). The secondary AluSx insertion within the TIR of Hsmar1 (#2) is represented as a blue diamond. The position of the deletion removing the stop codon of the "SET-only" gene (#3) is indicated by a black lightning bolt. The de novo conversion from noncoding to exonic sequence is shown in green, and a bent dashed blue line represents the creation of the second intron (#4), whose two ends are splice sites, shown as short thick vertical blue lines. © The National Academy of Sciences

The function of the gene is not yet known, but evidently the protein it encodes, 671 amino acids in length, is broadly expressed. Also, the portion of it derived from a mobile element appears to be under strong purifying selection. And this portion binds to a 19-base-pair DNA binding site of which the human genome contains more than 1500 perfect or near-perfect copies. This ubiquity suggests to the researchers that there is "a previously uncharacterized mechanism by which the circuitry underlying complex regulatory networks may be rapidly established." That mechanism could be part of the software management system that eukaryotic genomes would need, if they can acquire new programs as proposed in cosmic ancestry. We believe that the core finding of this study, in which exon-sized strands of DNA have been relocated and joined to make a new gene, supports the case for cosmic ancestry's mechanism.

3 May 2006
Genes undergo rapid mutation and selection immediately after transfer, according to a pair of biologists studying bacteria at McMaster University. First they note that the rate of gene insertion and deletion is usually underestimated by the standard techniques, and is greatest "at the tips of phylogeny." Using a comprehensive method of analysis, they write:

• ...During the evolutionary time period required for one substitution per site, an entire gene could possibly have been inserted/deleted about five times in the [fastest evolving] group.
• If this is an evolutionarily stable situation, then most of the laterally transferred genes must be lost shortly after their insertion during evolution.
• ...Genes that have been recently transferred into these hosts have a higher percentage of nonsynonymous substitutions. Together, the recently transferred genes not only have faster evolutionary change but also have higher Ka/Ks ratios.
• ...Gene movement in bacteria should be considered as a result of the dynamic process of passive uptake and of quick selection on those genes appropriate for the current bacterial niche or their rapid elimination.