"We conclude that the replication initiation protein (Rep)-related sequences of geminiviruses, nanoviruses and circoviruses have been frequently transferred to a broad range of eukaryotic species, including plants, fungi, animals and protists. Some of the transferred viral genes were conserved and expressed, suggesting that these genes have been coopted to assume cellular functions in the host genomes. We also identified geminivirus-like and parvovirus-like transposable elements in genomes of fungi and lower animals, respectively, and thereby provide direct evidence that eukaryotic transposons could derive from ssDNA viruses."

"In the last two decades there have been dramatic changes in our understanding of how evolution works. We used to believe that changes only took place through small mutations in our DNA that accumulated over time. But in this case we found a huge cut-and-paste operation that altered wide areas of the genome to create large-scale morphological change."

1500 unexpressed genes, awaiting recruitment for a major evolutionary advance, defy darwinian logic. But they, and the "cut and paste" method of their deployment and regulation, are confirmations for cosmic ancestry.

Schematic drawing of the domain structure of a choanoflagellate syntaxin (linked rectangles), and sequence alignments of the N-peptide of syntaxin (left) and of the conserved N-peptide binding site (right) are shown. Choanoflagellate sequences (bottom row) are compared to those (ascending) of sea anemone, nematode, fruitfly, and 3 or 4 mouse alleles. [Figure and caption adapted from Burkhardt et al., 2011]

In cosmic ancestry, genes exist before they are deployed. Research under this paradigm would look for examples of them. Here is one. There are lots more.

Thanks for your questions, Ken Jopp and Pedro Pereira.

1 September 2011

Antibiotic resistance genes are much older than modern antibiotics, according to a team who recovered the genes in a layer of uncontaminated mud 20 feet deep near Bear Creek in the Yukon Territory. "The ancient bacteria in the sediments turned out to contain all the major genes that enable modern bacteria to resist antibiotics.... This work firmly establishes that antibiotic resistance genes predate our use of antibiotics."

"Vancomycin resistance took the clinical community by surprise when it emerged in pathogenic enterococci in the late 1980s...." This and other similar developments were initially taken to indicate that antibiotic resistance can evolve very rapidly. Soon it became apparent that resistance genes can spread quickly among bacteria by horizontal gene transfer (HGT). But now it apears that many of the resistance genes predate, by at least 30,000 years, the existence of the antibiotics they counteract.

Genes that exist before there was any selective pressure to program them are a jarring puzzle for darwinism. They are a standard prediction of cosmic ancestry.

Evidence for even older life on Earth comes from rocks whose isotopic fractionation is best explained by cellular metabolism, so the case for old life is strong. And if life appeared on Earth so promptly after the planet cooled, panspermia looks like a reasonable explanation.

David Wacey et al., "Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia" [

This work provides good support for "pseudo-panspermia," the theory that space provides the starter ingredients for a prebiotic soup. Of course, we think that organic compounds in space may well be postbiotic. Consequently, we wonder if a suite of organics remaining from dead cells, after millions of years in space, might also resemble the meteorites' contents. Nonetheless, we welcome this support for a version of panspermia.

Michael P. Callahan et al., "Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases" [

Oliver and Greene write: "TEs can act to generate genetic novelties and thus specific phenotypic traits in numerous ways. Besides passively promoting exon, gene or segmental duplications (or deletions) by unequal recombination, or by disruption of genes via insertion, TEs can actively contribute to gene structure or regulation via exaptation. On multiple occasions, TEs have been domesticated to provide the raw material for entire genes or novel gene fusions. More frequently, TEs have contributed partially to individual genes through exonization after acquisition of splice sites. Independent exons generated by TEs are often alternatively spliced, and thereby result in novel expressed isoforms that increase the size of the transcriptome."

"The generation of novel gene sequences during evolution seems to be heavily outweighed by genetic or epigenetic changes in the transcriptional regulation of pre-existing genes. Consistent with this, much evidence indicates that a major way in which TEs have acted to functionally modify primate genomes is by actively inserting novel regulatory elements adjacent to genes, thus silencing or enhancing expression levels or changing expression patterns, often in a tissue-specific manner."

"A role for TEs in evolution has long been recognized by many, yet its importance has probably been underestimated. Using primates as exemplar lineages, we have assessed specific evidence, and conclude that it points strongly to an instrumental role for TEs... in engineering the divergence of the simian lineage from other mammalian lineages. TEs, particularly Alu SINEs, have essentially acted as a huge primate-restricted stockpile of potential exons and regulatory regions, and thereby have provided the raw material for these evolutionary transitions."

In a 2009 article titled, "Transposable elements: powerful facilitators of evolution", the same biologists observe:

Oliver and Greene also classify the TEs implicated above into four categories, one of which includes endogenous retroviruses. This inclusion only adds to the growing recognition of the association between TEs and viruses. We now suspect that our original focus on viruses, strictly defined, as agents of horizontal gene transfer may have been too narrow.

• Transposable elements... can cause genetic changes of great magnitude and variety.
• TEs are ubiquitous and extremely ancient....
• ...Although harmful to some individuals, they can be very beneficial to lineages.
• TEs can build, sculpt, and reformat genomes by both active and passive means
• TEs have ancient origins that are traceable to prokaryotes.
• TEs often comprise a large, if not massive, fraction of the eukaryotic genome.
• Periodic infestations of genomes by novel TEs predict 'punctuated equilibrium'....
• Many TE families are conspicuously lineage-specific....
• ...TEs [have] the potential to explain why certain other animal clades are anomalously large....
• TEs [may be] a prerequisite for evolutionary radiation
• TE activity increases under conditions of stress.
• TEs are differentially active in the germ line and during early embryogenesis
• ...Given their ancient origins, the biological and evolutionary impact of TEs is probably still underestimated, since much of their influence may now be untraced, and untraceable.

We have long believed that evolutionary progress depends on genetic programs acquired by HGT in a biologically open system. Beginning in 2001, we sponsored research at the University of Oklahoma to explore this hypothesis by seeking the sources of uniquely human gene families. We think the work from Murdoch University, including the 99 primate-specific traits, supports our hypothesis.

Another recent article, by University of Rochester biologist John H. Werren, asks if TEs and other selfish genetic elements (SGEs) persist "because of their ability to replicate within genomes" or "because they promote the ability of populations to adapt and evolve." He favors the former, but either assumption is consistent with darwinism. Of course, the darwinian framework needs to include an account of the "origin" of these elements, but the account seems to us very sketchy and elusive. We note that the origins of SGEs are not actually observed. Instead, TEs, for example, look "extremely ancient." Under cosmic ancestry they would have to be, to participate in the earthly development of preexisting cosmic life.

Genetic instructions for developing limbs and digits were present in primitive fish millions of years before their descendants first crawled on to land....
The genetic switches that drive the expression of genes in the digits of mice are not only present in fish, but the fish sequence can actually activate the expression in mice.
...The new experiments suggest that the genetic switch controlling limb development was in fact present deep in Earth's evolutionary tree.
There previously was the idea that these switches had to be generated from scratch de novo, but no, they already existed, they were already there.
There is a whole universe of questions that are opened up by this discovery.

These comments come from a team at the University of Chicago Medical Center who compared similar genetic regions in humans, mice, chickens, frogs, and two fish species. They found that the genes that regulate the development of limbs and digits existed before the appearance of limbs and digits. Members of the same research team have studied this issue for years; the conclusion is well supported.

It is said that when J.B.S. Haldane was asked what evidence could destroy his confidence in the theory of evolution, he answered, "fossil rabbits in the Precambrian." They would be out of order in the darwinian narrative. We think the same logic should apply to genes appearing out of order, because there was no opportunity for darwinian trial-and-error to program them. (That existing programs also, luckily, happen to precisely perform new functions is a weak, implausible, ad hoc proposal.) But in cosmic ancestry, genetic programs always exist before the functions they encode.

This example is only one on a fast-growing list of genes older than they should be. They should be as troubling to darwinism as fossil rabbits in the precambrian. If they aren't, perhaps Karl Popper was correct to suggest that the darwinian theory of evolution is impervious to evidence.

Like Harry, our allegiance goes to science. Unlike him, we are not sure that life can originate from nonlife. The evidence so far is not encouraging. But if life cannot originate from nonlife, we will not abandon science. Yet that's the choice that must be made, according to almost everyone. How did that idea originate?