24 February 2008
An intuitively unlikely evolutionary event has, in fact, occurred at least twice in primates — Cesar A. Virgen et al.

In the strong version of panspermia, species acquire new genetic programs by importing them, whole or in parts. After new sequences are acquired, powerful software management systems may duplicate, relocate, assemble, optimise and test them for usefulness. This acquisition-and-deployment process would have outcomes ranging from lethal to beneficial. Darwinian natural selection would purge the worst and retain the best acquisitions for future generations. If this scenario is correct, there shoud be evidence for it in the fast-growing databases of genomic sequences. There is such evidence. Among prokaryotes evolution by gene transfer is already the rule. Among multicelled eukaryotes, sequences still recognizable as having been introduced by viruses often outnumber regular genes, and apparent examples of beneficial genetic programs that emerged by the above scenario are accumulating too rapidly to keep count.

Adapted from Stoye and Yap

If a given genetic program emerged this way among eukaryotes, couldn't it have emerged more than once? One would think so. Now, research by three different medical research teams upholds this expectation. Their evidence shows that a gene conferring HIV immunity in monkeys was created by the same process at least twice. The gene, TRIMCypA, was created when a sequence encoding cyclophilin A (CypA) was inserted in a specific location, deposing another sequence in a certain predecessor gene (TRIM5). It happened in South American owl monkeys and in Old World macaques. The two insertions were clearly separate events, because in owl monkeys CypA lies between the seventh and eighth exons, but in macaques it is downstream of the eighth exon. Also in macaques the deposed sequence (B30.2) includes an extra fragment (exon 7) not deposed in owl monkeys, and the resulting immunities pertain to different HIV types.

Cesar A. Virgen et al., from The Rockefeller University elaborate —

• Previously, the generation of a chimeric gene encoding a TRIM5-CypA fusion protein was thought to be an improbable event that occurred uniquely in owl monkeys.... However, essentially the same protein has been generated in pigtailed macaques via an independent retrotransposition event.
• That the same fusion protein has arisen twice, independently, during primate evolution seems intuitively astonishing.
• ...It is even conceivable that a single ancient retroviral pandemic led to the selection and convergent evolution of the TRIMCyp protein in both Old and New World monkeys.

Darwinists now acknowledge that eukaryotes may acquire useful new genetic programs by gene transfer, although most say the phenomenon is rare. Darwinists do not attempt to explain how or why acquired programs subsequently become properly assembled. More luck, probably. But HIV immunity by the same insertion in the same gene, twice in a row? Virologist Greg Towers thinks, It's like lightening has struck twice.

22 February 2008
All scientific theories are subject to revision as more data are gathered and analysed. But a pair of cosmologists have now proposed that the big bang theory may be exempt from this process. They suggest that only now — and not later — cosmologists may have specially privileged access to the ultimate truth about the universe. They write —

...Must science in the future always reflect more empirical knowledge than existed in the past? Our recent work suggests that on cosmic timescales, the answer is no. We may be living in the only epoch in the history of the universe when scientists can achieve an accurate understanding of the true nature of the universe.

16 February 2008

The choanoflagellate genome, like the genomes of many seemingly simple organisms sequenced in recent years, shows a surprising degree of complexity.... Many genes involved in the central nervous system of higher organisms, for example, have been found in simple organisms that lack a centralized nervous system — Nicole King

More metazoan genes came before metazoa. Following the sequencing of Monosiga brevicollis, two biologists at the University of California, Berkeley, discuss the unexpected cadherin genes found in it. Cadherin genes are essential for metazoan development, as cells differentiate and bind to form various organs and tissues. M. brevicollis is a unicellular choanoflagellate. Unicellular organisms do not undergo cell differentiation and the development of organs and tissues. "Given the absence of overt cell adhesion in M. brevicollis, one might expect choanoflagellates to have fewer cadherin genes than metazoans," to put it mildly. Yet this choanoflagellate has 23 cadherin genes, even more than are found in Drosophila melanogaster, the well-studied fruitfly.

"Monosiga brevicollis leads a unicellular lifestyle and is not known to form cell-cell contacts. Therefore, the biological processes mediated by choanoflagellate cadherins remain enigmatic." For darwinism, certainly. For darwinism, this surprise calls for new speculation. Did other choanoflagellates use the cadherin binding function to form colonies? Did the crucial metazoan functions luckily accompany this primtive one?

In the strong version of panspermia, genetic programs exist before they are expressed. The programming in cadherin genes had to be somewhere before the ancestors of higher animals acquired it. For cosmic ancestry, finding genes in organisms unready to use them is not a surprise, but an endorsement.

15 January 2008

Graph shows the number of brachiopod species that were extant (black line), that originated (red spikes), and that went extinct (blue spikes) during a ten-million year period in the Lower and Middle Ordovician. The second surge is "perfectly contemporaneous" with the very first impacts following "the largest documented asteroid breakup event during the past few billion years."

Did meteors cause the Great Ordovician Biodiversification Event? An international team of geologists and paleontologists has observed that the sudden 4-fold diversification of seafloor creatures about 470 million years ago coincided with an intense bombardment of meteorites. "The precise coincidence between these two events is established by bed-by-bed records of extraterrestrial chromite, osmium isotopes and invertebrate fossils in Middle Ordovician strata in Baltoscandia and China."

A strictly darwinian account for a diversification event caused by a meteor bombardment is unknown. But with cosmic ancestry there are two plausible, non-exclusive scenarios. The meteor bombardment could have accompanied the delivery of new genetic programs from space, and/or the environmental changes it caused could have triggered the deployment of silent genetic programs already in Earth's biosphere.

15 January 2008
Did life begin on a radioactive beach? An astrobiologist at the University of Washington in Seattle, "has added to the existing long and varied list of hypotheses" for the origin of life. He has "demonstrated in laboratory experiments that [1-8 percent uraninite in sand] could produce the chemical energy to generate some of the molecules in water which produce amino acids and sugars – key building blocks of life...."

The origin-of-life problem has a software aspect and a hardware aspect. Efforts on the software aspect have produced nothing. The newest proposal seems even to retreat from the hardware aspect to something antecedent: Can anyone propose an environment that could foster some of the the materials necessary for the origin-of-life? Yes, a Washington astrobiologist can. For that we admire his imagination and diligence. But we think he has not reduced even the hardware aspect of the origin-of-life problem. Rather, he recognizes more of its magnitude.

14 January 2008
Extrasolar planets are the subject of a recent interview with Dimitar Sasselov, the Director of Harvard's Origins of Life Initiative. About 270 "exoplanets" have been confirmed so far, with more seen weekly. The ones detectable with today's methods are all larger than Earth, and many of these have surprisingly low densities. Still, planets from two to ten times the size of Earth may be earthlike "rocky" or "ocean" planets. The handful of these already confirmed are probably too hot or too cold, but ones with a suitable temperature range could possibly harbor life. New instruments like the French-led COROT, launched in December 2006, and NASA's Kepler, scheduled for launch in early 2009, will help us find them and see if they do.

4 January 2008
A sudden diversification of life..., if confirmed,... reinforces the idea that major evolutionary innovations occurred in bursts. A team of of paleontologists from Virginia Polytechnic Institute and State University in Blacksburg found that the oldest assemblage of Ediacaran plant fossils, from 575-565 million years old, contains every form of plant life subsequently seen throughout the entire Ediacaran. The diversification must have happened suddenly. Named the Avalon explosion, its pattern is similar to that seen for the Cambrian Explosion of animal life at least 30 million years later; and its timing coincides exactly with a sudden infusion of oxygen into the oceans.

Rapid explosions of diversity among plants or animals are not consistent with Darwin's original theory whereunder all evolution is slow and gradual. Amendments to accomodate evidence for "punctuated equilibrium" have been necessary. But rapid evolutionary changes are consistent with cosmic ancestry, where apparently novel genetic programs are actually already available. And if an environmental change immediately triggered the Avalon explosion, preexisting genetic programs for the new forms would seem to be required.