20 May 2008
How a virus became a retroposon is detailed in a report by French virologists and genetecists. Studying LTR (long terminal repeat) retroposons, very abundant in the mouse genome, they conclude that these derive from an ancestral retrovirus that has reached the germline of a remote rodent ancestor and has been 'endogenized.' The main steps in the process were the loss of the virus's env gene and the alteration of its plasma membrane targetting signal to target instead the endoplasmic reticulum membrane. The resulting retroposon subsequently multiplied to approximately a thousand copies in the mouse genome, 30% of which are still active today.

The research benefited from an unusual situation: both the progenitor element and the derived intracellularized retrotransposon still coexist in a functional state within their host. The progenitor retrovirus retains its env gene, whose protein product, the report notes, may even be further involved in the horizontal transfer of other endogenous retroviruses...[!]

Retrotransposons proliferate within genomes, expanding and rearranging them. This activity is known to have major evolutionary effects. And retrotransposons appear to be closely related to viruses. Now we learn some specifics about how they may evolve from viruses.

20 May 2008
Caltech reconsiders life on Mars in an illustrated retrospective article with lots about the Viking mission and others. The illustrations include one of sunset over Gusev crater photographed by JPL's Mars rover "Spirit" —

Douglas L. Smith, "The Fall and Rise (and Fall?) of Life on Mars" [

22 April 2008
Richard Dawkins endorses panspermia in a movie about Intelligent Design (ID). Interviewed in dim light by actor Ben Stein, Dawkins says that the intelligent design of life on Earth might be detectable if the designers were highly evolved creatures who spread life through space by panspermia long ago. Wow, we're pleased by this development in Dawkins' thinking. Of course he adds that the first creatures must have evolved in the strictly darwinian manner. Of course.

The movie, "Expelled," is pretty much a food fight between darwinists and proponents of creationism / ID. For one question, is Intelligent Design the same as creationism? Early in the movie, proponents of ID say no, the designer need not be God. But later on the movie seems to be all about belief in God.

The most discouraging thing is the message that there are only two choices about evolution — a message pounded in with images of the Berlin Wall. The darwinists are entirely complicit with the IDers in this false dilemma. Do both sides secretly enjoy this fight? So it seems.

We liked getting a closer look at some well-known darwinian proponents and opponents, including a few we already know. We wish the movie had said more about the science issues and less about the political ones. But sometimes the science issues were at least framed well. And ID proponent William Dembski, whom we have criticized elsewhere, made only arguments with which everyone should agree. For visual effects we especially liked a computer animation of the interior of a eukaryotic cell.

If you like a food fight, you may like the movie.

21 April 2008
Placental genes have ancient origins. Two geneticists at Stanford University reached this conclusion in a comprehensive study that asked, "What are the evolutionary origins of genes that play specific... roles in placentation?" First, they identified those genes as being the 757 ones preferentially expressed – above a specified threshold – in the placenta during development. They "found evidence that the basic placental structure relied largely on co-option of ancient genes."

Then, seeing that the expression profiles of those genes change markedly during development, they separately analyzed the ones expressed in the mature placenta. They concluded that those ones are "rodent specific and recently evolved." Furthermore, "In the mature human placenta, 24.0 to 29.9 percent of genes …are primate specific...." And they continued, "…While order- or species-specific modifications may have occurred, the rapid trophoblast development and differentiation found in all eutherian mammals is likely based upon a program already established in their last common ancestor."

We note that none of this has anything to do with the origin of genes. Knox and Baker use "origin" misleadingly — the earliest-detected example of a given gene is designated as its "origin". But how any given gene actually originated is not a question they consider.

They do speculate that duplication and divergence may have produced some new functions. For example, in mice, "While some of the Prl [prolactin-like] gene family members appear to mimic the biological actions of prolactin itself, others, including many of those we have found to be characteristic of the mature placenta, are believed to possess novel biological actions."

Even if this belief is true, the novel actions may come from programming already present and ready to be activated by directed mutations on the right few nucleotides. Of course, we recognize that this speculation of our own needs additional support — but directed mutation has become an accepted phenomenon. Meanwhile, the de novo composition of genetic programs or subroutines of more than, say, 50 ordered nucleotides, remains undocumented.

In sum, this study of today's genomes concludes that as the past is examined more and more deeply, placental genes have identifiable predecessors... until they don't. This shift is not gradual, but abrupt. The gradual composition of placental genes is not observed. Most placental genes are apparently ancient, but some show up only more recently, without detectable predecessors. How any of them originated is not known or even considered.

If anyone knows of a study that convincingly accounts for the origin of a genetic program or subroutine, we would like to hear about it!

11 April 2008
Earth's first animal... was probably significantly more complex than previously believed. This is the conclusion of a new study that used more than 100 computers to analyze the most data, so far, to map the evolutionary history of animals. "Among the study's surprising findings is that the comb jelly split off from other animals and diverged onto its own evolutionary path before the sponge." The comb jelly has complex features like specialized tissues and a nervous system, and the sponge doesn't.

1) The comb jelly evolved its complexity independently of other animals, after it branched off onto its own evolutionary path.	2) The sponge evolved its simple form from more complex creatures. © NSF

"This was a complete shocker," says Casey Dunn, lead author. "So shocking that we initially thought something had gone very wrong." The article, Nature's cover story, reports that the comb jelly "could only have achieved its apparent seniority over the simpler sponge via one of two new evolutionary scenarios: 1) the comb jelly evolved its complexity independently of other animals, after it branched off onto its own evolutionary path; or 2) the sponge evolved its simple form from more complex creatures...."

In spite of the unprecedented volume of data already analysed, the research team thinks the conclusion "should be viewed as provisional until more data are considered." Meanwhile, we note that other recent studies have reached similar conclusions — finding that complex genetic programs either are older than they should be, or arose independently more than once. With darwinian logic, either way, it's a jarring surprise. But with the logic of cosmic ancestry all genetic programs are very old and can be distributed widely by gene transfer mechanisms.

Jarring to us is a different puzzle: Why is it considered unscientific to question a theory as fallible as neo-darwinism?

3 April 2008
What is the origin of eukaryotic RNA polymerases? Three geneticists in France ask this question in a study that compares related polymerase sequences across all domains of life. They find that a previously unaccountable component of eukaryotic RNA polymerase is closely related to a "G" polypeptide found in archaeal RNA polymerase. Thus they have identified "a last missing link between the core structure of archaeal and eukaryotic RNA polymerases."

It will be assumed that this study adds weight to the already monumental case supporting darwinian evolution. In the darwinian paradigm, genetic programs such as eukaryotic RNA polymerase are built up incrementally from simpler precursors. Here someone has found a "missing link" that ties the eukaryotic program to one in archaea, which are older and simpler than eukaryotes. It shows that eukaryotic RNA polymerases originated by darwinian evolution, right?

Loss of G or Gain of G

Wrong. The study shows that the G polypeptide is present in some lineages and absent in others. The French team offer two scenarios to account for this pattern. "The first posits that all eukaryotic and archaeal RNA polymerases derive from an ancestral enzyme equipped with all of the eukaryotic core subunits," some of which were subsequently lost in various lineages. Of course, this pattern — a complex common ancestor and simpler descendants — is the very opposite of darwinism.

"A second scenario ...states that the G protein was specifically acquired by Crenarchaea after they diverged from Euryarchaea...." Until recently, this possibility might have been overlooked. But if a genetic program or component was acquired by gene transfer, the phenomenon supports strong panspermia (cosmic ancestry). In sum, either the whole program was there at the beginning, or parts of it came later, from nowhere. In no way does this study show that eukaryotic RNA polymerases originated by darwinian evolution.

In our opinion, a similar, mistaken assumption is made about most studies like this one. That is, people often assume that darwinian evolution's ability to compose new genetic programs has been demonstrated when it hasn't been. If darwinian evolution can compose wholly new genetic programs, there there should be unequivocal evidence. We haven't seen it.