24 September 2009
TEs are probably as old as life itself and have been an integral, active, and both destructive and constructive component of genomes. Two Stanford geneticists make this observation in commentary on an analysis (by others) of the activity of certain transposable elements (TEs) in rice. They also remark, about 90% of human DNA is made up of TEs. That's even more than we reported three days ago. Anyway, it's a lot. (See shaded box for geneticist Mark Batzer's comments on the difference.)

6:07 PM | from Mark Batzer: Short answer we are only talking about retroelements. Many older elements have also contributed but are no longer recognizable as such. So about 50 percent from recognizable modern elements and another 40 or so from older elements of many different classes. So both numbers are right just a question of how hard you look.

Josefa González and Dmitri Petrov, "MITEs—The Ultimate Parasites" [

21 September 2009
Nearly half of the human genome is derived from transposable elements (TEs). Most of these, approximately one-third of the human genome, are "non-LTR" retrotransposons. Now two distinguished geneticists have reviewed the effect of this group on human evolution. The huge volume of genomic data available today enables them to reconstruct the process in far more detail than only a decade or two ago, much as new telescopes improve our view of the stars. The details now apparent are eye-opening. The box below gives one small example.

Evolutionary analyses indicated that the three transduction events all took place ~7-14 Myr ago, as humans and African great apes share all four AMAC1 copies, whereas orangutans and other primate and non-primate species that have been analysed only possess the ancestral AMAC1L3 gene. Experimental studies indicated that, in addition to AMAC1L3, at least two of the three transduced AMAC1 genes are expressed in human tissues. RNA transcript sequence analyses of the expressed AMAC1 duplicates further revealed that the promoter sequence had been duplicated along with the AMAC1 coding sequence as part of the 3' transduction process. This indicates that retrotransposon-mediated gene transduction can duplicate not only coding regions of genes but also their regulatory regions; therefore, genes retain their functional potential after duplication, and retrotransposon-mediated duplication can lead to the rapid generation of functional gene families. Figure adapted from Xing et al. © 2006 The National Academy of Sciences USA.

The review begins with brief primer on TEs. Some are not retrotransposons, but DNA transposons. Among the rest, some are Long Terminal Repeat (LTR) retrotransposons, characterized by nucleotide sequences at their ends that are repeated hundreds or thousands of times. Viruses use these repeats to insert their genes into our genomes. In other words, human LTR elements are endogenous retroviruses. Most of these were inserted into our genomes more than 25 million years ago and are inactive now. The review focuses on the remaining ones, the non-LTR retrotransposons.

These are subdvided into four categories, but enough primer already. The bottom line is that non-LTR retrotransposons are very active in humans. "The impact of non-LTR retrotransposons on human genome evolution largely results from their extremely high copy numbers (for example, there is one Alu insertion every 3 kb on average) and their continued activity over tens of millions of years.... The current rate of Alu retrotransposition has been estimated as approximately 1 insertion for every 20 births in humans.... [T]he majority of Alu elements were inserted ~40 Myr ago following a peak of amplification during which there was approximately one new Alu insertion in every birth...."

Not surprisingly, this retrotransposon activity can cause problems. "Examples of human genetic disorders caused by de novo L1, Alu and SVA insertions continue to accumulate, and 65 cases have been shown to cause heritable diseases...." In theory, standard Darwinian selection would eventually eliminate lineages with such defects. This process by itself would be only havoc for our species.

But the human genome also has a number of regulatory systems to suppress or modify the activity of retrotransposons. And occasionally, their genetic tinkering produces a beneficial genetic novelty, as in the illustrated example above. Retrotransposons can even bring together "elements that have been present in the genome for a long time."

Along with our regulatory systems, could retrotransposons and other TEs be active components of the genomic software management systems that cosmic ancestry requires? Such systems would recognize and assemble genetic programs previously acquired in exon-sized blocks. Then standard darwinian evolution could select-for and optimize the programs — or select-against and eliminate them. We think TEs are likely components of these systems. Otherwise, they are hard to explain.

17 September 2009
The gain and loss of exons has contributed to the evolution of new features. Evidence for this surmise comes from Japanese and Californian geneticists whose primary interest is slightly different: domain shuffling in vertebrate genomes. The geneticists conclude that domain shuffling is important, and they notice that domains are frequently gained or lost during evolution. "These genes are likely to have gained new functional roles by acquiring new domains, and are likely to be involved in phenotypic evolution," they comment.

Domain structure of a vertebrate protein compared to three amphioxus sequencess and one sea urchin sequence.

Exons are the coding portions of genes, separated by noncoding portions called introns. Introns (and consequently, exons) were first recognized more than thirty years ago, and their evolutionary purpose has been a contentious subject ever since. How could interruptions in genes be a good thing? A dozen years ago we suggested, "Introns make more sense if evolution is a constructive process requiring the assembly of blocks of instructions imported from outside the cell."

Evidence that exons encoding the studied domains were ever gradually composed is not apparent in the new report. Rather, in the reconstruction of the past, exons seem to simply show up, already composed; or else they were present in the most ancient studied species. This supports our prediction, "If a new genetic program arrives by the strong panspermia process, intervening species should possess either nearly identical versions of it ...or nothing similar...."

If the studied domains were not gradually composed by mutation-and-natural-selection, how did they acquire their programming? Could they be encoded by random, "junk" DNA that luckily contains working programs or subroutines? No. Simple math makes it forbiddingly unlikely that any random domain except a trivially small one of, say, fifteen or fewer codons would be functional. Meanwhile, the studied domains appear to average about 150 codons in length; the largest one is longer than 3,000 codons.

The geneticists' conclusion concerning domain shuffling also interests us, because, "In the evolutionary mechanism we advocate, new genetic programs are acquired whole or in a few large pieces and then assembled by genetic software with rule-following, puzzle-solving capabilities."

In cosmic ancestry, genetic programming is as old as life itself. During evolution the program components need assembly and optimization, but the essence is there already. If so, some of the silent DNA is not random, or "junk," but instead it contains components of programs ready to become active. We think the data support this expectation.

14 September 2009
If we didn't know about life we wouldn't believe it.... — Richard Dawkins

On this website we maintain that the darwinian account of evolutionary progress and the origin of life is implausible. Charles Darwin's best-known living advocate apparently agrees. Dawkins' words come from a weekend newspaper article illustrated with facing images of Darwin and Michaelangelo's God; and he continues —except, of course, that there'd be nobody around to do the disbelieving! Religious zealots use similar rhetoric: If you don't believe the given dogma you are heretics, infidels, damned, excluded from the holy kingdom — you don't exist.

Later, Dawkins asks and answers, And how is the trick done? ...Darwinian evolution, the nonrandom survival of randomly varying coded information. We know, as certainly as we know anything, that this is the process that has generated life on our own planet. But if we know it so certainly, howcome a majority of educated American adults don't believe it?

"Extraordinary claims require extraordinary evidence," Carl Sagan said. This rule is often quoted, but what makes a claim extraordinary? A fair criterion might be this: It's an extraordinary claim if most people don't believe it. By this criterion Dawkins' answer, "the nonrandom survival of randomly varying coded information," remains an extraordinary claim — for which extraordinary evidence is still lacking. Shouldn't we at least consider other theories?

26 August 2009
"The Origin of Life on Earth" is one of six main articles in a Scientific American Special Issue: "Understanding Origins". We are grateful that the title of this article includes the words "on Earth" and that the authors briefly mention panspermia in a sidebar. But "Fresh clues hint at how the first living organisms arose from inanimate matter" is the subtitle and thrust of the article. Among the clues are recent experiments pertaining to the RNA world, and experiments in which lipid membranes form spheres and grow tails that may "break up into many smaller spheres."

The authors acknowledge many unsolved problems, and phrases like "it seems plausible ...perhaps ...could have ...would have" often appear. But doubts are forgotten by the last sentence: "At that point, the RNA world became the DNA world, and life as we know it began." As usual, all of the inquiry pertains to the hardware problem. The software problem is not even mentioned, unless you count sentences like, "Next, the organisms might have added protein making to their bag of chemical tricks."

24 August 2009
Most of our genes... were transferred from an endosymbiont. So writes Carl Zimmer in Science, in the latest essay in a series honoring "the Year of Darwin." The subject of this essay is the origin of eukaryotes. The statement, if true, powerfully affirms the importance of horizontal gene transfer (HGT) for the evolution of eukaryotes. Of course endosymbiosis is HGT in wholesale fashion, and the subsequent migration of genes from an endosymbiont to the eukaryotic nucleus is well-documented. But most of our genes by this one method? This is eye-opening.

Other methods of HGT, such as transduction by viruses, have also contributed many genes to eukaryotic species. We think it is time for mainstream science to recognize the importance of HGT in the evolution of eukaryotes.

21 August 2009
I find it fascinating that this prokaryotic symbiosis could so profoundly shape the evolution of life, and thereby set the stage for the formation of an oxygen-rich atmosphere and for the emergence of eukaryotic organelles. The symbiosis of two disparate prokaryotes to form the double-membrane prokaryotes appears to have done more than just introduce a new combination of genes into a cell.... [It] represents a radically new structural design.

So writes UCLA molecular biologist and astrobiologist James Lake, after studying evidence for a prokaryotic merger that would predate the appearance of eukaryotes. This would be another example of evolution that advances by combining pre-existing genetic components. And in this case, the components would have been whole prokaryotic genomes.

18 August 2009
NASA scientists have discovered glycine, a fundamental building block of life, in samples of comet Wild 2 returned by NASA's Stardust spacecraft. The sample was tiny, but carbon isotope testing indicates that the glycine was not a terrestrial contaminant. The discovery of glycine in a comet supports the idea that the fundamental building blocks of life are prevalent in space, and strengthens the argument that life in the universe may be common rather than rare said Dr. Carl Pilcher, Director of the NASA Astrobiology Institute. In this carefully worded statement Pilcher leaves open the possibility that the glycine could be, not a precursor but, a remnant of life.

Stardust passed through dense gas and dust surrounding the icy nucleus of Wild 2 on January 2, 2004. ...A special collection grid filled with aerogel... gently captured samples of the comet's gas and dust. The grid was stowed in a capsule which detached from the spacecraft and parachuted to Earth on January 15, 2006. Since then, scientists around the world have been busy analyzing the samples....

11 August 2009
...The source [for Mars' methane] must be 600 times more intense than originally assumed, which is considerable even by Earth's geological standards. This observation comes from a study of the regional plumes of methane that come and go seasonally on Mars. In Paris, a computer model (illustrated) best matched the phenomenon if approximately 150,000 tons of methane emerge within less than 200 days from a localized source. The study concentrated on mechanisms that could destroy the methane so quickly, but the source interests us more. Could it be biological? Hopefully, forthcoming missions like ESA's will enable us to find out.

25 July 2009
Spermatozoa of all species can take up exogenous DNA or RNA molecules and internalize them into nuclei. ...The reverse-transcribed sequences behave as extrachromosomal, biologically active retrogenes and induce novel phenotypic traits in animals.

Four medical researchers at the Istituto Superiore di Sanità in Rome concluded this while studying the phenomenon over several years. They note that sperm cells appear to have special receptors and machinery for facilitating such acquisitions. Even though the acquired genes are phenotypically expressed, they are usually not integrated into the main chromosomes and they are progressively lost during adult life. The researchers named the phenomenon Sperm-Mediated 'Reverse' Gene Transfer (SMRGT). They are especially interested because it exemplifies non-mendelian inheritance.

This acquisition system is news to us, and we are surprised to learn that genes can be expressed in development without being integrated into the main eukaryotic chromosomes. Rarely however, using mice, the researchers observed SMRGT genes that are integrated to become part of the main chromosomes of the affected lineage. Thus the phenomenon can certainly contribute to the cumulative macroevolutionary progress that animals on Earth have exhibited. This research reinforces our view that the reach of gene transfer is virtually unlimited, as it must be in cosmic ancestry.

23 July 2009
Primate-specific genes were inserted de novo, not generated by gradual divergence from non-primate genes. This conclusion comes from three geneticists who identified in the human genome 131 transcriptional units (TUs) that are found only among primates. These TUs ranged from 176 to more than 4,000 nucleotides in length, the average being around 1,500 nucleotides. The research team took care that their own methodology did not prevent them from recognizing gradual divergence —

Candidate primate-specific TUs might be conserved in nonprimates, but may have undergone accelerated sequence evolution, making their conservation unrecognizable in distant lineages and obscuring their shared origins from ancestral nonprimate genes. We do not believe exceptional divergence to be a major complication, because lowering the liftOver minMatch threshold did not improve detection of nonprimate alignments (see Materials and Methods). Accordingly, primate-specific TUs are consistent with de novo insertions, not sequence divergence.

The selection criteria were stringent, and the team expects many more primate-specific genes to be ultimately identified. But already, the report should startle darwinists, because the studied genes have no credible darwinian source. For darwinism, their unlikely sudden appearance is a virtual miracle. Is anyone paying attention?

Meanwhile, the result is consistent with our prediction: If a new genetic program arrives by the strong panspermia process, intervening species should possess either nearly identical versions of it ...or nothing similar....

12 July 2009
Phobus-Grunt will fly specimens of Earthly life to Mars and back. The specimens will include thale cress, tardigrades, brewer's yeast, the bacterium deinococcus radiodurans, and a variety of microbes found in Siberian permafrost. The round trip is planned to take 34 months. If the Earthly specimens survive after exposure to space for so long, the case for panspermia will be strengthened. The Russian mission will also attempt to return a sample of soil from Mars' moon Phobos. Launch is scheduled for October, 2009.

8 July 2009
Astrobiology XII: Instruments, Methods, and Missions will be held 4-6 August 2009 in San Diego, California, USA. This conference is part of the SPIE Optics + Photonics multidisciplinary technical exhibition and conference. (SPIE is "an international society sponsoring light-based research.") The Astrobiology XII Conference Chairs are Richard B. Hoover of NASA Marshall Space Flight Center, Gilbert V. Levin of Arizona State University and Alexei Yu. Rozanov of the Russian Federation Paleontological Institute. Conference sessions will cover —

• Microfossils and Biomarkers in Meteorites and Ancient Terrestrial Rocks
  
• Instrumentation for Astrobiology
• Mars, Venus, and Astrobiology
• Microbial Extremophiles
• Astrobiology and Planetary Protection

3 July 2009
Sponges don't have a nervous system, or even neurons, but they do have a surprising number of the building blocks that would be needed to put a nervous system together. This sentence comes from one of a series of essays about Charles Darwin, this essay reviewing what is known about the origin of nervous systems in higher animals. For darwinists, the picture is deeply puzzling. "...Some of the key molecular building blocks of neurons predate even the first multicellular organisms."

The genome of one studied species contains the genes for proteins typically found on the receiving side of a synapse. "Yet electron microscope studies have failed to find synapses in sponges." UCSB neuroscientist Kenneth Kosik, who led the study, comments, "Thus, the function of these synaptic scaffolding proteins in a sponge is a mystery...."

But we see a consistent story emerging. Many different studies find that essential genes existed before the evolution on Earth of the features they encode. This order of events is required in cosmic ancestry. Finding genes for neurons in primitive species that lack neurons is an especially telling example.