What'sNEW July–September 2009
29 September 2009
...HGT from multiple sources is shown to be able to generate and optimize novel evolutionary characters in eukaryotes....
Gregory P. Fournier, Jinling Huang and J. Peter Gogarten, "Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life" [abstract], doi:10.1098/rstb.2009.0033, p2229-2239 v364, Phil. Trans. R. Soc. B, 12 Aug 2009.
Viruses and Other Gene Transfer Mechanisms is the main related webpage — What'sNEW about HGT |
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.)
Metazoan Genes Older Than Metazoa? is our main webpage about genes older than the features they encode.
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.
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.
Richard Cordaux and Mark A. Batzer, "The impact of retrotransposons on human genome evolution" [abstract], doi:10.1038/nrg2640, p691-703 v10, Nature Reviews Genetics, Oct 2009. 17 September 2009
Richard Cordaux and Mark A. Batzer, "The impact of retrotransposons on human genome evolution" [abstract], doi:10.1038/nrg2640, p691-703 v10, Nature Reviews Genetics, Oct 2009.
17 September 2009
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.
Takeshi Kawashima et al., "Domain shuffling and the evolution of vertebrates" [abstract], doi:10.1101/gr.087072.108, p1393-1403 v19, Genome Res., Aug 2009. 14 September 2009
Takeshi Kawashima et al., "Domain shuffling and the evolution of vertebrates" [abstract], doi:10.1101/gr.087072.108, p1393-1403 v19, Genome Res., Aug 2009.
14 September 2009
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?
Richard Dawkins, "Man vs. God" [link], p W1-W2, The Wall Street Journal, 12-13 Sep 2009. 4 September 2009 1 September 2009 26 August 2009
Richard Dawkins, "Man vs. God" [link], p W1-W2, The Wall Street Journal, 12-13 Sep 2009.
4 September 2009
1 September 2009
26 August 2009
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."
In the same issue a briefer article, "The Eye," includes an interesting observation: "The basic structure of our eyes is similar in all vertebrates, even lampreys, whose ancestor branched away from ours about 500 million years ago. By that time, therefore, all the basic features of the eye must have already existed...." But this conclusion is not supported by any direct evidence that the basic features of eyes existed then on Earth. It is less speculative to conclude only that the genetic programs for eyes already existed. This conclusion is reinforced by evidence from genomics: the same gene controlling eye development is shared by fruitflies, mice, and squid. Genetic programs that wholly precede the features they encode are confounding for strict darwinism, but required in cosmic ancestry.
David Castelvecchi, "The Eye," p 86 v 301, Scientific American, Sep 2009. 24 August 2009
David Castelvecchi, "The Eye," p 86 v 301, Scientific American, Sep 2009.
24 August 2009
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.
Carl Zimmer, "On the Origin of Eukaryotes" [summary], doi:10.1126/science.325_666, p 666-668 v 325, Science, 7 Aug 2009. 21 August 2009
Carl Zimmer, "On the Origin of Eukaryotes" [summary], doi:10.1126/science.325_666, p 666-668 v 325, Science, 7 Aug 2009.
21 August 2009
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.
James A. Lake, "Evidence for an early prokaryotic endosymbiosis" [abstract], doi:10.1038/nature08183, p 967-971 v 460, Nature, 20 Aug 2009. 18 August 2009
James A. Lake, "Evidence for an early prokaryotic endosymbiosis" [abstract], doi:10.1038/nature08183, p 967-971 v 460, Nature, 20 Aug 2009.
18 August 2009
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....
NASA Researchers Make First Discovery of Life's Building Block in Comet, Bill Steigerwald, NASA Goddard Space Flight Center, 17 Aug 2009. 11 August 2009
Franck Lefèvre and François Forget, "Observed variations of methane on Mars unexplained by known atmospheric chemistry and physics" [abstract], doi:10.1038/nature08228, p 720-723 v 460, Nature, 6 Aug 2009. 30 July 2009 28 July 2009 25 July 2009
NASA Researchers Make First Discovery of Life's Building Block in Comet, Bill Steigerwald, NASA Goddard Space Flight Center, 17 Aug 2009.
11 August 2009
Franck Lefèvre and François Forget, "Observed variations of methane on Mars unexplained by known atmospheric chemistry and physics" [abstract], doi:10.1038/nature08228, p 720-723 v 460, Nature, 6 Aug 2009.
30 July 2009
28 July 2009
25 July 2009
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.
Ilaria Sciamanna et al., "Retrotransposons, reverse transcriptase and the genesis of new genetic information" doi:10.1016/j.gene.2009.07.011, Gene, online 21 July. 23 July 2009
Ilaria Sciamanna et al., "Retrotransposons, reverse transcriptase and the genesis of new genetic information" doi:10.1016/j.gene.2009.07.011, Gene, online 21 July.
23 July 2009
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....
Sen-Kwan Tay et al., "Global discovery of primate-specific genes in the human genome" [abstract], doi:10.1073/pnas.0904569106, p 12019-12024 v 106, Proc. Natl. Acad. Sci. USA, 21 Jul (online 6 Jul) 2009. 21 July 2009 12 July 2009
Robin McKie, "The first Earthling to journey to Mars - Conan the Bacterium" [link], The Observer, London, 12 Jul 2009. 8 July 2009
Sen-Kwan Tay et al., "Global discovery of primate-specific genes in the human genome" [abstract], doi:10.1073/pnas.0904569106, p 12019-12024 v 106, Proc. Natl. Acad. Sci. USA, 21 Jul (online 6 Jul) 2009.
21 July 2009
12 July 2009
Robin McKie, "The first Earthling to journey to Mars - Conan the Bacterium" [link], The Observer, London, 12 Jul 2009.
8 July 2009
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.