What'sNEW
20 November 2008
Life has a role in the origin of minerals according to geophysicist Robert Hazen of the Carnegie Institution. Thousands of minerals can form only in special environments that are produced only by life. Many of them, like azurite and malachite, require an oxygen-rich atmosphere. Of the approximately 4,300 known mineral species on Earth, perhaps two thirds of them are biologically mediated. This is principally a consequence of our oxygen-rich atmosphere, which is a product of photosynthesis by microscopic algae according to a new report Hazen's team.
Some of these minerals from living environments can persist unchanged for billions of years, providing a way to detect very ancient life. We wonder, are any life-influenced minerals to be found in meteorites? We hope this question is not overlooked.
Robert Hazen et al., "Mineral evolution" [abstract.pdf], p 1693-1720 v 93, American Mineralogist, Nov-Dec 2008.
Mineral kingdom has co-evolved with life, Carnegie Institution of Washington, 13 Nov 2008. [
Robert Hazen interview.mov]
Earth's Minerals Evolved, Too, by Phil Berardelli, ScienceNOW Daily News, 14 Nov 2008.
Microbes drove Earth's mineral evolution, doi:10.1038/news.2008.1226, by Ashley Yeager, NatureNews, 14 Nov 2008.
Gaia is a related CA webpage.
18 November 2008
...Borrowing a couple of genes.... challenges the notion that higher organisms must rely on their own genes to evolve. These comments follow an investigation asking how a hybrid of the British common groundsel weed (pictured) came to have its large yellow petals (right). The international team determined that the change was initiated when the groundsel's ancestor acquired a cluster of regulatory genes from a Sicilian species introduced some 300 years ago. The transfer likely resulted from cross-pollenation. The biologists write, Our results ...show how gene transfers between species may play an important part in the evolution of key ecological and morphological traits.
These biologists believe that this example is noteworthy because the identity of the transfered genes and their source are unusually well established. This establishment was easier because the events were relatively recent. And that the transferred genes are regulatory ones is well worth knowing. But documented examples of horizontal gene transfers (HGT) — of all sorts, by a variety of means, conferring new traits among eukaryotes — are not rare. These examples sustain a fundamental prediction of cosmic ancestry. The analysis of British groundsel flower petals only adds to this growing body of evidence.
Minsung Kim et al., "Regulatory Genes Control a Key Morphological and Ecological Trait Transferred Between Species" [abstract], doi:10.1126/science.1164371, p 1116-1119 v 322, Science, 14 Nov 2008.
Hey Bud, Spare Some Genes? by Elizabeth Pennisi, ScienceNOW Daily News, 13 Nov 2008.
Viruses and Other Gene Transfer Mechanisms is the main CA webpage about HGT [ What'sNEW about HGT ]
4 November 2008
Only a Theory, by Kenneth R. Miller, springs from the federal trial in 2005, when creationism/ID lost its bid to become part of the public school curriculum in Dover, Pennsylvania. Miller links that case to a "broader assault on scientific reason" that he believes to be underway. But before opening that discussion he must rebut, once again, claims that that Darwinism is not a sufficient scientific explanation of evolution. This rebuttal is what interests us.
As many do, Miller exploits the ambiguous meaning of "evolution." He cites (a) the history of life on Earth [which virtually everyone accepts] and (b) examples of adaptation [or microevolution, which proponents of ID accept] in support of (c) the Darwinian mechanism behind macroevolutionary innovation [which is the main issue, for which a & b are irrelevant]. Fortunately, he also looks more closely at a few examples of Michael Behe's "irreducible complexity."
One of those examples is the evolution of the immune system in jawed vertebrates. For Behe it is too complex to have been composed by Darwinian mutation-and-natural-selection. Miller rebuts Behe by citing studies which ...reached their climax in 2005 when the exact transposon from which the immune system evolved was conclusively identified (p 73). Miller's reference for this climactic identification is an article by a pair of geneticists at the Genetic Research Information Institute in Mountain View CA, published online by PLoS Biology in June 2005. We have now studied that paper. Its abstract states:
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The V(D)J recombination reaction in jawed vertebrates is catalyzed by the RAG1 and RAG2 proteins, which are believed to have emerged approximately 500 million years ago from transposon-encoded proteins. Here we show that the approximately 600-amino acid "core" region of RAG1 required for its catalytic activity is significantly similar to the transposase encoded by DNA transposons that belong to the Transib superfamily. This superfamily was discovered recently based on computational analysis of the fruit fly and African malaria mosquito genomes. Transib transposons also are present in the genomes of sea urchin, yellow fever mosquito, silkworm, dog hookworm, hydra, and soybean rust.... |
Miller thinks the perception of this scenario has elucidated the evolution of this key part of the immune system. (Here again, Miller's "evolution" is ambiguous.) Actually, the scenario affirms that the critical parts of the system were encoded by transposon-related genes that must have already existed in more primitive species lacking this kind of immune system. By some means of gene transfer, the jawed vertebrates acquired the genes. After acquisition, some assembly and optimization followed. But most of these facts have been known since 1998.
In no way does this evidence show that the needed genes incrementally "evolved" by darwinian mutation-and-natural-selection. Instead, the scenario presents a jarring puzzle for darwinism: How could the essence of this genetic program come into being before it could be affected by natural selection? But darwinians ignore these logical gaps, hoping the rest of us will grow weary and welcome a change of subject.
Eventually Miller argues that creationism/ID's alternative for explaining complex genetic programs is not clear. We agree. We think both programs, darwinism and creationism/ID, are flawed. We wish a third alternative such as cosmic ancestry would get consideration.
Kenneth R. Miller, Only a Theory: Evolution and the Battle for America's Soul, ISBN:9780670018833, Penguin Group (USA) Inc., 12 Jun 2008.
Vladimir V. Kapitonov and Jerzy Jurka, "RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons" [article], doi:10.1371/journal.pbio.0030181, v 3 n 6 e181, PLoS Biology, Jun 2005.
Viruses and Other Gene Transfer Mechanisms is the main CA webpage about HGT [ What'sNEW about HGT ]
Evolution versus Creationism is a related CA webpage.
...A Third Alternative, by Klyce and Wickramasinghe is a related CA reprint.
Comparing Darwinism, Creationism/ID and Cosmic Ancestry is a related CA webpage.
Michael Behe's book The Edge of Evolution, is reviewed in What'sNEW, 18 Jun 2007.
Michael Behe testified ...in a lawsuit ...in Dover PA, What'sNEW, 19 Oct 2005.
We owe the repertoire of our immune system to one transposon insertion... 450 million years ago...., What'sNEW, 25 Aug 1998.
30 October 2008
Horizontal transfer (HT) of DNA transposons has apparently produced evolutionary innovation in mammals, according to biologists at the University of Texas, Arlington. This is believed to be the first "unequivocal evidence for the repeated HT of a DNA transposon" into tetrapods, including 5 mammalian orders. The transposon family, named SPACE INVADERS (SPIN), has a spotty distribution pattern among species, unsimilar placement within different genomes, and a very high level of conservation. Together these facts indicate that horizontal transfer is the likeliest means of acquisition.
- "The only plausible scenario is that active and nearly identical SPIN elements were introduced horizontally, and relatively recently, into several tetrapod species and subsequently spawned different waves of SPIN amplification along these species lineages.
- "There is little doubt that SPIN amplification not only added megabases of DNA to the genomes, but it also promoted lineage-specific changes in chromosomal architecture and fueled evolutionary innovation.
- "Despite ...outstanding questions, our data provide evidence that HT has contributed significantly to diversifying and shaping the genomes of mammals and other tetrapods.
- "These findings are startling given the barriers apparently opposing the entry of exogenous DNA into the sequestered germline of animals."
Various other methods of horizontal transfer of genetic material are already known to have important evolutionary effects among eukaryotes. With a striking example, the horizontal transfer of DNA transposons is added to the list.
| This is a remarkable and unexpected finding, because it suggests that the ancestors of these species, some of which occupied different continents, were infiltrated by the same transposon at roughly the same time — Damon Lisch |
Elsewhere we have written, "If a new genetic program arrives by the strong panspermia process, intervening species should possess either nearly identical versions of it ...or nothing similar." The data in this study are consistent with that supposition.
John K. Pace II et al., "Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods" [abstract], doi:10.1073/pnas.0806548105, p 17023-17028 v 105, Proc. Natl. Acad. Sci. USA, 4 Nov (online 20 Oct) 2008.
Damon Lisch, "A new SPIN on horizontal transfer" [extract], doi:10.1073/pnas.0809525105, p 16827-16828 v 105, Proc. Natl. Acad. Sci. USA, 4 Nov (online 30 Oct) 2008.
'Space invader' DNA infiltrated mammalian genomes, by Jessica Griggs, NewScientist.com news service, 20 Oct 2008.
Viruses and Other Gene Transfer Mechanisms is the main CA webpage about HGT [ What'sNEW about HGT ]
New genetic programs in Darwinism and strong panspermia is the CA webpage containing our words quoted just above.
Thanks, Cédric Feschotte, who says, It's like a pandemic, and one that can infect species that weren't genetically or geographically close.
25 October 2008
On Mars, plumes of methane hundreds of kilometres across bloom and dissipate in less than a year. With methane concentrations reaching 60 parts per billion, the volume of methane appearing and vanishing so quickly in these hotspots must come from a powerful source. Apparently, methane on Mars is produced several orders of magnitude faster than previously suspected. Now NASA is asking, could methanogenic bacteria be the source?The analysis of the short-lived plumes comes from a team led by Michael Mumma (pictured), of NASA's Goddard Space Flight Center in Greenbelt, Maryland. It was presented at a meeting of the American Astronomical Society in Ithaca, New York, 11 October.
Plumes of methane identified on Mars, by Eric Hand, NatureNews, 21 Oct 2008.
Life on Mars is a related CA webpage. Search for "methane".
21 October 2008
Hundreds of genes from bacteria are found in diatom genomes. An international team reports —
- Horizontal gene transfer between bacteria and diatoms is pervasive....
- Bacterial genes in diatoms do not appear to be derived from any one specific source, but from a range of origins....
- Many of the genes shared between diatoms and bacteria encode components that are likely to provide novel metabolic capacities, ...novel cell wall components, and to provide unorthodox mechanisms of DNA replication, repair and recombination for a eukaryotic cell.
- We therefore propose that gene transfer from bacteria to diatoms, and perhaps vice versa, has been a common event in marine environments and has been a major driving force during diatom evolution.
Chris Bowler et al., "The Phaeodactylum genome reveals the evolutionary history of diatom genomes" [abstract], doi:10.1038/nature07410, p 239-244 v 456, Nature, 13 Nov (online 15 Oct) 2008.
Ronald P. Kiene, "...Genes in the glass house" [html], doi:10.1038/456179a, p 179-181 v 456, Nature, 13 Nov 2008.
Viruses and Other Gene Transfer Mechanisms is the main CA webpage about HGT [ What'sNEW about HGT ]
20 October 2008
Residue from one of Stanley Miller's experiments in 1953-54 has been found to contain all 20 of life's amino acids. After Miller died in 2007, two of his former students, James Cleaves and Jeffrey Bada, recovered his vials and lab notes and undertook the analysis.
 A: Volcanic plume with lightning. B: The experimental setup that might simulate this environment. C: Amino acids and concentrations detected. |
Miller originally used three different setups for his experiments. The famous classic setup used a spark discharge aparatus. Another setup (see diagram) added a steam aspirator to increase the gas flow rate through the system. None of the three setups produced detectable quantities of more than half of life's 20 amino acids. But with today's state-of-the-art instruments, analysts at the Goddard Astrobiology Analytical lab could detect much lower concentrations than Miller could. In residue from the spark discharge setup with a steam aspirator, all 20 are detectable today.
Miller's origin-of-life experiments were staged in a highly reducing atmosphere, as the early Earth was assumed to possess. That assumption is no longer accepted, a reversal that reduces the impact of the original experiments. But the spark discharge setup with a steam aspirator "possibly simulates the spark discharge synthesis by lightning in a steam-rich volcanic eruption." Such an environment might produce, locally and briefly, the assumed reducing atmosphere. This possibility has led to the new suggestion that life may have gotten its starter ingredients in a lightning-riddled volcanic plume.
Even if life's 20 amino acids could be created in volcanic plumes, tremendous problems would remain for the hardware aspect of the origin-of-life problem. And the seldom-mentioned software aspect of the problem is even more difficult. But speculation continues unabated.
Adam P. Johnson et al., "The Miller Volcanic Spark Discharge Experiment" [abstract], doi:10.1126/science.1161527, p 404 v 322, Science, 17 Oct 2008.
Did Volcanoes Spark Life on Earth?, by Phil Berardelli, ScienceNOW Daily News, 16 Oct 2008.
Volcanoes May Have Provided Sparks and Chemistry for First Life, by Bill Steigerwald, NASA Goddard Space Flight Center, 16 Oct 2008.
Volcanoes May Have Provided Sparks of First Life, Scripps Institution of Oceanography, University of California, San Diego, 16 Oct 2008.
'Lost' Miller-Urey experiment created more of life's building blocks, Indiana University, 16 Oct 2008.
The RNA World is the main CA webpage about origin-of-life theories, with links to more about Miller.
Thanks, Stan Franklin and Newswise.com.
11 October 2008
A short video about pseudo-panspermia from The Learning Channel is online. In three minutes, NASA's Chris McKay, Dave Deamer of the University of California at Santa Cruz, and astrobiologist Christopher Chyba promote the delivery of the ingredients for life to Earth by asteroids or comets. "But what of the blueprint – the recipe...?," the narrator asks. For the software aspect of the origin-of-life, Chyba is appropriately humble: "...An almost overwhelming kind of step."
It Came From Outer Space: Panspermia, Howstuffworks.com, n.d.
Modern Panspermia, a section of CA's webpage Panspermia Asks New Questions, explains pseudo- and other versions of panspermia.
Three YouTube videos about panspermia are linked from What'sNEW, 22 Apr 2008
The RNA World is our main webpage about origin-of-life theories.
Thanks, Google Alerts.
9 October 2008
Three more early works by Fred Hoyle and Chandra Wickramasinghe can now be downloaded in full for free from this website. The PDF pages are scanned images.
Fred Hoyle and Chandra Wickramasinghe, Living Comets, University College Cardiff Press, 1985.
Fred Hoyle, Chandra Wickramasinghe and John Watkins, Viruses from Space, University College Cardiff Press, 1986.
Fred Hoyle and Chandra Wickramasinghe, Space Travellers: The Bringers of Life, University College Cardiff Press, 1981.
Hoyle and Wickramasinghe's Analysis of Interstellar Dust is a related CA webpage with a list of Selected Resources.
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