What'sNEW July - September 2014
L. Ilsedore Cleeves et al., "The ancient heritage of water ice in the solar system" [abstract], doi:10.1126/science.1258055, p 1590-1593 v 345, Science, 26 Sep 2014.
Earth has water older than the Sun by Elizabeth Gibney, Nature News, 26 Sep 2014.
Arnaud Belloche et al., "Detection of a branched alkyl molecule in the interstellar medium: iso-propyl cyanide" [abstract], doi:10.1126/science.1256678, p 1584-1587 v 345, Science, 26 Sep 2014.
The Singapore team noted, "Of the ASC base pairs, 99.7% were noncoding, suggesting that novel anthropoid functional elements were overwhelmingly cis-regulatory." The importance of reguatory changes is already well-known, but this high fraction is still surprising.
They also observed, "Unexpectedly, transposable elements (TEs) contributed to >56% of ASCs...." We are not surprised by this, because, in cosmic ancestry, genetic elements that are imported, multiplied, relocated and tested, like TEs, are essential for evolutionary advances.
The most interesting part, to us however, goes unremarked by the Singapore research team. Consider the regulatory ASCs that enable the major advances, in anthropoid vision and nervous systems, for example. Many of them are present in non-primates as well. But there they are unconstrained — not in use. Why is programming for those anthropoid-specific features there at all?
Genetic programs that are available before they are deployed confound strict darwinism and confirm cosmic ancestry.
Ricardo C.H. del Rosario, Nirmala Arul Rayan and Shyam Prabhakar, "Noncoding origins of anthropoid traits and a new null model of transposon functionalization" [Open Access abstract], doi:10.1101/gr.168963.113, Genome Res., online 20 Jul 2014.
Rosetta comet lander gets a touch-down site by Elizabeth Gibney, Nature News, 15 Sep 2014.
Comet Rendezvous is a related section of the local webpage, "Can the Theory Be Tested?
...A quantitative assessment of the contributions of vertical inheritance and HGT [Horizontal Gene Transfer] to the evolution of prokaryotes based on the topological comparison of thousands of phylogenetic trees suggested that nearly two-third of evolutionary events originate from HGT. Furthermore, evidence has been presented that HGT rather than gene duplication is the principal contributor to the evolution of gene families in prokaryotes.
...Some groups appear to have vast, "open" supergenomes.
The analysis of prokaryotic genome dynamics described here unequivocally shows that rapid gene flux involving extensive loss of genes and families, partially balanced by gain of new gene families via HGT, is the principal mode of microbial evolution. Indeed, the estimated rates of gene family gain and loss in some groups of bacteria are such that multiple genes appear to come and go over the time required for a single nucleotide substitution to occur in an evolving gene.
Given that the great majority (typically, around 90%) of nucleotide substitutions in evolving microbial genomes are silent and even among those that affect protein sequences, many are effectively neutral, it seems indisputable that the rapid gene flux is the most important route of change in prokaryotic evolution. Notably, the present results show substantially greater rates of gene family loss and gain compared to family contraction and expansion rates. Thus, the gene flux is not only rapid and extensive but often leads to qualitative changes in the gene repertoires. In general terms, these results emphasize that prokaryotic evolution is largely driven not by small variations, such as single nucleotide substitutions, but by much more dramatic changes brought about by HGT and gene loss.
These words come from a new article by five recognized experts at NIH who conducted a comprehensive analysis of the genome dynamics in 35 groups ...of closely related microbial genomes. To us these observations reaffirm the case for a complete paradigm shift in the theory of evolution — for prokaryotes. No longer is the neo-darwinian process of mutation-and-selection expected to account for much: ...Extreme divergence of duplicated genes that could lead to the appearance of a new family is highly unlikely on the short evolutionary scale of an ATGC [Alignable Tight Genome Cluster]. Clearly, the mainstream account of new genetic programs among prokaryotes is awash. The apparent new source is HGT. But this paradigm shift is not getting the attention it deserves.
We expect a corresponding paradigm shift — for evolution among eukaryotes — also to emerge. There, too, the evidence favoring HGT is overwhelming and the paucity of evidence for neo-darwinan creation of new genes is scandalous. Meanwhile, in cosmic ancestry, HGT is the expected source for new genes.
Pere Puigbò, Alexander E Lobkovsky, David M Kristensen, Yuri I Wolf, Eugene V Koonin, "Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes" [Open Access abstract | pdf], doi:10.1186/s12915-014-0066-4, 12:66, BMC Biology, 21 Aug 2014.
The Plait Affair...: Wiliam Napier defends Wickramasinghe on The Cosmic Tusk, accessed 10 Sep 2014.
Life on Europa, Other Moons, Other Planets? has related links. Thanks, Larry Klaes via facebook.
Life on Europa, Other Moons, Other Planets? has related links.
Lateral gene transfer is now recognized to be much more extensive and widespread than it was previously assumed to be; occurring in most orders and often among them.
Scientists find traces of sea plankton on ISS surface, ITAR-TASS News Agency, 19 Aug 2014.
'We're ALL aliens': ...plankton on the ISS is proof that life on Earth came from outer space, Daily Mail Online, 21 Aug 2014.
Microbial life found living on the exterior of the International Space Station, say reports, The Independent, 21 Aug 2014.
Thanks, Richard Hoover and Chandra Wickramasinghe, for comments with links, 20 Aug 2014.
Life in Space? Crew Members Return to Earth With Marine Plankton, Sputnik News, 11 Nov 2014.
Richard Hoover and Gil Levin respond to several well-credentialed critics concerning the evidence for fossilized microbial life in meteorites, life on Mars and panspermia. A comment from Chandra Wickramasinghe is included, 9-14 Aug 2014.
...Our in silico results suggest that the known underground repertoire of E. coli enzymes can substantially increase the range of utilizable carbon sources available to this organism.... We speculate that the contribution of underground metabolism to adaptation to new environments might be even more pronounced in eukaryotes, where metabolic network expansion by means of horizontal gene transfer has a less prevalent role compared with bacteria.
The analysts are puzzled to note that the studied "underground reactions" apparently have not been exploited so far. They guess that the environments where the reactions might be helpful have simply not been encountered. And they found "no evidence" that the unexploited reactions might be harmful, lest that might be supressing their expression. They do not ask how the helpful catalysts might have evolved by darwinian trial-and-error if there were no trials. But for several hundred, only-beneficial catalysts, isn't that an obvious question?
In cosmic ancestry, all genetic programs are very old, and they must be installed, virtually complete, before they can be activated for testing and, if deployed, optimization. We think this analysis of underground reactions supports our view.
Richard A. Notebaart, Balázs Szappanos, Bálint Kintses et al., "Network-level architecture and the evolutionary potential of underground metabolism"
[Open Access abstract], doi: 10.1073/pnas.1406102111, p 11762Ė11767 v 111, Proc. Natl. Acad. Sci. USA, 12 Aug 2014.
We also suggest that this study may further explain the 2008 announcement that cloned, quarantined E. coli had evolved aerobic citrate metabolism. Links about that long-running experiment are at Lenski et al. on the webpage "In Real or Artificial Life, Is Evolutionary Progress in a Closed System Possible?"
CORRECTION, 18 Aug: In this posting we ask "how the helpful catalysts might have evolved by darwinian trial-and-error if there were no trials." We mistakenly thought that the underground reactions were encoded by DNA strands different from the ones encoding the primary catalysts (as in common examples of subfunctionalization following gene duplication.) No. The underground reactions in this in silico analysis are, in most cases, among the capabilities of the primary catalysts, which were expressed. However, all of these reactions are confined to narrow ranges, close to the primary activity, in our observation. An occasional apparent exception is not sufficient to generalize this phenomenon as broadly as darwinists do. If the phenomenon were so broadly capable, it should be be possible to demonstrate in quarantined experiments. So far it isn't. Of course, we regret our misunderstanding.
Rosetta craft makes historic comet rendezvous by Elizabeth Gibney, doi:10.1038/nature.2014.15681, Nature News, 6 Aug 2014.
Rosetta's Rendezvous, Astronomy Picture of the Day's version of ESA's photo, 7 Aug 2014.
Comets: The Delivery System is a related CA webpage.
Comet Rendezvous is the related section of the CA webpage, "Can the Theory Be Tested?".
Thanks, Bill Smith, for the comparison with Mt. Baker, the ESA link, and commentary, 7 Aug.
Erik Fischer et al., "Experimental evidence for the formation of liquid saline water on Mars" [abstract], doi:10.1002/2014GL060302, p 4456-4462 v 41, Geophysical Research Letters, 16 Jul 2014.
"Recipe for liquid water on Mars" [html], doi:10.1038/511008b, p 8 v 511, Nature, 3 Jul 2014.
Life On Mars! is the main related CA webpage.
Tracing mankindís fascination with our origins and purpose: Chandra Wickramasinghe delivers the Ray Wijewardene Memorial Lecture in Colombo, Sri Lanka, 31 Jul, by Smriti Daniel, Sunday Times, 4 Aug 2014.
When Worlds Collide by Nalaka Gunawardene, Ceylon Today, 8 Aug 2014.
Chandra Wickramasinghe has a related essay and links. Thanks, Robert Cobb.
Spotlight Live: The Hunt for Other Worlds Heats Up: a panel discusion with astronomers who specialize in extrasolar planets, c. 36 min., The Kavili Foundation, 9 Jul 2014. Thanks, Newswise.
The Third Way: evolution in the era of genomics and epigenomics, accessed 10 Jul 2014.
Comparing Darwinism..., Evolution versus Creationism, ...A Third Alternative and a 2011 pdf are related local webpages. Thanks, Stan Franklin and Bob Sweeney.
When Life Went Global by Johnny Bontemps, Astrobiology Magazine (+PhysOrg.com), 7 Jul 2014.
Introduction... and Gaia are related CA webpages. Thanks, Stan Franklin.
These words come from a 2010 essay, by Nigel Goldenfeld (pictured) and Carl Woese, that argues for a new, physics-based perspective on biology. We think their dissatisfaction with the Modern Synthesis — its very foundation is questionable — is not overstated. We note that one problem they highlight, the speed of evolution, is easily solved with horizontal gene transfer (HGT).
Nigel Goldenfeld and Carl Woese, "Life is physics: evolution as a collective phenomenon far from equilibrium" [abstract | pdf], arXiv:1011.4125 [q-bio.PE], 18 Nov 2010. Their reference for the example of recipient-controlled HGT is:
Goldenfeld and Woese also comment: Experiments on digital oganisms are an accurate and informative methodology for understanding the process of evolution because the entire phylogenetic history of a population can be tracked, something that is much more difficult–but not impossible–to do with natural organisms. Experiments on digital organisms can be performed over time scales relevant for evolution, and can capture universal aspects of evolutionary processes.... If the physics-based perspective is to prove fruitful, evidence might first appear in digital experiments. We will continue to watch for that. The essay is well-written and thought-provoking.
Computer Models of Evolution is the first of several CA webpages related to "experiments on digital organisms".
Maxime Bruto et al., "Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes" [abstract], doi:10.1098/rspb.2014.0848, n 1789 v 281, Proc. R. Soc. B, 22 Aug (online 2 Jul) 2014.