What'sNEW October - December 2013
Alfred S. McEwen et al., "Recurring slope lineae in equatorial regions of Mars" [abstract], doi:10.1038/ngeo2014, p 53-58 v 7, Nature Geoscience, online 10 Dec 2013.
Koonin, a Senior Investigator at NIH and Editor-in-Chief of Biology Direct, sees all the current research and integrates it with existing knowledge to the extent possible. This integration, however, requires major amendments to the prevailing paradigm, and he is blunt about that. "...Our understandng of evolution—and with it the very nature of biology—have forever departed from the prevailing views of the twentieth century that today look rather naïve and somewhat dogmatic" (p x).
Koonin is impressed by "a remarkable contrast between the relative evolutionary stability of individual genes, many of which retain their indentity over hundreds of millions or even billions of years of evolution, and the maleability of composition and architecture of genomes that change orders of magnitude faster" (p 77). Here and elsewhere, he reinforces to us the view that genes could be older than life on Earth. Of course, he does not go that far. Rather, in support of the basic darwinian belief that life can originate, probably on this planet, he is quite inventive. Yet nowhere in the book do we see any credible accounting for new genes. Instead, he mentions only briefly, "...the emergence of a new gene, typically via gene duplication, followed by radical divergence...," with no further elaboration (p 331). Radical divergence erases the details, apparently.
Horizontal Gene Transfer (HGT) is very well known to him. "...Even a gene that is found in all modern cellular life forms might not be inherited from LUCA: Its ubiquity could instead result from an HGT sweep" (p 331). He also classifies viruses as a huge separate "empire" of life that interacts furiously with all cellular life. "...These findings suggest that the Virus World largely 'builds' the genomes of cellular life forms and so shapes the evolution of life in general" (his italics, p 301). Wow, he knows that?
We learned more than ever about the details and varieties of, and difficulties for, the RNA World and other origin-of-life theories. Koonin admits, "The difficulty of the problem cannot be overestimated" (p 329). Yet he is hopeful. How hopeful? "We are even starting to develop scenarios for the origin of cells that may go beyond sheer speculation" (p 401)! His own speculations include a "Many Worlds" construct in which our biological world is vanishingly unlikely — the weak anthropic principle, he says (p 384). Please remind us, why is panspermia considered so outrageous? Nevermind. We were tremendously edified by The Logic of Chance. But also discouraged. Apparently, no amount of difficulty weakens darwinism's faith enough to admit for consideration alternatives like cosmic ancestry.
Eugene V. Koonin, The Logic of Chance: The Nature and Origin of Biological Evolution, ISBN-10: 0-13-254249-8, FT Press, 31 Aug 2011.
Gil Levin, Honorary Professor at The Buckingham Centre for Astrobiology, demands that NASA release evidence of Martian life Under the Freedom of Information Act [pdf | docx], Press Release from BCAB, 14 Dec 2013.
Life on Mars! is the main related CA webpage.
Mars has organics, according to NASA's new analysis of data from the Curiosity Rover. This development reverses the main objection (no organics detected) to the positive results from the life-detecting LR experiments on the Viking landers in 1976-77. May we please reconsider? Perhaps we have already found (dormant microbial) life on Mars.
Richard A. Kerr, "New Results Send Mars Rover on a Quest for Ancient Life" [summary], doi:10.1126/science.342.6164.1300, p 1300-1301 v 342, Science, 13 Dec 2013.
R.J. Worth, Steinn Sigurdsson and Christopher H. House, "Seeding Life on the Moons of the Outer Planets via Lithopanspermia" [abstract | pdf], doi:10.1089/ast.2013.1028, v 13 n 12, Astrobiology, online 5 Dec 2013; and [abstract], arXiv:1311.2558 [astro-ph.EP], 11 Nov 2013.
How Life-Bearing Rocks from the Chicxulub Asteroid Impact must have Spread through the Solar System, The Physics arXiv Blog, 18 Nov 2013.
Life Could Have Hitched a Ride to the Moons of Jupiter and Saturn by Charles Q. Choi, Astrobiology Magazine, 9 Dec 2013.
Dinosaur asteroid 'sent life to Mars' by James Morgan, BBC News, 11 Dec 2013.
Dinosaur-killing asteroid might have sent life to Mars..., CBS News, 11 Dec 2013.
Merci, Jacob Navia, for pointers to the Physics arXiv. Thanks, Bob Sweeney and Google Alerts.
Mars lake 'much like early Earth' by Jonathan Amos, BBC News, San Francisco, 9 Dec 2013.
Ancient Mars lake could have supported life, Curiosity rover shows by Mike Wall, Space.com (+Fox News), 9 Dec 2013.
J. P. Grotzinger et al., "A Habitable Fluvio-Lacustrine Environment at Yellowknife Bay, Gale Crater, Mars"
D. T. Vaniman et al., "Mineralogy of a Mudstone at Yellowknife Bay, Gale Crater, Mars"
S. M. McLennan et al., "Elemental Geochemistry of Sedimentary Rocks at Yellowknife Bay, Gale Crater, Mars," and a press release from Stony Brook University (+Newswise)
D. M. Hassler et al., "Mars' Surface Radiation Environment Measured with the ...Curiosity Rover"
D. W. Ming et al., "Volatile and Organic Compositions of Sedimentary Rocks in Yellowknife Bay, Gale Crater, Mars"
K. A. Farley et al., "In Situ Radiometric and Exposure Age Dating of the Martian Surface," Science, online 9 Dec 2013.
Life on Mars! is a related local webpage. Thanks, Bob Sweeney and Doron Goldberg.
...Europa's choppy ocean looks friendly to life by Nicola Guttridge, NewScientist, 1 Dec 2013.
Life on Europa, Other Moons, Other Planets? has related links.
Earth Evolution: The Intersection of Geology and Biology: an educational poster from the Howard Hughes Medical Institute, 15 Nov 2012.
The topics range widely and his knowledge is deep and up-to-date. Of course, we were disappointed that he showed little interest in panspermia, and instead concentrate[s] on a terrestrial origin of life (p 31). And although his thoughts on evolution are confined to strict darwinism, he is at least aware of the evidence for gene transfer and for genes older than their corresponding phenotypes (p 77-79).
"Gaia" is not listed in the 7-page index, but Catling knows plenty about the evolution of planetary atmospheres, plate tectonics, and other environmental processes that interact and coevolve with life. In fact, he is co-authoring a forthcoming book, Atmospheric Evolution on Inhabited and Lifeless Worlds. We will be especially interested to know his considered thoughts about Titan, with its abundant methane, on which he comments briefly, already, here. Of course life makes methane, and methane has profound Gaian effects.
Today's book begins by asking "What is astrobiology?" Catling answers with some history and some alternative definitions, including his favorite, a branch of science concerned with the study of the origin and evolution of life on Earth and the possible variety of life elsewhere. To anyone interested in these issues, we recommend the book.
David C. Catling, Astrobiology: A Very Short Introduction, ISBN:978-0-19-958645-5, Oxford University Press, Jan 2014.
The analysis considers 71 kinds of TFs and plots their distribution among eukaryotes. The results are entirely about the gain or loss of TFs, or their enrichment in number. By using comparative genomics, we show that plants and animals required richer transcriptional machineries compared with other eukaryotic multicellular lineages. Many TFs look much older than necessary, because they are found in simpler species with no apparent use for them. And for all TFs, too old or not, the term "origin" actually refers to their first appearance, not to any gradual darwinian evolution.
In cosmic ancestry, evolutionary advances follow the installation and deployment of existing genetic programs. In strict darwinian evolution however, genetic programs cannot already exist before deployment. Rather, the deployment and the "origin" of any genetic program must happen concurrently, while natural selection uses trial-and-error to compose the program. We carefully follow the scientific literature to see which scenario is actually observed. Today again, we discern the former scenario, and evidence for darwinian program-composition is conspicuously missing.
Meanwhile, members of the same team observed T-box genes that apparently existed before their deployment. The T-box transcription factors are key players in animal development and they were considered strictly animal-specific. We show that T-box genes have instead an important premetazoan evolutionary history, being present in several nonmetazoan unicellular taxa. More jarring news for strict darwinism. We welcome informed comments.
Alex de Mendoza, Arnau Sebé-Pedrós et al., "Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages" [abstract], doi:10.1073/pnas.1311818110, Proc. Natl. Acad. Sci. USA, online 25 Nov 2013.
Interview: Beyond Darwin: evolvability and the generation of novelty doi:10.1186/1741-7007-11-110, v 11 n 110, BMC Biology, 7 Nov 2013.
Interview: Beyond Darwin: evolvability and the generation of novelty doi:10.1186/1741-7007-11-110, v 11 n 110, BMC Biology, 7 Nov 2013.
After Kepler with Dimitar Sasselov, Søren Meibom, and David Latham (60-min. YouTube video), taken 17 Oct 2013.
Events for the Public, Harvard-Smithsonian Center for Astrophysics.
Paul Davies, "Are We Alone in the Universe?" [html], The New York Times, 18 Nov 2013.
5 November 2013 — a What'sNEW article about evidence for abundant Earth-like planets.
c Thanks, Christine Pulliam, Charlie Newman and Harmon Dunathan.
Newly discovered protist suggests evolutionary answers, questions, Mississippi State University (+Newswise), 13 Nov 2013.
Researchers Discover New Organism, University of Arkansas (+Newswise +PhysOrg.com), 17-18 Sep 2013.
Metazoan Genes Older Than Metazoa? has many examples of genes older than they "should" be.
Macroevolutionary Progress Redefined... is a related local webpage.
We suggest that organic material can survive capture and [interplanetary] transport in products of extreme impact processing....
Kieren Torres Howard et al., "Biomass preservation in impact melt ejecta" [abstract], doi:10.1038/ngeo1996, Nature Geoscience, 10 Nov 2013.
Meteor impact trapped ancient swamp plants in glass by Lisa Grossman, New Scientist, 11 Nov 2013.
Thanks, Martin Langford; and Gabriel Manzotti, who writes, "ALIEN hitch-hikers could be riding across the solar system in chariots of glass."
Erik A. Petigura, Andrew W. Howard and Geoffrey W. Marcy, "Prevalence of Earth-size planets orbiting Sun-like stars", doi:10.1073/pnas.1319909110, PNAS , online 4 Nov 2013.
Bioinformaticians from Columbia University and Stanford have employed algebraic topology to model the evolution of certain viruses. The resulting, multi-dimensional figures are not at all like darwinian trees. We note that horizontal evolution is a basic prediction of cosmic ancestry.
Joseph Minhow Chan, Gunnar Carlsson and Raul Rabadan, "Topology of viral evolution" [abstract], doi:10.1073/pnas.1313480110, Proc. Natl. Acad. Sci. USA, online 29 Oct 2013.
http://www.vz.ru/news/2013/10/29/657174.html, original Russian news release by Maxim Semenov, and
Google Translate's English version, 29 Oct 2013.
We are pleased that Eigen sees inventive evolution and the origin-of-life as closely related problems, both beset by the software issue. For that he prefers the term "information," and often qualifies it with "meaning," so he deals head-on with the topic of our interest. A substantial portion of the book is about entropy and the second law of thermodynamics, including how evolution and the origin-of-life may get around [the logical analog of] this law — again, perfect for us. He acknowledges the difficulties: "At this stage it suffices to conclude that a closed and formal system cannot generate any information that is not inherent in its algorithms..." (p 285). And immediately he notices that the biosphere is not closed. But he means that it is open to energy and matter, not genetic programs as cosmic ancestry requires. His ultimate affirmative solution is too subtle for us to grasp.
At the 5th Annual Conference on Bioastronomy in Capri, Italy, in 1996, I met Manfred Eigen. Following his paper there on the same themes, I asked a question: Can he name any convincing example in which substantial new encoded programming has been self-generated within a closed system? He reacted with hostility: "What does that have to do with what we are discussing here?" I was completely surprised and abashed by his reaction. I did not then know that only a creationist would dare to ask such a question, and creationists are always treated with contempt. I meekly rephrased and he replied, but his reply provided no satisfaction — nor any convincing example. None in the new book either. I wonder if he would be interested in the challenge of the "Evolution Prize" that we promoted in 2006.
Twenty years ago, Eigen believed the origin-of-life required "proteins first." Now he has switched allegiance to the RNA World. Apparently, he thinks the hardware problem is better solved that way. For cosmology, Eigen accepts the big bang, but he acknowledges variants of the theory that would allow life from the eternal past. We wish he would let himself entertain that possibility.
The book is full of anecdotes and references to other 20th century scientists, most of whom he knows personally. Our disagreements aside, it's a very readable, informed, probing, exhaustive discussion of issues related to the origin of life. And he plans a sequel of five more chapters. Wow.Manfred Eigen, From Strange Simplicity to Complex Familiarity: A Treatise on Matter, Information, Life and Thought, ISBN-13: 9780198570219, Oxford Unversity Press [publsher's promo], 18 Jul 2013.
The RNA World... references Eigen's earlier "proteins first" position.
The Second Law of Thermodynamics, Can Computers Mimic Darwinian Evolution? and the "Next" pages, including
The Evolution Prize... are related local webpages.
Manfred Eigen (1927-2019) by Georgina Ferry, Nature, 28 Feb 2019.
...Christner managed to revive several different types of bacteria from near the bottom of the Guliya ice cap on the Qinghan-Tibetan plateau in Western China – ice that is 750,000 years old.
Markus Dieser, John R. Battista and Brent C. Christner, "Double-strand DNA break repair at -15°C" [abstract], doi:10.1128/AEM.02845-13, Applied and Environmental Microbiology, online 27 Sep 2013.
Prof. W.M. Napier defends Chandra Wickramasinghe against blogger Phil Plait in an open letter [docx | pdf], 25 Sep 2013.
Matthew Z. DeMaere et al., "High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake" [abstract], doi:10.1073/pnas.1307090110, Proc. Natl. Acad. Sci. USA, online 30 Sep 2013.