What'sNEW Jan - Apr 2020
Luisi cares about the philosophy underlying the research and has much to say about topics like contingency vs. necessity, the role of religion, the definition of life, autopoiesis, synthetic biology, and minimal life. The Subject index contains about 400 entries, including one for panspermia.
"The hardware" is the title of Chapter 2. This makes us hopeful that the software problem will get equal treatment. Indeed, Luisi frequently mentions the difficulty of creating or finding long-enough, properly sequenced chains of amino-acids and nucleotides. But nothing more in the 11 chapters. Naturally, a biochemist will know the hardware better. And perhaps there's nothing more to say about the software anyway, we suggest.
This book is a big resource: 37 pages of references, c. 300 entries in the Names index, and – our favorite – a 15-page Appendix of open questions. Luisi is convinced that life originated on Earth, but every chapter mentions difficulties and unknowns. He is a thoughtful, probing, skeptical origin-of-life scientist. We wish he would take a closer look at cosmic ancestry.The Emergence of Life: From Chemical Origins to Synthetic Biology, Second Edition, by Pier Luigi Luisi, 478 pages, Cambridge University Press, 2016 [ToC with Summaries]. Thanks for your help, Katrina Halliday.
The RNA World: and Other Origin-of-Life Theories has background and updated links.
Computer Models of Evolution discusses the software problem.
Replicase activity is the first essential property of life, he observes. RNA polymers of 100 nucleotides or so exhibit this activity, but ones of only 40-60 nucleotides may exist. Even if so, forming a continuous RNA strand only that long is a problem. It's difficult because the nucleotides tend to aggregate. The formation or one or two long-enough polymers (just the structure, regardless of sequence) he calls an abiogenesis event. After mathematical analysis, he concludes, ...the expected number of abiogenesis events is much smaller than unity when we observe a star, a galaxy, or even the whole observable universe. But if this entire universe is larger than the observable one by a factor of 10^78 or so, then, long-enough RNA polymers become likely somewhere within it. That's how an abiogenesis event is possible.Emergence of life in an inflationary universe (Open Access), by Tomonori Totani, Scientific Reports, 03 Feb 2020.
The RNA World: and Other Origin-of-Life Theories has background and updated links.
The End and the Big Bang has brief discussion related to multiple universes. Thanks, Theodore Rigley.
Dr. Ted Steele Talks by George Howard, Cosmic Tusk, 16 Apr 2020.
17-19 Apr: Chandra Wickramasinghe: atmospheric transmission | Ted Steele: sequencing and testing | Reg Gorczynski: widespread exposure | Brig Klyce: mutations; and 24 Apr 2020: more from Gorczynski on Italy.
Evolutionary biologist Brandon Ogbunugafor quotes this passage in a thoughtful, open-access review. He especially appreciates what Maynard Smith's article "can teach us about the art of constructing useful and subversive analogies" (subversive?). Now, fifty years later, functional proteins look more like sentences with forty-letter words, and evolutionary theorists no longer depend on point mutations except for optimization within narrow ranges.
Maynard Smith also wrote about major transitions in evolution. These would require, to sustain the analogy, whole new sentences, paragraphs, chapters and volumes. Nowadays, evolutionary theorists take words and sentences as given, and rely on fortunate acquisitions and rearrangements of them for the new paragraphs and chapters. This scenario is appealing, but to many it is implausible, or certainly incomplete. In any case, today's dawinism suffers from a glaring lack of experimental support for its most important claims. Even a computer model, in principle, could demonstrate these claims, but that's also lacking.
Before long, the commemoration praises Maynard Smith for his "unambiguous rebuttal" of creationism/intelligent design (the subversives?). And gridlock still paralyzes evolutionary theory. There must be another way.A Reflection on 50 Years of John Maynard Smith's 'Protein Space' (Open Access), by C. Brandon Ogbunugafor, doi:10.1534/genetics.119.302764, Genetics, 01 Apr 2020.
Neo-Darwinism... is our main related webpage, with discussion and links about fitness landscapes.
The Evolution Prize confronts the lack of evidence. Evolution vs Creationism elaborates on the gridlock.
The general theme is that genetic programs already in existence get rearranged to produce macroevolutionary advances. Thus, what may look miraculous is actually rather simple; only some easy assembly is required.
We welcome his observation that many genetic programs come from viruses. Nowhere does Shubin suggest that selection pressure caused any program to be invented on a blank slate — hooray! And we were intrigued to know that William Bateson coined the term genetics, before the word gene was in use. The book is full of delight like that.
"Nothing, of course, begins at the time you think it did," wrote playwright Lillian Hellman. It is Shubin's favorite sentence, because it captures the point that genetic programs were already available before each macroevolutionary advance. And we agree, they were. But Shubin somehow believes the story is now complete. He is not surprised if, for example, hundreds of genes, all required for placental birth, were acquired at different times from viruses, and properly coordinated and deployed,. The new capability was enabled simply "by a change of function," as Darwin wrote. Luckily, programming for the new function was there all along.
This looks miraculous to us. Genetic programming that precedes its own deployment needs a source such as cosmic ancestry. Without that, for just an enjoyable, edifying, up-to-date history of the consensus Darwinian theory of evolution, Shubin's book is excellent.Some Assembly Required: Decoding Four Billion Years of Life, from Ancient Fossils to DNA by Neil Shubin, ISBN 9781101871331, Pantheon Books, 17 Mar 2020. Neo-Darwinism... is our related webpage with updated links.
Viruses are part of evolution, Chandra Wickramasinghe interviewed by Predrag Slijepcevic (+Cosmic Tusk), 08 Apr 2020. The entire sequence of the Coronavirus Genome, with explanation and illustrations by Jonathan Corum and Carl Zimmer, The New York Times, 03 Apr 2020.
Thanks, Nature Briefing. Viruses... has a primer and updates.
Deep microbial proliferation at the basalt interface in 33.5-104 million-year-old oceanic crust by Yohey Suzuki et al., doi:10.1038/s42003-020-0860-1, Communications Biology (Open Access), 02 Apr 2020.
...researchers have discovered living cells inside exceedingly old, cold oceanic crust in the middle of the South Pacific. It isn't yet clear how these new microbes are managing to survive–and yet, there seem to more than a million times more of them, for the same volume of rock, than in the younger crust.
Bizarre life-forms found thriving in ancient rocks beneath the seafloor by Robin George Andrews, National Geographic, 02 Apr 2020.
Bacteria in rock deep under sea inspire new search for life on Mars, MarsDaily, 03 Apr 2020.
Thanks, Ronnie McGhee and Stan Franklin.
Life on Mars! has history and updates. Bacteria... has more about their hardiness.
SSoCIA 2020: conference webpage, The Society for Social and Conceptual Issues in Astrobiology.
Hemolithin: a Meteoritic Protein containing Iron and Lithium by Malcolm. W. McGeoch, Sergei Dikler, Julie E. M. McGeoch, arXiv, 22 Feb 2020.
Protein discovered inside a meteorite by Bob Yirka, Phys.org, 03 Mar 2020. ...alien protein inside a meteorite? by Leah Crane, NewScientist, 03 Mar 2020.
Comets: The Delivery System has a primer and updates.
Thanks, Martin Langford, Jerry Chancellor and Stan Franklin.
James Powers has reservations about this report, 07 Mar 2020.
Limited Archaean continental emergence reflected in an early Archaean 18O-enriched ocean by Benjamin W. Johnson and Boswell A. Wing, Nature Geoscience, 02 Mar 2020. Gaia is related.
Interestingly, the flu often seems to come from China — Hong Kong Flu, Asian Flu, and now COVID-19. Hoyle and Wickramasinghe had an intriguing hypothesis to explain this. Viral particles landing as cometary dust from above the atmosphere could take a year or more to drift down to Earth's surface. Wind turbulence can speed this up. The jetstream is obligated to bounce high in the stratosphere over the Himalayas, Earth's tallest mountain range. Downwind, the jetstream would descend over the plain of China. There viral particles from space would likely first make landfall. Fred Hoyle and Chandra Wickramasinghe, Diseases from Space [5Mb local PDF], J.M. Dent and Sons Ltd., 1979.
Fred Hoyle, Chandra Wickramasinghe and John Watkins, Viruses from Space [5Mb local PDF], University College Cardiff Press, 1986. Viruses... is related.
07 Feb 2018: Every day, more than 800 million viruses...
04 Feb 2020: more from Wickramasinghe, Steele et al.
Greg Irwin comments; discussion ensues, 29 Feb 2019.
Coronavirus tracking website with data, maps, updated several times per day, by Avi Schiffmann.
Discovery on Vera Rubin Ridge - Trace Fossils on Mars? [Kindle version at Amazon], by Barry E. DiGregorio, 07 Feb 2020. Life on Mars! has background and more.
Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes by Nikolaos Vakirlis, Anne-Ruxandra Carvunis and Aoife McLysaght, eLife, 18 Feb 2020.
We have long advocated HGT for supplying all "new" genes. If these remain dormant for many generations and an HGT source is not apparent, instead they will be designated de novo, provenance unknown. But if, as supposed, such genes are ancestrally present without HGT, in DNA that was never-deployed in the new role, yet is now somehow ready for optimizing selection, we have a question: Where does the programming come from? Regarding the few orphans that these geneticists think may have gradually, completely diverged from unrecognizable predecessors ...same question.
An attempt to answer our question also comes from these researchers and their affiliates. Overall, our results support an experiential model for de novo gene birth whereby a fraction of incipient proto-genes can subsequently mature and, as adaptive changes engender novel selected effects, progressively become established in genomes in a species-specific manner (see illustration). However, ...while emerging sequences show no evidence of encoding a useful protein product in the present state of the organism, they have the potential to do so in the future. ...We are standing by.
We are pleased that orphan genes are increasingly recognized for their ubiquity and importance. And we welcome the close scrutiny of gradual divergence. We think its power is limited to microevolution.Genes from scratch - far more common and important than we thought, Trinity College Dublin (+PhysOrg.com), 17 Feb 2020, and New and Maybe Important, Genome Web, 19 Feb 2020.
Where Do New Genes Come From? by Viviane Callier, Quanta, 09 Apr 2020.
Viruses... is all about HGT. 04 Jan 2016 and 21 Aug 2016 are postings about de novo genes.
Three New Human Genes... cites McLysaght on de novo genes, with updates since 2009.
...Finding Life Is Space's Final Frontier by Brad King, The Wall Street Journal, 07 Feb 2020.
The Coronavirus May Have Come From Space by N.C. Wickramasinghe and E.J. Steele, viXra, 06 Feb 2020.
Coronavirus latest: infections in China pass 20,000, Nature News, 04 Feb, updated until 22 Apr 2020.
Influenza from Space?, first posted Jan 2000, has related discussion and updates.
Antioxident genes before oxygen are consistent with cosmic ancestry, in which genes always come first.
Metazoan Genes Older Than Metazoa? and Genes Older Than Earth? have many more examples.
What if the Universe has no end? (lots from Penrose), by Patchen Barss, BBCNews, 19 Jan 2020.
The End and the Big Bang and The Beginning have related discussion and updated links.
Our Cosmic Ancestry in the Stars: The Panspermia Revolution and the Origins of Humanity, by Chandra Wickramasinghe, Kamala Wickramasinghe and Gensuke Tokoro, Bear & Company, 14 May 2019.
Chandra Wickramasinghe has a background essay and updated links.
Methanogenic Archaea Can Produce Methane in Deliquescence-Driven Mars by Deborah Maus et al., Scientific Reports, 08 Jan 2020. Life on Mars! has links about methane there. Thanks, Theodore Rigley.
Bet 44: our original posting at Long Bets, now part of The Long Now Foundation.
...I only want to draw attention to an important test that the standard theory [of evolution] has not yet met.