January '23 What'sNEW Sep - Dec 2022
The ribosome is a big molecular machine that assembles proteins within cells. At its heart is the Peptidyl Transferase Center, where amino acid residues are connected, one-by-one. At a crucial step, the inner chamber of the PTC (illustrated) rotates 180 degrees to carry its tiny cargo forward. This by itself is amazing.
The current literature review is focused on the nature of the extant PTC and its proposed ancestor, the proto-ribosome, with 14 pages of illustrated text and 275 references. It observes that that some parts of the ribosome are able to retain function independently. Important metal ions may have been even more important earlier. Some RNA nucleotides may be substituted without harm (see left). They elaborate:
"In one study on yeast ribosomes, the rRNA mutations involving universally or highly conserved bases in the PTC region resulted in subtle structural rearrangements. However, these changes had a minimal effect on the overall translational accuracy, aminoacyl-tRNA binding, or PTC activity. Thus, the extant PTC rRNA could accommodate a certain level of plasticity without affecting the overall PTC function. Such plasticity could well be attributed to the functional groups and likely be a clue to its functionally generalized pasts. ...Overall, the structural organization of the extant PTC is characterized by a property defined as an "induced-fit mechanism" (conformational change). ...Such a mechanism, in turn, is thought to confer an extraordinary ability to the ribosome to handle substrates of various sizes."
For a proposed historical reconstruction of evolution at the molecular level, this is as good as it gets. But there is room for doubt about the whole line of research. Even the suggestions from these world experts are gappy and speculative. At this rate, the RNA World seems unlikely to explain the origin-of-life in this century. I suspect George Fox would agree.
I think a more fruitful question is "Where does life come from?" Methodical pursuit of this question makes panspermia a viable possibility. The Houston research team is fully aware of panspermia and many of its implications, but they pay insufficient attention to their own observation quoted first above. Maybe life was there all along,"The Peptidyl Transferase Center: a Window to the Past," by Madhan R. Tirumalai, Mario Rivas, Quyen Tran and George E. Fox, doi:10.1128/MMBR.00104-21, Microbiology and Molecular Biology Reviews, Dec 2022.
George Fox, Department of Biology and Biochemistry, University of Houston.
29 Dec: Fox replies, "Although the PTC might appear to be from an RNA World I think most of us think there was an RNA-peptide world Very early."
The RNA World and Other Origin-of-Life Theories has history and updates.
Testing Darwinism versus Cosmic Ancestry has relevant discussion.
Viruses and Other Gene Transfer Mechanisms has updates with thousands of examples of HGT.
The writers consider a wide range of issues, often referencing quantitative analysis. Comets, hardy bacteria, various technologies, planetary protection, life detection and ethical questions all come under discussion. Well worth reading. Among the other articles, several deal directly with the recent interstellar visitor, 'Oumuamua. Another article (reviewed yesterday) gives a concise history of panspermia.Directed Panspermia Using Interstellar Comets by Christopher P. McKay, Paul C.W. Davies, and Simon P. Worden, Astrobiology, Dec 2022
Astrobiological Implications of Interstellar Material in the Solar System [ToC], special issue of Astrobiology, edited and introduced by Paul C.W. Davies and S. Peter Worden, online 06 Dec 2022.
How is it Possible? includes Cosmic Ancestry's early speculations about comets intentionally seeded with life, and — when a lifeless body becomes exposed — the roles of extremophiles, HGT and Gaia.
Gaia, Bacteria: The Space Colonists and
Comets: The Delivery System are related.
Mitton is not confined by the usual hidden assumptions. For example, he mentions, without dismissing, the logic that leads to life with no origin. He is aware that organics in meteorites may be remnants of biology. He admits that evolution and the origin-of-life have shared difficulties. And he fully acknowledges the contributions of Chandra Wickramasinghe and Fred Hoyle.A Short History of Panspermia from Antiquity Through the Mid-1970s by Simon Mitton, Astrobiology, Dec 2022
Hoyle and Wickramasinghe's Analysis of Interstellar Dust has more about them.
Introduction: More Than Panspermia includes a brief history. Mitton's has much more.
CRISPR tools found in thousands of viruses..., Nature News, 23 Nov 2022.
Viruses and Other Gene Transfer Mechanisms has a primer and many examples of HGT.
Sep - Nov 2022: emails with Adam S. Wilkins.
Virus-derived gene transfer agents benefit host cells by providing templates for DNA repair by Andrew S. Lang, PLoS Biol, 08 Nov 2022; re:
Prophage-like gene transfer agents promote Caulobacter crescentus survival and DNA repair during stationary phase by Kevin Gozzi et L., PLoS Biol, 03 Nov 2022.
10 Mar 2021: New genes can be acquired only via HGT..., affirming HGT among prokaryotes, with links.
Remembering author Kurt Vonnegut, who would have turned 100 on Friday, 7-minute excerpt of interview, Morning Edition, NPR, 11 Nov 2022.
Of course, cosmic ancestry is at odds with the consensus big bang theory, because a beginning from a super-hot single point, with nowhere to hide, would sterilize everything. Fortunately, Peebles also wonders what the universe was doing before it was expanding, and says that we have no coherent theory of the "beginning" of the universe. Good.
I was pleased to learn that Mach's challenging skepticism had lasting influence, and to learn more about Einstein's path to General Relativity. George Gamow's role in the development of today's cosmology was bigger than I knew. Fred Hoyle's multiple contributions are acknowledged and explained. Cosmology is a collaborative enterprise, and Peebles knows who contributed what, and when.
Peebles has a lot to observe about how science advances. Some discoveries come almost simultaneously from different scientists, "Merton's multiples," he names them. Some ideas are originally accepted for their elegance and simplicity. Some insights are simply "in the air." Major breakthroughs usually come from "small science," whose papers have only a few authors.
The examples come from cosmology, but the book is largely about the logic and philosophy of science in general. I also think about that subject, with examples from a different field, evolution. The contrast is striking:
While cosmologists may work independently, they heed others and notice evidence from any source that may be relevant. If an anomaly arises, it is investigated. Resolving differences is an unstated, obvious goal. And the assumptions underlying the whole enterprise are not exempt from scrutiny. This freedom keeps the subject healthy and lively. By comparison, today's theory of evolution is ridgidly blindered, gridlocked.
Peebles writes "a 'persuasive case' [applies] to theories that pass enough tests of prediction to persuade the community to accept the theory...." By that criterion, the Modern Synthesis (including EES, etc.) is obviously not persuasive. Its defenders respond that the unpersuaded are not members of the "community."
"At the heart of the science wars is surely the difficulty of communication between different cultures with different traditions," Peebles says, referring to conflict with "anti-science." A skeptical alternative such as cosmic ancestry is not "anti-science," but mainstream biology frames all skepticism that way. "The mismatch makes fertile ground for misunderstandings," Peebles concludes. These words come from a distinguished scientist who well understands the practice of science. Highly recommended.The Whole Truth: A Cosmologist s Reflections on the Search for Objective Reality by P. J. E. Peebles, Princeton University Press, 02 Aug 2022.
21 Nov 2019: comments from an interview with James Peebles.
The End and the Big Bang includes evidence inconsistent with a hot big bang from a single point.
Multiple Horizontal Acquisitions of Plant Genes in the Whitefly Bemisia tabaci by Clément Gilbert and Florian Maumus, Genome Biology and Evolution, Oct 2022.
26 Mar 2021: more about transferred whitefly genes.
Viruses and Other Gene Transfer Mechanisms has a primer and many updates with examples.
Weldon, Bateson, and the origins of genetics: Reflections on the unraveling and rebuilding of a scientific community by Lea K. Davis, PLoS Gen, 27 Oct 2022.
How Genes Can Leap From Snakes to Frogs in Madagascar by Veronique Greenwood, Quanta, 27 Oct 2022.
28 Apr 2022: about the original study of retroposons transferred from snakes to frogs.
Viruses... cites more than 2,000 examples of HGT, including every gene category.
Thanks, Google Alerts and Adam S. Wilkins. Adam, please notice also:
Scientists Catch Jumping Genes Rewiring Genomes, by Max Kozlov, Quanta, 12 May 2021.
Surface waves and crustal structure on Mars by Doyeon Kim et al., and
Largest recent impact craters on Mars: Orbital imaging and surface seismic co-investigation by L. V. Posiolova et al., Science, 27 Oct 2022.
...It Came From Space. by Kenneth Chang, The New York Times, 27 Oct 2022.
Thanks, Rob Cooper. Life on Mars!, cites various, noteworthy evidence.
Effects of Desiccation and Freezing on Microbial Ionizing Radiation Survivability... by William H. Horne et al., Astrobiology, online 25 Oct 2022. Desiccation and freezing greatly increased radiation survival....
Bacteria..., and Life on Mars!, have background and updated information.
Thanks, Google Alerts and George Nickas.
New research suggests that the membrane protecting the spore stores electrical energy as a "biological capacitor," accumulating and integrating signals from the environment while the spore is chemically inert. Upon reaching a threshold, the capacitor triggers Germination and the cell resumes normal life. Of course, this would be crucial for panspermia.
...short nutrient pulses result in step-like changes in the electrochemical potential of persistent spores. During dormancy, spores thus gradually release their stored electrochemical potential to integrate extracellular information over time. It would be hard to invent a neo-darwinian explanation for the programming underlying this capability.Electrochemical potential enables dormant spores to integrate environmental signals by Kaito Kikuchi et al., Science, 06 Oct 2022.
An electric alarm clock for spores by Jonathan Lombardino and Briana M. Burton, Science, 06 Oct 2022.
...How Dormant Bacteria Calculate Their Return to Life, UC San Diego (+Newswise), 06 Oct 2022.
Bacteria: The Space Colonists has background and updates about their hardiness.
Robust Software Management begins with a brief discussion of endospores.
Sep 2022: Raju Pookottil, a member of "The Third Way of evolution," reacts to cosmic ancestry.
Jun-Sep 2022: My side of a conversation with biochemist and molecular biologist James A. Shapiro (excerpt below).
Metabolic novelty originating from horizontal gene transfer is essential for leaf beetle survival by Roy Kirsch et al., doi:10.1073/pnas.2205857119, PNAS, 26 Sep 2022. Also, a stinkbug benefits from cross-kingdom HGT. It seems to be everywhere.
A new antimicrobial peptide, Pentatomicin, from the stinkbug Plautia stali, by Yudai Nishide et al., Nature, 04 Oct 2022. Notably, orthologous sequences were also detected from a horseshoe crab, cyanobacteria and proteobacteria, suggesting the possibility of inter-domain horizontal gene transfers of Pentatomicin and allied protein genes.
Viruses... cites more than 2,000 examples of HGT, crossing all kingdoms.