What'sNEW Apr - Jun 2022
| 27 Jun 2022 |
What'sNEW about HGT
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Vertical inheritance is foundational to Darwinian evolution, but fails to explain major innovations such as ...the origin of photosynthesis in eukaryotes. Horizontal (or lateral) gene transfer does explain such innovations, as shown in a new analysis. It considers Darwinian proposals and finds them unsupported.
 "Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events" by Auden Cote-L'Heureux, Xyrus X. Maurer-Alcalá and Laura A. Katz, ed. by Cédric Feschotte, PLoS Genet., 22 Jun 2022.
 Thanks, Jim Powers, for a pointer to a related article:
"Adaptive Evolution of C4 Photosynthesis through Recurrent Lateral Gene Transfer" by Auden Pascal-Antoine Christin et al., Current Biology, 06 Mar 2012.
 Viruses and Other Gene Transfer Mechanisms cites many related examples.
Skepticism is foundational to cosmic ancestry. Which major innovations are explained - credibly and adequately - by neo-darwinian evolution?
| 14 Jun 2022 |
What'sNEW about HGT
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...the occurrence of auxiliary metabolic genes indicates that RNA viruses cause reprogramming of diverse host metabolisms, including photosynthesis and carbon cycling....
"Diversity and ecological footprint of Global Ocean RNA viruses" by Guillermo Dominguez-Huerta, Ahmed A. Zayed et al., Science, 09 Jun 2022.
Viruses... has examples of viruses that supply genetic programming to cellular life.
Asteroid Ryugu contains "protein-forming" amino acids, according to the Japanese space agency, JAXA. Its mission to Ryugu returned samples that geochemicists have been examining for a year now. Amino acids are confirmed, but preliminary reports don't say which ones they are. The idea that amino acids from space may contribute to the origin of life on Earth –pseudo-panspermia– is the slant this news is getting. And for edification, today's news release from Okayama University is quite informative about the formation of asteroids and comets.
"...A recent study of the Asteroid Ryugu...." from Okayama University [html | pdf], 10 Jun 2022.
"Building Blocks of Life Were Found on an Asteroid..." by Ben Turner, Live Science, 10 Jun 2022.
Thanks, Jacob Navia.
Comets... and
...Interstellar Dust have our slant on organics from space.
More about Ryugu comes from Science and NYT commentary, but no mention of organics.
"Samples returned from the asteroid Ryugu are similar to Ivuna-type carbonaceous meteorites" by Tetsuya Yokoyama, Kazuhide Nagashima et al., Science, 09 Jun 2022; and
"Asteroid Samples May 'Rewrite the Chemistry of the Solar System'" by Kenneth Chang, The New York Times, 09 Jun 2022.
Comet Rendezvous is a related section of "Can The Theory Be Tested?"
I was born in 1939 to a Crown colony of the British Empire which was Ceylon.... Chandra Wickramasinghe talks about his career of discovery in science, and the implications of what he has seen.
 interview with Savithri Rodrigo for Sri Lankan TV, 60-min. YouTube video, online 03 Jun 2022.
interview with Indeewari Amuwatte for Hydepark, 40-min. YouTube video, online 30 May 2022.
Chandra Wickramasinghe has an introductory essay and updates.
| 07 Jun 2022 |
What'sNEW about HGT
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It is predicted that human endogenous retroviruses contributed 9% of the genome, an additional 30% works in coordination with the retroviral elements, and an additional 50% has unknown function.
Since our 20,000 human genes make up less than 2% of the human genome, this is noteworthy. The American Society for Microbiology is taking notice.
"Viruses Inside Us..." by Elise Phillips, ASM journal (+Mirage), 06 Jun 2022.
Thanks Google Alerts.
Viruses... has links to many related examples.
The Origin of Life is an active, well-funded field of research. Two of its recognized experts discuss the very latest developments in a Quanta Magazine podcast. Harvard's Jack Szostak postulates a "cyanide world" that would have preceded the RNA world. Astrobiologist/paleogeneticist Betül Kaçar seeks clues about the first ribosome. Both are optimistic, and the interviewer doesn't ask hard questions.
"How Could Life Evolve From Cyanide?" Steven Strogatz interviews Jack Szostak and Betül Kaçar for Quanta Magazine [transcript], 01 Jun 2022.
The RNA World... has more, including an excerpt from the transcript.
Philosophical evolutionary biologists give the Origin of Life problem a wide-ranging open-access review. Almost every approach is included as they deconstruct the issue by varying constraints along three axes (see figure). Panspermia gets poor treatment and evidence for life elsewhere is discounted. They admit, ...no one has ever observed the spontaneous formation of living matter from nonliving matter.... But they see no reason to doubt that it happens anyway. In answer to the question in the title of the paper, cosmic ancestry endorses "Where does life come from?"
"The Origin of Life: What Is the Question?" by Christophe Malaterre, Cyrille Jeancolas and Philippe Nghe, doi:10.1089/ast.2021.0162, Astrobiology, 25 Apr 2022.
The RNA World... includes history and updates.
What Is Life? has relevant discussion.
George Nickas comments, 25 May 2022.
| 16 May 2022 |
What'sNEW about HGT |
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The gene regulatory network controlling the development of germ cells may have been rewired by endogenous retrovirus (ERV) insertions during hominoid evolution. This suggestion comes from virologists, genomicists and veterinarians using "multiomics" and genomics data, including a comparative transcriptome analysis between humans and macaques. An endogenous retrovirus "fine-tuning" a network regulating germ cells in primates — even humans? That should get our attention!
A hominoid-specific endogenous retrovirus may have rewired the gene regulatory network shared between primordial germ cells and naïve pluripotent cells, by Ito J, Seita Y, Kojima S, Parrish NF, Sasaki K, Sato K, PLoS Genet, e1009846, 12 May 2022.
Viruses... has links to countless examples of HGT advancing eukaryotic evolution.
17 May 2022: My email restates the foundational principle of cosmic ancestry.
Ongoing and Future Missions Should Search for Life As We Know It, says astrobiologist Christopher Carr in an open access article comparing Earth and Mars. Now that Mars' planetary history is roughly apparent, he thinks that chances for an origin of life as we know it were better, for much longer, there. Others have thought likewise.
Resolving the History of Life on Earth by Seeking Life As We Know It on Mars, by Christopher E. Carr, doi:10.1089/ast.2021.0043, Astrobiology, 25 Apr 2022.
...Life may have started on Mars, by Nicole Karlis, Salon, 08 Feb 2021.
I agree wholeheartedly with the bold statement, but for other reasons. By cosmic ancestry, all of life is related. Besides, evidence for our kind of life on Mars is already noteworthy. My main disagreement is with the origin-of-life theorizing. As usual, the hardest part, genetic programming, is ignored.
Life on Mars! describes lots of evidence. Note especially A fossil on Mars....
The RNA World includes discussion and links about the software problem.
| 11 May 2022 |
What'sNEW about HGT
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Instead of evolving to produce poison, some distantly related fungi became toxic through a process called horizontal gene transfer, scientists say.
Genes and evolutionary fates of the amanitin biosynthesis pathway in poisonous mushrooms, by Hong Luo et al., doi:10.1073/pnas.2201113119, PNAS, 09 May 2022.
...Mushrooms Borrowed Toxin From a Mysterious Source, by Veronique Greenwood, The New York Times, 09 May; also Bob Yirka, PhysOrg, 10 May 2022.
Thanks for the full paper and helpful comments, Hong Luo.
Viruses... has links to countless examples of HGT advancing eukaryotic evolution.
Most US kids have caught the coronavirus..., by Smriti Mallapaty, Nature, 05 May 2022.
Darwin's Radio by Greg Bear is full of issues that seem timely today. A worldwide viral epidemic creates panic. A vaccine is quickly developed but public trust is low and the virus persists. Government health agencies respond with heavy-handed measures including quarantine and mandatory treatment. All this in a SciFi novel of 1999.
Other issues in the book relate even more directly to cosmic ancestry. Anthropologists think they find evidence of human speciation in centuries-old human remains. A dormant ancient virus is reactivated by environmental (social?) developments. The virus causes an evolutionary advance in humans. The theory of evolution faces a possible paradigm shift. Maverick scientists can see the way, but the science establishment will not be influenced.
There are fallibile heroes and redeemable villains. The characters and the settings are evocatively described. With plenty of plot, lots of drama and a surprise ending, Darwin's Radio is everything SciFi should be. I was first drawn to it because Greg Bear gave a paper to the American Philosophical Society in 2003, "When Genes Go Walkabout".
Darwin's Radio by Greg Bear, Ballantine / Random House, 1999.
28 Feb 2006 "Can Viruses Make Us Human" references Bear's paper, published Sep 2004.
Mars Sample Return is a proposed mission to return samples from the surface of Mars to Earth. There is a 30-day window for the public to comment, at the first link below:
National Environmental Policy Act; Mars Sample Return Campaign, NASA, 14 Apr 2022.
Mars Sample Return, NASA homepage, with video link.
Thanks, Barry DiGregorio.
Life on Mars! has history.
| 28 Apr 2022 |
What'sNEW about HGT
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Our finding of these extensive [horizontally transferred LINE elements] mediated by parasites provides a mechanism for the rapid and broad taxonomic transmission of genetic elements. A collabortion of mostly Japanese biologists observed that a blood-sucking parasite has transferred a widespread LINE retrotransposon, BovB, between snakes and frogs at least 54 times in the past 85 million years. Whether bacteria, viruses, or whole blood cells from the host carry the retrotransposon is not clear. But the importance of HGT in eukaryotic evolution is clear by now, I hope.
Geography-Dependent Horizontal Gene Transfer from Vertebrate Predators to Their Prey by Chiaki Kambayashi et al., doi:10.1093/molbev/msac052, Molecular Biology and Evolution, 11 Apr 2022.
Frogs have acquired DNA from snakes with the help of parasites by Jake Buehler, New Scientist, 26 Apr 2022.
 30 Oct 2022: Quanta looks at this phenomenon.
Viruses... has links to thousands of examples of HGT affecting evolution.
All 5 of the DNA and RNA nucleobases have now been found in carbonaceous meteorites. Newer techniques enable the identification of trace amounts of cytosine, uracil, and thymine as small as parts per trillion. Finding these components of DNA and RNA in the Murchison, Murray, and Tagish Lake meteorites is promoted as good news for origin-of-life research. They would be ingredients for a pre-biotic soup.
I call that pseudo-panspermia. But the news would also support cosmic ancestry, because life-related and other complex organics from space look like remnants and degradation products of life.
Identifying the wide diversity of extraterrestrial purine and pyrimidine nucleobases in carbonaceous meteorites by Y. Oba, Y. Takano, Y. Furukawa et al., Nature Communications, 26 Apr 2022.
All of life's nucleic acids could have extraterrestrial origins by Anthony King, Chemistry World, 27 Apr 2022.
All of the bases in DNA and RNA have now been found in meteorites by Liz Kruesi, Science News, 26 Apr 2022.
Meteorites ...contain key ingredients for life by Tatyana Woodall, Popular Science, 26 Apr 2022.
Thanks, Walter Klyce, Zach Baker, David Cotton, Ted Steele and Kenneth Augustyn.
08 Sep 2021: NASA says complex molecules are a sign of life.
Hoyle and Wickramasinghe's Analysis of Interstellar Dust has essential background.
Comets: The Delivery System has related discussion.
Amino Acid Asymmetry in the Murchison Meteorite! cites evidence (chirality) not mentioned in the study.
...shallow water may be critical, not only to double ridge formation, but also to Europan ice-shell dynamics, exchange, and ultimately habitability.
Double ridge formation over shallow water sills on Jupiter's moon Europa, by Riley Culberg et al., doi:10.1038/s41467-022-29458-3, Nature Communications, 19 Apr 2022.
Icy Moon Europa May Host Water Near the Surface, by Colin Stuart, Sky & Telescope, 19 Apr 2022.
Life on Europa, Other Moons, Other Planets? and Earth-analogs...
I seldom read science fiction, but the newest one from Becky Chambers caught my attention. In To Be Taught..., four veteran astronauts, bio-enhanced to withstand the hazards of space, travel for 28 years to explore a system of planets that likely bear life. One of the crew on Lawki 6 engagingly tells the story, while Earth gradually fades in memory and priority. Of course, extraterrestrial life is everywhere. In crisis, the explorers seek consensus and usually find it. The book is brief, captivating and thought provoking. I plan to read more from Chambers.
In a postscript she asks, "What, if any, responsibility do science fiction writers have to champion real science?" My thought: at least don't mislead us. In a long discourse about chirality Chambers seems unaware that amino acids from space, if not fully racemic, are always biased toward left-handedness. This implicates life as we know it – Lawki. Her mother, an astrobiologist, could have told her.
To Be Taught, If Fortunate: a Novella, by Becky Chambers, Harper Voyager, Sep 2019.
This means life could have begun as little as 300 million years after Earth formed.
Metabolically diverse primordial microbial communities in Earth's oldest seafloor-hydrothermal jasper, by Dominic Papineau et al., doi:10.1126/sciadv.abm2296, Science Advances, 13 Apr 2022.
Diverse life forms may have evolved earlier than previously thought, University College London, 13 Apr 2022.
Microfossils may be evidence life began 'very quickly'..., The Guardian, 13 Apr 2022.
Life Before 3850 Million Years Ago? has updates about evidence for early life.
The RNA World... has more about the time problem for any origin-of-life.
George Nickas replies with a comment.
...the first database of surface reflection for biota from icy environments to provide a tool for upcoming space- and ground-based telescopes that will search for life in the cosmos.
Color Catalogue of Life in Ice: Surface Biosignatures on Icy Worlds, by Lígia F. Coelho et al., Astrobiology, online 10 Mar 2022.
Life on Europa... has links about icy worlds with intriguing coloring.
17 Apr 2009: life under Antarctic ice colors a glacier there.
Mutations in non-coding regulatory DNA sequences can alter gene expression, organismal phenotype and fitness. This is opening sentence of a study that used high-throughput gene sequencing alongside artificial intelligence to study the regulation of a specific gene in yeast. Only three or four point mutations in the regulator can drastically amplify or reduce the expression of the regulated gene. Apparently, a few regulatory mutations could affect size, survivability, reproductive rate and a full range of phenotypic variables.
The new study is comprehensive and worth studying. But so far, all quarantined experiments in biology or computer models only explore the potential of the genetic programming already installed. None has produced wholly new programming. Until they do, the far-reaching claims of neo-darwinism continue to lack experimental support.
The evolution, evolvability and engineering of gene regulatory DNA, by E.D. Vaishnav, C.G. de Boer, J. Molinet et al., doi:10.1038/s41586-022-04506-6, Nature, 09 Mar 2022. Using our models, we study expression divergence under genetic drift and strong-selection weak-mutation regimes to find that regulatory evolution is rapid and subject to diminishing returns epistasis; that conflicting expression objectives in different environments constrain expression adaptation; and that stabilizing selection on gene expression leads to the moderation of regulatory complexity.
An oracle for gene regulation, by Andreas Wagner, Nature, 17 Mar 2022.
In Real or Artificial Life... includes updates about the best quarantined biological experiments.
10 Mar 2021: artificial intelligence is used to analyze prokaryotic evolution.
The claim is the Tanis creatures were killed and entombed on the actual day a giant asteroid struck Earth ...66 million years ago when the reign of the dinosaurs ended and the rise of mammals began. —
BBC News, 06 Apr 2022.
A team of archaeologists studying the Tanis fossil site in North Dakota for several years has found specimens that are extraordinarily well-preserved. We've got so many details with this site that tell us what happened moment by moment..., says Robert DePalma, the graduate student leading the dig. BBC's publicity promotes a forthcoming 90-minute TV documentary with David Attenborough:
Dinosaurs: The Final Day..., 15 Apr 2022.
Shards of Asteroid That Killed the Dinosaurs May Have Been Found in Fossil Site, by Kenneth Chang, The New York Times, 07 Apr 2022.
Thanks, Carole Deforest.
The same fossil site also made the news three years ago.
The Day the Dinosaurs Died, by Douglas Preston, The New Yorker, 29 Mar 2019.
A seismically induced onshore surge deposit at the KPg boundary, North Dakota, by Robert A. DePalma et al., doi:10.1073/pnas.1817407116, PNAS, 01 Apr 2019. ...fish, densely packed in the deposit, contain ejecta spherules in their gills and were buried by an inland-directed surge....
Astonishment, skepticism greet fossils claimed..., by Colin Barras, Science, 01 Apr 2019.
The methane on Mars, Titan, Enceladus, Pluto, comets and extrasolar planets is likely biological.
The case and context for atmospheric methane as an exoplanet biosignature, by Maggie A. Thompson et al., doi:10.1073/pnas.2117933119 PNAS, 30 Mar 2022; and commentary:
Methane could be the first detectable indication of life beyond Earth, by Tim Stephens, UC Santa Cruz
+PhysOrg.com, 28 Mar 2022.
Thanks, Stan Franklin.
The case for methane as a biosignature stems from its instability in the atmosphere. Because photochemical reactions destroy atmospheric methane, it must be steadily replenished to maintain high levels.
| 05 Apr 2022 |
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Prokaryotes acquire new genetic programming via horizontal gene transfer (HGT). Bacteriophages (viruses) facilitate the process. Physicians and epidemiologists are interested because pathogenic bacteria often become drug-resistant via HGT. New insights now come from a medical team based in Glasgow. They conclude that a common "selfish" mobile genetic element (SaPI), provides additional benefits to their host cells ...promoting the survival of the entire bacterial population, including those that have acquired foreign genetic material. This knowledge could lead to new treatments. And it improves our understanding of bacterial evolution.
Phage-inducible chromosomal islands promote genetic variability by blocking phage reproduction and protecting transductants from phage lysis, by Rodrigo Ibarra-Chávez et al., doi:10.1371/journal.pgen.1010146 PLoS, 28 Mar 2022.
Bacteriophages: New hope in combatting bacterial diseases, Proteon Pharmaceuticals, Poultry World, 04 Apr 2022.
Viruses... has background and links about HGT.
10 Mar 2021: new hub for prokaryotic evolution.
Bacteriophages ...are estimated to be the most abundant biological entities on the planet. ...They are key mediators of horizontal gene transfer (HGT) via transduction.
Did the formation of Earth's solid iron inner core enable life's Cambrian Explosion? New research shows that very hot pressurized iron loses heat and solidifies faster than previously thought. This means that Earth's solid core must be much younger than the planet itself. Meanwhile, sometime between 565 and 535 million years ago, Earth's magnetic field strengthened dramatically. And seismic data, new and old, are clarifying our picture of the planet's inner structure. Maybe the solid core restored the magnetic field, which in turn protected the newly emerging life forms and their environment. Intriguing, with implications for other planets.
"The planet inside", doi:10.1126/science.abq2618 by Paul Voosen, Science, 31 Mar 2022.
Gaia introduces James Lovelock's theory of life and the planet affecting each other.
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