What'sNEW
We discover hundreds of thousands of regulatory elements that emerged very recently in evolution and are specific to primates and humans, and are not present in other mammals.
— Kyle Kai-How Farh, VP of artificial intelligence at Illumina and coauthor of a new study in Nature.
 "Identification of constrained sequence elements across 239 primate genomes," by L.F.K. Kuderna, J.C. Ulirsch, S. Rashid et al., doi:10.1038/s41586-023-06798-8, Nature, 29 Nov 2023.
"Whole-genome alignment with primates reveals DNA elements conserved in humans" (summary), Nature, 29 Nov 2023.
"Comparison of 239 Primate Genomes Reveals Conserved Regulatory Sequences," by Andrea Anderson, GenomeWeb, 29 Nov 2023; re:
As the burgeoning data from genome sequencing is submitted to
powerful computers, we are sure to encounter surprises. It will help to look with open eyes. Me too.
 New genetic programs...: cosmic ancestry predicts, "...nearly identical versions... or nothing similar...."
| 23 Nov 2023 |
What'sNEW about HGT
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...the potential of horizontal gene transfers in eukaryotes....
"Horizontal acquisition of a DNA ligase improves DNA damage tolerance in eukaryotes," by E. Nicolas, P. Simion, M. Guérineau et al., Nature, 22 Nov 2023.
Viruses... has many examples of HGT across all of life.
Whatever their inconsistencies, all molecular clock estimates published to date indicate that animals began to diversify much earlier than fossils suggest. So wrote Harvard paleontologist Andrew Knoll in 2003. Since then, the issue has not gone away. Now a statistician and a paleobiologist suggest that flawed methodology creates the problem.
"...A Critical Examination of Relaxed Molecular Clock Age Estimates of the Bilaterian Animals and Placental Mammals," by Graham E Budd and Richard P Mann, Systematic Biology, 11 Sep 2023; and commentary:
"Genes are often uninformative for dating species' origins," by Matt Pennell, Nature, 22 Nov 2023.
By cosmic ancestry, genes are always older than their first expression.
Metazoan Genes Older Than Metazoa? and
Genes Older Than Earth? have examples.
| 17 Nov 2023 |
What'sNEW about HGT
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Extracellular vesicles play a much greater role in horizontal gene transfer in the ocean than previously assumed.
"Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space," by D. Lücking, C. Mercier, T. Alarcón-Schumacher et al., ISME Commun., 17 Oct 2023.
"Much more than waste: Tiny vesicles exchange genetic information between cells in the sea," Max Planck Institute for Marine Microbiology (+ScienceDaily), 16 Nov 2023.
10 Mar 2021: local hub for HGT among bacteria, with updated links.
Viruses... mentions transformation, the acquisition of DNA from the environment.
Pseudo-Panspermia gets a fresh endorsement from Cambridge University.
"Can comets deliver prebiotic molecules to rocky exoplanets?" by R.J. Anslow, A. Bonsor and P.B. Rimmer, Proc. R. Soc. A., 15 Nov 2023.
"'Bouncing' comets could deliver building blocks for life to exoplanets," University of Cambridge, 15 Nov 2023.
 Thanks, PhysOrg.com and Google Alerts.
"Cometary Delivery of Organic Molecules to the Early Earth," by Christopher F. Chyba, Paul J. Thomas, Leigh Brookshaw and Carl Sagan, Science, 27 July 1990.
Comets: The Delivery System has an overview and updates since 1998.
...New Questions describes various types of panspermia.
There are about 181,000 annotated exons within the approximately 20,000 known, protein-coding human genes. But "the human genome contains over a million autonomous exons" (including the annotated, coding ones.) They were identified using the 3' and 5' splice sites which characterize them.
These findings reinforce speculation that much of the "dark matter" transcriptome may be a by-product, or even an expected component, of the regulation of known genes, as well as a source of novel genetic entities. If the extra exons contain potentially useful genetic programming, with no evidence of neo-darwinian trial-and-error, cosmic ancestry gains implicit support.
The human genome contains over a million autonomous exons, by Nicholas Stepankiw, Ally W H Yang and Timothy R Hughes, Genome Res., published in advance, 09 Nov 2023.
Human Genome Search describes a discontinued research project with relevant discussion and updates.
Robust Software Management is even more impressive if it can handle this much complexity.
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With the failure of these many efforts science was left in the somewhat embarrassing position of having to postulate theories of living organisms which it could not demonstrate. After having chided the theologian for his reliance on myth and miracle, science found itself in the unenviable position of having the create a mythology of its own: namely the assumption that what, after long effort, could not be proved to take place had, in truth, taken place in the primeval past.
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Loren Eisley (1907-1977) was a respected anthropologist, ecologist and essayist. He drew deep satisfaction and wonder from the majesty of life, describing it in rich, resonant prose. When his collection of fourteen essays, The Immense Journey, was published in 1957, it became a surprise bestseller. The above quotation appears in the final one, "The Secret of Life." Another one, excerpted next, is titled "The Flow of the River."
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...more delicate, elusive , quicker than fins in water, is that mysterious principle known as "organization," which leaves all other mysteries concerned with life stale and insignificant by comparison. For that without organization life does not persist is obvious. Yes this organization itself is not strictly the product of life, nor of selection. Like some dark and passing shadow within matter, it cups out the eyes' small windows or spaces the notes of a meadowlark's song in the interior of a mottled egg. That principle—I am beginning to suspect—was there before the living in the deeps of water.
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The Immense Journey: An Imaginative Naturalist Explores the Mysteries of Man and Nature, by Loren Eisley, 1957.
Dr. Richard Hoover, astrobiologist and former NASA astrophysicist, will give a lecture about his journey in science and discoveries along the way. This event is free and open to the public at the U.S. Space & Rocket Center's Discovery Theater, Huntsville AL, 2PM, Sunday, 12 Nov 2023.
...Microfossils in a Carbonaceous Meteorite includes a list of Hoover's collected articles.
Is it safe to bring samples of Mars to Earth? Some say no.
"Searching for life on Mars isn't worth the risk to Earth," by Paul Marks, New Scientist, 01 Nov 2023.
07 Nov 2023: NASA vs ICAMSR from Barry DiGregorio.
Life on Mars! has more.
| 06 Nov 2023 |
What'sNEW about HGT
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When and where did COVID-19 first infect people? A comprehensive review of this issue, looking at archived samples from around the world, indicates that human infections became widespread earlier and more rapidly than previously known. For example, in mid-November 2019, SARS-CoV-2 RNA suddenly spiked and remained high in the sewage of Florianópolis, Brazil (graph). Blood and tissue samples from France, Italy and the US Northwest tell a similar story. So the evidence is clear that the virus was circulating both in China and internationally by November 2019 at the latest. We can also say with strong confidence that it was not circulating prior to July 2019, and it may not have been around before October 2019....
"The Evidence COVID-19 Was Spreading Around the World in Late 2019," by Will Jones, Brownstone Institute, 02 Jan 2023. (Brownstone Institute has an advocacy agenda, but the data are unchallenged.)
Where did the coronavirus that caused the pandemic come from? The rapid worldwide detection indicates that it was spread by global winds, not strictly by personal contact. And remember, there was an airburst high over Northeast China, 11 Oct 2019 – likely the remains of a spent comet whose orbit Earth was crossing. These facts make cometary panspermia hard to dismiss as a possible source for the virus. Immunologist and panspermia affiliate Ted Steele comments:
"Dear Will,..." by Ted Steele, local docx, 08 Jan 2023.
Origin of new emergent Coronavirus and Candida fungal diseases—Terrestrial or cosmic?, by Edward J Steele et al., doi:10.1016/bs.adgen.2020.04.002, Adv Genet, 14 Jul 2020.
"Brilliant Midnight Fireball Lights Up Sky Over Northeast China" by Tariq Malik, Space.com, 13 Oct 2019.
27 Feb 2020: How has Coronavirus spread?
07 Feb 2018: More than 800 million viruses per square meter per day descend from the high atmosphere....
Influenza from Space? Many related updates follow an exchange in The Guardian, 2000.
Viruses... has a primer and updates.
Mounting evidence indicates that there may be multiple ways to sustain liquid-water oceans over billions of years. Tides and radioactivity are the best known ways, but Saturn's tiny moon Enceladus, whose surface features active geysers (pictured), may need more. A new review about nearby moons with likely oceans has history, insights and speculations:
"These Moons Are Dark and Frozen. So How Can They Have Oceans?" by Robin George Andrews,
Quanta Magazine, publicised 03 Nov 2023.
Meanwhile, Geysers on Earth host life with extreme survival capabilities. "The fact that life can grow on Earth in those particular conditions tells us something about the biological potential" in places like Enceladus, Europa or even Mars, according to astrobiologist Alfonso Davila.
"Old Faithful Is Boiling, Smelly and the Perfect Home for These Living Things," by Sarah Derouin,
The New York Times, 27 Oct 2023.
Life on Europa, Other Moons, Other Planets? and Earth-analogs for those environments has related links.
Bacteria: The Space Colonists discusses their hardiness and versatility.
And another proposal: Here, we integrate basic ecological and evolutionary concepts with chemical reaction network dynamics to provide a conceptual model for primordial evolution in spatially structured chemical ecosystems and the subsequent adaptive emergence of cellular individuation and genetic encoding.
"The ecology-evolution continuum and the origin of life," by David A. Baum et al., J. R. Soc. Interface, Nov 2023.
Another new understanding of evolution comes from non-biologists. It begins, ...a new approach to understanding and quantifying selection is necessary. I notice the reluctant acknowledgment that the consensus theory of evolution doesn't work — that should be the headline. But, since anti-scientific creationists would also welcome that announcement, quieter is better. And the opening must be immediately filled. Hence, "Assembly Theory." ...By reimagining the concept of matter within assembly spaces, AT provides a powerful interface between physics and biology.
"How purposeless physics underlies purposeful life," Nature, 04 Oct 2023; re:
"Assembly theory explains and quantifies selection and evolution," by A. Sharma, D. Czégel, M. Lachmann et al., Nature, 04 Oct 2023.
A new law of evolution is proposed by an interdisciplinary team including geochemist Robert Hazen of the Carnegie Institution for Science. We ...propose a time-asymmetric law that states that the functional information of a system will increase over time when subjected to selection for function(s). ...we propose a 'law of increasing functional information.' The PNAS paper was supported by research grants from the Templeton Foundation, NASA and Carnegie. Information theorist Stuart Kauffman was among those reviewing early drafts. Under "Results," the team makes clear that the new law pertains to everything including life. It's getting a lot of notice.
"Scientists and philosophers identify nature's missing evolutionary law," Carnegie Institution, 16 Oct 2023; and:
"Nature's missing evolutionary law identified," Cornell University, 16 Oct 2023; re:
"On the roles of function and selection in evolving systems," by Michael L. Wong et al., PNAS, 16 Oct 2023.
If the new law is valid, it should have testable consequences. We wonder if this team would be willing to subject its theory, as it pertains to biology or computer models, to scientific testing. We will ask.
The Evolution Prize..., 2006, was one proposed test for theories of evolution.
The Second Law of Thermodynamics has related discussion.
The RNA World... has related discussion.
23 Oct 2023: email to co-author Jonathan Linune, cc to Robert Hazen.
George Church: Prove it.
"Panspermia," 3,700 words by Balazs Bradak of Kobe University, edited by Pamela Weintraub, Aeon, 17 Oct 2023.
Thanks, Ted Steele, who rightly notices that the article "fails to give proper scientific accreditation and priority for the work of Sir Fred Holye and Professor N Chandra Wickramasinghe...." He has asked them to correct the oversight. (Aeon acknowledges the communication, 26 Oct 2023.)
Hoyle and Wickramasinghe's Analysis of Interstellar Dust has history.
| 20 Oct 2023 |
What'sNEW about HGT
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"Massive horizontal gene transfer and the evolution of nematomorph-driven behavioral manipulation of mantids," by Tappei Mishina et al., Cur. Biol., 19 Oct 2023.
"Stolen genes allow parasitic control of behavior," Riken, 20 Oct 2023.
Thanks, Google Alerts.
The activities of transposable elements are no longer perceived as peripheral ...but as deeply integrated into the physiology, development and evolution of species.
"Transposable elements:
McClintock's legacy revisited," by Cédric Feschotte,
NRG | local pdf, 18 Sep 2023.
 Chandra Wickramasinghe talks about life-related chemistry on Bennu and other bodies, interviewed by Mayank Chhaya, posted on YouTube, 14 Oct 2023
"NASA's Bennu Asteroid Sample Contains Carbon, Water," by Abbey A. Donaldson, NASA, 11 Oct 2023.
"NASA Unveils First Glimpse of 'Scientific Treasure' Collected From Asteroid," by Kenneth Chang, The NewYork Times, 11 Oct 2023. ...all life on Earth uses only one of the two mirror forms of amino acids and other complex organic molecules. If Bennu contains more of the mirror form used by life,... what could that possibly mean?
Amino Acid Asymmetry in the Murchison Meteorite! has a suggestion.
We can only detect laterally acquired genes that are retained until the present. Those detected therefore likely represent the tip of the iceberg....
"Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage," by Pauline Raimondeau et al., New Phytologist, 04 Oct 2023.
"...grasses take evolutionary shortcut by borrowing genes from their neighbours," by Alice Fletcher, University of Sheffield +EurekAlert!, 02 Oct 2023.
Viruses... has a primer and very many updates about HGT.
The finding ...could suggest that the Kuiper belt either extends much farther than once thought or ...that a "second" belt exists. When the New Horizons spacecraft went past the assumed limit of the Kuiper belt, the count from the dust detector did not fall off as expeeted. Meanwhile, a dozen larger objects lying beyond that distance have been discovered using the ground-based Subaru Telescope (red orbits in illustration). They're likely comets, too.
"Puzzling objects found far beyond Neptune hint at second Kuiper belt," by Paul Voosen, Science, 03 Oct 2023.
Comets: The Delivery System has history and updates.
| 02 Oct 2023 |
What'sNEW about HGT
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Viruses by Marilyn Roossinck is the best primer about them you are likely to find. The variety of viruses, in form and genetic system and capacity, is much more than most people realize. Roossinck pays attention to their effects on animals and plants; many individual species of viruses are featured in illustrated two-page chapters with territory world maps. Also discussed are vaccination, innate and acquired immunity, mosquitoes, control of host behavior, the Spanish flu, pioneering researchers like Rosalind Franklin and more. I especially like the colorful illustrations and charts on almost every page. Suitable for your coffee table!
Roossinck well knows that most viruses cause no harm, and that viruses are often endogenized. She even comments, "About 30% of the protein adaptations that make us human have been shaped by the viruses that infected our ancestors." She knows that viruses are everywhere, they are easily transferred, and the vast majority of them are completely unknown. But she makes no extrapolation from these facts, and her chapters on evolution are strictly conventional.
From my cosmic ancestry perspective, the implications are overwhelming. Given the ubiquity of viruses, we animals and plants must get new exposure every day. That gives macroevolution a ready and credible mechanism. I am susprised that mishaps like birth defects and disease aren't even more frequent. How do our systems safely cope with that genetic traffic? And what potential would lie in the vast store of unknown genes that viruses carry?
Viruses: A Natural History by Marilyn J. Roossinck, Princeton University Press, 02 May 2023.
Viruses... has my own learning curve. Roossinck has a much fuller story.
07 Feb 2018: Every day, more than 800 million viruses are deposited per square metre....
Robust Software Management suggests that genomes would have systems to cope with genes from viruses.
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