ญญWhat'sNEW in Cosmic Ancestry, beginning January 2021

What'sNEW Jan - Mar 2021

26 Mar 2021 What'sNEW about HGT |
Whitefly hijacks a plant gene In cosmic ancestry, horizontal gene transfer (HGT) is the ultimate source for all "new" genes. For prokaryotes, that principle is now well accepted. We believe it applies to eukaryotic life as well. Examples are countless. Here's another one:
Whitefly hijacks a plant detoxification gene that neutralizes plant toxins by Jixing Xia, Zhaojiang Guo, Zezhong Yang et al., Cell, 25 Mar 2021. ...we show that, through an exceptional horizontal gene transfer event, the whitefly has acquired the plant-derived phenolic glucoside malonyltransferase gene BtPMaT1.
First Report of Horizontal Gene Transfer Between Plant and Animal by Emma Yasinski, The Scientist, 25 Mar 2021.
Plant to insect horizontal gene transfer: empowering whiteflies by Louis-Valentin Méteignier et al., TiG, 30 Apr 2021.
Thanks Thanks, Stan Franklin and Nature briefing.
10 Mar 2021: the paradigm shift for prokaryotes looks complete.
Viruses... cites more than 1,500 examples of HGT in all kingdoms.

26 Mar 2021
Convergent Evolution describes the appearance of similar features or systems in unrelated species. Standard theory has difficulty explaining it, although horizontal gene transfer could surely account for some of it. For microevolutionary convergence, an interesting possibility deserves mention — directed mutation. This is the enhanced substitution rate of a few specific nucleotides, apparently prompted by environmental stress, producing positive selection. How this might be managed is not known. For one example, it seems to have enabled many species of Atlantic herring to quickly adapt to redder light in the Baltic Sea. Is directed mutation also active in the new coronavirus? Coronavirus
Mutations in at least eight different positions in the spike protein are simultaneously on the rise around the world....
The Coronavirus Variants Don't Seem to Be Highly Variable So Far by Vaughn Cooper, Scientific American, 24 Mar 2021.
Thanks Thanks, Nature briefing.
Convergent Evolution has discussion and related links.
27 Aug 2019: about directed mutation in the Atlantic herring.

The Orgueil meteorite (Atlas of microfossils)
16 Mar 2021
A new examination of the Orgueil meteorite is published, after a years-long collaboration by biochemists, microbiologists and astrobiologists — seven Russians and one American. The bi-lingual document includes history, new high-definition photographs of microfossils, and detailed analysis of the meteorite's chemistry. The case that the fossils are biological is strong. This is surely the definitive story of Orgueil.

The Orgueil meteorite (Atlas of microfossils) by Alexei Yu. Rozanov, Richard B. Hoover et al., Joint Institute for Nuclear Research, Russia, Oct 2020.
More about Orgueil.

11 Mar 2021
...Meteor over Vermont shook buildings, NASA says, CBS News, 10 Mar 2021.
...meteorite found in wake of U.K. fireball..., CBS News, 09 Mar 2021.
Thanks Thanks, Rob Cooper and Peter Thompson.

10 Mar 2021
There is a basic set of genes shared by almost all prokaryotes, the "core" genome. But far more prokaryotic genes are "singletons," found in only one genome. Not too many land in between. What accounts for this U-shaped distribution?

Experts in biotechnology information have submitted this question to computer modelling. From thousands of bacterial genomes, their graph (shown) has the characteristic shape: almost 4,000 genes were singletons, and 20 genes were shared among almost 2,000 of the genomes. With varying assumptions about the rate of gene gain and loss, and about the size of the available gene pool, their models can produce a similar distribution. Their first assumption: New genes can be acquired only via HGT, whereas other mechanisms, such as duplication followed by divergence and de novo gene birth, are disregarded.

models of prokaryotic pangenome evolution "Assessment of assumptions underlying models of prokaryotic pangenome evolution" [
open-access link] by Itamar Sela, Yuri I. Wolf and Eugene V. Koonin, doi:10.1186/s12915-021-00960-2, BMC Biology, 10 Feb 2021.
15 Oct 2020: HGT can potentiate future adaptation.
18 Dec 2018: Horizontal Gene Transfer (HGT) is the only source....
10 Sep 2014: ...HGT is the principal contributor....
15 Mar 2006: The paradigm for evolution among prokaryotes has shifted.
26 Sep 2005: Common bacteria share an infinite gene pool?
12 Jun 2000: Among bacteria, HGT is "all there is," says Ernst Mayr.

07 Mar 2021
Genes allowing oxygen metabolism were present among bacteria 3.1 billion years ago, according to two biochemists who analyzed 700 of those genes in today's species. The date is surprisingly early, because oxygen became widely available only after the Great Oxygenation Event, 2.4 billion years ago. With neo-darwinian logic, the researchers at the Weizmann Institute of Science conclude that oxygen must have been available for bacterial metabolism already, at the earlier time. Otherwise, without oxygen, the genes would not have evolved.
"The evolution of oxygen-utilizing enzymes suggests early biosphere oxygenation" [
abstract] by Jagoda Jablonska and Dan S. Tawfik, Nature Ecology & Evolution, 25 Feb 2021.
"Life could use oxygen long before it was abundant" [link] by Robert F. Service, Science, 05 Mar 2021.

We think the inference that oxygen was already available is unnecessary. Genes that precede the features they encode are noticed everywhere. In cosmic ancestry, genes always come first.
12 Feb 2021: Everything necessary was already there, a recently described example.
Metazoan Genes Older Than Metazoa? cites hundreds of examples.
Genes Older Than Earth? affirms the early presence of the oxygen-related genes.
Gaia: We think bacterial life arrives with the capability to make an environment suitable for advanced life, and the genetic programming for advanced life is already available.

26 Feb 2021
Probable Impossibilities Is Life Special? In his newest book, Alan Lightman answers, Yes, of course. With welcome highlights from the history of science he explains why we no longer think that life depends on an immaterial vital ingredient. Rather, life is special because "our atoms are arranged in a special way." He doubts that human souls exists independent of matter, although most American adults think otherwise. A universe without life is conceivable, but he thinks it could have no meaning without conscious minds. I align closely with Alan. I wish I could convince him that microbial life or its remains could constitute a non-negligible fraction of interstellar dust.

"Is Life Special?" is the title of just one of 17 brief, rich essays in this book. These range very widely, including, "What Came Before the Big Bang" and "The Ghost House of My Childhood." Lightman is a prolific author who masters science and lyricism equally well. Now he has given us a neat new collection of wisdom and reflections.

He has held a dual faculty appointment in science and the humanities at Harvard and MIT. In 2006, he founded the Harpswell Foundation, which "equips young women in Southeast Asia with leadership skills, education, and a supportive network." Alan is also an Advisory Director of this website's sponsor, and a valued friend.

Probable Impossibilities: Musings on Beginnings and Endings by Alan Lightman, Pantheon, 09 Feb 2021.
"All and Nothing", review by Andrew Crumey, The Wall Street Journal, 13-14 Mar 2021.

Jezero crater landing site
26 Feb 2021
Perseverance's primary mission is to search for evidence of past life.

"Perseverance will explore history of ancient lake" [link], by Paul Voosen, Science, 26 Feb 2021.
Life on Mars! has recent history about the search for life there.
A fossil on Mars... photographed by NASA, 27 Feb 2004.

22 Feb 2021
...over 140,000 virus species in the human gut, half of which are new to science, Wellcome Sanger Institute, 18 Feb 2021.
Infographic: Trans-kingdom Interactions in the Gut by Catherine Offord, The Scientist, 01 Feb 2021.
...phages interact directly with mammalian cells in the gut, too.

21 Feb 2021 What'sNEW about HGT |
DNA transposons promote exon shuffling Where do new genes come from? We think they first come when strands of DNA or RNA, pieces of genetic programming, are acquired by some form of transfer (HGT). After acquisition, the pieces must be properly installed. A recent study probes one example of this mechanism. The pieces are Transposable Elements (TEs).
TEs interacting within their host genome provide the raw material to generate new combinations of functional domains that can be selected upon and incorporated within the hierarchical cellular network. ...Our findings confirm that exon shuffling is a major evolutionary force generating genetic novelty.
"Recurrent evolution of vertebrate transcription factors by transposase capture" [
link], by Rachel L. Cosby et al., doi:10.1126/science.abc6405, Science, 19 Feb 2021; and commentary:
Transposon domain capture may be a common source of new genes and molecular innovation across the tree of life.
"New genes from borrowed parts" [link], by Aaron Wacholder and Anne-Ruxandra Carvunis, doi:10.1126/science.abf8493, Science, 19 Feb 2021.
'Jumping genes' repeatedly form new genes over evolution by Krishna Ramanujan, Cornell University, 19 Feb 2021.
Thanks Thanks, Martin Langford.
Viruses... has links about HGT as the primary source for new genes.

Meanwhile, the standard explanation for new genes is that they gradually diverged from existing genes or even existing "junk". But a very substantial number of genes are "orphans," without identifiable predecessors, or they are "de novo" genes, activated from silent DNA without benefit of mutation-and-selection. Standard darwinism has no good explanation for them. Now, a study concludes that most of them are not produced by divergence.
For a long time, divergence was considered to be the only realistic evolutionary explanation for the origin of new gene families, while de novo emergence has only recently been appreciated as a widespread phenomenon. The persistent presence of orphans and TRGs in almost every genome studied to date despite the growing number of available sequence databases demands an explanation. ...Overall, our findings are consistent with the view that multiple evolutionary processes are responsible for the existence of orphan genes and suggest that, contrary to what has been assumed, divergence is not the predominant one.
"Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes" [link], by Nikolaos Vakirlis, Anne-Ruxandra Carvunis and Aoife McLysaght, doi:10.7554/eLife.53500, eLife 2020;9:e53500, 18 Feb 2021.
"Genetic Novelty: How new genes are born" [link], by Urminder Singh and Eve Syrkin Wurtele, doi:10.7554/eLife.55136, eLife 2020;9:e55136, 19 Feb 2021.

15 Feb 2021
...we are still discovering previously unseen types of sub-ice shelf communities far from open water.
Breaking All the Rules: The First Recorded Hard Substrate Sessile Benthic Community Far Beneath an Antarctic Ice Shelf by Huw J. Griffiths et al., doi:10.3389/fmars.2021.642040, Frontiers in Marine Science, 15 Feb 2021.
Scientists Surprised To Find Life Under Antarctic Ice, WBUR News, 15 Feb 2021.
Life on Europa... has links about life deep under frozen oceans, on Earth and possibly elsewhere.

13 Feb 2021
Dumas et al., 2021 How did the human brain evolve? This question gets deep treatment by three geneticists and brain-specialists in Quebec and France. They looked at the sequences of almost all protein-coding genes in humans, with special attention to the brain-related ones. These they compared to alignable sequences in our primate relatives, including archaic humans, to learn how the genes may have evolved.

Most brain-related genes were seen to be under strong purifying selection. Others, including genes likely to govern brain size, show evidence of positive selection, or excessive non-synonymous nucleotide substitutions. The full, groundbreaking study is available online.

Many major innovations characterize the evolution of life on Earth. Steps leading to the nervous system in primates are among them. Such innovations require lengthy genetic programs. In our view, these programs must originally arrive by some form of gene transfer, which may come soon before, or long before the programs are deployed. Major innovations may be termed "macroevolution."

Microevolution, by contrast, readily comes from nucleotide point substitutions. Plenty of evidence now shows that these mutations may often be under positive selection, and this may even be targeted at specific nucleotides. We do not doubt that microevolution may explore and optimize the potential of innovative programming, after it is installed. Is this how the human brain attained its size?

Systematic detection of brain protein-coding genesunder positive selection during primate evolutionand their roles in cognition by Guillaume Dumas, Simon Malesys and Thomas Bourgeron, doi:10.1101/gr.262113.120, Genome Res., online 13 Jan 2021.
Thanks Thanks, lead author Guillaume Dumas, for affirmative feedback and suggested edits.
Macroevolutionary Progress Redefined... explains how macro- differs from microevolution and suggests that the latter might expand an organ like the brain.

12 Feb 2021
Mature features are detected in an early galaxy [
link], by Julie Wardlow, Science, 12 Feb 2021; re:
A massive stellar bulge in a regularly rotating galaxy 1.2 billion years after the Big Bang [link], doi:10.1126/science.abc1893, by Federico Lelli et al., Science, 12 Feb 2021.
The End... has more about puzzles for the standard big-bang theory.

12 Feb 2021
phylogeny of fish and tetrapods "All these studies tell us that the origin of tetrapods was something waiting to happen," says Borja Esteve-Altava, an evolutionary biologist at Pompeu Fabra University in Barcelona, Spain. Genetically, "Everything necessary was already there" before vertebrates came ashore, nearly 400 million years ago. This excerpt comes in a review of soon-to-be-released articles in Cell. Teams of geneticists have concluded that many genes enabling animals to live on land existed long before they were depolyed. Genetic programs that come before the features they encode surprise darwinism and support cosmic ancestry.

"Genes for life on land evolved earlier in fish" [
link], by Elizabeth Pennisi, Science, 12 Feb 2021.
Kun Wang et al. Xupeng Bi et al., M. Brent Hawkins et al., Cell, online Feb 2020.
Our findings reveal a latent, limb-like pattern ability in fins that is activated by simple genetic perturbation.
Metazoan Genes Older Than Metazoa? and
Genes Older Than Earth? have related discussion and links.

10 Feb 2021 What'sNEW about HGT |
HGT may be the primary means of macroevolution for all of life. Examples are too numerous to count. For another one, Canadian geneticists see evidence that a protein suspected to have an important regulatory role was installed by transposons into many species dozens of times. First, the observation that [a binding protein and the transposon that carries it] are found mainly among a few disparate classes of eukaryotes [including humans and coelacanths] suggests horizontal movement of the transposon between very different branches, even though these classes ...inhabit very different environments.
Coelocanth unchanged Diverse Eukaryotic CGG Binding Proteins Produced by Independent Domestications of hAT Transposons, by Isaac Yellan et al.,
abstract with pdf link, Molecular Biology and Evolution, 09 Feb 2021.
Coelacanth Hasn't Spent 65 Million Years Unchanged After All by Tessa Koumoundouros, ScienceAlert, 10 Feb 2021.
Thanks Thanks, for helpful feedback, lead author Isaac Yellan.
Viruses and Other Gene Transfer Mechanisms
has related links.

It's so much more explanatory to say [life is] spreading all across the universe, and we caught it too, it didn't start here — Gary Ruvkun, astrobiologist and geneticist, Harvard Medical School
...life may have started on Mars by Nicole Karlis, Salon, 08 Feb 2021.
Life on Mars!

07 Feb 2021 What'sNEW about HGT |
...horizontal gene transfer can provide a fast track channel for the evolution of novelty....
"Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer" by Eivind A. B. Undheim and Ronald A. Jenner, doi:10.1038/s41467-021-21093-8,
link, Nat Commun, 05 Feb 2021.
Viruses and Other Gene Transfer Mechanisms has related links.

03 Feb 2021 What'sNEW about HGT |
Our results indicate that as-yet-undiscovered fossils from unknown viruses remain hidden in animal genomes.
"Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome" by Shohei Kojima et al., doi:10.1073/pnas.2010758118,
abstract, PNAS, 02 Feb 2021.
Viruses and Other Gene Transfer Mechanisms has related links.

28 Jan 2021
Life on Venus claim faces strongest challenge yet by Alexandra Witze, Nature, 28 Jan 2021.
Purported phosphine on Venus more likely sulfur dioxide by James Urton, University of Washington +Newswise, 27 Jan 2021.
"Claimed detection of PH3 in the clouds of Venus is consistent with mesospheric SO2" by Andrew P. Lincowski et al., arXiv:2101.09837 [astro-ph.EP], 25 Jan 2021.
"Complications in the ALMA Detection of Phosphine at Venus" by Alex B. Akins et al., arXiv:2101.09831 [astro-ph.EP], 24 Jan 2021.
14 Sep 2020: phosphene reported in Venus' atmosphere.

Meanwhile, veteran astrobiologists propose a framework for estimating the chance of life on Venus.
The Venus Life Equation by Noam R. Izenberg et al., doi:10.1089/ast.2020.2326, Astrobiology, 28 Jan 2021.

23 Jan 2021 What'sNEW about HGT |
Alexander P. Hertle et al., 2021 Whole organelles can transfer between plant cells of different species. The reach of HGT continues to surprise us.
Horizontal genome transfer by cell-to-cell travel of whole organelles by Alexander P. Hertle et al., Science Advances, 01 Jan 2021; and commentary:
Plant Cells Swap Organelles by Abby Olena, The Scientist, 07 Jan 2021.
Plant Cells of Different Species Can Swap Organelles (with video), by Viviane Callier, Quanta, 20 Jan 2021.
Viruses and Other Gene Transfer Mechanisms is our main webpage about HGT, with updates since 1997.

20 Jan 2021
Constructive Neutral Evolution – the hypothesis postulating that molecular mechanisms can evolve in the absence of evolutionary benefits.      Trends in Genetics, Feb 2021.
Where do new genetic programs come from? Now, a newly named phenomenon, Constructive Neutral Evolution, is getting attention.
Functional Long Non-coding RNAs Evolve from Junk Transcripts by Alexander F. Palazzo and Eugene V. Koonin, doi:10.1016/j.cell.2020.09.047, Cell, 25 Nov 2020.
...junk transcripts provide the raw material... for functional innovation with relatively little adaptation involved.
Testing Darwinism... discusses the need for demonstrations.

14 Jan 2021
Orange K-type stars may be better than our sun for hosting living planets. For one thing, they last longer.
...Another Important Aspect of Planets That Could Host Life by Michelle Starr, ScienceAlert, 13 Jan 2021.
Thanks Thanks, Stan Franklin. The simplified chart tells the story.

12 Jan 2021 What'sNEW about HGT |
The role of viruses in evolution is becoming further recognized and explored. Even the eukaryotic nucleus may derive from large DNA viruses — they produce nucleus-like enclosures. Today the suggestion is no longer startling and skepticism is waning. The viruses can readily supply complex genetic programming that is otherwise unexplained.

The eukaryotic system to uncouple transcription from translation is complex and employs hundreds of genes that act in concert. Medusavirus Ancestor in a Proto-Eukaryotic Cell: Updating the Hypothesis for the Viral Origin of the Nucleus by Masaharu Takemura, doi:10.3389/fmicb.2020.571831, Front. Microbiol., 03 Sep 2020.
Evidence supporting a viral origin of the eukaryotic nucleus by Philip J.L. Bell, doi:10.1016/j.virusres.2020.198168, Virus Research, Nov 2020. The eukaryotic system to uncouple transcription from translation is complex and employs hundreds of genes that act in concert.
Did Viruses Create the Nucleus? The Answer May Be Near by Christie Wilcox, Quanta, 25 Nov 2020.
19 Nov 2020, 26 Sep 2019 and 24 Sep 2019: related news.
Viruses... has updates since 1997.

11 Jan 2021
The Milky Way is full of habitable real estate....
The Occurrence of Rocky Habitable Zone Planets Around Solar-Like Stars from Kepler Data, by Steve Bryson et al., arXiv, 05 Nov 2020.
...A new galactic survey holds a clue by Nadia Drake, National Geographic, 02 Nov 2020.

09 Jan 2021
Simon Turner et al., 2021 ...the meteorites must have been exposed to liquid within the past million years. That's the conclusion of an international, interdisciplinary team who noticed "nonequilibrium distributions" of uranium and thorium isotopes in several carbonaceous chondrites. In some instances, water apparently flowed even after the meteorites broke free from their parent bodies. The report doesn't mention it, but their conclusion supports the theory that comets may be wet enough to support life for very long times.
Carbonaceous chondrite meteorites experienced fluid flow within the past million years by Simon Turner et al., Science, 08 Jan 2021.
Meteorites From the Beginning of the Solar System May Have Carried Water Quite Recently by Isaac Schultz, Gizmodo, 09 Jan 2021.
Thanks Thanks, Stan Franklin.

Decades ago, Hoyle and Wickramasinghe proposed a surprising way for radioactive isotopes to keep ice melted inside comets. Their research is wide in scope, mathematical, and deeply probing.
Biological Activity in the Early Solar System in its Outer Reaches by Fred Hoyle and Chandra Wickramasinghe, chapter 7, Living Comets [7Mb pdf], University College Cardiff Press, 1985.
Comets: The Delivery System has discussion, references, and updates since 1998.

04 Jan 2021
Modern Science is uniquely powerful because, in Newton's day, it began to follow the "Iron Rule of Explanation". That's the thesis of The Knowledge Machine by Michael Strevens. The rule, profusely elaborated, dictates what counts as a legitimate move in the game of science. Most of what formerly qualified no longer does. I found Strevens' restrictions as confining as a straight-jacket. Eventually we see that he has misgivings, too! The Knowledge Machine

One manifestation of the Iron Rule is the "Tychonic Principle": the importance of observations with accuracy out to many decimal places. Kepler's use of Tycho's voluminous data exemplifies this principle. So would the careful measurement of the bending of starlight in the solar eclipse of 1919 — in theory at least. But the eclipse data were not very precise. In their interpretation, Eddington's prejudice had a much bigger role than precision. In general, Strevens' contentions — that early science was so primitive, the Scientific Revolution was so abrupt, and science is at last fully objective — seem debatable to me.

While reading the book, I often wanted to raise a hand and ask a question. Sometimes Strevens came around to the issue, but not always. For example, Strevens says that the Iron Rule guarantees consensus, which allows continuity, which he deems important. But sometimes consensus is completely lacking, as in the theory of evolution. How life evolves is one of the most contentious issues in the history of science. I see no consensus there, only crisis. Strevens has studied Thomas Kuhn but seems little persuaded by him.

Thanks to the Iron Rule, Strevens says, "Always there is something that even the most bitter enemies can agree to do next: another test." This is starkly wrong. The schism between Darwinism and Intelligent Design illustrates this. From my third-party perspective, the gridlock is especially obvious.

Still, I quite enjoyed reading The Knowledge Machine. I love knowing more about Aristotle, Francis Bacon, Descartes, Galileo, Newton, Kelvin, D'Arcy Thompson, Whewell and many others, in well-told episodes and colorful vignettes. Strevens' writing is easygoing, his scholarship is very impressive, and his ambivalence about his own Iron Rule is intriguing.

The Knowledge Machine: How Irrationality Created Modern Science, by Michael Strevens, Liveright, 13 Oct 2020.

...the questions that brought me to this topic, however urgent, are sometimes seduced into slumber by the cunning charms of a pressing plot. Analysis, however, is a light sleeper. — Jill Lepore, The Name of War
ps: Strevens prompts me to attempt to restate my own principles for science. In brief: To explain a phenomenon, one must show its material causes. By this criterion the standard big bang, quantum entanglement, and Intelligent Design are unexplained. Furthermore, the material causes must be ones that can be demonstrated. If so, the origin of life and ongoing macroevolutionary progress remain unexplained. To depend on material causes is, frankly, a faith. But if any phenomenon has immaterial causes, it falls outside the scope of science.
The Beginning quotes David Hume on the scope of science.
pps: I once asked Intelligent Design proponent Michae Behe, How does ID work? He admitted that ID's mechanism is unknown. He pointed out that Newton's theory of gravity, likewise, lacked a mechanism. But Newton's theory enabled astronomers to make many useful, precise predictions about the motion of the planets. With that level of demonstration, a material cause is almost assured. (Does quantum entanglement merit similar assurance?)
correspondence with Michael Behe, 12-25 Jun 2013.

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