What'sNEW Jan - Mar 2021
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, 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.
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, Nature briefing.
Convergent Evolution has discussion and related links.
27 Aug 2019: about directed mutation in the Atlantic herring.
More about Orgueil.
...meteorite found in wake of U.K. fireball..., CBS News, 09 Mar 2021.
Thanks, Rob Cooper and Peter Thompson.
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."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.
"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.
"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.
"Perseverance will explore history of ancient lake" [link], by Paul Voosen, Science, 26 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.
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, 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.
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.
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, 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.
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.
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.
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, 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!
"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.
"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.
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.
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.
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.
...Another Important Aspect of Planets That Could Host Life by Michelle Starr, ScienceAlert, 13 Jan 2021.
Thanks, Stan Franklin. The simplified chart tells the story.
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.
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.
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, 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.
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 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.