What'sNEW Apr - Jun 2023
"Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses," by Kaiyi Jiang et al., doi:10.1101/2023.06.13.544871, bioRxiv, online 14 Jun 2023.
"Fanzor is a eukaryotic programmable RNA-guided endonuclease," by Makoto Saito et al., doi:10.1038/s41586-023-06356-2, Nature, draft, 28 Jun 2023.
"...CRISPR-like system in animals that can edit the human genome," by Leah Eisenstadt, MIT News, 28 Jun 2023.
"Fanzor: First CRISPR-Like System Found in Eukaryotes," Genetic Engeneering and Biotechnology News, 30 Jun 2023. The new study demonstrates that RNA-guided DNA-cutting mechanisms are present across all kingdoms of life.
Thanks, Google Alerts.
Viruses... points to many examples of HGT to and among eukaryotes.
Robust Software Management in eukaryotes is further exemplified by this gene editing feature.
The mismatch between the apparent ages of genes – compared to the fossils that their expression would have left – is not going away. An international team of Earth scientists have a new theory to reconcile the mismatch, at least with respect to the genes for eukaryotic membrane sterols. Finding "abundant protosteroids in sedimentary rocks of mid-Proterozoic age," they envision a wholly separate eukaryotic phylogeny (illustrated in magenta) prior to the Last Eukaryotic Common Ancestor (LECA). All but one of its branches went extinct, leaving only chemical traces in ancient rocks.
08 Mar 2017: ...simple sterol biosynthesis existed well before the diversification of living eukaryotes....
Metazoan Genes Older Than Metazoa? has examples.
Genes Older Than Earth? has examples.
The Tree of Life has related discussion.
"Detection of phosphates originating from Enceladus's ocean" by Frank Postberg et al., Nature, 14 Jun 2023.
"A 'Soda Ocean' on a Moon of Saturn Has All the Ingredients for Life" by Katrina Miller, NYT, 14 Jun 2023.
"Owen Gingerich, 93, Who Delved Into the Cosmos and Saw God, Dies" [link], The New York Times, 12 Jun 2023.
"... intelligent design" [pdf], by Owen Gingerich, Science & Theology News, Nov 2005.
Gingerich is wrong to dismiss the deep schism between proponents and opponents of the theory of evolution. I agree with ID, the theory of evolution does not begin to explain how life or its genetic programming "originates." But "occasional input" from an immaterial source would undermine science. So I am somewhat relieved that Gingerich admits, "...frankly it lies beyond science to prove the matter one way or the other," although that suggests that the rift will never go away. Cosmic ancestry is a way to repair the theory of evolution. It follows scientific principles wthout insulting Gingerich's belief in a "created cosmos."
PS From Brig: Cosmic ancestry provides "occasional input" by HGT, but it's not immaterial or supernatural.
"Spatial variations in aromatic hydrocarbon emission in a dust-rich galaxy" [link], by J.S. Spilker, K.A. Phadke, M. Aravena et al., doi:10.1038/s41586-023-05998-6, Nature, 05 Jun 2023.
"Webb Space Telescope detects universe's most distant complex organic molecules" [link], by Lois Yoksoulian, University of Illinois at Urbana-Champaign +Phys.org, 05 Jun 2023.
Hoyle and Wickramasinghe's Analysis of Interstellar Dust.
"Genes and evolutionary fates of the amanitin biosynthesis pathway in poisonous mushrooms" [link], by Hong Luo et al., doi:10.1073/pnas.2201113119, PNAS, 09 May 2022.
"Distantly related mushrooms gained the ability to make toxin via horizontal gene transfer" [link], by Bob Yirka, Phys.org, 10 May 2022.
Viruses... points to many examples of HGT to and among eukaryotes.
"Unconceived alternatives and conservatism in science:
the impact of professionalization, peer-review,
and Big Science," by P. Kyle Stanford, doi:10.1007/s11229-015-0856-4, Synthese, 30 Aug 2015.
10 Mar 2021: New genes can be acquired only via HGT....
"JWST spots biggest water plume yet spewing from a moon of Saturn," by Alexandra Witze, Nature, 18 May 2023.
"...Surprisingly Large Plume Jetting From ...Enceladus," Webb Space Telescope, 30 May 2023.
Life on Europa, Other Moons, Other Planets?... has related links.
...Concerted Evolution? A new study shows that duplicated human sequences have undergone accelerated point mutations. Single-nucleotide variant (SNV) density is significantly elevated (60%) in duplicated DNA when compared to unique DNA.... (Red and dark green, respectively, in figure.) The team from The University of Washington School of Medicine and the UC Santa Cruz Genomics Institute estimate, "at least 23% of this increase is due to the action of interlocus gene conversion (IGC) between paralogous sequences that essentially diversify allelic copies through concerted evolution."
Robust Software Management [incomplete] has comments on this capability. RSM would also facilitate macroevolution, by managing the installation (and testing, rejection, mothballing, etc.) of newly acquired programming, which HGT can supply. RSM is well demonstrated in computers.
27 Aug 2019: a striking example of convergent microevolution.
26 Mar 2021: another possible example pertaining to the coronavirus.
Duplication Makes A New Primate Gene? has discussion and links about sub- vs. neo-functionalization.
Why Sexual Reproduction? includes early remarks about Gene Conversion.
Macroevolutionary Progress Redefined... lists examples of macro- and microevolution.
"We used a mutation rate of 7.8×10^-9 mutations per nucleotide position per generation." Sounds promising, and the research is deep. But they never ask the most basic questions. How likely is it that a strand of 1,000 random nucleotides will not be interrupted by a stop codon? About 10^-7. How likely is it that its protein product will be a working member of any of life's 10^12 known protein families. Maybe, with lots of room for variants, something like 10^-40. Unlikely, right? A theory that anticipates de novo genes deserves consideration."Neutral Models of De Novo Gene Emergence Suggest that Gene Evolution has a Preferred Trajectory," by Bharat Ravi Iyengar and Erich Bornberg-Bauer, Molecular Biology and Evolution, doi:10.1093/molbev/msad079, 03 Apr 2023.
...De Novo Genes has background and links.
08 May 2023: Lead author Barat Ravi replies with comments.
"The 'Hurtful' Idea of Scientific Merit," by Jerry Coyne and Anna I. Krylov, WSJ, 28 Apr 2023. Ideology of a different sort infects Coyne himself. Yes, life on Earth has evolved. But Coyne insists that today's theory of evolution is adequate to explain things it can't, like where new genetic programming comes from. He ignores the lack of proof and the doubts of many or most educated adults. He rules out the need for a serious alternative. None of this is unusual, but isn't it also an ideology?
"Scientists discover antibiotic resistance genes in clouds," Newswise, 27 Apr 2023; re:
"Quantification of antibiotic resistance genes (ARGs) in clouds at a mountain site..." [link], by Florent Rossi et al., Science of The Total Environment, 20 Mar 2023.
Now this team has identified a specific recombinase that recognizes target sites for the Starship and facilitates insertion; they call it Captain. They also note that past contributions of HGT may be hard to detect because the clues degrade; HGT may be as important for yeast as it is for bacteria. "...Already implicated in chemical resistance, pathogenicity, and fungal domestication, the study of Starships represents an exciting avenue toward increasing our understanding of how fungi rapidly evolve numerous traits that impact upon human activities." Taking that avenue would be a breakthrough.
"Starships are active eukaryotic transposable elements mobilized
by a new family of tyrosine recombinases" [link], by Andrew S. Urquhart et al., doi:10.1073/pnas.2214521120, PNAS, 06 Apr 2023. Also see:
Intelligent Design (ID) sees that today's theory of evolution is deeply flawed. I generally agree with their critiques. Now, with informative commentary, a website promoting ID shows unusual interest in Starships and the power of HGT. Could cosmic ancestry at least supply the mechanism ID lacks? That would be a breakthrough!"Starship Enterprise: Fungal Transposons Boldly Go" [link], by David Coppedge, Evolution News, 26 Apr 2023. It's time for eukaryotes like us to look at our transposons anew.
Thanks, Google Alerts.
Evolution vs. Creationism has comments and links about ID.
...A Third Alternative (2003) has related discussion.
29 Apr 2023: my email to an anonymous proponent of ID: Common ground?
"...our data indicate that bacterial S41 peptidase genes have been acquired at least three independent times during eukaryotic evolution, including one instance that gave rise to vertebrate IRBP [interphotoreceptor retinoid-binding protein] and its unique role in the vertebrate visual cycle.
"Taken together, our work reveals further evidence that bacterial genes provide a rich source of evolutionary novelty, not just to other bacterial species, but to eukaryotes as well....
"...[A]cquisition of foreign genetic material has the potential to punctuate eukaryotic evolution by providing immediate functional novelty."
"Bacterial origin of a key innovation in the evolution of the vertebrate eye" [link], by Chinmay A. Kalluraya, Alexander J. Weitzel, Brian V. Tsu and Matthew D. Daugherty, doi:10.1073/pnas.2214815120, PNAS, 10 Apr 2023.
"Horizontal transfer of vertebrate vision gene IRBP into the chordate ancestor," by Anthony K. Redmond and Aoife McLysaght, PNAS, 14 Aug 2023.
Theorists have wondered, could surprising, complex, emergent behaviour like that somehow produce new instructions that lead to increasingly complex emergent behaviour, without limit? Is that how life evolves? After much investigation ...apparently not. ALife is now pursuing research on multiple fronts, and the optimism of a decade or more ago is now muted. I wish they did not assume (as the article's writer does) that Earthly life is an actual quarantined demonstration. It's time to discard that assumption. Without it, evolution is open to a complete rethink. It needs that."Life Evolves. Can Attempts to Create 'Artificial Life' Evolve, Too?" [link | animation], by Shi En Kim, Scientific American, 06 Apr 2023.
Computer Models of Evolution is the first of six related webpages, including
The Evolution Prize, now dormant. It could return if there's demand.
03 Jun 2021: in email I suggest that human activity may exemplify emergence.
What Is Life? deals with the article's opening question.
"Intelligence as a planetary scale process" [link], by Adam Frank, David Grinspoon and Sara Walker, International Journal of Astrobiology, 07 Feb 2022. What Earth Systems Science took from Gaia Theory was its recognition of the biosphere as a principal driver of planetary evolution....
Gaia has history and updates.
They notice, "viruses contain genetic information that can be transferred on massive scales." Some transfers have contributed significant features and capabilities to earthly life, and our genomes host abundant evidence of past transfers.
Ongoing HGT from viruses presents a puzzle to today's theory of evolution, yet it gets little mention. HGT and the astounding store of unknown genes in viruses could portend a huge paradigm shift. Might those genes affect future life? Could viruses be the primary source for evolutionary innovation? But these astrovirologsts have turned their attention elsewhere, wth much to explore."Astrovirology: how viruses enhance our understanding of life in the Universe" [link], by Gareth Trubl et al., doi:10.1017/S1473550423000058, International Journal of Astrobiology, 05 Apr 2023.
Viruses Drive Evolution: Kenneth M. Stedman et al., Jan 2018.
Viruses and Other Gene Transfer Mechanisms has many examples of viral genes that contribute to evolution.
Cosmology and the Origins of Life by N. Chandra Wickramasinghe, Jayant V. Narlikar and Gensuke Tokoro, Journal of Cosmology, posted 04 Apr 2023. ...the widespread distribution of biologically relevant molecules throughout the Galaxy and beyond is clear. It must come from life.
Life beyond the limits of our planetary system by N. Chandra Wickramasinghe, Journal of Cosmology, posted 04 Apr 2023.
But the puzzle is no less puzzling today. The philosophy that relies on "selfish genes" and sees mostly "junk DNA" can only propose implausible accounting for introns. Introners deepen the mystery.
Introns: a Mystery has an introduction and updates since 1996.
Robust Software Management begins to develop this concept with examples.