What'sNEW Jul - Sep 2025
...high rates of organic carbon burial caused by elevated levels of atmospheric carbon dioxide, climate-sensitive phosphorous mineral weathering, and phosphate regeneration from marine sediments can turn warming events into ice ages. ...We need a fresh look into the operation of Earth's thermostats.
 "Instability in the geological regulation of Earth's climate," by Dominik Hülse and Andy Ridgwell, doi:10.1126/science.adh7730 and Editor's Summary, Science, 25 Sep 2025.
It is not something we ever expected to see :o) Andy
 Gaia is the theory about processes that can shape the biosphere for advanced life. They are not immediate. Surprising, wide swings in temperature or sea level are well documented. For example:
11 Aug 2023: Major "tipping points"....
01 Jun 2019: 500 million years ago....
Intraterrestrials, by Karen G. Lloyd, describes archaea that can persist in very deep submarine sediments for millions of years. Using "Gibbs free energy," Lloyd explains that they cannot reproduce, but only replace parts as needed. I was amazed. I guess this very slow metabolism is why most of them cannot be cultured in a lab. Nevertheless, over long times, these archaea can have crucial gaian effects on the biosphere. She proposes to name them aeonphiles (same root and pronunciation as eon.) To explain how they got that way, under the mainstream theory of evolution, she wonders if drastic environmental events like earthquakes or volcanoes, once per eon, must accelerate their lives.
I wondered if crash-landing on a planet, or passing near the hot sun might accelerate their lives. However, panspermia is not her interest. She hardly mentions endospores with no metabolism at all. But her title tells me she is on the right track. The fun of the book is her narration of the far-flung field research trips, in episodes from exhausting to harrowing to hilarious.
Intraterrestrials: Discovering the Strangest Life on Earth, by Karen G. Lloyd, Princeton University Press, 2025.
Bacteria: The Space Colonists has lots about prokaryotic survival.
| 12 Sep 2025 |
What'sNEW about HGT
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Bacteria evolve by horizontal gene transfer (HGT). This is not in duspute. But now, another mechanism that can facilitate this has been noticed. European biologists have observed that ...tailless capsids... can hijack different phage tails to form chimeric infectious particles... contributing to bacterial evolution. The interdisciplinary team saw "capsid-forming phage-inducible chromosomal islands," widespread among multiple species of bacteria. Once released, I would think they look just like other normal phages, but their formation process appears different. The medical world is concerned if this is another pathway for the spread of antimicrobial resistance (AMR), which, of course, it is. And it is one more path for bacterial evolution by HGT.
"Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization," by Lingchen He1, Jonasz B. Patkowski et al, Cell, online 09 Sep 2025.
"Tail-Swapping "Pirate" Phages Expose New Route for AMR," Genetic Engineering & Biotechnology News, 11 Sep 2025.
...phage satellites can "steal" tails from unrelated viruses....
 Thanks, Google Alerts.
How Prokaryotes Evolve
Viruses and Other Gene Transfer Mechanisms cites abundant evidence of HGT across all kingdoms.
NASA says minerals in Jezero Crater may be signs of past life. This was the subject of a widely publicised online news release at 11AM EDT today. A sample, named "Sapphire Canyon," was the focus of the event. It contains tiny spots that have chemical signatures perhaps left by biology (note scale; click to enlarge.) Most of the analysis was released earlier, but a new open access paper by almost a hundred scientists promises a closer look. A sample return mission to facilitate the investgation is still under consideration, along with robotic and/or manned missions with capability for in situ testing.
"NASA Says Mars Rover Discovered Potential Biosignature Last Year," by Jessica Taveau, NASA, 10 Sep 2025.
"Redox-driven mineral and organic associations in Jezero Crater, Mars," by Hurowitz, J.A., Tice, M.M., Allwood, A.C. et al, Nature, 10 Sep 2025.
"In a Rock on Mars, NASA Sees 'Clearest Sign of Life' So Far," [really?] by Kenneth Chang, The New York Times, 10 Sep 2025.
Life on Mars! cites lots of evidence from missions and studies since Viking.
| 06 Sep 2025 |
(revised 12 Sep)
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How Does Life Evolve? The interested public wants to know, specifically, how life acquires new capabilities. Life depends on genetic programming, so, logically, new capabilities come from new programming, "new genes." Chinese horticulturalists agree, writing, The origin of new genes with novel functions drives adaptive evolution and the innovation of lineage-specific phenotypes. That leads to the next question:
Where do new genes come from? The same researchers continue, New genes can emerge through various processes, such as horizontal gene transfer, retrotransposition, gene fission, gene fusion, gene duplication, and de novo origin. Notice that all but the last of these are rearrangements of existing genes. Only the last ones, "De novo genes ...emerge from noncoding DNA and lack evolutionary history." They may be entirely derived from non-coding sequences, or they may be chimeric, including segments from transposable elements or existing genes. This study recognizes 178 likely ones in "baifeng," a species of peach. All were absent in nine closely related peach species, and 158 of them were confirmed to be transcriptionally active. All of this is clear enough. But then it becomes murky:
"De novo genes can evolve 'from scratch' from noncoding sequences, acquiring novel functions...." The interested public understands evolve as used here to mean acquire a new function by an incremental Darwinian process of mutation-and-selection. The evolutionary process is automatically assumed, because neo-darwinian dogma requires it. But no evidence for such a process is observed — de novo genes "lack evolutionary history." Instead, when first observed, a de novo gene is already active, or is available to be activated. It already is an "existing gene."
If so, that means all "new genes" are rearrangements of existing genes. The de novo ones, chimeric or whole, would merely be the newest ones, because their novel sequences arrived [in the genome of the species under study] only recently. Over time, they would be able to incorporate additional segments, a suggestion that gains support in the study. "...[T]he transition from shorter de novo genes to longer conserved genes involves the recruitment of ...alternative exons...." This assembly and rearranging would need guidelines analogous to ones in word-processors such as grammar- syntax- and spellcheck. (Some of this assembly could precede activation, as chimeric ones may demonstrate.) The concept needs further exploration, of course, but it could be easily demonstrated in computer models, and it looks like what we observe. The de novo genes in baifeng peaches would be just another illustration of the way evolution uses available, "existing genes."
"De novo gene integration into regulatory networks via interaction with conserved genes in peach," by Yunpeng P. Cao, Yuepeng P. Han et al, Horticulture Research, 05 Sep 2025.
"New genes from scratch: how peach creates novel traits," Chinese Academy of Sciences via Newswise, 05 Sep 2025.
...De Novo Genes, our main page on this topic, begins with de novo human genes.
A Wordcount for Comparson has a deconstructive essay with important links.
The Beginning discusses life with no origin.
What Difference Does It Make? has early, relevant thoughts.
Robust Software Management: our name for a genomic operating system with guidelines.
10 Mar 2021: Evolution with "existing genes" is fully demonstrated in prokaryotes.
Difficulties for the Origin-of-Life get a wide-ranging review by Robert G. Endres, a systems biologist and biological physicist at Imperial College, London. He knows that life requires lengthy genetic programming ("software"), so it's a perceptive, edifying review. But he never questions the assumption that life must originate.
"The unreasonable likelihood of being...," by Robert G. Endres, arXiv:2507.18545, [pdf | abstract], 25 Jul 2025.
"The Math Says Life Shouldn't Exist...," by Mark Thompson, SciTechDaily, 31 Aug 2025.
The RNA World... describes a variety of Origin-of-Life theories.
The Second Law of Thermodynamics has related discussion.
The Beginning has related speculations, including this excerpt from V. I. Vernadskii, 1926:
None of the exact relationships between facts which we know will be changed if ...life always existed and had no beginning....
These findings support a dynamic, lengthy co-oxygenation history for the atmosphere and oceans—marked by long-term positive coupling and short-term negative feedbacks–offering a coherent explanation for the anomalous Neoproterozoic carbon cycles and the protracted, episodic rise of complex life.
"Two-billion-year transitional oxygenation of the Earth's surface," by Wang, H., Li, C., Peng, Y. et al, doi:10.1038/s41586-025-09471-4, Nature, 27 Aug 2025.
Gaia has background about processes that can shape the biosphere for advanced life.
How is it Possible? includes early, minimal thoughts about how natural "terraforming" mght proceed.
| 17 Aug 2025 |
What'sNEW about HGT
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The study ...reinforces the role of horizontal gene transfer in plant adaptation to land environments.
"Lost in time, found in bacteria: tracing the roots of plant terpene genes," Chinese Academy of Sciences, 17 Aug 2025.
"Discovery of bifunctional diterpene cyclases/synthases in bacteria supports a bacterial origin for the plant terpene synthase gene family," by Xinlu Chen, Meimei Xu et al, doi:10.1093/hr/uhae221, Horticulture Research, 03 Aug 2024.
Viruses... cites abundant evidence for gene transfer from bacteria to eukaryotes.
We investigate the evolution of microbial metabolisms from the last universal common ancestor to the extant biota through comparative phylogenomics, reconciling the evolution of the genes that underpin metabolic pathways with a time-calibrated tree of life. This sentence introduces an analysis by an international, interdisciplinary team studying the emergence of Gaian processes that co-engineer the biosphere. They elaborate, The metabolic interplay among organisms drives the recycling of the core elements needed for life, collectively modulating Earth's land, air, oceans and climate.
The genes that carry the programming for the metabolic pathways appear to have emerged very early. For example, the figure here illustrates pathways inferred to have already existed by 4 Ga (black), then by 3.5 Ga (teal) and by 3 Ga (red). Furthermore, horizontal gene transfer (HGT) plays a big role in the accumulation of the necessary genes, with useful genes potentially being transferred across large phylogenetic distances.... They speculate about how specific metabolic processes may have become "fixed," but not about the sources of the underlying genes.
I welcome their close attention to the role of Gaia in the history of life on the planet. They even discuss two versions of Gaia, "entropic" and "Darwinized." And they suggest that observing other biospheres may be illuminating. This makes me wonder about Titan, since Life is ...the main vector of nitrogen input to the biosphere. Although the analysis uses the words originate and evolve misleadingly, it is very informative. Recommended.
"The emergence of metabolisms through Earth history and implications for biospheric evolution," by Moody ERR, Williams TA, Álvarez-Carretero S, Szöllősi GJ, Pisani D, Lenton
TM and Donoghue PCJ, doi:10.1098/rstb.2024.0097, Philos Trans R Soc Lond B | PubMed, 07 Aug 2025.
Gaia has a brief introduction with updates.
How is it Possible? includes speculations about how Gaia could help life become established on a planet.
...Older Than Metazoa?, and
...Older Than Earth? have evidence for old genes and "complexity early."
| 05 Aug 2025 |
What'sNEW about HGT
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The first step in the evolution of sex chromosomes is the acquisition of a sex-determining gene by an autosome. This matter-of-fact sentence introduces a review of recent progress on how sex chromosomes evolved. The latest question is, How did recombination between the two chromosomes become suppressed? (Some existing theories require "luck.") A new study in PLoS, comparing different populations of sticklebacks, sheds new light on this subject.
"Sex chromosome evolution in action in fourspine sticklebacks," review by Beatriz Vicoso, Trends in Ecology & Evolution, doi:10.1016/j.tree.2025.06.010, open acess, online 05 Jul 2025. (click figure to enlarge.)
"The fourspine stickleback (Apeltes quadracus) has an XY sex chromosome system with polymorphic inversions on both X and Y chromosomes," by Zuyao Liu et al, PLoS Genet., doi:10.1371/journal.pgen.1011465, 09 May 2025.
It's the matter-of-fact opening, a statement of accepted science, that gets my attention. In brief, one ordinary chromosome acquired a "sex determining" gene; then it underwent losses and became a sex chromosome. Where the acquired gene came from is an unnoticed issue for mainstream theory, but fortunately, it was available. This sequence surprises the consensus theory of evolution and supports cosmic ancestry.
Why Sexual Reproduction? has related discussion.
Viruses and Other Gene Transfer Mechanisms lists very many examples of whole-gene acquisition by eukaryotes.
"RETRACTED: A Bacterium ...Using Arsenic Instead of Phosphorus," Science, 24 Jul 2025.
Related discussion, by Valda Vinson and H. Holden Thorp, Editor's Blog, Science, 24 Jul 2025.
02 Dec 2010: "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus"
The ingredients for life originated in space. This is the first sentence of a report from German and American astronomers using the Atacama Large Millimeter/submillimeter Array who saw evidence of ethylene glycol and glycolonitrile in a protoplanetary disk in Orion. I welcome the growing acceptance of this weak version of panspermia that I call "pseudo-panspermia." It's a small step.
"Complex organic molecules found in young star's disk hint at cosmic origins of life," Max Planck Society via Phys.Org, 24 Jul 2025; re:
"A Deep Search for Ethylene Glycol and Glycolonitrile in the V883 Ori Protoplanetary Disk," by Abubakar M. A. Fadul et al, ApJL 988 L44, 24 Jul 2025.
Complex organics in space were once considered virtually impossible. Now, the evidence is not disputed. But mainstream science still seems blind to a glaring alternative — the complex organics might be postbiotic, not prebiotic. Intriguingly, co-author Kamber Schwarz comments, Our results suggest that protoplanetary disks inherit complex molecules from earlier stages.... Right.
Hoyle and Wickramasinghe's Analysis of Interstellar Dust has background and updates.
23 November 2006: a review of Kyle Stanford's book about blind spots that hinder science.
Thanks, Jacob Navia, for your alert and a poetic message, "truth slowly emerges."
A Breakthrough in origin-of-life research is announced by a team at Harvard. Their optimism is impresssive.
"Self-reproduction as an autonomous process of growth and reorganization in fully abiotic, artificial and synthetic cells," by Juan Pérez-Mercader et al, PNAS [Open Access pdf | epub], 27 May 2025; and commentary:
"A step toward solving central mystery of life on Earth," by Kermit Pattison, The Harvard Gazette, 22 Jul 2025.
The RNA World and Other Origin-of-Life Theories has background and lists many alternatives.
NASA finds new interstellar comet passing through solar system, CBS News, 03 Jul 2025.
...Astronomers discover third interstellar object, by David Dickenson, Universe Today via Phys.Org, 02 Jul 2025.
New interstellar comet will keep a safe distance from Earth, NASA says, by Marcia Dunn, APNews, 03 Jul 2025.
Comets: The Delivery System: has background and updates.
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NASA says minerals in Jezero Crater may be signs of past life. This was the subject of a widely publicised online news release at 11AM EDT today. A sample, named "Sapphire Canyon," was the focus of the event. It contains tiny spots that have chemical signatures perhaps left by biology (note scale; click to enlarge.) Most of the analysis was released earlier, but a new open access paper by almost a hundred scientists promises a closer look. A sample return mission to facilitate the investgation is still under consideration, along with robotic and/or manned missions with capability for in situ testing.
