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 have systems to cope with genes from viruses.
"...haul of asteroid dust and rock returns to Earth," by Alexandra Witze, Nature, 24 Sep 2023.
"NASA spacecraft delivering biggest sample yet from an asteroid," by Marcia Dunn, Phys.Org, 20 Sep 2023.
Comet Rendezvous has related history and updates.
I love to see deep into the history of science, with its human drama unhidden, as when Paul Ehrenfest witnesses the early development of quantum theory. Eugene Wigner says that von Neuman was the first to understand what Kurt Gödel had proven, and it affected him profoundly. Richard Feynman admits that thoughtless youthful striving and competitiveness at Los Alamos largely propelled us to Hiroshima and Nagasaki.
In Sydney Brenner's telling, von Neuman foresaw the logic of DNA replication and translation even before the discovery of DNA. In another remembrance from Wigner, von Neuman thought that a computer-based version of life might reach "a threshold, a tipping point that, if surpassed, would kick off an evolutionary process in the machines, leading to... offspring of ever-increasing complexity." When von Neuman died, in 1957, computers were extremely primitive by today's stardards, but today the fantasy remains alive – and unattained. In an included sequel, computers wth Artificial Intelligence defeat all humans in games of skill. That would please von Neuman.The MANIAC by Benjamin Labatut Random House, coming 03 Oct 2023.
Thanks, Mark Frederick at the Memphis bookstore, Novel.
Computer Models of Evolution is the first of several related pages.
"Webb Discovers Methane, Carbon Dioxide in Atmosphere of K2-18b," NASA/SCTI and Newswise, 11 Sep 2023; re:
"Carbon-bearing Molecules in a Possible Hycean Atmosphere," by Nikku Madhusudhan et al., arXiv:2309.05566, submitted 11 Sep 2023.
The Life of Super-Earths, by Dimitar Sasselov, tells why they may be better suited than Earth for advanced life.
Life on Europa, Other Moons, Other Planets?..., has links about other candidates.
Dimethyl sulfide is the subject of Jacob Navia's comments, 17 Sep 2023.
"The MillenniumTNG project: the galaxy population at z ≥ 8," by Rahul Kannan et al., M.N.R.A.S., Sep 2023. The early release science results from JWST have yielded an unexpected abundance of high-redshift luminous galaxies.... This indicates either an incomplete understanding of the new JWST data or a need for more sophisticated galaxy formation models..., or even deviations from the standard ΛCDM model.
"The Story of Our Universe May Be Starting to Unravel," by Adam Frank and Marcelo Gleiser, The New York Times, 02 Sep 2023. We may be at a point where we need a radical departure from the standard model....
The End and the Big Bang has lots of recent updates.
An 'alien meteorite' probably didn't slam into Earth...? by Alexandra Witze, Nature, 06 Sep 2023; also:
"Did interstellar debris fall to the sea floor?..." by Daniel Clery and Paul Voosen, Science, 08 Sep 2023; re:
...Spherules of Likely Extrasolar Composition in the Pacific Ocean..., by Abraham Loeb et al., arXiv, 29 Aug 2023.
We notice a shift in our earthly perspective: in a few decades the presence in nearby space of abundant interstellar material including comets has quietly become well accepted. Seldom mentioned is something even more interesting: the interstellar dust that Stardust encountered appeared to contain very large organic molecules.
Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome, by B. van Dijk, P. Buffard, A.D. Farret al., doi:10.1038/s43705-023-00294-, ISME Commun., 17 Feb 2023.
10 Mar 2021: a local hub for HGT among bacteria, with updated links.
Viruses... points to many examples of HGT across all kingdoms.
The story begins with an informative historical review of the science of evolution, including close scrutiny wth the new polarizing filter. "Materialism without reductionism...," for example. Then Reiss and Ruse move to issues of health, sex and gender, race, even Gaia, and guess what. They, also, are torn between the two conflicting points of view. The suggested solution comes in Chapter 9, "God and the New Biology."
I notice that the conflict vanishes in less political sciences. Weather forecasting readily incorporates global phenomena such as el niño without needing a new philosophy. For the theory of evolution, yes, there is a crisis as serious as any in the history of science. But the problems are compounded by faulty assumptions and questions that science cannot answer. If we get those right, the theory of evolution can bypass the gridlock, and God can stay safely above the fray.The New Biology: A Battle between Mechanism and Organicism, by Michael J. Reiss and Michael Ruse, ISBN:9780674972247, Harvard University Press, 20 Jun 2023.
Evolution vs Creationism has related history, comments and links.
Some Things Are Simply Given: a related essay (local pdf, close to return.)
27 Jul 2002: RNA World: the latest.
The RNA World has discussion, history and updates.
Systematic evaluation of horizontal gene transfer between eukaryotes and viruses, by N.A.T. Irwin, A.A. Pittis, T.A. Richards, T.A. and P.J. Keeling, doi:10.1038/s41564-021-01026-3, Nature Microbiology, 31 Dec 2021.
Viruses... points to many related examples.
The most striking tipping point in the cenozoic occurred 34 million years ago, when Antarctica drifted away from the other continents, atmospheric CO2 declined and the climate cooled. Antarctica acquired glaciers and sea ice. They reflected sunlight away and further cooled the ocean. Sea level abruptly dropped about 70 meters and began to oscillate in a lower range (see graph).
The study also looks more closely at the last 3 million years, with worrying thoughts: Human activity is now rapidly pushing the Earth system towards the limits of its safe operating space.... This concern is supported by actual observations impacting numerous tipping elements through very drastic tipping cascades. This paves the way for a possible upcoming major transition, which might lead us to climate conditions that are fundamentally different from what has been observed in the recent or more distant past...."A punctuated equilibrium analysis of the climate evolution of cenozoic exhibits a hierarchy of abrupt transitions" [link], DD. by Rousseau, W. Bagniewski and V. A. Lucarini, Scientific Reports, 12 Jul 2023.
"Huge tipping events dominated the evolution of the climate system," University of Copenhagen via Newswise, 09 Aug 2023.
Gaia has more about how life and the planet affect each other.
"Sustained wet–dry cycling on early Mars" by W. Rapin, G. Dromart, B.C. Clarket al., Nature, 09 Aug 2023.
"...possible seasonal climate patterns on early Mars" [link], Los Alamos National Laboratory, 09 Aug 2023.
Thanks, Rob Cooper and Newswise. Life on Mars! has more.
"Our Galaxy Is Home to Trillions of Worlds Gone Rogue" by Katrina Miller, The New York Times, 06 Aug 2023.
"Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities" by Sonya A. Widen, Israel Campo Bes et al., Science, 30 Jun 2023.
We hypothesize that Mavericks... integrate into the genome of their host and passively replicate until an environmental factor triggers the formation of infective particles.
"Selfish, Virus-Like DNA Can Carry Genes Between Species" by Saugat Bolakhe, Quanta Magazine, 03 Aug 2023.
Viruses... points to many related examples.
"Scientists woke up a 46,000-year-old roundworms from Siberian permafrost" by Carolyn Y. Johnson, The Washington Post, with video, 27 Jul 2023; re:
"A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva" by Anastasia Shatilovich, Vamshidhar R. Gade et al., PLoS Genet., 27 Jul 2023.
Thanks, Walter Klyce and Bob Sweeney.
"Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems" by S.E. Ruff, P. Humez, I.H. de Angelis et al., Nature Communcations, 13 Jun 2023.
"Underground Cells Make 'Dark Oxygen' Without Light" by Saugat Bolakhe, Quanta Magazine, 17 Jul 2023.
Bacteria: The Space Colonists introduces their surprising capabilities.
Life on Europa, Other Moons, Other Planets? and Earth-analogs for those environments has relevant links.
"Carbonaceous dust grains seen in the first billion years of cosmic time" by Joris Witstok, Irene Shivaei, Renske Smit et al., Nature, 19 Jul 2023.
"James Webb Space Telescope makes 1st detection of diamond-like carbon dust in the universe's earliest stars" by Robert Lea, Space.com, 19 Jul 2023.
Thanks, Jim Powers, who has convinced me to wonder: How did the first stars form without dust?
The End... discusses reasons to question the usual big-bang story.
"Horizontal gene transfer underlies the painful stings of asp caterpillars..." by Andrew A. Walker et al., PNAS, 10 Jul 2023.
"Centipede Venom Is A Cocktail Of Genetic Material Nicked From Bacteria And Fungi" by Rachael Funnell, commentary from IFL Science, 05 Feb 2021; re:
"Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer", by Eivind A. B. Undheim and Ronald A. Jenner, open-access link, Nature Communications, 10 Mar 2021.
"A new human embryonic cell type associated with activity of young transposable elements allows definition of the inner cell mass" by Manvendra Singh et al., PLoS Biol., 20 Jun 2023.
"An Ancient Battle Is Playing Out in the DNA of Every Embryo" by Celia Ford, Wired, 17 Jul 2023.
Viruses... points to many related examples. (Identified genes occupy less than 2 percent of our genetic material.)
"Diverse organic-mineral associations in Jezero crater, Mars" by S. Sharma, R.D. Roppel, A.E. Murphy et al., Nature, 12 Jul 2023.
"Mars Life Reveal?..." by Leonard David, Inside Outer Space, 15 Jul 2023.
Thanks, Barry DiGregorio, who comments on Leonard David's blog.
Life on Mars! has discussion and updates about the Viking Mission. Organics are there!
The new analysis looks at point mutations in existing genes over "Long-scale" and "Short-scale" timespans. The changes shown over the former also require genetic programs acquired by transfer, but these are not mentioned. A figure in commentary by Bush & Goriely illustrates the difference between macro- and microevolution:
"Evolution of the germline mutation rate across vertebrates" by Lucie A. Bergeron et al., doi:10.1038/s41586-023-05752-y, Nature, 01 Mar 2023.
"Fine-tuning germline mutation rates across evolution" by Stephen J. Bush and Anne Goriely, TiG, Aug 2023.
Does Micro- Explain Macro-? and Macroevolutionary Progress Redefined... have related discussion.
"These six distant galaxies captured by JWST are wowing astronomers," by Alexandra Witze, Nature, 30 Jun 2023.
The End... discusses reasons to question the usual big-bang story.