On the occurrence of cytochrome P450 in viruses by David C. Lamb, Alec H. Follmer, Jared V. Goldstone et al., doi:10.1073/pnas.1901080116, PNAS, 05 Jun 2019. Thanks, Martin Langford. Viruses... has more.
Gaia mentions plate tectonics that help to stabilize Earth's climate. Maybe also on Venus, in its past?
Climate history gets increasingly difficult in the deeper past. (10,000 years of human civilization only comes at the last .002% of the graph.) The Smithsonian project neeeded wide collaboration among various disciplines, lots of detective work and some computer modelling. The research is ongoing but obviously, some kinds of life flourished when Earth was hotter. Gaia theory had supposed that the temperature range in the deep past was only half as wide. Losing the polar ice caps again looks inevitable. Maybe climate instability helps to explain the Fermi paradox? Lots to think about! Project traces 500 million years of roller-coaster climate by Paul Voosen, Science, 24 May 2019.
Gaia discusses Lovelock's theory of climate stability. 02 Feb 2016 and 14 Aug 2017: about Fermi's paradox.
One of the biggest surprises from DNA sequencing data is that many eukaryotic "orphan" genes have no detectable predecessors. Other de novo ones come from open reading frames that apparently never underwent selection for their roles. They seem to need only to be switched on. A new survey of research about these genes includes a table counting the known or suspected ones in two dozen eukaryotic categories. In arthropods, for example, 65,000 orphan genes have been identified so far.
These genes have no ready explanation under mainstream darwinian theory, but suggestions are not lacking. Perhaps the selection process was so rapid and thorough that the orphan's homology with its ancestral gene is erased? Or selection for an outdated, unknown function luckily also prepares the de novo gene for its role?
Such speculations lack plausibility, and demonstrations in quarantined biology or computer models do not succeed. Meanwhile, genes that "seem to have come from nowhere" are required in cosmic ancestry.De novo gene birth by Stephen Branden Van Oss and Anne-Ruxandra Carvunis, doi:10.1371/journal.pgen.1008160 [Open Access], PLoS Genetics, 23 May 2019.
Genes Older Than Earth? takes issue with the term "birth." It implies a process of gestation which is not observed.
New genetic programs... contains an early, primitive, proposed investigation to seek the source of new genes.
Three New Human Genes... has become our main webpage about de novo genes.
In other words, in this case, the needed genes are already there. We think genes always come first.
Are developmental shifts the main driver of phenotypic evolution in Diplodus spp.... by Paolo Colangelo et al., BMC Evolutionary Biology, 21 May 2019.
Life on Europa, Other Moons, Other Planets?... has links about ice-covered oceans and lakes. Thanks, Rob Cooper.
If prokaryotes all come from a common single ancestor, their lines of descent, logically, should branch like a tree. But with only today's genomes, of course it would be challenging to reconstruct the form this tree took billions of generations ago. Horizontal gene transfer (HGT), rampant among prokaryotes, makes it much more challenging. And when eukaryotic sexual reproduction appears, the difficulty is again compounded.
The trickster microbes that are shaking up the tree of life, doi:10.1038/d41586-019-01496-w, Nature, 14 May 2019.
New genetic programs... promotes a test. Metazoan Genes Older Than Metazoa? and Genes Older Than Earth? report clues we have noticed.
...this biosphere ...goes way, way down. ...scientists have still never hit sterile rock.
...microbes use the rock itself as a source of energy.
...under the South Pacific gyre ...were microbes trapped in sediment that was at least 100 million years old.
These quotations come in a brief essay about the deep biosphere, an environment of renewed interest. Biologists already knew that bacteria come in a wide variety, but now we glimpse a whole new world of them. If bacteria are so durable, resourceful and ubiquitous, perhaps they could persist in space and survive on other planets?Zombieland: The vast world of hidden microbes miles beneath your feet by Graham Lawton, NewScientist, 08 May 2019. Thanks for sharing the complete article, Martin Langford.
02 Oct 2018 and 10 Dec 2018: related reports. Bacteria... has more about their survival capabilities.
...the Phytophaga GH45s have adapted to substrate shifts.
These observations come from a thoroughgoing analysis of certain cellulase genes in leaf-eating beetles.
We suppose that macroevolutionary advances must be ultimately supplied by the horizontal gene transfer (HGT) of lengthy new programming. The acquired enzyme analysed here, for example, is more than 200 amino acids (600 exonic nucleotides) long. After installation, we think accelerated point mutations allow new genes and their duplicates to become optimized for new situations. Optimization (microevolution by our definition) may be possible with only a few (1 - 10) amino acid substitutions in the right places, as Busch et al. report (see chart, right). In sum, this study describes a scenario that matches our suppositions.Functional diversification of horizontally acquired glycoside hydrolase family 45 (GH45) proteins in Phytophaga beetles [PDF] by André Busch, Etienne G. J. Danchin and Yannick Pauchet, BMC Evolutionary Biology, doi:10.1186/s12862-019-1429-9, 10 May 2019.
...we combined functional and phylogenetic analyses to unravel the origin, evolution and functional diversification of the GH45 family in Phytophaga beetles.
Macroevolutionary Progress Redefined... explains how macro- and microevolution are different. Viruses... is our main page about HGT.
Robust Software Management... mentions adaptive (accelerated) and directed (targeted) mutation.
Thanks, Google Alerts. 01 Nov 2017: A passing object adds evidence for interstellar panspermia.
Also of note to us, 60% of the Medusavirus genes, 279, are unfamiliar ones with unknown functions. So called "ORFan" genes are starting to look numberless, and they are especially abundant among large viruses. If ORFan genes are widely available from viruses, are they an inventory of potential de novo genes, the ones that "seem to have come from nowhere" in the evolution of eukaryotes?Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water by Genki Yoshikawa et al., doi:10.1128/JVI.02130-18, J Virol, online 03 Apr 2019.
New giant virus may help scientists better understand the emergence of complex life, Tokyo University of Science (+Science Daily), 26 Apr 2019. The results of an evolutionary analysis done by the authors suggest that in the evolution tree, the Medusavirus DNA polymerase lies at the origin of the DNA polymerase found in eukaryotes. ...this could mean that our DNA polymerase probably originated from Medusavirus or one of its relatives.
Viruses...: background and links about viral genes in eukaryotic evolution.
13 Jun 2018 and 25 Jan 2013: more about ORFans. 13 May 2011: an archive of cellular genes in viruses?
Three New Human Genes has links and more about de novo genes. Thanks, Stan Franklin and Martin Langford.
Forearc carbon sink reduces long-term volatile recycling into the mantle by P.H. Barry et al., Nature, 24 Apr 2019.
Major deep carbon sink linked to microbes at volcanic island chains, National Science Foundation, 24 Apr 2019.
...Microbes could influence Earth's geological processes..., University of Tennessee (+Newswise), 25 Apr 2019.
Gaia has comments about the burial of carbon on the ocean floor.
Mystery of the Universe's Expansion Rate Widens with New Hubble Data, Space Telescope Science Institute (+Newswise), 25 Apr 2019. The universe seems to be expanding faster than all expectations by Michael Greshko, National Geographic, 25 Apr 2019. The universe may be a billion years younger than we thought... by Corey S. Powell, NBC News, 18 May 2019. Thanks, Rob Cooper and Stan Franklin.
The discrepancy suggests that there's something in the cosmological model that we're not understanding right.
Large Magellanic Cloud Cepheid Standards Provide a 1% Foundation for the Determination of the Hubble Constant and Stronger Evidence for Physics Beyond ΛCDM by Adam G. Riess et al., doi:10.3847/1538-4357/ab1422, arXiv:1903.07603v2, 28 Mar 2019. The End and the Big Bang is related.
Saltational symbiosis by Jan Sapp, Theory Biosci, Sep 2010.
...Is it not time, for the advancement of science, to drop the adjective "Darwinian" from evolution?
Hundreds of thousands of marine viruses discovered in world's oceans by Erin I. Garcia de Jesus, Nature, 25 Apr 2019.
Marine DNA Viral Macro- and Microdiversity from Pole to Pole by Ann C. Gregory, et al., doi:10.1016/j.cell.2019.03.040, Cell, 16 May 2019. Thanks, Martin Langford.
A new study begins with the premise that protein domains are the basic units of meaning in genomes. The researchers, from the University of Alabama in Birmingham and the National Institutes of Health, compare them to words in a written language. They demonstrate that protein domains and words occur with mathematically similar patterns and frequencies, apparently following similar grammars. We welcome this insight, because it suggests a tool for the toolkit that we think life's evolution needs.Consider an analogy we have offered before: word-processing programs can identify spelling, syntactical and gramatical errors, and suggest or make corrections. Even if some passages are out of order, the error-recognition logic could be deployed to properly order them. Now consider genomes. Suppose some protein domains, usually between a hundred and a thousand nucleotides long, are out of place. If genomes have an analogous capability, they could properly order the domains. The new study strengthens our view that genomes could have such capabilities.
14 Jun 2016: more software management. The Second Law... explains why entropy is a confusing term.
Discovery of a Meteor of Interstellar Origin by Amir Siraj and Abraham Loeb, arXiv:1904.07224v1, 15 Apr 2019.
Harvard Scientists Say Earth Was Struck by an Interstellar Object 5 Years Ago by Peter Dockrill, Science Alert; &
Interstellar object hit Earth and it could explain how life began by Sean Martin, Express.co.uk, 17 Apr 2019.
08 Feb 2018 & 15 Oct 2018: more from Loeb et al.. Thanks, Google Alerts and Justin Willingham.
Another Mars meteorite may carry traces past life, namely the partially-melted remains of iron-oxidizing bacteria. The structures require interpretation, but the observed carbon isotope anomaly usually comes from life, on Earth anyway.
Mineralized biosignatures in ALH-77005 Shergottite - Clues to Martian Life? by Ildikó Gyollai et al., doi:10.1515/astro-2019-0002, De Gruyter, Jan 2019; and commentary, MarsDaily, 05 Apr 2019.
Claimed Signs of Life in a Martian Meteorite by Dirk Schulze-Makuch, airspacemag.com, 06 May 2019.
Thanks, Ronnie McGhee and Rob Cooper. Life on Mars! has lots about ALH84001.
Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation by Hyeonsoo Jeong et al., doi:10.1371/journal.pgen.1007995, Nature Scientific Reports, 11 Apr 2019.
The authors focus on bacteria and yeast cells, but Stress response-up-regulated mutation mechanisms have been discovered in plants, flies, and human cells. Edited by W. Ford Doolittle, the article concludes, regulated mutagenesis mechanisms greatly increase the probability that the useful mutations will occur at the right time, thus increasing an organism's ability to evolve and, possibly, in the right places. Assumptions about the constant, gradual, clock-like, and environmentally blind nature of mutation are ready for retirement..
The findings are consistent with our belief that genomes must have robust software management systems to keep them functional and adaptable. (And the necessary high-fidelity DNA repair might be difficult to evolve, the report mentions.) Robust software management would also manage horizontal gene transfer (HGT), which stress may also induce. We mention HGT in order to clarify its role in cosmic ancestry —
We agree, rearrangements within an existing genome can have profound effects, both positive and negative. For a positive one, suppose that a silent beneficial gene needs only to be turned on, or a key exon needs relocation. If this change is effected and inherited, a beneficial evolutionary step is enabled. But if the gene or exon is not available, stress alone cannot induce that evolutionary step. In other words, there is a near limit to the range of evolution within a quarantined genome. Suppose an evolutionary step requires a unique strand of, say, 200 or more properly sequenced nucleotides. If the strand is not already present, the evolutionary step will not occur. Of course, HGT could supply it. But without HGT, macroevolutionary progress would soon halt, we believe.
We scan the literature regularly for relevant evidence, and HGT is obseved frequently enough, in all domains. Also, we have proposed research programs in biology and in computer models to test the importance of HGT, with no serious takers. Meanwhile, we welcome these straightforward observations from Fitzgerald and Rosenberg.
Is Evolutionary Progress ...Possible? has discussion and updates about a long-running quarantined experiment.
Macroevolutionary Progress Redefined: Can It Happen Without Gene Transfer? has related discussion.
Viruses... is our main webpage about HGT.
2018 2017 2016 2015 2003: various examples of stress-induced or non-randonm HGT.
The Second Law of Thermodynamics makes our argument logically. Robust Software Management... is incomplete.
The Beginning and Evolution vs Creationism mention questions asking, "...in the first place?"
On Earth biological sources ...produce 95% of the methane in our atmosphere.