What'sNEW July - September 2017
Life Before 3850 Million Years Ago? has more links about very old life.
Thanks, George Nickas and Stan Franklin.
Examining non-LTR retrotransposons in the context of the evolving primate brain by Sara Linker et al., doi:10.1186/s12915-017-0409-z, BMC Biology, 11 Aug 2017.
Viruses and Other Gene Transfer Mechanisms has more about evolution by HGT.
New genetic programs in Darwinism and strong panspermia includes predictions that are supported by the above graph and accompanying research.
Here again, HGT apparently provides a genetic program for macroevolutionary progress among eukaryotes. And the program could serve no related purpose in the donor species, so there was no apparent opportunity for darwinian mutation-and-selection to compose it. Here again, the evidence surprises standard darwinism and supports cosmic ancestry.Origin of the Reflectin Gene and Hierarchical Assembly of Its Protein, by Zhe Guan, Tiantian Cai et al., doi:10.1016/j.cub.2017.07.061, Current Biology, 07 Sep 2017.
Research group discovers the origin of octopuses' instant modulation of body coloration, by Zhou Yijing, PhysOrg.com, 11 Sep 2017. Thanks, Google Alerts.
Viruses and Other Gene Transfer Mechanisms has links to a hundred or more similar examples.
Goldenfeld thinks that HGT with viruses helps their bacterial host adapt to changing light faster than the bacteria alone could, because genes undergo point mutations more rapidly in viruses. That's pretty interesting, even if the necessary mutations are few. Of course, delivering photosynthesis genes by HGT originally is already interesting.
He also notices that evolution was rapid when life first emerged on Earth, but is slower now. Following a computer simulation, he observes, ...life automatically shuts off the horizontal gene transfer once it has evolved enough complexity. ...It's still trying to do horizontal gene transfer, but almost nothing sticks.
With respect to the origin of life, he says, ...given that life started as something physical and not biological, [life's start] is fundamentally a physics question. He further believes, There was definitely simpler life before [3.8 billion years ago] – life that didn't even have genes.... Evolution was going on before genes even existed.... We understand the physics-related grounding for this position, the big bang. But from the perspective of biology, life without genes is pure conjecture. And the theory of evolution, gridlocked in public opinion, needs fresh conjecture. So, thanks, Nigel. Please, carry on!Seeing Emergent Physics Behind Evolution, an interview with Nigel Goldenfeld, Quanta Magazine, 31 Aug 2017.
Viruses... has more about photosynthesis delivered by HGT. (Search the page for "photosynthesis".)
The RNA World has lots about origin-of-life theories.
7 Jul 2014, an earlier entry about Goldenfeld.
6 Oct 2009, ...compelling documentations of horizontal gene transfer in eukaryotes..., Woese and Goldenfeld.
04 Dec 2018: Nonhomologous end-joining and retroelements ...in the evolution of advanced life [Goldenfeld et al.]
How Cells Hack Their Own Genes, Institute of Molecular Biotechnology (+Newswise), 23 Aug 2017.
We recognize the need to establish a webpage for discussion and links about robust software management.
Right away we get deep into the story of the Burgess shale, whose fossils Conway Morris re-examined with fresh eyes, and which Gould publicised in Wonderful Life (1989). Soon, Losos introduces his own specialty, lizards, and his lifelong study of them. Researches by other evolutionary specialists also pertain the original question, and their personal stories are entertaining.
Losos wants to tackle the question experimentally, so projects like Richard Lenski's years-long culturing of cloned bacteria get close attention. We were delighted to read about the Rothamstead Research Station in England, with some experiments begun more than a century ago. And we especially enjoyed learning about odd species like the aye-aye of Madagascar, with astonishing features like ever-growing incisors and "an elongate, skeletal middle finger capable of rotating in any directon."
Losos's eventual answer is: both. Evolution repeats itself sometimes, but often doesn't. While we enjoyed and recommend the book, we wish the question were treated from a perspective beyond strict darwinism. Most of the evolution probed in detail is micro-evolution, by which we mean evolution attainable with only a few point-mutations, so not forbiddingly improbable. (We were pleased to learn a term for changes requiring no germ-line genetic mutations, "phenotypic plasticity".) When macro-evolution is observed, the genetic changes that may produce it get insufficient attention. Computer models are not mentioned. We wish that evolutionary biologists who are truly curious would ask this question: Where do new genetic programs come from?Improbable Destinies: Fate, Chance, and the Future of Evolution, by Jonathan B. Losos, Riverhead Books, Aug 2017.
Neo-Darwinism: The Current Paradigm has sections about Punctuated Equilibrium and Convergent Evolution.
Rewinding the Tape is a related section under "Can the Theory Be Tested".
Macroevolutionary Progress Redefined... considers micro- and macro-evolution.
23 Aug 2017: Author Jonathan Losos responds.
A mathematical astronomer from Arkansas proposes a plausible and sobering solution to Fermi's paradox:
Here we argue that ...the typical technological species becomes extinct soon after attaining a modern technology and that this event results in the extinction of the planet's global biosphere.
Implication of our technological species being first and early by Daniel P. Whitmire, International Journal of Astrobiology, online 03 Aug 2017 (+alternate with author's summary).
The Implications of Cosmic Silence, University of Arkansas (+Newswise), 11 Aug 2017.
Gaia has more about the longterm fate of living planets.
Milky Way's Origins Are Not What They Seem, by M. Fellman, Northwestern University (+Newswise), 26 Jul 2017.
Given how much of the matter out of which we formed may have come from other galaxies, we could consider ourselves space travelers or extragalactic immigrants.
Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice by Catriona P. Harkins et al., doi:10.1186/s13059-017-1252-9, Genome Biology, 20 Jul 2017.
Methicillin resistance was out there before methicillin, Nature Research Highlights, 24 Jul 2017.
...MRSA Genesis Occurred Years Before Clinical Introduction of Methicillin, GenomeWeb, 21 Jul 2017.
Metazoan Genes Older Than Metazoa? and Genes Older Than Earth? are related local webpages.
It apears that there is much more cometary material in the Oort Cloud than previously known. Their orbits place these large comets in interstellar space, where they might stray to and from orbits around other nearby stars. This traffic would increase the likelihood of interstellar panspermia.
Large, Distant Comets More Common Than Previously Thought, Jet Propulsion Laboratory, NASA, 25 Jul 2017.
Debiasing the NEOWISE Cryogenic Mission Comet Populations by James M. Bauer et al., n 2, v 154, The Astronomical Journal, 14 Jul 2017.
Comets: The Delivery System has more. Thanks, George Nickas.
Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses by Ito J, Sugimoto R, Nakaoka H, Yamada S, Kimura T, Hayano T, et al., doi:10.1371/journal.pgen.1006883, PLoS Genet, uncorrected proof online 12 Jul 2017.
Viruses... has much more about HGT. Robust Software Management is incomplete.
The [bacterial] immunity system works just as efficiently as ours, except our system functions at the protein recognition level, whereas CRISPR works at the nucleic acid recognition level — Ailong Ke, professor of molecular biology and genetics, Cornell UniversityBringing bacteria's defense into focus by Bill Steele, Cornell Chronicle (+Newswise), 30 Jun 2017; re:
Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System by Yibei Xiao et al., doi:10.1016/j.cell.2017.06.012, Cell, 29 Jun 2017.
The image shows an aerogel array for collecting dust on NASA's Stardust mission.
Thanks, Chandra Wickramasinghe and Martin Langford.