What'sNEW January - March 2017
In the legend for the figure here they write, "...The three Cyanobacteria classes likely acquired aerobic respiration independently after the rise of oxygen (atmospheric oxygen is represented by the red shading). Squares and triangles indicate acquisitions of complex III, whereas circles and diamonds indicate acquisitions of complex IV. ...Square brackets denote operon fusions, and a red 'X' indicates putative loss of ETCs." The report continues, "If true, we expect that other phyla will exhibit the same pattern for aerobic respiration as the Cyanobacteria—a lack of aerobic respiration in their last common ancestor, with a later acquisition involving lateral gene transfer."
The term "origin" appears in the article and title, but it seems to mean "first deployment." Certainly, coordination and testing must follow the acquisition of genes and other genetic components to complete the installation of programs for aerobic respiration, photosynthesis, or any comparable evolutionary innovation. But the "origin" of any complex functional genetic program remains unobserved and unexplained. Meanwhile, evidence for horizontal gene transfer (HGT) grows daily. We think the underlying assumptions about evolution need to be reconsidered.On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria, by Rochelle M. Soo, James Hemp et al., doi:10.1126/science.aal3794, Science, 31 Mar 2017; and commentary:
How Cyanobacteria went green, by Robert E. Blankenship, Science, 31 Mar 2017.
Viruses... is our main related webpage. Testing Darwinism... is another related webpage.
These distinguished cosmologists have witnessed the bias with which the story of modern cosmology is usually told. For one example: until 1998, the big bang theory confidently held that the expansion of the universe is decelerating. Then the very opposite, acceleration, was discovered. The shock was quickly swallowed with no mention of an interesting fact: acceleration was a basic prediction of the steady-state theory, the leading alternative. Although the original steady-state theory of Gold, Bondi and Hoyle is now abandoned, a newer "quasi-steady-state" cosmology (QSSC), which Fred Hoyle also helped to develop, is well-explained and supported in the book. Along the way we learn about the contributions of astronomers seldom noticed elsewhere, like Viktor Ambartsumian and Hans Arp, to name only two.
Burbidge and Narlikar confess that no theory today satisfactorily explains all the data, and since 2008, this situation has not improved. Meanwhile, dogmatic support for the big bang inhibits scientific imagination and hinders progress. The dogma also requires life to somehow originate, which, to us, looks forbiddingly improbable.Facts and Speculations in Cosmology, by Jayant Narlikar and Geoffrey Burbidge, ISBN-13: 9780521865043, Cambridge University Press, 2008.
The End and the Big Bang has more. George Nickas replies with comments, 27 Mar 2017.
The pristine interior of comet 67P revealed by the combined Aswan outburst and cliff collapse, by M. Pajola et al., Nature Astronomy, online 21 Mar 2017.
Why a NASA spacecraft could bounce, crunch or sink on icy Europa, by Alexandra Witze, Nature, 21 Mar 2017.
Life on Europa... has related links.
7 Alien 'Earths' May Be Swapping Life via Meteorites, by Shannon Hall, NationalGeographic, 22 Mar 2017.
TRAPPIST-1... our first notice about these planets, posted 22 Feb 2017.
Thanks, Bob Sweeney, Stan Franklin and Google Alerts.
...the tree of life is infected by viruses from the root to the leaves — Patrick Forterre, Mart Krupovic and David Prangishvili, Cellular domains and viral lineages, Trends in Microbiology, October 2014.
Viruses... is our main related webpage. Thanks, Suzan Mazur.
Seeing through mythologies and debunking them is what real science is all about — Robert B. Laughlin,
A Different Universe: Reinventing Physics from the Bottom Down, Perseus Books, 2005.
The chart shows the number of KZFP-like genetic units (including pseudogenes) in indicated genomes, ordered by taxonomic class. To us, the study provides another example of evolutionary progress made possible by pre-existing genetic programs that have been imported into the genomes of receptive species, perhaps in pieces, perhaps long ago.
KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks, by Michaël Imbeault, Pierre-Yves Helleboid and Didier Trono, doi:10.1038/nature21683, Nature, online 08 Mar 2017.
Study suggests complex life was present on Earth 2.33 billion years ago, by Jennifer Chu, MIT News Office (+Physorg.com), 06 Mar 2017. Thanks, Stan Franklin.
Metazoan Genes Older Than Metazoa? and Genes Older Than Earth? cite many more examples of complexity early.
To make sense of this apparent absurdity within a strictly darwinian paradigm, Krupovic and Koonin ultimately imagine unexplained, unobserved "origins." But we endorse their fully-grounded observations: These findings reveal a stronger connection between the virosphere and cellular life forms than previously suspected. ...this view is compatible with the scenario of multiple recruitment events occurring throughout the course of evolution of life.
Multiple origins of viral capsid proteins from cellular ancestors, by Mart Krupovic and Eugene V. Koonin, doi:10.1073/pnas.1621061114, PNAS, online 06 Mar 2017.
New Evidence for a Water-Rich History on Mars, by Glenn Roberts Jr., Lawrence Berkeley National Laboratory (+Newswise), 06 Mar 2017. Life on Mars! has lots about water there.
Survivability and growth kinetics of methanogenic archaea at various pHs and pressures: Implications for deep subsurface life on Mars, by Navita Sinha et al., doi:10.1016/j.pss.2016.11.012, Planetary and Space Science, Feb 2017.
Is Anything Tough Enough To Survive on Mars?, by Bob Whitby, Arkansas Center for Space and Planetary Sciences (+Newswise), 28 Feb 2017. Bacteria... has more about their survival capabilities.
Evidence for early life in Earth's oldest hydrothermal vent precipitates, by Matthew S. Dodd, Dominic Papineau et al., doi:10.1038/nature21377, Nature, 01 Mar 2017.
Cells adapt ultra-rapidly to zero gravity, UZH News (+ScienceDaily), 28 Feb 2017; re:
Rapid adaptation to microgravity in mammalian macrophage cells, by Cora S. Thiel et al., Scientific Reports, doi:10.1038/s41598-017-00119-6, online, 27 Feb 2017.
Thanks, Chandra Wickramasinge, for noticing: if life comes from space, it's less paradoxical.
Evolution of Cells, Genomes and Proteins, a conference at Nanyang Technological University, 1-3 Feb 2016.
The distribution of recognized protein superfamilies shows extensive overlap among the 3 domains of life (diagram). The "complexity early" which this distribution reconfirms is a jarring surprise for darwinists. We wish the surprise would prompt them to notice cosmic ancestry, which predicts, "Life can only descend from ancestors at least as highly evolved as itself." Meanwhile, mainstream speculations about the origin of life and the tree of life must be wrong. Two experts in "the structural classification of proteins" (SCOP), discuss its use and implications in a recent interview:
Viruses... has links to many examples of the horizontal transfer of genetic material affecting eukaryotes.
Seven temperate terrestrial planets around the nearby ultracool dwarf star TRAPPIST-1, by Michaël Gillon et al., doi:10.1038/nature21360, Nature, 23 February 2017.
Scientists discover 7 'Earthlike' planets orbiting a nearby star by Sarah Kaplan, The Washington Post, 22 Feb 2017.
"On the eve of War, Churchill wrote essay about extraterrestrial life," by Traci Watson, USA Today, 16 Feb, 2017. He was not "sufficiently conceited to think that my sun is the only one with a family of planets."
Life on Europa, Other Moons, Other Planets?... has related links. Thanks, Bob Sweeney and Ronnie McGhee.
"Life's beginnings" [jpeg], by Chandra Wickramasinghe, London Times, 27 Feb, 2017.
Naica's crystal caves hold long-dormant life by Jonathan Amos, BBC, 18 Feb 2017.
Weird Life Found Trapped in Giant Underground Crystals, by Victoria Jaggard, NationalGeographic, 17 Feb 2017.
Bacteria... is a related webpage. Thanks, Stan Franklin.
Now more ESPs are seen among a newly-designated clade of archae named Asgard. They include a subunit of eukaryotic DNA polymerase, a eukaryotic ribosomal protein, key components of the eukaryotic cytoskeleton and membrane trafficking proteins. The schematic representation of a eukaryotic cell (right) highlights ESPs that have been identified in Asgard archaea, with colored tables indicating their distribution among those species.
The overall picture indicates that the archaeal ancestor of eukaryotes already contained many key components underlying the emergence of cellular complexity that is characteristic of eukaryotes, this research team says in summary. As darwinists, they suppose that an archaeal ancestor must have had some use for the ESPs after all. But in cosmic ancestry, genes always come first. If they weren't often found in species preceding the need for them, we would be surprised.
Asgard archaea illuminate the origin of eukaryotic cellular complexity, Katarzyna Zaremba-Niedzwiedzka et al., doi:10.1038/nature21031, Nature, 19 Jan 2017; and commentary:
email to Ted Steele on the origin of life, 17 Feb 2017.
The researchers are specifically interested in the phylogeny and ultimate origin of the mimiviruses. Were their [viral?] ancestors even more complex, or less complex? Despite many theories, the origin and evolution of mimiviruses remains a breathtaking mystery. It is not yet possible to exclude any specific scenario of giant viruses' evolution.
Darwinian logic does exclude the scenario we prefer. In cosmic ancestry, viruses are the main vector for the horizontal transfer (HGT) of cellular genes into species that can use them. We are not surprised if mimiviruses contain genes for tRNAs, protein synthesis, translation factors and more.
The analysis of translation-related gene set boosts debates around origin and evolution of mimiviruses, Jônatas Santos Abrahão, Rodrigo Araújo et al., PLOS Genetics, 16 Feb 2017.
Localized aliphatic organic material on the surface of Ceres, by M. C. De Sanctis et al., doi:10.1126/science.aaj2305; and commentary: Dwarf planet Ceres and the ingredients of life, by Michael Küppers, Science, 17 Feb 2017.
Life's Building Blocks Found on Dwarf Planet Ceres by Mike Wall, 16 Feb 2017.
Thanks for an alert, Ronnie McGhee. Life on Europa, Other Moons, Other Planets?... has related links.
Eugene V. Koonin interviewed by Suzan Mazur, Huffington Post, transcript online 03 Feb 2017. ...multi-cellular eukaryotes ...are actually a derived and highly constrained evolutionary subset of the biosphere.
Advances in biodiversity: metagenomics and the unveiling of biological dark matter, by Robert J. Robbins, Leonard Krishtalka and John C. Wooley, doi:10.1186/s40793-016-0180-8, Stand Genomic Sci., online 09 Sep 2016.
We take this synopsis from a comprehensive new study by geographers at the University of Exeter, UK, who modeled the processes in the biosphere that produce and consume oxygen. Its history, including the long stasis, is puzzling. With isotope data, they make a plausible case that mineral, tectonic, biological, climatic, weathering and sedimentary processes with feedback loops can explain it. The study also supports our belief that slow Gaian processes can make a planet habitable, and then more advanced life can develop and flourish without delay.
Gaia has a primer and related links.
Gaia is a possibly related webpage. Did bacteria make the methane?
The $2.4-billion plan to steal a rock from Mars, by Alexandra Witze, Nature News Feature, 18 Jan 2017.
Life on Mars! has historical information and links.
Communication between viruses guides lysis-lysogeny decisions, by Zohar Erez et al., doi:10.1038/nature21049; and commentary: ...Phages make a group decision by Alan R. Davidson, Nature, 18 Jan 2017.
...the choice [between lysis and lysogeny] in some phages is also profoundly influenced by communication, by means of small molecules, between phages infecting other cells in a culture. We know that horizontal gene transfer (HGT) by viruses affects evolution. This new discovery makes their power among prokaryotes even more impressive. Viruses... has a primer and related links.
The new method, pioneered in Joe Thornton's lab, apparently opens a new way to study adaptation. In our understanding, adaptation on the scale examined here would be categorized as microevolution. Macroevolution, by contrast, requires wholly new genetic programs that have not been shown to come from adaptive mutations of one or a few nucleotides. Therefore, the same method cannot be simply extended for studying macroevolution. Nevertheless, we are intrigued. ...because of technical and conceptual advances, it should now be possible to experimentally assess the causal predictions of many previously untested or weakly tested hypotheses of historical molecular adaptation....Discovery overturns long-held genetic belief, The University of Chicago Medicine (+PhysOrg.com), 03 Jan 2017; re:
Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster, by Mohammad A. Siddiq et al., doi:10.1038/s41559-016-0025, Nature Ecology & Evolution, online 13 Jan 2017.
Thanks, Stan Franklin and Bob Sweeney. Testing Darwinism versus Cosmic Ancestry is a related local webpage.
Macroevolutionary Progress Redefined... reconsiders the difference between micro- and macroevolution.
In a new, wide-ranging essay, Eugene V. Koonin of the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, considers the fitness landscapes of prokaryotes (large populations) versus eukaryotes (small populations). The latter allow for greater inventiveness, he concludes. To cope with this inescapable burden [introns], eukaryotes have evolved a global solution, the highly efficient splicing machinery. ...The nucleus itself may have evolved as a damage-control device that prevents the exit of unprocessed transcript to the cytoplasm. (How are these not more "Just-So" stories?)
Koonin is well aware of horizontal gene transfer (HGT) and de novo gene origination: mobile genetic elements (MGE) ...genes have been recruited for essential functions at key stages of eukaryotic evolution. But where the programming for these functions comes from is not a concern to him. If he wants a theory of evolution with testable predictions, may we suggest testing his predictions with quarantined experiments in biology or computer models?Splendor and misery of adaptation, or the importance of neutral null for understanding evolution, by Eugene V. Koonin, doi:10.1186/s12915-016-0338-2, BMC Biology, 23 Dec 2016.
Testing Darwinism versus Cosmic Ancestry and The Evolution Prize are related local webpages.
Neo-Darwinism: The Current Paradigm has a section with links about Fitness Landscapes.
New research provides another example of genetic systems older than standard darwinism expects them to be. The report also confirms that the subject retroviruses can be transferred across diverse species and become permanently installed into their genomes. Genetic programs that look too old, and horizontal gene transfer (HGT) by viruses are phenomena that surprise darwinism and support cosmic ancestry.Ancient retroviruses emerged half a billion years ago, by Carrie Arnold, Nature, 10 Jan 2017, re:
Marine origin of retroviruses in the early Palaeozoic Era, by Pakorn Aiewsakun & Aris Katzourakis, doi:10.1038/ncomms13954, Nature Communications, online 10 Jan 2017.
Viruses..., Metazoan Genes Older Than Metazoa? and Genes Older Than Earth? are related local webpages.
The Search for Extraterrestrial Genomes (SETG), homepage at MIT.
Thanks, Google Alerts.
Introduction: More Than Panspermia has historical information.
What Is Life? is a related local webpage.
The RNA World and Other Origin-of-Life Theories is a related local webpage.