What'sNEW Jul - Sep 2019
Our results strongly suggest that these transfers and the diversification of NCLDVs predated the emergence of modern eukaryotes, emphasizing the major role of viruses in the evolution of cellular domains.
Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes by J. Guglielmini et al., doi:10.1073/pnas.1912006116, 24 Sep 2019.
Viruses ... has related examples. Genes Older Than Earth? is possibly related.
A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators by David M. Needham, Susumu Yoshizawa, Toshiaki Hosaka et al., doi:10.1073/pnas.1907517116, PNAS, online 23 Sep 2019.
Viruses as Modulators of Interactions in Marine Ecosystems, Kiel University, 26 Sep 2019.
Viruses and Other Gene Transfer Mechanisms cites many related examples. Thanks, Martin Langford.
Enceladus Lights Up Saturn's Inner Moons by Paul Gilster, Centauri Dreams, 19 Sep 2019.
Life on Europa...? has links about Jupiter's and Saturn's moons.
CORRECTION: The bulk density of Enceladus is 1.61 - NASA.
Another Interstellar Visitor Is Headed Our Way by Bob King, Sky & Telescope, 11 Sep 2019. Thanks, Centauri Dreams.
Comets: The Delivery System has more.
Initial characterization of interstellar comet 2I/Borisov by Piotr Guzik et al., Nature Astronomy, 14 Oct 2019.
Thanks, William Smith and Chandra Wickramasinghe.
Hoyle and Wickramasinghe's Analysis... and Fred Hoyle Interviewed... have more.
Geological and Geochemical Constraints on the Origin and Evolution of Life by Norman H. Sleep, doi:10.1089/ast.2017.1778, Astrobiology, 12 Sep 2018 (the figure has been adapted); and commentary:
How geology tells the story of evolutionary bottlenecks and life on Earth by Sarah Wild, Astrobiology, 14 Oct 2018.
Life Before 3850 Million Years Ago? has related evidence. The RNA World describes origin-of-life theories.
Transposable elements (TEs) are ubiquitous in eukaryotic genomes. Their activity is normally suppressed by chaperone complexes. Heat can reactivate TEs by disabling the chaperone complexes. Now, new research from Italy illuminates key details of this process. In germ cells, a specific heat shock protein, Hsp70, liberates TEs by mechanisms which differ from the ones in somatic cells. With active TEs in the germline, the next generation will have more new variants for natural selection to choose among. In this way, an experience in a parent's lifetime, heat stress, can heritably influence future generations. (This sounds like Lamarckism.) And the system is not confined to fruitflies.
The human genome is made up of perhaps 70% transposable elements. How in the world has this ongoing internal attack not driven all life to extinction? The answer is because transposable elements are kept in check by a number of mechanisms in cells, including piRNAs.... This exquisite system involves the formation of a "library" of transposable elements encoded in an organism's genome, a codex of all of the transposable elements the organism has ever encountered, a reference to which all other sequences can be compared....The piRNA system is limited to the germ plasm, where its components are loaded into eggs and sperm....
Cappucci, Noro et al. have probed the details of an important evolutionary mechanism, a kind of "adaptive mutation". In response to stress, the next generation is born with new variation, unlocked by programming already in the genome.In the presence of drastic environmental changes, Hsp70 plays a key dual role in increasing both the survival probability of individuals and the genetic variability in their germ cells. The consequent increase of genetic variation in a population potentiates evolutionary plasticity and evolvability.
The Hsp70 chaperone is a major player in stress-induced transposable element activation by Ugo Cappucci, Fabrizia Noro et al., doi:10.1073/pnas.1903936116, PNAS, 03 Sep 2019. Robust Software Management... is incomplete.
Life on Europa, Other Moons, Other Planets? and Earth-analogs for those environments has related links.
Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells by Yanxiao Zhang et al., Nature Genetics, 19 Aug 2019.We observe that viruses and the elements they introduce play a powerful, essential role in macroevolutionary progress, even among eukaryotes. We think the evidence is overwhelming.
Viruses and Other Gene Transfer Mechanisms cites hundreds of related examples.
We categorize adaptations like this as microevolution, and we are pleased that the specific genetic changes underlying this example are known. We suspect that software management capabilities within genomes make such directed mutation possible. Else it seems magical. We hope that understanding how genomes are able to conduct directed mutation will become an active topic for study.
...visual adaptation to the new light environment was achieved through a recent and rapid selective sweep on a mutation in the rhodopsin gene. Furthermore, this exact same amino acid change has occurred at least 20 separate times in fish species transitioning from marine to brackish or freshwater environments. This is a remarkable example of convergent evolution.Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin by Jason Hill et al., doi:10.1073/pnas.1908332116, PNAS, 26 Aug 2019.
Convergent Evolution has related discussion. Robust Software Management... is a related, incomplete webpage.
08 Apr 2019: ...regulated mutagenesis mechanisms greatly increase the probability that the useful mutations will occur at the right time, ...and, possibly, in the right places.
Coordinated biotic and abiotic change during the Great Ordovician Biodiversification Event: Darriwilian assembly of early Paleozoic building blocks by Alycia Stigall et al., Palaeogeography, Palaeoclimatology, Palaeoecology, 15 Sep 2019. Early Species Developed Much Faster Than Previously Thought, Newswise, 16 Aug 2019.
Gaia has background and updates. Neo-Darwinism... discusses fitness landscapes and punctuated equilibrium.
Dust from asteroid breakup ...may have led to a boom in animal life by Joshua Sokol, Science, 18 Sep 2019.
Dust from a giant asteroid crash caused an ancient ice age, Field Museum, 18 Sep 2019. Thanks, Martin Langford.
A medical team has begun the effort to sequence the entire human microbiome by starting in the digestive tract. The Boston doctors analyzed 3,500 samples containing almost 46 million genes. More than half of the genes were "singletons", unique to each individual. This ratio likely extends to the entire human microbiome, but already, the number of unfamilar genes in the digestive tract is astonishing, even to us. And the finding supports our contention that so-called "new" genes actually already exist.The Landscape of Genetic Content in the Gut and Oral Human Microbiome by Braden T. Tierney et al., doi:10.1016/j.chom.2019.07.008, Cell Host & Microbe, 14 Aug 2019.
Microbial Fingerprinting by Ekaterina Peshiva, Harvard Medical School (+Technology Networks), 14 Aug 2019.
Thanks, Google Alerts.
Metazoan Genes Older Than Metazoa? and
Genes Older Than Earth? are related.
In darwinian philosophy, genes are composed by mutation-and-selection for ongoing or incipient functions. So, plausible, non-eukaryotic functions will need to be proposed for at least some of the ESPs. (But how did the genes get the programming for their eukaryote-specific functions? Nevermind.)
In cosmic ancestry, genes precede their functions. ESPs found in prokaryotes support this expectation.Scientists glimpse oddball microbe that could help explain ...complex life by Jonathan Lambert, Nature, 09 Aug 2019.
07 May 2015: Lots more about Lokiarchaea. 19 Feb 2017: ESPs in Lokiarchaea and other archaebacteria.
Metazoan Genes Older Than Metazoa? cites similar evidence since 1996. Genes Older Than Earth? has more.
Isolation of an archaeon at the prokaryote-eukaryote interface by Hiroyuki Imachi et al., Nature, 15 Jan 2020.
Meet the relatives of our cellular ancestor by Christa Schleper and Filipa L. Sousa, Nature, 15 Jan 2020.
...insight into early complex life on Earth, The Guardian, 15 Jan 2020. Thanks, Gordon Cooper.
The End and the Big Bang has related discussion and updates. Thanks, Karen Roberts.
The second thesis is that Intelligent Design (ID) does work. Well, if so, how does it work? When Meyer mentions causes now in operation (p 349), and titles a section A Cause Now in Operation (p 360), we become especially alert. But no causes ever appear. Meyer explains that ID is not a strictly material process or mechanism (p 395). He thinks it can still be scientific.
The book would probably edify anyone interested in evolution. And the gridlock imposed by Darwinism and ID remains in place. There must be another way.Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design, by Stephen C. Meyer, Harper One, 2013.
Evolution versus Creationism has discussion and links.
Compare Darwinism, Creationism/ID, Cosmic Ancestry
...we know that nature has been busy cross-contaminating worlds for the past 4 billion years.
Tardigrades Were Already on the Moon by Caleb A. Scharf, Scientific American, 08 Aug 2019.
Thanks, William Smith and Stan Franklin. I thought Scharf was skeptical. Anyway, good to hear.
...'Water bears' stuck on the moon after crash, BBC News, 07 Aug 2019.
11 Mar 2002: Tardigrades in space? and 18 May 2011: Project BIOKIS... are related.
Symphony of genes, University of Vienna (+Newswise), 05 Aug 2019; re: Ancient animal genome architecture reflects cell type identities by Bob Zimmermann et al., Nature Ecology & Evolution, 05 Aug 2019.
Metazoan Genes Older Than Metazoa? cites similar evidence since 1996. Genes Older Than Earth? has more.
Enceladus: First Observed Primordial Soup Could Arbitrate Origin-of-Life Debate by Amit Kahana, Philippe Schmitt-Kopplin and Doron Lancet, doi:10.1089/ast.2019.2029, Astrobiology, online 22 Jul 2019. The authors curtly dismiss the possibility that the organics might already include amino acids or other byproducts of life. They are aware that many carbonaceous meteorites contain amino acids, but apparently, not that these consistently exhibit remnant lifelike chirality. Panspermia is never mentioned. And of course, in an article about prebiotic soup, the software problem is left to others.
Life on Europa, Other Moons, Other Planets? has links about candidates for hosting life, including Enceladus.
The RNA World and Other Origin-of-Life Theories has history and updated links.
The Second Law of Thermodynamics and the six "Next" pages are all about the software problem.
02 Aug 2019: George Nickas replies with comments and questions.
In one featured protein, 20 out of 224 residues showed strong evidence of positive selection (tall red or blue lines.) Only a few of these 20 were in the enzymatic binding sites (colored bars in lower box.) Most residues showed evidence of only neutral mutations without any detectable effect (grey-colored "lawn"). To us the changes in this protein look like optimization by directed mutation, an example of microevolution. Yet this and similar changes seem to be involved in the evolution of placental birth — macroevolution by any definition. What can be said?
First, the study was focussed on only orthologous genes. If an H. formosa gene had no orthologs in the sister species, it was ignored. We wish the Dutch team would now ask if any acquired or newly activated DNA of any description "may have played a role in the evolution of the placenta." We think that might also be illuminating.The genome of the live-bearing fish Heterandria formosa implicates a role of conserved vertebrate genes in the evolution of placental fish by Henri van Kruistum et al., BMC Evolutionary Biology, 26 Jul 2019.
Neo-Darwinism... Macroevolutionary Progress Redefined... & Testing Darwinism... are related webpages.
27-30 Jul 2019: First author van Kruistum replies to our reqest for clarification. Very helpful!
Parasitic plants steal genes to become better parasites by Nick Carne, Cosmos, 23 Jul 2019.
Viruses and Other Gene Transfer Mechanisms has lots about the role of HGT in evolution.
Thanks, Stan Franklin and Google Alerts.
26 Aug 1996: Arlo 'n' Janis features life on Mars. Thanks, Polly Cooper. We shoulda posted this long ago.
Prebiotic Chemistry of Pluto by D.P. Cruikshank et al., Astrobiology, online 16 Jul 2019.
(How do they know that the organics are prebiotic?)
...the darker parts of our genetic heritage, Lund University (+Science Daily), 19 Jul 2019. Thanks, Martin Langford.
Evolution and ecology of plant viruses by Lefeuvre, P., Martin, D.P., Elena, S.F. et al., doi:10.1038/s41579-019-0232-3, Nat Rev Microbiol, 16 Jul 2019.
Plant viruses may be reshaping our world, ASU via PhysOrg.com, 17 Jul 2019. Thanks, Google Alerts.
The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions by Alessandro W Rossoni et al., doi:10.7554/eLife.45017, eLife, 31 May 2019.
Hayabusa2 touched down on Ryugu to collect material from beneath the surface.
Japanese spacecraft probes asteroid's guts for first time, Nature News, 10 Jul 2019.
What If Life Did Not Originate on Earth? by Isaac Chotiner, The New Yorker, 08 Jul 2019.
Thanks, Glenda Ruby. 06 Jan 2017: more on Ruvkun.
The linked interview led us to his recent TED-style lecture explaining how genomics and early life point to panspermia:
...Interstellar Communication with Microbes..., YouTube, 17 Apr 2019. 21 Dec 2017: more on Zubrin.
How is it Possible? includes our early speculations about intentionally undertaking panspermia to avoid extinction.
Before a bacterial gene can even operate in a eukaryotic cell, it has some major biological hurdles to overcome. It must acquire introns, a promoter sequence, and a termination sequence. It also has to be able to interact fruitfully with existing host genes. ...Researchers are trying to understand how this enormous leap occurs.
...against slim odds, some of these bacterial genes have introduced novel and critical functions to their new hosts. These transfers, say researchers, are an overlooked source of fodder for evolutionary transformation in complex organisms.
Horizontal gene transfer (HGT) is not overlooked in cosmic ancestry. We think it is essential for evolutionary progress. We highly recommend the new open-access review article by Viviane Callier....Gene transfers from bacteria and viruses may be shaping complex organisms, doi:10.1073/pnas.1909030116, by Viviane Callier, PNAS, 09 Jul 2019.
Viruses and Other Gene Transfer Mechanisms is our main related webpage.
Robust Software Management in Genomes begins our attempt "to understand how this enormous leap occurs."
Study suggests asteroids might play key role in spreading life by Peter Reuell, posted on Physorg.com (originally Harvard Gazette), 09 Jul 2019. Thanks, Ted Steele. 11-15 Oct and 09 Feb 2018: more about this study. Recently ( 23 Jun) another astronomer reported that neighboring stars may swap life-bearing cometary material frequently. We welcome endorsements of panspermia, but these recent studies are only about the transfer of physical material. It would be fanciful to assert that life is out there without the pioneering work by Fred Hoyle (1915-2001) and Chandra Wickramasinghe (b. 1939). Beginning in the 1960s, they made careful spectrographic analyses of interstellar dust. By 1980 they had found solid evidence for organic molecules and even whole bacteria in the dust. Their research gave interstellar panspermia its most substantial support.
Hoyle and Wickramasinghe's Analysis of Interstellar Dust has an historical outline. Comets... has more.
04 July 2019: Chandra Wickramasinghe reviews the development of cometary panspermia theory.