COSMIC ANCESTRY | Quick Guide | Site Search | What'sNEW - Later - Earlier - Index | by Brig Klyce | All Rights Reserved

What'sNEW September - December 2015

30 Dec 2015 What'sNEW about HGT |
It is even argued that HGT has been highly active and important since the beginning of cellular life and that the complexity of life, as we know it, may not have evolved without HGT.
Horizontal transfer of short and degraded DNA has evolutionary implications for microbes and eukaryotic sexual reproduction by Søren Overballe-Petersen and Eske Willerslev, doi:10.1002/bies.201400035, Bioessays, Oct 2014.
Thanks Thanks, Tobias Mourier. > Viruses and Other Gene Transfer Mechanisms is the main related CA webpage.

16 Dec 2015 What'sNEW about HGT |
...We identified up to hundreds of active foreign genes in animals, including humans, suggesting that HGT provides important contributions to metazoan evolution.
Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes by Alastair Crisp, Chiara Boschetti et al., doi:10.1186/s13059-015-0607-3, Genome Biol. [PubMed abstract | pdf], 15 Mar 2015.
Horizontal gene transfer is not a hallmark of the human genome, by Steven L. Salzberg, doi:10.1186/s13059-017-1214-2, Genome Biology, 08 May 2017 NEW (Rebuttal).

We argue that the introduction of transposable elements by horizontal transfer in eukaryotic genomes has been a major force propelling genomic variation and biological innovation.
Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution by Sarah Schaack, Clément Gilbert and Cédric Feschotte, doi:10.1016/j.tree.2010.06.001, Trends Ecol Evol [abstract], Sep 2010.
> Viruses and Other Gene Transfer Mechanisms is the main related CA webpage.

> The Director of SETI says that an apparent biological fossil on Mars can be ruled nonbiological by geologists, with no need to consult biologists, 13-15 Dec 2015.

10 Dec 2015
...The arrival of this new group [diplobasts] was accompanied by a small number of novel proteins (specified by previously nonexistent genes).... Many triploblast groups are associated with an entirely new collection of previously nonexistent proteins, mediating previously unprecedented functions. — Stuart A. Newman, Professor of Cell Biology and Anatomy, New York Medical College
Are We Toys?, HuffPost Science, 8 Dec 2015. Thanks Thanks, Kevin Hatfield.

Standard darwinism is perplexed by genetic programs that seem to have come from nowhere. They are a basic prediction of cosmic ancestry. For example, see > New genetic programs Darwinism in and strong panspermia.

7 Dec 2015 What'sNEW about HGT |
We compare our assembly to a recently published one for the same species and do not find support for massive horizontal gene transfer.
The genome of the tardigrade Hypsibius dujardini, Georgios Koutsovoulos et al., doi:10.1101/033464, BioRxiv, 1 Dec 2015; and commentary:
...How Much Foreign DNA Tardigrades Actually Have by Victoria Turk, Motherboard, 7 Dec 2015. Later:
No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini, Georgios Koutsovoulos et al., doi:10.1073/pnas.1600338113, PNAS, online 3 May 2016.
24 Nov 2015
Approximately one-sixth of the genes in the tardigrade genome were found to have been acquired through horizontal transfer.... Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade, Thomas C. Boothby, Bob Goldstein et al., doi:10.1073/pnas.1510461112, PNAS, online 23 Nov 2015.
A huge chunk of a tardigrade's genome comes from foreign DNA, University of North Carolina, 23 Nov 2015.
...More than 6,600 genes ...were obtained through horizontal gene transfer from bacteria, fungi, and other organisms. ...Horizontally Acquired Genes in Water Bear Genome, Genome Web, 24 Nov 2015. Thanks Thanks, Google Alerts.
> Viruses and Other Gene Transfer Mechanisms is a related CA webpage.

23 Nov 2015 What'sNEW about HGT |
Genetic residue from ancient viral infections has been repurposed to play a vital role in acquiring pluripotency, the developmental state that allows a fertilized human egg to become all the cells in the body.
Ancient viral molecules essential for human development by Krista Conger, Stanford Medicine (+PhysOrg.com), 23 Nov 2015. Thanks Thanks, Stan Franklin.
The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming by Jens Durruthy-Durruthy, Vittorio Sebastiano, et al., Nature Genetics, 23 Nov 2015.
> Viruses and Other Gene Transfer Mechanisms is a related CA webpage.

Three things Rosetta taught us +3 we don't know about Comet 67P: c. 5 min. video from Nature.com, 18 Nov 2015.
A Sudden Jet on Comet 67P, Astronomy Picture of the Day, 18 Nov 2015.

NASA Is Sending a Spacecraft Deep Inside an Alien Geyser by Mark Strauss, National Geographic, 27 Oct 2015.

A Search for Extra-Terrestrial Genomes (SETG), NASA (+MIT), 15 Nov 2015. Thanks Thanks, Bill Smith.

> Chandra Wickramasinghe sends thoughts from the Indian Institute of Technology, Kharagpur, 11 Nov 2015.

9 Nov 2015
The Rosetta Mission Asks: Did Comets Bring Life to Earth? 2-min. video from NASA JPL, 5 Nov 2015.
Professor Chandra Wickramasinghe: comments, 8 Nov 2015. Thanks Thanks, Bill Smith and Ronnie McGhee.
29 Oct 2015
67P/Churyumov–Gerasimenko Mainstream science cannot explain the abundant O2 in the atmosphere of comet 67P. Instruments on ESA's Rosetta spacecraft detected the oxygen consistently over months of observation. Current Solar System formation models do not predict conditions that would allow this to occur.

Methane is also present. Responding to this surprise, ESA investigator Kathrin Altwegg says, ...The combination of methane and O2 was a hint that you had life, but on our comet we have both methane and O2, but we don't have life.....

The evidence points squarely at life. Altwegg's assurance that the comet is lifeless makes no sense. But the roar of consensus can be intimidating.

Abundant molecular oxygen in the coma of comet 67P/Churyumov-Gerasimenko, by André Bieler et al., doi:10.1038/nature15707, p 678-681 v 526, Nature, 29 Oct 2015.
Oxygen found on comet in Rosetta mission... by Deborah Netburn, Los Angeles Times, 28 Oct 2015.
...Most surprising discovery ...so far by Ian Sample, The Guardian, 28 Oct 2015.
Thanks Thanks, Ken Augustyn and Doron Goldberg for alerts, and Kevin Keogh for additional comments and a link:
Life detection by atmospheric analysis by Dian R. Hitchcock and James E. Lovelock, Icarus, Sep 1967.
> What'sNEW under Comet Rendezvous has links to Rosetta updates. > Comets... is a related local webpage.

29 Oct 2015
...The last unicellular ancestor of animals was already capable of elaborate specification of cell types.
Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals, by Alex de Mendoza et al., doi:10.7554/eLife.08904, eLife Journal, 14 Oct 2015.
Gene regulation predates animals, doi:10.1038/526612e, p 612-613 v 526, Nature, 29 Oct 2015.
> Metazoan Genes Older Than Metazoa? and > Genes Older Than Earth? are related CA webpages.

28 Oct 2015
A fossil on Mars resembles one on Earth. The Martian fossil (left, picture width = c. 2cm) was photographed with the Microscopic Imager camera of NASA's Opportunity rover on sol 34 of that mission (27 Feb 2004), at Mars' Meridiani Planum, once a wet environment. The Earthly one (right, scalebar = cm) is identified as Reteocrinus elongatus, a marine animal in the crinoid family, which flourished in the paleozoic era. This example was recovered by Percy Raymond in 1931, in Upper Ordovician sediments in Montgomery County, Tennessee, and placed in the Harvard Museum of Natural History. The segmenting, branching, triangular crotch and cup or "crown" structure, considered together, make a convincing match, and the sizes are comparable. The spearpoint-like plate on the Martian fossil is also diagnostic of crinoids. Looks like former life on Mars.
Crinoid fossil from Harvard Museum Fossil on Mars
Opportunity :: Microscopic Imager :: Sol 034: uncropped image and legend from NASA.
Thanks Thanks, Richard B. Hoover, for the photo from the Harvard Museum, taken 4 Oct 2015.
Did NASA's Opportunity rover find evidence for life on Mars in 2004? posted 26 Jul 2013.
> The Director of SETI comments: geologists say the fossil is not biological, 13-15 Dec 2015.
> Astrobiologist and Mars specialist Frances Westall writes, 'look-alikes' is not enough, 15 Jun 2016.
> A geologist who works with NASA on Mars missions writes, "...It could be a fabric related to recrystallization of the sulfate minerals," 4 Oct 2016.
> Life on Mars! is a related local webpage.
Ron McGhee thinks a rock at the Spirit rover landing site may be petrified wood, emailed 1 Nov 2015.

Astrobiology, Oct 2015
26 Oct 2015
Astrobiology is the leading peer-reviewed international journal for astronomers, biologists, chemists, geologists, microbiologists, paleontologists, and planetary scientists designed to advance our understanding of life's origin, evolution, and distribution in the universe. This authoritative journal disseminates the most current findings and discoveries coming out of recent interplanetary exploration and laboratory - and field-based research programs.

Astrobiology, Oct 2015. This entire issue is available online.
Thanks Thanks, Sherry L. Cady, Editor-in-Chief [disclaimer].


21 Oct 2015
...It seems that Europa's ice has been penetrated often in the past, and possibly in geologically recent time.... Astrobiological materials could be transported to the ocean via these impact-created conduits.
Journal of Geophysical Research
Impact breaching of Europa's ice: Constraints from numerical modeling, by Rónadh Cox and Aaron W. Bauer, doi:10.1002/2015JE004877, Journal of Geophysical Research, 14 Oct 2015.
Did Comets Spark Alien Life in Europa's Oceans? by Larry O'Hanlon, Discovery.com (+Space.com), 14 Oct 2015.
Thanks Thanks, Ronnie McGhee.
> Life on Europa, Other Moons, Other Planets?... has links to more about possible life elsewhere.

20 Oct 2015
Carbon isotopes that may point to life have been found in 4.1 billion-year-old zircon. The geochemists at UCLA and Stanford who report the finding say that the subject inclusions are likely not contaminants, and the isotopic fractionation is consistent with a biogenic origin and may be evidence that a terrestrial biosphere had emerged by 4.1 Ga, or ~300 My earlier than has been previously proposed. Life on Earth so early would be well-explained by panspermia. Life on Earth may have started almost instantaneously, says coauthor Mark Harrison.
Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon, by Elizabeth A. Bell et al., doi:10.1073/pnas.1517557112, PNAS, online 19 Oct 2015.
Scientists may have found the earliest evidence of life on Earth by Julia Rosen, Science, 19 Oct 2015.
Life on Earth likely started 4.1 billion years ago by Stuart Wolpert, UCLA (+SpaceDaily +Physorg.com), 19 Oct 2015.
Life on Earth May Have Started Almost Instantaneously, The Daily Galaxy, 21 Oct 2015.
Thanks Thanks, Ronnie McGhee, Rob Sheldon and Stan Franklin.
> Life Before 3850 Million Years Ago? and > The RNA World are related local webages.

19 Oct 2015
Neo-Darwinism just needs to be left behind so that the universe of learning, of finding out about nature, opens up properly — Mae-Wan Ho [interviewed in]
The Paradigm Shifters: Overthrowing the 'Hegemony of the Culture of Darwin', by Suzan Mazur, Caswell Books, 17 Nov 2015.

16 Oct 2015
PNAS 13 Oct 15 cover Algal ancestor of land plants was preadapted for symbiosis. That's the title of an open-access article by an international collaboration of geneticists, microbiologists and affiliated specialists who write, The ability of the first land plants to form symbiotic associations with beneficial fungi was [a] critical innovation.... Yet they conclude that genes essential for this symbiosis predated the first land plants. It's another example of genes that appear to be available before they are needed. Standard darwinism must invent new stories to explain them. Cosmic ancestry requires them.

Algal ancestor of land plants was preadapted for symbiosis by Pierre-Marc Delaux et al., doi:10.1073/pnas.1515426112, PNAS, online 5 Oct 2015.
Thanks Thanks, Sascha Wageringel, for alerts and encouragement.
> Metazoan Genes Older Than Metazoa? and > Genes Older Than Earth? are related CA webpages.
> Pierre-Marc Delaux, lead author, disagrees with our comments, 23 Oct 2015.

15 Oct 2015
A 500-year experiment to monitor bacterial dormancy is launched in Edinburgh and London.
Suspended animation by Alex Riley, Aeon, 15 Oct 2015. Thanks Thanks, George Nickas.
> Bacteria: The Space Colonists is a related CA webpage.

9 Oct 2015 What'sNEW about HGT |
...Comparative analysis of eukaryotic cells and genomes indicates that the signature advanced functional systems of the eukaryotic cells were already present in the last eukaryotic common ancestor (LECA).
...The emergence of these fundamental facets of advanced cellular organization presents a challenge of such scale that Darwin’s famous scenario for the evolution of the eye looks like a straightforward solution to an easy problem.
...[T]he only consistent characterization of the evolutionary status of eukaryotes is as archaeo-bacterial chimeras.
...It turns out that the evolutionary relationship between archaea and eukaryotes is not limited to the core of information-processing systems but also involves several genes and entire gene suites that are essential for eukaryotic intracellular organization. Surprisingly, however, these homologs of the signature eukaryotic genes are scattered among different archaea.
...The newly achieved clarity in our understanding of these key aspects of eukaryogenesis calls for reassessment of some of the most general concepts in biology. The first one is the representation of the entire history of life as a single evolutionary tree....
BMC Biology
Eugene V. Koonin,
Archaeal ancestors of eukaryotes: not so elusive any more, doi:10.1186/s12915-015-0194-5, 13:84 BMC Biology, 5 Oct 2015.
Thanks Thanks, Martin Langford. And Stan Franklin.

We agree and we thank NIH's Eugene V. Koonin for his insights, but something troubles us. In this article the term "origin" appears about 40 times overall. The meta-message is that now, with previously unknown origins revealed, everyone can relax. What? If something originated, that would mean that it did not already exist. But Koonin explains that the genes for most eukaryotic systems were "already present." The term "origin" seems to have a different meaning in the darwinian paradigm, something like "proof of prior existence." No. Don't relax yet.

Eukaryotic genes that exist before eukaryotes confound standard darwinism and confirm cosmic ancestry.

> The Tree of Life, > Metazoan Genes Older Than Metazoa? and > Genes Older Than Earth? are related CA webpages.
Numerous genes for Eukaryotic Signature Proteins (ESPs) have been found in Archaea, What'sNEW, 7 May 2015.
> Viruses and Other Gene Transfer Mechanisms is a related CA webpage.

28 Sep 2015
The dark streaks, known as recurring slope linae There is water on Mars! This is the latest news from NASA. Alfred S. McEwen, professor of planetary geology at the University of Arizona and the principal investigator of images from a high-resolution camera on the Mars Reconnaissance Orbiter, reports the detection of hydration salts in dark streaks on slopes on Mars. These must have formed in the presence of liquid water within only days before their detection. This evidence virtually proves the earlier suggestion that recurring dark streaks on Mars are traces of flowing water. (NASA's computer-generated false-color Mars image here exaggerates the vertical dimension by 1.5x.)

> Life on Mars! includes links to c. 75 earlier reports of water on Mars. Search the page for "water" or "ocean".
NASA Confirms Evidence That Liquid Water Flows on Today's Mars, NASA, 28 Sep 2015.
Signs of Liquid Water Found on Surface of Mars... by Kenneth Chang, The New York Times, 28 Sep 2015.
Martian salt streaks 'painted by liquid water' by Jonathan Amos, BBC News, 28 Sep 2015.
Thanks Thanks, Polly Klyce Pennoyer, Richard Hoover, Martin Langford and NPR.
et seq:
Seasonal Streaks Point to Recent Flowing Water on Mars, Astronomy Picture of the Day, 30 Sep 2015.
Mars find suggests our solar system is awash with life by Chandra Wickramasinghe, The Guardian, 30 Sep 2015.
> Chandra Wickramasinghe sends a copy of his letter "Life on Mars," published in The Times, 2 Oct 2015.
Neil deGrasse Tyson – Water on Mars: 6-min. YouTube video with Bill Maher, 2 Oct 2015.
Thanks Thanks, Justin Willingham.

27 Sep 2015 What'sNEW about HGT |
Nearly 65% of the proteins encoded by Mollivirus have no known homologs. So says Barbara R. Jasny in commentary on a report of a newly observed giant virus whose genome encodes 523 proteins. In addition to the majority of unfamilar genes, 16% have homologs in another giant virus, and 10% have homologs in the virus's usual host. Intriguingly, the virus remains viable after 30,000 years in Siberian permafrost.

Genes without discernable provenence, genes where they aren't needed, genes acquired by horizontal transfer, and frozen giant viruses that can persist indefinitely? All of this surprises standard darwinism and supports cosmic ancestry.

In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba by Matthieu Legendre, Audrey Lartigue et al., doi:10.1073/pnas.1510795112, E5327–E5335, n 38 v 112, PNAS, 22 Sep 2015.
Giant virus varieties keep growing by Barbara R. Jasny, doi:10.1126/science.349.6255.1501-e, Science, 25 Sep 2015.
> Viruses and Other Gene Transfer Mechanisms is a related local webpage.
> Robert Temple alerts us to related earlier research by the same French team, 11 Sep 2015.

24 Sep 2015 What'sNEW about HGT |
Ever-evolving mosiac The nuclear genome is an ever-evolving mosaic of DNA acquired from different sources — John M. Archibald

Gene transfer in complex cells, commentary in Nature on:
Endosymbiotic origin and differential loss of eukaryotic genes by Chuan Ku et al., doi:10.1038/nature14963, p 427-432 v 524, Nature, 27 Aug 2015.
> Viruses and Other Gene Transfer Mechanisms is a related local webpage.


15 Sep 2015 What'sNEW about HGT |
Reticulate Evolution The abundant occurance of lateral gene transfer in all three domains of life has only been recognized in recent years. Molecular phylogenetic reconstructions ...now provide conclusive evidence for "alien" or exogenous DNA uptake....

Nathalie Gontier, ed.,
Reticulate Evolution, v 3, Interdisciplinary Evolution Research, ISBN:978-3-319-16344-4, Springer International Publishing, 10 Jul 2015.
Thanks Thanks, Stan Franklin, for mentioning this book.
> Viruses... is a related local webpage.

13 Sep 2015
30,000-year-old giant virus 'comes back to life' by Rebecca Morelle, BBC News, 4 Mar 2014.
Thanks Thanks, Robert Temple >.

New Pluto Images from NASA’s New Horizons: It’s Complicated, NASA, 10 Sep 2015. Thanks Thanks, Lawrence Klaes.

Remnants of Life Found Half a Mile Below the Seafloor by Dirk Schulze-Makuch, Air & Space, 9 Sep 2015. "Similar deep habitats might be found on other worlds." Thanks Thanks, Bill Smith.

Wallis MK and Wickramasinghe NC, "Pluto's Surprises: Mountain Tectonics, Methane and Evidence of Biology," doi:10.4172/2332-2519.1000135, Journal of Astrobiology & Outreach, 27 Jul 2015.

4 Sep 2015
We have found thousands of transcripts that are human- and/or chimpanzee-specific and which are likely to have originated de novo from previously non-transcribed regions of the genome. We have observed an enrichment in transcription factor binding sites in the promoter regions of these genes.... [S]ome of the genes encode new functional proteins ...which may have contributed to phenotypic novelties in human evolution. These are among the observations made by European researchers in genomics and related specialties who analyzed RNA sequence data from humans, chimps and other species. They undertook the study because they believe, as they state at the outset, The birth of new genes is an important motor of evolutionary innovation.

They saw that many important genes were formerly silent, open reading frames (ORFs) that were recruited into service by newly acquired promoter sequences. This phenomenon is becoming well-known, and the previously silent ORFs are now designated de novo genes. They comment, ...In de novo gene evolution the full sequence space can be potentially explored....

Yes, theoretically. But not in the real world. Even a gene of only 300 nucleotides has 4^300 or about 10^180 possibilities in its sequence space. Allowing for very wide latitude in the protein product, the exponent might be effectively halved; even so, ~10^90 possibilities? A sequence space that large to fully explore? Thousands of times? The entire human genome has room for only about 10^7 such sequences. Where on Earth would this exploration be taking place? Where at all?

The "birth" of new genes is not an observed phenomenon. We only call them "new" because they were first observed or first activated in the species under study. It would be more fruitful to ask where the genes come from, how they got here, etc., as in cosmic ancestry.

Jorge Ruiz-Orera et al., "Origins of de novo genes in human and chimpanzee," arXiv:1507.07744 [q-bio.GN], 28 Jul 2015.
A Surprise Source of Life's Code by Emily Singer, Quanta Magazine (+Scientific American), 18 Aug 2015.
> Conserved Non-Genic Sequences, > A Wordcount for Comparison, > Three New Human Genes, > New genetic programs in Darwinism and strong panspermia, > Human Genome Search and > Neo-Darwinism... are related CA webpages. Thanks, Thanks Ken Jopp!
04 Jan 2016: We discuss a new version of Jorge Ruiz-Orera et al., published in PLoS, 31 Dec 2015.

COSMIC ANCESTRY | Quick Guide | Site Search | What'sNEW - Later - Earlier - Index | by Brig Klyce | All Rights Reserved