What'sNEW January - March 2014

16 March 2014 What'sNEW about HGT |
Michael Syvanen, Ph.D. It is difficult to imagine a more radical restructuring of evolutionary and biological thinking than that which would result from the incorporation of HGT into the structure of phylogenetic relationships.
Michael Syvanen, "Evolutionary Implications of Horizontal Gene Transfer" [
abstract], v 46 p 341-358, Annual Reviews Genetics, Dec 2012.
> Horizontal Gene Transfer, Michael Syvanen and Clarence I. Kado, eds., May 1999.
> Viruses and Other Gene Transfer Mechanisms is the main related CA webpage.

13 March 2014
Neil deGrasse Tyson
Cosmos: A Spacetime Odyssey, hosted by astrophysicist Neil deGrasse Tyson, premiered Sunday and Monday on Fox, National Geographic and other affiliated TV networks. The series is modeled on the 1980 one on PBS hosted by Carl Sagan; his widow, Ann Druyan, is the executive producer. Tyson, influenced by Sagan, makes the science compelling. Twelve more weekly episodes will follow, beginning Sunday night at 9/8c, 16 Mar 2014.
...New 'Cosmos' Series Brings TV Science Full Circle by Alan Boyle, NBC News, 7 Mar 2014.

7 March 2014
"Traditional evolutionary biology began in the 1930s with the 'modern synthesis', which fused Darwin's theses on phenotypic variation and selection with Mendel's concepts of genetic inheritance to explain the source of biological diversity. This synthesis predated knowledge that genes were made of DNA and of the structure of DNA and how it replicates. Thus, molecular mechanisms could not be integrated into concepts about how phenotypic variation is generated. Instead, assumptions had to be made about the origins of the variation that drives evolution. Among the cornerstone assumptions were that mutations are the sole drivers of evolution; mutations occur randomly, constantly, and gradually; and the transmission of genetic information is vertical from parent to offspring, rather than horizontal (infectious) between individuals and species (as is now apparent throughout the tree of life). But discoveries of molecular mechanisms are modifying these assumptions."
Susan M. Rosenberg and Christine Queitsch, "Combating Evolution to Fight Disease" [
summary], doi:10.1126/science.1247472, p 1088-1089 v 343, Science, 7 Mar 2014.
Science > Neo-Darwinism: The Current Paradigm is the main related CA webpage.
> Viruses and Other Gene Transfer Mechanisms is a related CA webpage.
> How is it Possible? includes mention of "adaptive mutation," now well-established.

5 March 2014 What'sNEW about HGT |
Newly discovered giant viruses, ...that dwarf most other viruses ...Researchers are beginning to realize that most organisms are in fact chimeras containing genes from many different sources — eukaryotic, prokary­otic, and viral alike.

Didier Raoult, "Viruses Reconsidered" [html], The Scientist, 1 Mar 2014.
Thanks Thanks, Stan Franklin.
> Viruses and Other Gene Transfer Mechanisms is the main related CA webpage.

Ed Yong, "Giant virus resurrected from 30,000-year-old ice" [html], doi:10.1038/nature.2014.14801, Nature, 3 Mar 2014.
Giant Virus Resurrected from Permafrost... by Tia Ghose, Yahoo News, 3 Mar 2014. Thanks Thanks, David Cotton.

...Pivotal advances in genetics—and other fields of biology—are also made by synthesizing disparate threads of extant information rather than generating new information from experiments or formal theory. William R. Rice, "The Synthesis Paradigm in Genetics" [abstract], doi:10.1534/genetics.113.160200, p 367-371 v 196, Genetics, 1 Feb 2014.

15 February 2014
Welcome to the astrobiology road mapping community. "This site is the home of the community developing the next generation of the Astrobiology Roadmap."

Set of terrestrial worlds T and subsets
3 February 2014
...A variety of processes exist that can make environmental conditions on a planet or moon more benign to life than is the case on Earth.
René Heller and John Armstrong, "Superhabitable Worlds" [html | pdf], doi:10.1089/ast.2013.1088, p 50-66 v 14, Astrobiology, 16 Jan 2014.
Star next door may host a 'superhabitable' world by Jeff Hecht, NewScientist, 31 Jan 2014.
> Life on Europa, Other Moons, Other Planets?... has links about other possibly habitable worlds.
Thanks Thanks, Theodore Rigley.

Earthlings may be extreme latecomers to a universe full of life....
Abraham Loeb, "The Habitable Epoch of the Early Universe" [
abstract], arXiv:1312.0613v2 [astro-ph.CO], 16 Jan 2014.
Did Alien Life Evolve Just After the Big Bang? by Katia Moskvitch, Space.com, 31 Jan 2014.
Thanks Thanks, George Stratton.

Old Mars rover finds signs of ancient water by Alexandra Witze, Nature, 23 Jan 2014.
> Life on Mars! is a related CA webpage.

Herschel Discovers Water Vapor Around Dwarf Planet Ceres, European Space Agency, 22 Jan 2014.
Water Found on Dwarf Planet Ceres, May Erupt from Ice Volcanoes by Tanya Lewis, Space.com, 22 Jan 2014.
Massive asteroid seen steaming off by Sid Perkins, Nature, 22 Jan 2014.

25 January 2014
The surfaces of tiny interplanetary dust particles are space-weathered by the solar wind, causing amorphous rims to form on their surfaces. Hydrogen ions in the solar wind react with oxygen in the rims to form tiny water-filled vesicles (blue). This mechanism of water formation almost certainly occurs in other planetary systems with potential implications for the origin of life throughout the galaxy. Credit: John Bradley, UH SOEST/ LLNL Water in interplanetary dust is a byproduct of solar wind and is therefore probably ubiquitous in the solar system, according to researchers in California and Hawaii. This news, added to the awareness of organics in space, has kindled new interest in pseudo-panspermia, the delivery of the "ingredidents of life" from space. The news also strengthens the likelihood that life is ubiquitous.

John P. Bradley et al., "Detection of solar wind-produced water in irradiated rims on silicate minerals" [abstract], doi:10.1073/pnas.1320115111, Proc. Natl. Acad. Sci. USA, online 24 Jan 2014.
Interplanetary dust particles could deliver water and organics to Earth and other terrestrial planets, University of Hawaii (+ScienceDaily +World Science), 24 Jan 2014.
Water found in stardust suggests life is universal, by Catherine Brahic, NewScientist, 24 Jan 2014.
> Hoyle and Wickramasinghe's Analysis of Interstellar Dust is a related CA webpage.
Thanks Thanks for alerts, Theodore Rigley and Stan Franklin.

24 January 2014
The earliest steps in de novo gene origination remain mysterious. Yet de novo genes are becoming recognized as possibly the major source for "new" genes. They are unexpressed strands of DNA that already contain genetic programming, needing only minor adjusting or optimising. They have no apparent expressed orthologs that could be used to support a darwinian origin. These genes appear to derive primarily from ancestral intergenic, unexpressed open reading frames (ORFs), with natural selection playing a significant role in their spread. ...These candidate polymorphic genes correspond to unique, intergenic sequence in the D. melanogaster reference genome..., are alignable to unique orthologous regions in the Drosophila simulans and Drosophila yakuba reference sequences, and show no significant BLASTP hits to the NCBI nr (nonredundant) protein database. The standard darwinian story of genetic programs gradually composed by trial-and-error does not work for de novo genes. Ignoring this failure is a mistake. Meanwhile, de novo gene origination, as now defined, is a basic prediction of cosmic ancestry.
Li Zhao et al., "Origin and Spread of de Novo Genes in Drosophila melanogaster Populations" [
abstract], doi:10.1126/science.1248286, Science, online 23 Jan 2014.
> Conserved Non-Genic Sequences and > A Wordcount for Comparison are related CA webpages.
> Three New Human Genes has become our main page about de novo genes.

20 January 2014
Philae landing on comet Rosetta awakens! After 31 months of hibernation, this comet-rendezvous mission of the European Space Agency (ESA) is ready to go back to work. Rosetta will soon chase down Comet 67P/Churyumov-Gerasimenko. Rosetta will stay in close orbit with the comet and ESA will deploy the Philae lander in November. If successful, it would be the first time a spacecraft has landed on a comet. Rosetta will spend 16 months closely observing the comet and carries 11 science instrument packages that will be used to identify the chemical composition of the comet as well as changes in temperature and gas activity as the object heats up.
Rosetta, homepage at ESA.
'Wake Up Rosetta' Live Stream..., International Business Times, 20 Jan 2014.
Rosetta wakes up and phones home by Elizabeth Gibney, Nature News Blog, 20 Jan 2014.
> Comet Rendezvous is a related section of the webpage, "Can The Theory Be Tested?"

20 January 2014
sea anemone (length = <1 inch) Geologists who drilled through the 270-meter-thick Ross Ice Shelf off Antarctica have observed a whole new ecosystem that no one had ever seen before. Intent on studying ocean currents, they were surprised to see thousands upon thousands of small sea anemones [example pictured] …burrowed into the underside of the ice..., fish that routinely swam upside down, ...polychaete worms, amphipods and a creature they dubbed 'the eggroll,' a 4-inch-long, 1-inch-diameter, neutrally buoyant cylinder that seemed to swim using appendages at both ends of its body…. The Antarctic discoveries have implications for the possibility of life that may exist on Europa, the ice-covered moon of Jupiter.
ANDRILL team discovers ice-loving sea anemones in Antarctica, University of Nebraska-Lincoln (+Newswise), 16 Jan 2014.
> Life on Europa, Other Moons, Other Planets?... has related links.

16 January 2014 What'sNEW about HGT |
Marine census chart
Environmental DNA (eDNA) in aquarium water correlates with the species living there, although some eDNA also arrives in the intake water. These observations come from a team at The University of Washington, studying the Monterey Bay Aquarium. Just a glassfull of sample water contains enough eDNA for the analysis. The analysist are pleased by this potential method for taking a census of life in any aquatic environment. We notice that the ubiquity of eDNA in the water multiplies the opportunities for horizontal gene transfer.

Kelly RP, Port JA, Yamahara KM and Crowder LB, "Using Environmental DNA to Census Marine Fishes in a Large Mesocosm" [html], doi:10.1371/journal.pone.0086175, 9(1): e86175, PLoS ONE, 15 Jan 2014.
DNA detectives able to 'count' thousands of fish using as little as a glass of water by Sandra Hines, The University of Washington (+Newswise), 15 Jan 2014.
> Viruses and Other Gene Transfer Mechanisms is a related CA webpage.

10 January 2014
If only those ideas get published that are considered orthodox..., progress of science will stall as it did for centuries in the Middle Ages — Milton Wainwright and Chandra Wickramasinghe
Milton Wainwright et al, "Biology Associated With A Titanium Sphere Isolated From The Stratosphere" [
pdf], doi:http://dx.doi.org/10.5334/jc.sr, Journal of Cosmology, 2013; and commentary from The University of Buckingham, "More Evidence of Life from Space: Isolation of a Remarkable Space-Derived Titanium Life Form" [local pdf], received 14 Dec 2013.

9 January 2014 *** What'sNEW about HGT |
human, chimp and orangutan chromosomes My favorite hypothesis is that at a key point in great ape evolution, there was a burst in retroviral activity — Edward Hollox, geneticist, University of Leicester, UK.
A Missing Genetic Link in Human Evolution by Emily Singer, Quanta Magazine (+ScientificAmerican.com), 2 Jan 2014.
Thanks Thanks for an alert, Jerry Chancellor.
> Human Genome Search... and
> Duplication Makes A New Primate Gene are related CA webpages.
> Viruses... is a related CA webpage

What'sNEW about HGT |.
*** Until now, "What'sNEW about HGT |" crosslinks were placed below the text and images of the article (as immediately above). The new placement, top right corner, makes them easier to find and use.

...Dr. Chandra Wickramasinghe...: 1-hour interview with Nancy du Tertre, online 27 Dec 2013.

2 January 2014
It appears that much of the genetic machinery necessary for a nervous system was present in the ancestor of all extant animals. Genes that appear to be older than the features they encode confound standard darwinism and confirm cosmic ancestry.
Joseph F. Ryan et al., "The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution" [
abstract], doi:10.1126/science.1242592, Science, online 13 Dec 2013.
> Metazoan Genes Older Than Metazoa? and > Genes Older Than Earth? are related CA webpages.
Thanks Thanks for an alert, Ken Augustyn.
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