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What'sNEW Archives, October-December 2003

December 31
SOS response pathway Stress can increase the rate of horizontal gene transfer. Microbiologists in Boston have confirmed this phenomenon in the bacterial species Vibrio cholerae after dosing it with an antibiotic, ciprofloxacin. The antibiotic prompts an "SOS response" and induces the transfer of genetic integrating conjugative elements (ICEs) among the bacteria. Some of the ICEs confer resistance to antibiotics, including ciprofloxacin.

The importance of gene transfer among bacteria is already fully accepted. Now we learn that the rate of gene transfer can be enhanced by environmental stress. We wonder how many forms of stress will enhance horizontal transfer among bacteria, and whether eukaryotes have a version of the same mechanism.

John W. Beaber, Bianca Hochhut and Matther K. Waldor, "SOS response promotes horizontal dissemination of antibiotic resistance genes" [abstract], p 72-74 v 427, Nature, 01 Jan 2004.
Horizontal Gene Transfer, class notes for Microbiology 316 at the University of Illinois, Urbana-Champaign, by Andrea Baker, 22 Sep 2001: "Natural genetic transformation is believed to be the essential mechanism for the attainment of genetic plasticity in many species of bacteria."
How is it Possible? mentions "adaptive mutation," an increase in the mutation rate when a need arises.
Viruses... is a CA webpage about horizontal gene transfer. [Next-What'sNEW about HGT-Prev]

Formalhaut Circumstellar Disk in infrared Infrared telescope sees hydrocarbons: "There are more organic molecules in the universe than what can be discerned in visible light. Using their new orbital infrared telescope [the Spitzer Space Telescope], astrophysicists are finding that the basic building blocks of carbon chemistry have found a primary place in some of the most unlikely spots...." [Thanks, Jerry Chancellor.]
First Images Show Organic Molecules, by Leslie Mullen, Astrobiology Magazine, 23 Dec 2003.
Analysis of Interstellar Dust is a related CA webpage.

gene distribution A species of coral contains many sequences matching ones from genes thought to be peculiar to vertebrates, such as genes associated with highly differentiated nervous systems. Furthermore, the coral shares significantly more genes with humans than it does with fruitflies, worms, or species in other non-mammalian kingdoms. The Australian geneticists who made this finding conclude, "Our preliminary survey ...appears to turn upside down several preconceived ideas about the evolution of animal genomes."

To make the finding conform to the darwinian paradigm, the writers must suppose, "Rather than being simple, the common metazoan ancestor was genetically complex, containing many genes previously considered to be vertebrate innovations." (Nothing like this phylogeny is suggested in the fossil record.) They must also suppose that the rate of gene loss accelerates significantly on the branches leading to non-mammalian kingdoms. (Else those kingdoms would have the genes as well.)

The evolution of new features — like the ones that differentiate humans from coral — depends on the acquisition of new genetic programs. Suppose these do not arise by the darwinian method, but arrive by horizontal transfer. In this case, the presence of human genes in coral, and not elsewhere, does not create a crisis. But it is still quite interesting!

R. Daniel Kortschak, Gabrielle Samuel, Robert Saint and David J. Miller, "EST Analysis of the Cnidarian Acropora millepora Reveals Extensive Gene Loss and Rapid Sequence Divergence in the Model Invertebrates" [abstract], p 2190-2195 v 13, Current Biology, 16 Dec 2003.
Coral reveals ancient origins of human genes, by Carina Dennis, Nature Science Update, 16 Dec 2003.
Viruses... is a CA webpage about horizontal gene transfer. [Next-What'sNEW about HGT-Prev]
Metazoan Genes Older Than Metazoa? is a related CA webpage.
Misinterpretation is the subject of a reply from Dan Kortschak, 12 Nov 2005.

AbSciCon The Third Astrobiology Science Conference will be held 28 March to 1 April 2004, at NASA's Ames Research Center, California. A list of confirmed speakers is available at the conference website, with registration, abstract submission and other details to follow.
AbSciCon, 28 Mar - 1 Apr 2004.
"Abstracts from the Astrobiology Science Conference 2004" [], NASA Ames Research Center, Moffett Field, CA, 28 Mar - 1 Apr 2004.

variation in CNGs vs genes
In mammals, the rate of change per million years (D/my) is less in CNGs than in protein- or RNA-encoding genes.
In mammals, CNGs are more numerous and better conserved than genes. CNGs are conserved non-genic sequences whose mean length is some 100 to 200 nucleotides. Seven geneticists studied over a dozen genomes including the green monkey, ring-tailed lemur, brush-tailed porcupine, rabbit, pig, cat, greater mouse-eared bat, white-toothed shrew, nine-banded armadillo, African elephant, tammar wallaby, and platypus to ascertain their properties. The immutability (see figure) and abundance of CNGs are more consistent with cosmic ancestry than darwinism, we suggest on a new webpage. [Thanks, Tom Ray.]
Conserved Non-Genic Sequences is the new CA webpage, with references and links to abstracts, 20 Nov 2003.
Neo-Darwinism... is a related CA webpage.
Human Genome Search at The University of Oklahoma is a related CA webpage.
New genetic programs in Darwinism and strong panspermia is a related CA webpage about the evolutionary significance of highly conserved genetic programs.

Microorganisms may have spread throughout the galaxy. That's the conclusion in two papers to be published simultaneously in the Monthly Notices of the Royal Astronomical Society. It is already known that microscopic life could cross interplanetary distances on debris blasted from a planet by a collision with an asteroid or comet. However, the enormous distances between stars have seemed an insurmountable barrier to colonising a galaxy. These new papers show ways around this barrier—

indirect route Max K. Wallis and N.C. Wickramasinghe, Cardiff Centre for Astrobiology, "Interstellar transfer of planetary microbiota" [abstract | pdf | local pdf], doi:10.1111/j.1365-2966.200, p 52-61 v 348 n1, Monthly Notices of the Royal Astronomical Society, Feb 2004:
Wallis and Wickramasinghe explain that life-bearing particles would be buried in and protected by comets, which escape from the Edgeworth Kuiper belt and reach proto-planetary discs and star-forming nebulae [see figure]. There sputtering releases the trapped micro-organisms to seed forming planetary systems.

W.M. Napier, Armagh Observatory, "A Mechanism for Interstellar Panspermia" [abstract | local pdf], doi:10.1111/j.1365-2966.2004.07287.x, p 46 v 348 n 1, Monthly Notices of the Royal Astronomical Society, Feb 2004:
"Napier finds that collisions with interplanetary dust will quickly erode the ejected boulders to ...tiny, life bearing fragments [that] may be thrown out of the solar system by the pressure of sunlight in a few years."

Spread of Life Throughout the Galaxy (1 page .pdf) [or 2 page .doc], Armagh Observatory Press Release by John McFarland, 31 October 2003.
Introduction... is a related CA webpage.
Panspermia Asks New Questions is a related CA webpage.
How Is It Possible? is a related CA webpage.
Earth sows its seeds in space, by Philip Ball, Nature Science Update, 23 Feb 2004.

Ancient river delta on Mars
photo width = c. 14 km
Water flowed on Mars for long times, according to the simplest interpretation of new NASA photos. They show forms apparently left by river deltas (right) and meanders, which brief flows or floods do not create — but longlasting rivers do.

Michael C. Malin and Kenneth S. Edgett, "Evidence for Persistent Flow and Aqueous Sedimentation on Early Mars" [abstract], p 1931-1934 v 302, Science, 12 Dec 2003.
Delta-Like Fan on Mars Suggests Ancient Rivers Were Persistent, Newsrelease 2003-151, NASA/JPL, 13 November 2003.
Distributory Fan Near Holden Crater, PIA04869, NASA/JPL/Malin Space Science Systems, 13 November 2003.
Distributary Fan: "Smoking Gun" ..., MGS MOC Release No. MOC2-543, 13 November 2003.
Life on Mars! is a related CA webpage.

ESA's Mars sample returner Europe's Mars sample return mission is planned for 2011, when a sample return capsule will be launched for orbit around Mars. Two years later, another spacecraft with Mars descent and ascent capabilities will follow. It will collect samples on Mars and then rendezvous with the return capsule in Mars orbit. The capsule will return to Earth for delivery to a planetary protection facility. The European Space Agency (ESA) says it is "a mission of tremendous scientific importance and the first robotic mission with a similar profile to a possible human expedition to Mars." [Thanks, Newshub.]

ESA’s first step towards Mars Sample Return, Bruno Gardini, ESTEC, 12 Nov 2003.
Life on Mars! is a related CA webpage.

To populate 10^10 suitable planets within the lifetime of the Galaxy would require about 33 generations with a doubling time of about 300 Myr.... W.M. Napier, "A Mechanism for Interstellar Panspermia," Monthly Notices of the Royal Astronomical Society, accepted October 2003.

Changing spots on Mars
photo width = c. 3 km
More changing spots on Mars have been photographed by the Mars Orbiter Camera. The ones shown here lie outside an impact crater (partly visible, upper left) in the south polar region of Mars. The largest spots in this photo have grown to about 200 meters in diameter in the martian spring. NASA believes, "As frost is removed from the patches of sand, it creates a pattern of dark spots." But others think the dark spots may be a life form (like mold?) that grows when the weather warms. [Thanks, Ron Baalke.]

Defrosting Scene, Mars Global Surveyor MOC Release No. MOC2-531 (with legend), and a larger image, 1 November 2003.
Dark spots which spread every Martian spring... is CA's first notice of the phenomenon, 7 Sep 2001.
More about the changing dark spots on Mars is CA's second notice of the phenomenon, 31 Jan 2002.
Life on Mars! is a related CA webpage.

Mudflow on Mars? Mudflows on Mars are well supported, according to a team of Spanish geologists. Studying images taken by NASA's Mars Orbiter Camera of the Gorgonum crater, they see formations that they cannot explain any other way. In Madrid, Astrobiology Magazine interviewed team members Roberto Oyarzun, Cristobal Viedma, Alvaro Márquez and Javier Lillo. [Thanks, Marsbugs.]

Mars and Muddied Waters?, Astrobiology Magazine, 29 Oct 2003.
MGS MOC Release No. MOC2-241, Malin Space Science Systems, 22 June 2000.
Life on Mars! is a related CA webpage.

Amino acids in meteorites are gaining favor as the starting ingredients for life on Earth. At a conference in Seattle, geologist Mike Engel and chemist Stephen Macko confirm that eight of life's standard twenty amino acids have been found in carbonaceous meteorites like Murchison. The non-presence of the other twelve is a puzzle — and it is evidence that the eight are not earthly contaminants. Why amino acids from space are predominantly left-handed, if they were produced nonbiologically, is another puzzle — for which we have another suggestion. Anyway, "pseudo-panspermia" is now well-accepted, and we will not complain. [Thanks, Larry Klaes.]

Geological Society Michael H. Engel and Stephen A. Macko, "The Significance of Protein Amino Acids in Carbonaceous Meteorites" [abstract], Geological Society of America, 3 Nov 2003.
Seattle Annual Meeting, Geological Society of America, 2-5 Nov 2003.
Extraterrestrial Enigma: Missing Amino Acids In Meteorites, ScienceDaily, 4 Nov 2003.
Life theories [lots about pseudo-panspermia], by Anne McIlroy, The Globe and Mail, 4 Oct 2003.
Panspermia Asks New Questions is a CA webpage that defines "pseudo-panspermia".
Comets... is a related CA webpage.
Amino Acid Asymmetry in the Murchison Meteorite is a related CA webpage.

Where the red rain fell The red rain of Kerala has been attributed to cometary panspermia by a pair of scientists from Mahatma Gandhi University. In the abstract of a recent paper, Godfrey Louis and A. Santhosh Kumar write:

"Red coloured rain occurred in many places of Kerala in India during July to September 2001 due to the mixing of huge quantity of microscopic red cells in the rainwater. Considering its correlation with a meteor airbust event, this phenomenon raised an extraordinary question whether the cells are extraterrestrial. Here we show how the observed features of the red rain phenomenon can be explained by considering the fragmentation and atmospheric disintegration of a fragile cometary body that presumably contains a dense collection of red cells. Slow settling of cells in the stratosphere explains the continuation of the phenomenon for two months. The red cells under study appear to be the resting spores of an extremophilic microorganism. Possible presence of these cells in the interstellar clouds is speculated from its similarity in UV absorption with the 217.5 nm UV extinction feature of interstellar clouds." [Thanks, Michael Paine and Chandra Wickramasinghe.]

Godfrey Louis and A. Santhosh Kumar, "Cometary panspermia explains the red rain of Kerala" [abstract | 20-page pdf], 5 Oct 2003.
Analysis of Interstellar Dust is a related CA webpage.
A dust storm caused the red rain...?, 24 Dec 2005.
A dust storm couldn't have caused the red rain..., 6 Jan 2006.
Chandra Wickramasinghe discusses the red rain in an online interview, 2 Aug 2006.
Jim Galasyn wonders if isotope analysis would be useful, 16 Aug 2006.
Robert Temple informs us about red rain in Burgundy in 1361, posted 22 Oct 2006.
The Red Rain of Kerala has historical precedents, 6 Feb 2008.
...Cells "from space"... is the subject of another news story pointed out by Stan Franklin, 11 Sep 2008.

panspermia The origin of the word "panspermia" is the subject of a question we posted on "Google Answers."
+ Hlabadie replied, "The scientific usage of the term can be traced back to the Ionian Greek philosopher Anaxagoras of Clazomenae, circa 450 B.C.
+ ...The term is first noted in English in 1690, according the Oxford English Dictionary, in the form *panspermatic*, appearing in William Leybourn's Cursus Mathematicus."
+ Blinkwilliams wrote, "According to the OED the term [panspermia] first appears in Robley Dunglison's Medical Lexicon from 1842."
Q: origin of a scientific term, Google Answers, 2 Oct 2003.
Introduction... is a related CA webpage.

Workshop Group
photo by B. Stedman
The NASA Astrobiology Institute Virus Focus Group held its first workshop in Portland Oregon, 16-17 October. It was chaired by former NAI head Barry Blumberg (1) and hosted by Portland State University's Ken Stedman (2). The possible role of viruses in the origin of life, methods of sampling microorganisms under ice, and viruses that infect extremophiles were among the subjects discussed.

My initial interest was to find out more about the role of viruses in evolution. I was intrigued to learn from Luis Ruedas (n.s.) of Portland State that mice infected with hantavirus live longer than uninfected mice. And Paul Turner (3) of Yale explained that viruses can generate "gene transfer agents" that contain host genes only — no viral genes. When the cell dies these may be released into the environment for possible incorporation into other genomes.

But my primary lesson was that the world of viruses is huge and mostly unknown. In this regard, Forest Rohwer (4) of San Diego State University observed that the number and variety of viruses in seawater are ten times those of the next-most abundant life form, bacteria. And by his estimate, less than .0002% of the bacteria-infecting viruses have been studied!

Virus Focus Group Workshop — 4 photos, 16-17 Oct 2003.
Virus Focus Group — homepage.
Virus Focus Group Annual Report, NASA Astrobiology Institute, July 2003 - June 2004.
Gut bugs sequenced — Nature Science Update reports on work by Rohwer, who says, "We're not even scratching the surface of what's out there." 14 Oct 2003.
Viruses... is a related CA webpage. [Next-What'sNEW about HGT-Prev]

Pevzner and Tesler
Pevzner and Tesler
Genetic "fault zones" are confirmed at the University of California. As we noted in June, bioinformaticians Pavel Pevzner and Glenn Tesler at UC San Diego, using computational analysis and comparison of the human and mouse genomes, surmised that humans have about 400 "fragile" regions where genetic rearrangement are likely. Now a team at UC Santa Cruz have confirmed the UCSD results, and have pinpointed the location of some of the fault zones. The research has implications for cancer and for human evolution. With respect to evolution we wonder, can scrambling blocks of genetic material produce novel genetic programs? Or could scrambling be a step in the assembly of existing genetic programs that were acquired in pieces?

W. James Kent et al., "Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes" [abstract], p 11484-11489 v 100, Proc. Natl. Acad. Sci. USA, 30 Sep 2003.
Sankoff and Nadeau, "Chromosome rearrangements in evolution: From gene order to genome sequence and back," p 11188-11189 v 100, Proc. Natl. Acad. Sci. USA, 30 Sep 2003.
From Genome Comparisons, UCSD Researchers Learn Lessons about Evolution and the Fight Against Cancer, the University of California, San Diego, 13 Oct 2003.
2003, June 19 [3rd paragraph]: Insertions and deletions, important for human evolution, occur at preferred sites.
How Is It Possible? discusses another example of accelerated genetic change, "adaptive mutation."

PNAS As the burgeoning genome databases are analysed, the sources for genetic programs are becoming apparent. For example, this week PNAS online notes, "An ancient retroviral element has a major impact on [human] gene expression." According to biologists from Canada and Sweden, a long terminal repeat (LTR) sequence from a retroviral element promotes a gene involved in the synthesis of an antigen in the human gastrointestinal tract and mammary gland. A viral infection installed this sequence into our lineage.

In the past decade, we have become aware of dozens of examples like this one in which a new genetic program or subroutine was acquired by horizontal transfer. However, for providing new functions, this process should be much less frequent than the mutation of sequences inherited vertically, according to the darwinian paradigm. If so, by now scores or hundreds of new examples illustrating that process — new genes written by mutation — should have been published. Where are those articles?

Catherine A. Dunn et al., "An endogenous retroviral long terminal repeat is the dominant promoter for human 1,3-galactosyltransferase 5 in the colon" [abstract], p 12841-12846 v 100 Proc. Natl. Acad. Sci. USA, 28 Oct 2003.
See for example, "[47] Human Genes Potentially Derived from Transposable Elements," Table 10.3, p 325, Lateral DNA Transfer, by Frederic Bushman, Cold Spring Harbor Laboratory Press, 2002.
Viruses... is a CA webpage listing many examples of gene transfer, especially under "What'sNEW." [Next-What'sNEW about HGT-Prev]

Ward I hear over and over, and I've stated it myself: Life must be easy to make, because we got it on Earth almost as soon as it could have evolved. Where's the science behind that? Those who are attempting to produce life in a test tube are getting nowhere. — Peter Ward, coauthor of Rare Earth, in remarks at a forum, "The Drake Equation Revisited," Palo Alto, CA, 26 August 2003.
The RNA World is a CA webpage about the origin of life.

National Geographic NASA will explore comets for clues about the origin of life. Comets are rich in organic compounds, scientists now generally agree. For example, "When European spacecraft analyzed dust particles from the Halley comet in 1986, it turned out to be some of the most organic-rich material measured in the solar system." In the new initiative, NASA will ask "how organic compounds are created in interstellar clouds" that precede stars, planets and comets. We hope the research is open to the full range of possible sources, including biology, for organics in space. Meanwhile, the paradigm whereunder space provides the ingredients for the prebiotic soup on Earth, "pseudo-panspermia," seems completely accepted. [Thanks, Larry Klaes.]
Did Comets Make Life on Earth Possible?, by Stefan Lovgren, National Geographic News, 2 October 2003.
Panspermia Asks New Questions is a CA webpage that discusses pseudo-panspermia.
Comets... is a related CA webpage.
Comet Rendezvous is a related section of the CA webpage, "Can the Theory Be Tested?".
COSMIC ANCESTRY | Quick Guide | What'sNEW - Later - Earlier - Index | by Brig Klyce | All Rights Reserved