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

What'sNEW Archives, November-December 2004

29 Dec 2004
Methane on Mars is number seven among the top ten astrobiology stories of the year, says Astrobiology Magazine.
Mysterious Martian Methane, Astrobiology Magazine, 29 Dec 2004.
Vladimir A. Krasnopolsky et al., "Detection of methane in the martian atmosphere: evidence for life?" [pdf], Icarus, 2004.
Life on Mars! is a related CA webpage. Search for "methane".

27 Dec 2004
Secondary symbiosis Plastid Portability — A team studying eukaryotic phytoplankton reports that the red plastids (organelles) incorporated into most of the microbes are apparently quite portable in evolution, by "secondary symbiosis." This is different from primary symbiosis, the apparent way whole free-living cells became organelles after they were engulfed by others. Organelles tend to lose most of their genes, contributing many to the eukaryotic nucleus. But following secondary symbiosis, the red plastids have retained some 200 protein-coding genes. The report even describes tertiary symbiosis, "where secondary photosynthetic symbionts were engulfed by a heterotrophic dinoflagellate host cell." We continue to be impressed by the variety and capacity of gene transfer mechanisms.
Paul G. Falkowski et al., "The Evolution of Modern Eukaryotic Phytoplankton" [
abstract], p 354-360 v 305, Science, 16 Jul 2004.
Viruses... has a What'sNEW section listing over 150 recent scientific developments related to gene transfer. [Next-What'sNEW about HGT-Prev]

Secondary symbiosis Now botanists from Canada and the US claim that red plastids are not more "portable" than green ones. Furthermore they write, "In all known cases of secondary endosymbiosis, the host nucleus must have acquired hundreds of genes encoding plastid-targeted proteins from the endosymbiont nucleus." This challenge and the original team's response only reinforce the evolutionary importance that we ascribe to gene transfer.
Patrick J. Keeling et al., "Comment on 'The Evolution of Modern Eukaryotic Phytoplankton'" [text], p 2191 v 306, Science, 24 Dec 2004.
Daniel Grzebyk et al., "Response to Comment on 'The Evolution of Modern Eukaryotic Phytoplankton'" [text], p 2191 v 306, Science, 24 Dec 2004.


The God Gene

Genes for religion? A new book by geneticist Dean Hamer suggests that we may have them. The idea is speculative, but it is consistent with our own speculations!
Dean H. Hamer, The God Gene: How Faith is Hardwired Into Our Genes [
publisher's promo], Doubleday, Sep 2004.
Jeffrey Kluger, "Is God in Our Genes?" [abstract], p 62-72 v 164 n 17, Time, 25 Oct 2004.
Carl Zimmer, "Faith-Boosting Genes" [text], Scientific American, Oct 2004.
What Difference Does It Make? is the CA webpage containing our related speculation.

NASA book cover

16 Dec 2004
A history of astrobiology from NASA's perspective is available.
Steven J. Dick and James R. Strick, The Living Universe: NASA and the Development of Astrobiology,
Rutgers University Press, 2004.
Jeffrey L. Bada, book review, "A Field with a Life of Its Own" [summary], p 46 v 307, Science, 7 Jan 2005.
The Living Universe, book review by Mark Motimer, Universe Today, 10 Dec 2004.
Introduction... is a related CA webpage.
Thanks Thanks, Larry Klaes.

14 Dec 2004
Microbes survived a short trip in space in an experiment at New Mexico's White Sands Missile Range in April 2004. Bacillus subtilis bacteria were attached to man-made granite meteorites placed on the outside of small rockets that caried them 70 miles high. Having endured the cold vacuum of space and heat of nearly 300 degrees Fahrenheit, ten percent of them were still viable upon returning to Earth. Microbiologist Wayne Nicholson at the Kennedy Space Center says additional, more realistic experiments are planned.
Micronauts Ride Rockets In Interplanetary Travel Tests, by Jim Tunstall, The Tampa Tribune, 13 Dec 2004.
The Tampa Tribune Bacteria... is a related CA webpage.
Thanks Thanks, Larry Klaes.

13 Dec 2004
Panspermia and life on Mars get serious consideration in a conference report featuring molecular geobiologist Carrine Blank and others. Space.com
Life-Swapping Scenarios for Earth and Mars, by Leonard David, Space.com, 13 Dec 2004.
Life on Mars! is a related CA webpage. Thanks Thanks, Ron McGhee.

10 Dec 2004
Evolution versus creationism was the topic on CNN last week. Within the past year, 24 states have gone through public debate about teaching evolution, said correspondent Tom Foreman. To discuss this simmering issue CNN invited a representative from each of the two sides to its "Paula Zahn Now" show. The most telling part of the program, we thought, was the following exchange:
    Paula Zahn
    Paula Zahn
  • Jason Lisle [Ph.D. in astrophysics, Cincinnati, affiliated with a pro-creationism group called Answers in Genesis] — Well, there's no neutral ground, is there? I mean, you're ultimately either for what God has said as word or against it. And that's what the real issue is here.
  • Paula ZahnEugenie?
  • Eugenie Scott [director of the National Center for Science Education, San Francisco] — No, we're treating this as if there are two alternatives, evolution, and the Institute, or the Answers in Genesis' version of creation.
Today's theory of evolution has profound problems; we agree with creationists to that extent. And the problems need to be addressed scientifically; there we agree with science. Yet the scientific establishment pretends that there are no major problems. It treats all suggestions thereof as creationism. Thus, science accepts creationism's premise: if the theory of evolution is missing something important, only religion can supply it. Both sides like to maintain this false dilemma. But it prevents scientific progress. We wonder how much longer the crisis will last.

Paula Zahn Now, transcript, 29 Nov 2004. Search the page for "evolution and creation".
Evolution vs Creationism is a related CA webpage.
...Is Evolutionary Progress in a Closed System Possible? is one of several CA webpages discussing a major problem with today's theory of evolution — its most important feature has not been (cannot be?) demonstrated.


A Wordcount for Comparison — Four days ago (just below), we discussed seven mechanisms by which new genes may originate, according to a 2003 review. Now, on a new webpage we attempt to quantify our analysis by counting essential terms chosen from the review. We count the number of times they appear in recent book of 400 abstracts by 1,200 eminent biologists. Is this too confusing?
A Wordcount for Comparison is the new CA webpage, posted 30 Nov 2004.

26 Nov 2004
jingwei The evolution of a new fruitfly gene is analyzed in PNAS by a team from the Universities of Chicago and Minnesota. The gene is jingwei, a member of the short-chain dehydrogenase reductase (SDR) family. This study indicates that it first arose 2.5 million years ago when sequences from two other fruitfly genes, Adh (another SDR) and Ymp, were combined (see figure). Their abstract concludes, "These data suggest that protein functional diversity can expand rapidly under the joint forces of exon shuffling, gene duplication, and natural selection."

In the opening paragraph of their report, Jianming Zhang et al. list all seven mechanisms by which they say genes may originate:

Much is known about the origins of new genes (1) by means of exon shuffling, gene duplication, retroposition, recruitment of transposable elements, horizontal transfer, gene [fusion]/fission, and the generation of coding regions from noncoding regions of the genome, each with many examples.
Reference (1) is a 2003 review, "The Origin of New Genes...," by Manyuan Long et al. (Long is the correspondence coauthor of the current PNAS paper.) The review lists the same seven mechanisms in a table and discusses them at length, citing 122 references. One of the seven mechanisms is horizontal transfer, and four others clearly amount to recombinations of exon-sized or longer sequences of nucleotides. (These five support the theory we promote on this website.) For the sixth mechanism, gene duplication, the comment in the table is vaguer than the others: "Many duplicates have probably evolved new functions." We note that jingwei, the example involving gene duplication in the current paper, was also shaped by an exon-sized recombination — and it is still an SDR!

The seventh mechanism, "the generation of coding regions from noncoding regions," was once the mainstay of darwinian theory. Indeed, it would provide all the salient examples of the sixth mechanism, by reincarnating duplicated genes that have gone silent for a time. But the 2003 review paper does not give "many examples" of this crucial darwinian mechanism. The discussion of it in the text reads in full —

De novo origination. Although the true de novo origination of new genes from previously non-coding sequnces is rare, there are genes with a portion of coding-region sequence that has originated de novo. For example, in the Drosophila sperm-specific dyenin intermediate chain gene Sdic, a previously intronic sequence has been converted into a coding exon22.
But introns were also once exon-sized [or larger] recombinations. Thus, even this carefully chosen example may ultimately support our theory that new genetic programs are acquired and installed in blocks, in genetically open environments, and not the theory that they are composed pointwise, de novo, in closed ones.

Jianming Zhang, Antony M. Dean, Frédéric Brunet and Manyuan Long, "Evolving protein functional diversity in new genes of Drosophila" [abstract], p 16246–16250 v 101, Proc. Natl. Acad. Sci. USA, 16 Nov 2004.
Manyuan Long, Esther Betrán, Kevin Thornton and Wen Wang, "The Origin of New Genes: Glimpses from the Young and Old" [abstract], doi:10.1038/nrg1204, p 865-875 v 4, Nature Reviews Genetics, Nov 2003.
Our What'sNEW items below of 23, 21 and 14 November contain closely related discussion.
Viruses... is a related CA webpage about evolution by gene transfer. [Next-What'sNEW about HGT-Prev]
...Is Evolutionary Progress in a Closed System Possible? is a related CA webpage.
Macroevolutionary Progress Redefined: Can It Happen Without Gene Transfer? is a related CA webpage.
6 August 2005: Parallel evolution has been observed in fruitflies.


Mars Methane on Mars was a primary topic at a meeting of the Division for Planetary Sciences of the American Astronomical Society this month in Louisville, Kentucky. Ultra-violet light shatters methane, so something must continue to release it into Mars' atmosphere. On Earth, methane is released by hot geochemcal processes like volcanoes, and by methanogenic bacteria. On Mars there are no signs of recent volcanoes or hot spots. Planetary scientist Dr. Vladimir Krasnopolsky of Catholic University in Washington DC believes bacteria are the "most plausible source." This idea is apparently gaining acceptance.
Kenneth Chang, "Methane in Martian Air Suggests Life Beneath the Surface" [
text], The New York Times, 23 Nov 2004.
Life on Mars! is a related CA webpage. Search the page for "methane".
Thanks Thanks, Larry Klaes.

23 Nov 2004
Human genes composed mainly of mobile elements (ME) have been identified by CalTech geneticist Roy Britten. In a brief paper he lists 49 "observed transcripts that match ME for >80% of their length." He concludes, "These observations add to the many known ways in which MEs have contributed to our evolution." Recently we asked, "Can a diverged gene acquire a new function by pointwise mutations only, or must it undergo exon-sized recombinations?" Britten's study seems to support the second alternative. His abstract reads —
Among all of the many examples of mobile elements or "parasitic sequences" that affect the function of the human genome, this paper describes several examples of functioning genes whose sequences have been almost completely derived from mobile elements. There are many examples where the synthetic coding sequences of observed mRNA sequences are made up of mobile element sequences, to an extent of 80% or more of the length of the coding sequences. In the examples described here, the genes have named functions, and some of these functions have been studied. It appears that each of the functioning genes was originally formed from mobile elements and that in some process of molecular evolution a coding sequence was derived that could be translated into a protein that is of some importance to human biology. In one case (AD7C), the coding sequence is 99% made up of a cluster of Alu sequences. In another example, the gene BNIP3 coding sequence is 97% made up of sequences from an apparent human endogenous retrovirus. The Syncytin gene coding sequence appears to be made from an endogenous retrovirus envelope gene.
PNAS Roy J. Britten, "Coding sequences of functioning human genes derived entirely from mobile element sequences" [
abstract], p 16825-16830 v 101, Proc. Natl. Acad. Sci. USA, 30 Nov 2004.
Haig H. Kazazian, Jr., "Mobile Elements: Drivers of Genome Evolution" [abstract], p 1626-1632 v 303 Science, 12 Mar 2004.
21 Nov 2004: our What'sNEW item asking "Can a diverged gene acquire a new function...."
Viruses... is the primary CA webpage about evolution by gene transfer. [Next-What'sNEW about HGT-Prev]
Human Genome Search... is a related CA webpage.
Almost all human genes contain duplicated sequences — other work by Britten described in What'sNEW, 5 Dec 2006.

22 Nov 2004
Apollo 12 Apollo 12 landed on the moon 35 years ago and returned to Earth with a camera in which NASA's laboratory found viable bacteria. The camera had been left on the moon by an unmanned mission 30 months earlier. Apparenty the germs had survived inside it during that time on the lunar surface. Or, could the lab have contaminated the camera after it was returned? While doubts about this instance remain, we now know that bacteria can survive in space.
Apollo 12 Remembered: Lunar Germ Colony Or Lab Anomaly? Astrobiology Magazine online, 21 Nov 2004.
Bacteria... is a related CA webpage with more about "that little bacteria who came back and lived".
Thanks Thanks, SpaceDaily.com.

21 Nov 2004
Nature Evidence that 1,183 human genes were "born" 3-4 million years ago, by duplication and divergence comes from continuing genome analysis by members of the International Human Genome Sequencing Consortium. (IHGSC was one of two teams who published a first draft of the human genome sequence in 2001.) They believe, "The birth of new genes is of interest because it provides raw material for adaptive evolution, with extra copies of genes able to undergo functional divergence in response to positive selection." According to current darwinian theory, this process can ultimately produce new genetic programs for new functions. IHGSC notes, "These genes often fall within larger clusters of paralogous genes including genes with greater divergence and reflecting older duplications." In a table they list the ones with the most duplicates (5 to 26) in 41 gene families. If any of the 1,183 studied genes has a function different enough to put it in a new family, that is not mentioned.

In our theory, duplication and divergence under positive selection can adapt and optimize a gene within a narrow range only. If abetted by directed mutation, as many examples imply, this process is quite remarkable. However, to go outside their narrow ranges and acquire new genetic programs, genes require new sequences that pointwise mutations will never compose, we think. If instead, these sequences are acquired by gene transfer, then powerful genetic operating systems with accessories like mobile elements, and processes like recombination and DNA repair, may subsequently piece them into place. If we're right, any diverged genes comprising wholly new genetic programs will exhibit whole insertions, and possibly deletions, of exons or similar-sized sequences. IHGSC's current analysis specifically ignored likely insertions and deletions in the studied duplicates, and ignored other possible duplicates altogether, if likely insertions and deletions were longer than the remaining sequence. Unsurprisingly, all of the duplicated genes in this study appear to exhibit adaptation and optimization within narrow ranges. None exemplifies the birth of new a function.

Can a diverged gene acquire a new function by pointwise mutations only, or must it undergo exon-sized recombinations? We suspect the latter. We see nothing in this study that indicates otherwise.

International Human Genome Sequencing Consortium, "Finishing the euchromatic sequence of the human genome" [abstract], p 931-945 v 431, Nature, 21 Oct 2004. Note especially, "Gene birth in the human lineage," p 943-944.
The human genome... is a What'sNEW item about the first published draft of the human genome sequence, 12 Feb 2001.
Humanoid gene arose abruptly? is well-documented example of the recombination we contemplate, in What'sNEW, 18 Feb 2003.
Viruses... is the primary CA webpage about evolution by gene transfer, with many examples listed under that page's What'sNEW section. [Next-What'sNEW about HGT-Prev]
Can Computers Mimic... Evolution? discusses gene duplication and subsequent divergence by pointwise mutation.
New genetic programs... poses a question like our last one, using the term "new genetic programs," instead of "new genes".


ragworm eyes
ragworm eyes
Vertebrate photoreceptor cells in a primitive invertebrate have been identified by German molecular biologists. Many biologists believe eyes must have evolved at least twice, because the opsins in vertebrate and invertebrate photoreceptor cells are so different. Now, a member of this team says, "We think both photoreceptor cells track back to one cell type."

Not everyone is convinced of this scenario. The Germans themselves "detected a highly conserved stretch of amino acids... that is shared among the [vertebrate] c-opsins but distinct in the [invertebrate] r-opsins." A connection between the c-opsins in ragworms and vertebrates is much better supported. Sequence similarities suggest that an evolutionary path between them could have been traversed by pointwise mutations.

A friend asked us if this research illustrates the darwinian evolution of eyes. We think instead that it shows how essential, conserved programs may adapt and be optimized within narrow ranges. And even if, as hypothesized, c- and r-opsins evolved from a single predecessor, it was probably also, already an opsin.

Detlev Arendt, Kristin Tessmar-Raible et al., "Ciliary Photoreceptors with a Vertebrate-Type Opsin in an Invertebrate Brain" [abstract], p 869-871 v 306, Science, 29 Oct 2004.
Elizabeth Pennisi, "Worm's Light-Sensing Proteins Suggest Eye's Single Origin" [abstract], p 796-797 v 306, Science, 29 Oct 2004.
Thurston Lacalli, "Evolutionary biology: Light on ancient photoreceptors" [text], p 454-455 v 432, Nature, 25 Nov 2004.
Marine worm sports two kinds of 'eyes', by Emma Marris, News@Nature.com, 28 Oct 2004.
Neo-Darwinism... is a related CA webpage.
Thanks Thanks, Stan Franklin, for additional discussion, 1 Nov 2004.


Cuscuta californica Plant-to-plant gene transfer is illuminated by geneticists at Indiana University. "We describe two new cases of horizontal gene transfer, from parasitic flowering plants to their host flowering plants, and present phylogenetic and biogeographic evidence that this occurred as a result of direct physical contact between the two. Our findings complement the discovery that genes can be transferred in the opposite direction, from host to parasite plant."

Jeffrey P. Mower et al., "Gene transfer from parasitic to host plants" [abstract], p 165-166 v 432, Nature, 11 Nov 2004.
Gene exchange between species is aided by parasitism, IU Media Relations, 8 Nov 2004.
Viruses... is a related CA webpage about evolution by gene transfer. [Next-What'sNEW about HGT-Prev]
Thanks Thanks, Jim Galasyn.


Other theories of evolution?! In the past few months, skirmishes between creationists and darwinists over the teaching of evolution have broken out in in Kansas, Georgia, Ohio, and Maryland. We think the gridlock between those two interest groups, by excluding other scientific alternatives, is detrimental to science. We advocate legitimate enquiry into darwinism's possible flaws, without abandoning scientific principles. Now a Pennsylvania school board may have opened a door for us. On 18 October 2004, by a 6-3 vote, the Dover Area School Board added these words to the science curriculum: Students will be made aware of gaps/problems in Darwin’s Theory and of other theories of evolution including, but not limited to Intelligent Design. The Origins of Life is not taught. We hope they really mean "not limited to...."
Joseph Maldonado, "'Intelligent design' voted in," York Daily Record, York County, PA, 19 Oct 2004.
Dover Area School District homepage and Press Release for Biology Curriculum, 19 Nov 2004.
A dubious first for "intelligent design", National Center for Science Education, 21 Oct 2004.
Hour One: Teaching Evolution, Science Friday, 19 Nov 2004.
Evolution vs Creationism is a related CA webpage.

15 Nov 2004
If you know too much, sometimes you won't make the obvious discovery.
— Ronald D. Ekers, President of the International Astronomical Union, speaking at New Mexico Institute of Mining and Technology, 10 Nov 2004.
Tom Treweek, "Jansky lecturer stresses importance of serendipity" [
text], El Defensor Chieftain, Socorro NM, 13 Nov 2004.
Ronald D. Ekers Selected for the 2004 Jansky Lectureship, National Radio Astronomy Observatory, 26 Oct 2004.
Thanks Thanks, Larry Klaes.

14 Nov 2004
The birth of a new gene unique to apes and humans is reported in Nature Genetics by Swiss geneticists Fabien Burki and Henrik Kaessmann. GLUD2 encodes an enzyme that functions in the brains of gibbons, orangutans, gorillas, chimps and humans, but is lacking in old-world primates and other studied mammals. By analyzing its phylogeny Burki and Kaessmann conclude that the gene arose after the duplication of GLUD1, a gene found in humans and apes, and also in more primitive species. The duplication apparently occurred between 23 and 18 million years ago, when the older gene was transcribed into RNA, edited to remove its introns, and reverse-transcribed into DNA as an intronless paralog. Subsequent divergence, perhaps driven by "positive" darwinian selection, turned the intronless copy into GLUD2. From these facts one might conclude that the darwinian evolution of a new genetic program by gene duplication and divergence, as theorized by Susumo Ohno, has been confirmed.

Nature Genetics Compared to its predecessor, the enzyme encoded by GLUD2 has 18 amino acid substitutions. The two that were fixed earliest are 100% conserved and are essential for the newer enzyme's brain-specific function. Another nine substitutions characterize differences among different apes and humans. The remaning seven aparently have little or no affect on function. Meanwhile, the enzyme encoded by GLUD1, lacking brain-specificity, has apparently remained unchanged. Both enzymes are versions of glutamate dehydrogenase (GDH).

We agree that gene duplication and divergence occur, and we have already supposed that intronless paralogs can be or become functional. Furthermore, we suspect that directed mutation — accelerated sequence changes in the right places — may assist "positive" selection. But we believe that these processes can only optimize existing genetic programs within very narrow ranges; we doubt that they can write new programs. The enzymes encoded by GLUD2 and GLUD1 differ by only a few amino acids, and both enzymes are versions of GDH. To us, this is a story about optimization within a narrow range. We think Ohno's theory still lacks confirmation.

Fabien Burki and Henrik Kaessmann, "Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux" [abstract], p 1061-1063 v 36 n 10, Nature Genetics, [online 19 Sep] Oct 2004.
Ajit Varki, "How to make an ape brain," p 1034-1036 v 36 n 10, Nature Genetics, Oct 2004.
Neo-Darwinism... is a related CA webpage.
Can Computers Mimic... Evolution? is a CA webpage that discusses Ohno's theory.
Human Genome Search at University of Oklahoma is a related CA webpage.


Was Darwin Wrong? is the cover story of this month's National Geographic. The writer concludes, "No," listing evidence from the traditional fields, biogeography, paleontology, embryology and morphology. He adds that newer fields such as molecular biology and genomics also confirm Darwin. And the photos are beautiful.

Was Darwin Wrong? None of the cited evidence addresses our question: Can darwinian evolution produce new genetic programs in closed systems? Nor is the possibilty of life from space even mentioned. At least US public opinion is not overlooked: "...Nearly half the American populace prefers to believe that Charles Darwin was wrong where it matttered most." And this preference has endured: "The most startling thing... is not that so many Americans reject evolution, but that the statistical breakdown hasn't changed much in two decades."

David Quammen, photographs by Robert Clark, "Was Darwin Wrong?" [interactive link], p 2-31 v 206, National Geographic, Nov 2004.
Evolution vs Creationism is a related CA webpage.
Is Sustained Macroevolutionary Progress Possible? is one of several CA webpages about tests in closed systems.
Thanks Thanks, Stan Franklin.


The NASA Astrobiology Institute will hold its biennial members' meeting 11-14 April 2005, in Boulder, Colorado.
NAI 2005 Biennial Meeting. Thanks Thanks, Marsbugs.
COSMIC ANCESTRY | Quick Guide | What'sNEW - Later - Earlier - Index | by Brig Klyce | All Rights Reserved