5:57 PM: Dear All, Here are links to the updated NASA JSC web site on new evidence for life on Mars. This site contains new information not in the November release and these sites are worth looking at:
http://www.nasa.gov/centers/johnson/news/releases/2009/J09-030.html [main press release]

The release includes the complete text of the just-published Geochemica paper which is mostly about the ALH84001 magnetite. The alternate hypothesis that this magnetite was made completely non-biologically has been the leading competing explanation for our biologic hypothesis for about 10 years now. We believe that this paper completely falsifies this alternative hypothesis. The Powerpoint presentation (converted to PDF) on the press release site explains this a bit more simply than the paper itself. The importance of this paper cannot be underestimated; this non-biological alternative hypothesis has been the main obstacle in the scientific community to our original hypothesis that the magnetites were made biologically, and until it could be falsified, our hypothesis could not gain widespread acceptance. This new paper shows unequivocally that the proposed hypotheses (thermal or shock decomposition of siderite (iron-rich carbonate)) simply will not work and will not produce most of the magnetites actually present in the meteorite. These data are indisputable. If this alternative hypothesis does not work, we are left with our original biologic hypothesis for the specific kinds of magnetite which are identical to those made by bacteria on earth.
http://www.nasa.gov/centers/johnson/pdf/403100main_life_on_mars.pdf [educational presentation: 59 charts] (slow loading)

At this site (part of the press release site) is a powerpoint (converted to PDF) presentation showing the status of the martian meteorite study, the status of Mars exploration, and plans for the future. This presentation has already been picked up by a number of teachers for use in their classrooms. Take the time to download it and run through it. Be sure and allow enough time for the animations at several charts to load and run (you may have to click on them) The animations include the carbonate pancake cartoon and the revolving magnetite crystals.
http://www.nasa.gov/centers/johnson/pdf/403089main_7441-1.pdf [abstract, doi:10.1117/12.832317, vol. 7441, SPIE Proceedings, 11 Sep 2009.]

The second paper just published (SPIE Proceedings) discusses the status of our ALH84001 meteorite studies, shows some new data on biomorphs in this meteorite, and shows a number of Scanning Electron Microscope images of biomorphs (potential martian microfossils) in two other martian meteorites, Nakhla which fell in Egypt in 1911 and Yamato 000593 which fell earlier in Antarctica and was recovered by the Japanese Polar Expedition a few years ago. The biomorphs in these last two meteorites are nearly identical, supporting our hypothesis that they formed on Mars; it is unlikely that microbes grown and fossilized in Antarctica would be identical to microbes grown and fossilized on a Nile delta field (or in the British museum where Nakhla has spent most of its terrestrial life). We see considerable carbon in Nakhla much of it associated with these biomorphs; Tim Jull of U of Arizona has shown that at least ~70% of the carbon in Nakhla is not terrestrial and therefore came from its original location (positively identified as Mars. Most biologists that I have shown these pictures to agree that they are likely microbial remains and fossils.
http://www.nasa.gov/centers/johnson/home/mars_meteorite.html [directory and new images]

This last feature consists of 20 SEM images of biomorphs in Nakhla and Yamato (on two pages), most of them previously unreleased and unpublished. These show a selection (from hundreds more) of the kinds biomorphs that we have found. We have found similar features in nearly all chips of Nakhla and Yamato 593 that we have investigated, and we think it very unlikely that these are contaminants from earth.

While we do not yet claim that we have rigorously proved that there is life on Mars, we believe that we are very close. In 2010 we plan to perform ion microprobe on a number of these biomorphs to try to determine unequivocally whether they were formed on Mars (textural or stratigraphic releationships already support that interpretation), and to unequivocally determine if they were made biologically rather than non-biologically (based on carbon isotope ratios and the presence of minor bio-elements such as nitrogen), although their complex texture and morphology certainly supports a biologic origin. If even a few of these features is shown by detailed chemistry to be martian in origin and is shown to be biologically produced, the presence of microbial past and possibly currently life on Mars becomes a near certainty. Regards, Dave ...David S. McKay | Johnson Space Center

Ancient life remains the most plausible explanation... the related What'sNEW article, 1 Dec 2009.
Life on Mars! is the related local webpage, with a special section, What'sNEW: ALH84001.

7:55 PM: Hi, I just want to say I concur with your analysis on the discovery of 3 human-specific genes that were purportedly recruited from ncDNA. It seems more logical to presume that a previously disabled gene in primates (due to a frameshift) had been reactivated in the human lineage for reasons that are still unclear. Could it be useful for mitigating the effect of lymphocytic leukemia?

Also, isn't it the case that the equivalent stretch of DNA in chimps is still coding, albeit for a shorter protein or has it lost its regulatory features entirely? That part is not clear in the paper by McLysaught. Regards, JH.

15 Dec / 10:07 AM: Dear Joe -- Thanks for the comments. I do not know the answers to your first question. For the second one, I think the paper would have mentioned it, if the chimp sequence is translated. But dunno. Perhaps another respondent will weigh in? Thanks again. Best regards. Brig

Three New Human Genes is the related webpage, posted 4 Sep 2009.

4:19 PM: Brig Klyce, Thanks for providing our paper in your references on CNGs. I'm interested in your take on our recent paper and how it relates to your thesis on panspermia. Although, I have a comment on this:

In cosmic ancestry, the CNGs themselves would have been horizontally acquired as well. The new data even seem to support that alternative according to criteria we stated in April 2002: "If a new genetic program arrives by the strong panspermia process, intervening species should possess either nearly identical versions of it... or nothing similar..." (4). These CNG's are even more nearly identical, among species from mice to humans, than we would have guessed.

I'm sure you realize that CNGs can be present for another reason (besides recent exogenous transfer) and that is of course - strong selection. The determination of the functions of ncRNAs is currently a particularly active area of research. Those newly discovered functions will likely provide a mechanism by which the necessity for strong selective pressure is explained. Coding regions are less weakly conserved because proteins do not need to be highly conserved to preserve function, i.e. they are mutationally robust in most cases - with the exception of a select number of catalytic residues. The functionally of CNGs may be less robust to mutation - which would necessitate strong conservation. The conservation alone does not sufficiently prove they are exogenic. In fact, unless acquired very recently or under strong selection, an exogenous sequence will appear to have experienced similar levels of drift as native sequence.

Gregory E. Sims, PhD | Computational Scientist | Lawrence Berkeley National Lab

22 Oct 2009 / 1:05 PM: Dear Dr. Sims -- Thank you for noticing. I am aware that strong selection can keep sequences constrained very tightly. But this leaves a problem for standard darwinian evolution -- how did the sequence "originate"? If by mutation and natural selection, then there must have been a time when they weren't so tightly constrained. But this supposition is not supported by evidence, as far as I know. Are there sequences that would support the darwinian account of gradual evolution of these CNGs?

In general, the version of panspermia that I promote is so radical that it is hard to grasp immediately. (It was for me, too.) In it, every genetic program must be supplied. Darwinian evolution can only shuffle, toggle and optimize supplied programs. So in "strong panspermia," every genetic program was ultimately supplied by some form of HGT, whether recently or eons ago.

The direct evidence for HGT as the source for genetic programs is accumulating steadily. But the main reason to consider this hypothesis is that the direct evidence for darwinian mutation-and-natural-selection as the source for genetic programs is so weak and indirect. Without the big bang as its foundation (everything must originate), it would be laughable, in my opinion.

I welcome your thoughts, as long as good will prevails! Thank you. Best regards. Brig

Conserved Non-Genic Sequences is the webpage prompting this exchange.

Panspermia.mp3: an hourlong interview about panspermia with Brig Klyce on AudioMartini (requires MP3 player), 29 Sep 2009.
Audiomartini with Rick Wood: homepage with links to all interviews.

Exotic life beyond Earth? Looking for life as we don't know it, PhysOrg.com, 18 Sep 2009.

If we didn't know about life we wouldn't believe it introduces the related What'sNEW article, 14 Sep 2009.

11:14 AM: Dear Brig ...I thought you would like to know that a new Journal of Cosmology has been launched -- http://journalofcosmology.com/About.html -- and I have been asked to be the Executive Editor of Astrobiology. An inaugural edition launched today focuses on "Panspermia".... All the best, Chandra | Chandra Wickramasinghe | New book details

Chandra Wickramasinghe contains a prepared statement of 1981, and links.

6:58 AM: Brig, Here's another example of hybridization that's "shocking" to darwinists, but utterly unremarkable from the CA point of view.... "The fusion of two distinct evolutionary lines is not supposed to work. According to received biological wisdom, any chimeras that result are meant to be evolutionary dead ends. Not for the first time, received wisdom appears to be wrong (New Scientist, 16 June 2007, p 48)." ...Jerry Chancellor | President | VisionTech Computer Services, LLC
13 more things: Hybrid life, NewScientist, 2 Sep 2009.
Viruses and Other Gene Transfer Mechanisms is the main related CA webpage.

6:32 PM: Dear Brig, as a regular visitor/user of your site, I would like to draw your attention to the two our papers that are now freely accessible at the web site of Biology Direct.... With best regards, Armen.... Armen Y. Mulkidjanian, Ph.D. | University of Osnabrück | School of Physics and School of Biology/Chemistry | Barbarastrasse 7 D-49076 | Osnabrück, Germany
On the origin of life in the Zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth.
On the origin of life in the Zinc world: 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
The RNA World is the main CA webpage about origin-of-life theories.

11:46 AM: Dear Dr Klyce, I am most pleased that Astrobiology Research Trust just honored Chandra Wickramasinghe. I had the pleasure of meeting Chandra recently at Budapest at: [Astronomy and Civilization, 10-13 Aug 2009] where he gave a superb lecture on panspermia. With regards, Subhash | Subhash Kak | Professor and Head | Department of Computer Science | Oklahoma State University
Comets contained oceans of liquid water during the first million years of their formation: is the related What'sNEW article, 23 Jul 2009.
Astrobiology Research Trust: homepage that mentions the recent honor.

11:04 AM: Hey Yo Bubba! ...I'll try to find time and attention to comprehend your exciting news from the cosmos...my problem is that I still think de Novo is something you park in de yard when you can't afford to buy de better kinda car. Love, Bubba
Primate-specific genes were inserted de novo... is the related What'sNEW article, 23 Jul 2009.

4:30 PM: Dear Brig, Thank you for posting a summary of our work on your website. I have a few comments:
the newly acquired retro-genes are not lost progressively during development but are lost after birth, progressively during adult life. These sequences can be in fact detected by PCR amplification, sometime also by Southern blot analysis, in tissues from young animals but are progressively lost in tissues from aged animals. This is shown in figure 3 which reports the comparative anlysis of DNA samples extracted from tail tissues of 20, 40 and 60 days old mice.
although maintained as non-integrated extrachromosomal structures, these retro-genes can indeed be sexually transmitted from one generation to the next because they are stored in spermatozoa. Therefore the corresponding phenotypic traits are also inherited by the progeny, although paradoxically in the absence of specific(s) chromosome-linked gene(s).
I am convinced that SMRGT process has played a role in evolution. Reverse transcriptase is encoded by retroltransposons which are stress-responsive elements, including among others exposure to UV, ionizing radiation, toxic agents and starvation. On these grounds it is reasonable to hypothesize that exposure to drastic environmental variations may have promoted bursts of newly synthesized retro-genes with ensuing sudden consequences on macroevolution.

Best, Corrado | L'Istituto Superiore di Sanità (ISS)...

6:27 PM: Corrado, thank you for these clarifications. ...With respect to heritability, I have been totally focussed on evolution that becomes permanent. Could the non-integrated extrachromosomal structures, the retro-genes, be thought of like bacterial plasmids -- permanent parts of the heritable genome in those species? Or, could they become integrated later, over longer times than you can experimentally observe? Thanks again for your help, and for your original work! Best regards.
6:37 PM: ...I have amended my text. I hope it's OK now. Still curious about my questions. Thanks. Brig
8:57 PM: One more question: you wrote --

although maintained as non-integrated extrachromosomal structures, these retro-genes can indeed be sexually transmitted from one generation to the next because they are stored in spermatozoa. Therefore the corresponding phenotypic traits are also inherited by the progeny, although paradoxically in the absence of specific(s) chromosome-linked gene(s).

I have now re-read your paper with that isue in mind. You say that the sperm of the F0 generation take up the DNA or RNA and that sequence is expressed in the F1 generation. Also the sperm of the F1 generation contain the acquired DNA or RNA. But did F1's sperm acquire it from the environment, as with F0? Or did F1's sperm inherit it from the parent, like a sex linked chromosome? In the latter case, isn't the inheritance now mendelian? Thanks. Brig

26 Jul / 7:33 AM: I'll try to answer to your questions:
I agree with your view that reverse transcriptase-generated extrachromosomal retro-genes can with time get integrated in genomic DNA and then fixed in the germ line. My guess is that such integrations occur mostly in the very early stages of embryonic developmant, 2- 4-cell stage embryos.
Spermatozoa are extremely reactive cells able to take up both DNA or RNA molecules and to deliver them to oocytes at fertilization. This is a distinctive feature of sprmtozoa of virtually all animal species, including human.
Reverse transcriptase-dependent retrogenes are sexually transmitted as extrachromosomal structures through spermtozoa from on generation to the next. It is not yet clear if oocytes do the same. Inheritance of non integrated sequences is quite unpredictable: we have observed a mosaic distribution, in the sense that they are present in some embryonic territories but not in others and therefore some organs of adult animals will be transformed while others will not. In ddition, these retro sequences are transient in adult tisues, are abundant in young nimals while their amount declines with age.

Best, Corrado

Spermatozoa of all species... is the What'sNEW article to which this correspondence refers, 25 Jul 2009.

8:05 PM: Brig, hope your well. Thought of you when I saw this:
How 'Invading' Bacteria Can Integrate Captured DNA Into Own Genetic Makeup, ScienceDaily, 2 Jun 2009.
Viruses and Other Gene Transfer Mechanisms is the main related CA webpage.

10 Jun | 7:43 PM: OK. How about this? You say that organisms fall from the sky. Here's one for ya!!
Mysterious tadpole rain in Japan (pics), Pink Tentacle, 10 Jun 2009.

Geographic Isolation Drives Evolution Of Hot Springs Microbe, ScienceDaily, 28 May 2009.

...Gene regulators may bind promiscuously, but they often do nothing by Lynn Yarris, Science@BerkeleyLab, 15 Feb 2008.

8:37 AM: Hi Brig... May be that some of the following links could be of your interest for your "the end and the big bang" webpage. The first (Narlikar's) paper, frames the present Standard cosmology in the right historical context and highlights its success and shortcomings. The second (Disney's) casts motivated doubts on the actual "Scientific" status of Cosmology. The last (Lopez-Corredoira's) suggests that the success of the present Standard Cosmological model, beyond its technical motivations, could someway rest also on the Mainstream (and Sidestream) Cosmologists social behaviour. Here Below a short and someway funny excerpt of this last paper.

"(..) 2.3. Psychological profile of cosmologists -- There are two main psychological profiles of cosmologists, with gradations of grey between them:

Heterodox: Possessed by the complex of unappreciated genius, too much "ego", normally working alone/individually or in very small groups, creative, intelligent, non-conformist. His/her (mostly males) dream is to create a new paradigm in science which completely changes our view of the Universe. Many of them try to demonstrate that Einstein was wrong, maybe because he is the symbol of genius and defeating his theory would mean that they are geniuses above Einstein. Most of them are crackpots.

Orthodox: Dominated by the groupthink, following a leader's opinion as in the "Naked king" tale, good workers performing monotonous tasks without ideas in large groups, specialists in a small field which they know very well, conformist, domestic. His/her dream is getting a permanent position at an university or research center, to be leader of a project, to do astropolitics (see Lopez-Corredoira 2008). Most of them are like sheep (or geese3), some of them with vocation of shepherds too.

The sociological reasons for favouring orthodox proposals might be related to the preference of domesticity in our civilization. Sheep rather than crackpots are preferred. Finding a promising change of paradigm closer to the truth among thousands of crazy proposals is very difficult; in orthodoxy, although absolute truth is not guaranteed, at least a consensus version of the truth is offered." EoE

Best Regards | Gabriel Manzotti | Monza | Italy

Einstein and cosmology by J.Narlikar -- Abstract: This review gives a historical account of how cosmology has developed since the 1917 paper of Albert Einstein. Today it is a frontier level science drawing on contemporary astronomy as well as contemporary physics, stretching both as far as extrapolations will permit. Thanks to numerous observations at different wavelengths, cosmologists today have their plates full. Extrapolations of laboratory tested physics are called for to understand all information within the framework of a standard model. The success and shortcomings of this approach are briefly discussed against the historical backdrop.
The Case Against Cosmology by M. J. Disney -- Abstract: It is argued that some of the recent claims for cosmology are grossly overblown. Cosmology rests on a very small database: it suffers from many fundamental difficulties as a science (if it is a science at all) whilst observations of distant phenomena are difficult to make and harder to interpret. It is suggested that cosmological inferences should be tentatively made and sceptically received
Sociology of Modern Cosmology by Martin Lopez-Corredoira -- Abstract: Certain results of observational cosmology cast critical doubt on the foundations of standard cosmology but leave most cosmologists untroubled. Alternative cosmological models that differ from the Big Bang have been published and defended by heterodox scientists; however, most cosmologists do not heed these. This may be because standard theory is correct and all other ideas and criticisms are incorrect, but it is also to a great extent due to sociological phenomena such as the "snowball effect" or "groupthink". We might wonder whether cosmology, the study of the Universe as a whole, is a science like other branches of physics or just a dominant ideology.
The End and the Big Bang is the referenced CA webpage.

11:59 AM: DNA analysis may be done on Mars for first time [by Ewen Callaway, NewScientist.com, 9 Apr 2009.]
"Chemical signs of life can be ambiguous, but Ruvkun and his team hope to find its unequivocal signature by sending a DNA amplifier and sequencer to Mars in the next decade. They're betting that any life on the Red Planet shares an evolutionary heritage with life on Earth, and therefore contains a similar genetic code – a requirement that other scientists say is too narrowly focused, since Martian life may have evolved independently and therefore may have very different chemistry."

Thought you might find this article interesting. ...Keep up the good work! ...Jerry

Life on Mars! is a related CA webpage.

3:42 AM: You probably have read this: Did the Ancient Crenarchaeal Viruses from the Dawn of Life Survive Exceptionally Well the Eons of Meteorite Bombardment? [Matti Jalasvuori, Jaana K.H. Bamford. Astrobiology. January/February 2009, 9(1): 131-137. doi:10.1089/ast.2007.0189]. I find it highly ironic that we have viruses in the wild with computers and we see them in nature so robust (billions of years?)... if the document has any validity. ...sorry about your [Memphis basketball] tigers, our jayhaws were very sadly (also?) intrepid this year ... cody

Viruses and Other Gene Transfer Mechanisms is the main related CA webpage.

1:38 PM: Hi my colleague Barbie Drillsma met you at the AAAS meeting in Chicago and passed me your card as she said you had expressed some interest in involvement. I gather you took a sponsorship brochure in Chicago but am attaching a PDF just in case. The brochure outlines a number of opportunities for involvement, but we are happy to discuss any other possibilities. Our website has plenty of detail on the programme and our supporters and can be found at www.wcsj2009.org. Anyway I thought I would mail to follow up this initial contact and to see if you would like to discuss further opportunities for involvement with this international meeting of science journalists. All the best and I look forward to hearing from you soon - Sallie Robins | Co-Director, World Conference of Science Journalists 2009 and Communications Manager, The Big Bang

7:07 PM: Dear Sallie -- Thank you for your message. Yes I am interested in coming to your June meting. May I tell you more? I am (I now realize) a blogger on the subject of panspermia. The version of panspermia I promote pertains not only to the origin of life on Earth, but also to evolution. My work gives me a rare perspective on the well-advertised debate between evolution and creationism/ID.

I have come to believe that science journalists usually do a terrible job on the subject of evolution. They are more like cheerleaders for the darwinist position. I believe they should be more like political reporters, who don't just automatically believe what the politicians tell them. Political reporters are often very well-informed, so they are able to probe and challenge and sometimes eventually help to uncover to the truth. (And evolutionary scientists are like politicians -- their jobs are at risk.)

While I think creationism/ID has no scientific answers to offer, I think the issues it raises are often real. That is, I think the mainstream theory of evolution has very major shortcomings. Perhaps these can be overcome, but so far the evidence is lacking. Meanwhile, the superficiality of the debate is severely hindering scientific progress.

I would like to opportunity to make a case like this to some science journalists. I would urge them to ask probing questions, and not to presume that science has no self-interest to protect. I could prepare a presentation with discussion to follow, or I could participate in some other way that would afford a similar opportunity.

My main interest is panspermia, but this would not be any kind of hidden agenda. After a short confession, my subject would be strictly as described above. I welcome the chance to discuss this further. Thank you. Best regards, Brig

Tuesday, March 03, 2009 12:26 PM: Many thanks for your response, unfortunately the programme is now fully formed, but of course we would welcome you attending as a delegate and of course then you can participate in the many debates and discussions that will take place both formally as part of the programme and more than likely late into the evening at receptions! Full details are available on the website. Maybe we will see you in London in June/July. All the best - Sallie

Evolution versus Creationism is a related CA webpage.

11:42 AM: Hi Brig, Following up on the discussion about our Space Invaders HT [horizontal transfer] story, I thought you may be interested to read this new piece [linked below]. It offers a bit more (speculative) thoughts on what could explain the mysterious invasion. This is an 'addendum' (i.e. a self-commentary) that just appeared in Communicative & Integrative Biology, an interesting new journal, multidisciplinary and open-access. ...Cheers, Cedric
Cédric Feschotte, PhD | Assistant Professor | Department of Biology | The University of Texas at Arlington

Clément Gilbert, John K Pace II and Cédric Feschotte, "Horizontal SPINning of transposons" [Open Access abstract], Communicative & Integrative Biology 2:2, 1-3; March/April 2009. "...Evidence that a family of DNA transposons ...independently invaded horizontally the genome of seven distantly related tetrapod species and subsequently amplified to high copy number in each of them."
The Feschotte Lab
Horizontal transfer (HT) of DNA transposons has apparently produced evolutionary innovation in mammals is our What'sNEW article to which Feschotte refers, 30 Oct 2008.