The genome ...implicates a role of conserved vertebrate genes in the evolution of placental fish
To/From: Henri van Kruistum | 27-30 Jul 2019
Dear Dr. van Kruistum -- I have commented on your article on my website about evolution and panspermia. I do not expect you to adopt my unorthodox view, but I would be grateful if you would check that I have not misunderstood your study.
BTW, I did not easily find out how many genes in H. formosa were not matched in the sister species. I said "ten to twenty percent." If this is dramatically wrong, please tell me. Thanks!
[later] I have revised my online comments [omitting the 10-20%]. I still invite your review. And thank you for the very thorough analysis presented in your paper. ...Brig
Hi Brig,
Thank you for commenting on my article. I think you got the 10-20 percent from figure 1, where you can see that ~80-85 percent of the guppy genome is covered by the H. formosa alignment. It is a little more complex than that, as genic regions are much more conserved between species than intergenic regions, and the assembly of the guppy is also a bit more complete. If I search for genic regions only between these species, the coverage would be higher than 99 percent, and only a handful of genes would have no match at all (way less than 1 percent).
This does not imply that the results that I find here capture all changes in the genome, as intergenic regions can also have an influence on gene expression and function. Right now I am investigating whether there are evolutionary patterns in these parts of the genome that may have a link to placenta evolution in livebearing fish. This is a work in progress still.
Late rejoinder -- Of course, non-coding DNA (such as transcription factors?) could have a role, right? And newly activated (de novo genes?) could be important? And "way less than 1 percent" could still be ...how many genes? 50? 100? ...Thank you!
Yes, there are many non-coding factors that may (and likely do) play a role, such as transcription factor binding sites, non-coding rna and more. Novel genes may arise from duplications, but my study focusses on closely related species, at those timescales the two copies are still very similar. However, it is possible that the new copy gains a new expression pattern and differentiates in this way. Based on unpublished results I would say around 50 is a good estimate indeed. ...So yes, the results I publish here are not likely the full story. I do believe they are a significant part of the story, and I hope to find the other parts in the coming years. ...Best regards, Henri
Cometary Panspermia | From: Chandra Wickramasinghe
04 July 2019 docx format
Dear Brig
With a veritable surge of new discoveries by many individuals and groups who are now assisting in the progress of astrobiology, it is worth recounting a history of relevant events that I myself have witnessed throughout a long career. When I began my research in astronomy in 1960 interstellar dust (the material that makes up a percent of the mass of the galaxy) was thought to be made of inorganic ice crystals. The origin of life was then regarded as being fully explained by the classic Miller-Urey experiments of the 1950's, so abiogenesis – the transition from non-life to life - was firmly set on Earth. Together with mentor and long-term collaborator Fred Hoyle I was the first to challenge the prevailing Oort-van de Hulst theory that ice grains can indeed even condense under interstellar conditions; and in 1962 we proposed the theory of carbon grain formation and of carbon dust in the outflows of carbon stars (1).
In 1974 I was also the first to propose an organic polymeric composition of interstellar dust (which we first thought was dominated by polyoxymethylene and later by polysaccharides) based on early infrared observations of both interstellar and circumstellar dust (2-4). Fred Hoyle and I were the first to attribute the famous 2175A bump in interstellar extinction to aromatic molecules in space (5); and shortly after this we began to discuss the idea of prebiotic organic molecules in space (6).
Following the pioneering astronomical observations by D.T. Wickramasinghe of a broad 3.4 micron absorption profile in the spectrum of GC-IRS7, Fred Hoyle and I next proposed our theory that biologically relevant organic dust was omnipresent in the galaxy (7) and that these were most likely to be derived from biology itself.
Not long afterwards we launched our theory of cometary panspermia and this was prompted to a large extent by D.T. Wickramasinghe's first infrared observations of a comet - comet P/Halley. All this was followed by further arguments and theorising that eventually led to us proposing that comets are the main incubators/amplifiers of microbes in the galaxy and throughout the cosmos (8,9).
By 1986 the concept of astrobiology as an emergent scientific discipline was actually proposed by us in public lectures and publications and nurtured in its formative years. In the past 2 decades after Fred Hoyle's death, I personally (together with a small team of collaborators) have continued to accumulate and review an every-increasing body of new data from diverse fields that supports the cosmic life theory that we had diligently nurtured for over 5 decades. A small sampling of the relevant publications are given in references (10)-(13). In total, there is a grand tally of over 250 peer reviewed journal papers, with more than 50 published in the journal Nature. A recent reappraisal of some the supportive data for life as a cosmic phenomenon is to be found in a recent publication by Edward J. Steele et al (14)
As I enter the 80th year of my life I am gratified by the convergence of a vast body of scientific research that seems to overwhelmingly support the ideas that Fred Hoyle and I had nurtured over many decades. On the other hand, an endemic failure to acknowledge, or even reference, our prior published work stands out as a sad commentary on modern scientific conduct and integrity.
Yours sincerely,
Chandra Wickramasinghe
References
1. "On graphite particles as interstellar grains", F. Hoyle and N.C. Wickramasinghe, Mon.Not.Roy.Astr.Soc., 124,417,1962
2. "Formaldehyde polymers in interstellar space", N.C. Wickramasinghe, Nature, 252, 462,1974
3. "Polyoxymethylene polymers as interstellar grains", N.C. Wickramasinghe, Mon.Not.Roy.Astr.Soc., 170, 11P,1974
4. "Formaldehyde polymers in comets", N.C. Wickramasinghe and V. Vanysek, Astrophys. Sp.Sc., 33, L19,1975
5. "Identification of the 2200A interstellar absorption feature", F.Hoyle and N.C. Wickramasinghe, Nature, 270, 323, 1977
6. "Prebiotic polymers and infrared spectra of galactic sources", N.C. Wickramasinghe, F. Hoyle, J. Brooks, and G. Shaw, Nature, 269, 674, 1977
7. "Infrared spectroscopy over the 2.9-3.9 micron waveband in biochemistry and astronomy", F. Hoyle, N.C. Wickramasinghe, S. Al-Mufti, A.H. Olavesen and D.T. Wickramasinghe, Astrophys. Sp.Sci., 83, 405-409, 1982
8. "The organic nature of cometary grains", N.C. Wickramasinghe, F. Hoyle, M.K. Wallis and S. Al-Mufti, Earth, Moon and Planets, 40, 101, 1988
9. "Comets - a vehicle for panspermia", F. Hoyle and N.C. Wickramasinghe, in Comets and the Origin of Life, ed. C. Ponnamperuma, D. Reidel Publishing Co., 1981
10. Comets and the Origin of Life (with J.T. Wickramasinghe and W.M. Napier) World Scientific and Imperial College Press, 2009
11. The Search for Our Cosmic Ancestry, World Scientific, 2015
12. Vindication of Cosmic Biology: Tribute to Sir Fred Hoyle, World Scientific, 2015
13. Our Cosmic Ancestry in the Stars, Inner Traditions, 2019
14. "Cause of the Cambrian Explosion – Terrestrial or Cosmic?", Edward J. Steele et al, Progress in Biophysics and Molecular Biology 136, 3e23, 2018
It seems obvious that both sides are preaching to the choir, and the lack of dialog will leave the questions gridlocked. In the YouTube interview, Behe was asked, What would they say?, and he gave his version of an imagined, unproductive conversation.
He briefly mentioned panspermia, very dismissively, evoking laughter. He repeated the standard critique -- it just pushes the question to another planet.
And he complained again that materialist scientists can't logically believe that minds are real. (Why can't my mind ...be an emergent property of my genome?)
David Raup said, in 1997, "On the creation-evolution debate, I foresee continued conflict. Both sides will continue to lie, cheat and steal to make their points." (My link to the interview, with Steve Brusatte on "Dino Land," has died.) Behe confirmed this. He spent lots of time on the dishonesty of darwinists. Then, when asked about the timing of receiving tenure vs coming out for ID, he said with a wink, "My momma didn't raise no fool." More laughter.
Behe wants to use science to prove that life violates the laws of science. I believe this is a logical impossibility. He claims that Occam's Razor favors Intelligent Design. What?!
Strictly within hard, materialistic science, panspermia answers where life comes from and how life evolves. Behe agrees with panspermia that it [the origin-of-life] couldn't have happened in the available time on Earth. Including all of the (standard big-bang theory) time and space multiplies the opportunity by 10^20 or so. That should help.
He also would say that some of life can't be explained even with that much opportunity. As you know, I agree about that. But if physical existence is eternal, life can be simply a "given" about the world, like matter, energy, space, etc. So, life "in the first place" becomes a non-issue. All we need for this is a modification of the big bang theory, which allows us to remain fully scientific. But Behe promotes the standard big bang theory at every opportunity.
Behe is not dumb, but his valid insights are having little influence. He seems fine with that.
Thanks again for the link. Best regards. | Brig Klyce
Darwin Overthrown | to Suzan Mazur | 09 Apr 2019
Dear Suzan – Thank you for the [review copy of Darwin Overthrown]. ...My early thoughts are, in random order —
I like Fodor a lot, as you do, but I found him hard to understand about natural selection. It seems entirely possible that cold weather could induce – by amino acid substitutions, regulatory changes or some epigenetic thing – sheep to grow longer wool. But he would not concede even that (the example with him was giraffe necks). And his refusal was an insistence that we don't know which trait is "selected for." I think it is often obvious. His logic here eludes me.
14-29 Jun 2010: correspondence with Fodor.
I am keenly interested in how evolution works. I am not especially interested in the funders' possible hidden agenda. I care about the experimental results.
I pay close attention to origin-of-life research, but it looks to me like alchemy – trying to make gold from lead – it will never work. I know this seems to put me into metaphysics, but I claim complete skepticism. I think the universal assumption that life must "originate" depends too heavily on the big bang theory, which is too new and too fluid to have that much authority. All the real-time evidence makes the origin-of-life look impossible. If it's impossible, that does NOT mean that science has to be abandoned – a very tyrannical assertion.
I am also only mildly curious about synthetic cells. If they get far enough along to begin writing (evolving?) genetic programs, I will tune in closely, because:
The origin-of-life problem has two aspects. 1) hardware – DNA, RNA, proteins, cells, etc. 2) software – the programming that genomes contain, the more difficult part. You note somewhere that the simplest cell has (300?) genes. Right. I have proposed computer testing to see if any truly new functional programs, of any kind, could be ...automatically invented in computer models. So far, none. Meanwhile, all the current research pertains to hardware only. Even there, very little to show.
I can point you to hundreds of examples of HGT in all domains. The HGT deniers will lose.
I love reading about all these researchers, a few of whom I know pretty well. Dimitar Sasselov and I don't always agree, but I am crazy about him. ...I met Andrew Pohorille when NASA's Center for Computational Astrobiology was announced. It was going to be a "very inclusive" community. I tried to interest him in a research project, but, no interest. A year or two later, when I sat by him at lunch, he behaved as if I carried the plague....
Brig Klyce | www.panspermia.org
Darwin Overthrown: Hello Mechanobiology, by Suzan Mazur, Caswell Books, 2019.
indisputable? | from John Lattanzio to Ted Steele et al. | 20 May 2018
Hi All -- to describe octopuses origins beyond the Earth as "indisputable" seems to be a bridge too far....!
I would say its not impossible and may be plausible. But far from "indisputable"..... Am I missing something??
Again - as someone new to the field - claiming beyond what can be truly defended to a skeptic does not do any good. If ne claim is seen as rubbish then people don;t listen to the rest. That is bad...
The fault is theirs! But humans are humans....we have to work with them :-)
JL | Professor John Lattanzio | School of Physics and Astronomy | Monash University | Victoria 3800 AUSTRALIA
29 Jun 2018: Lattanzio keynotes the Annual Meeting of the Astronomical Society of Australia, 25 Jun 2018.
20 May 2018 | 3:44 AM | from Ted Steele
Dear John: I think it is very important to read our paper very carefully as it reviews and deduces the most parsimonious conclusions from the data. https://doi.org/10.1016/j.pbiomolbio.2018.03.004
It is a paper of deep analysis for communication to all scientists in plain English prose. We have made that very clear up front and throughout the tortuous peer review process which took 12 months. We do not pull our punches, and I personally will not now.
For me, at this stage of this decisive debate - as that is what it is now - a very real and deep Paradigm Shift is underway globally ( I have been involved in these and it is now a no holds barred fight as they always are like this). This cannot be avoided in a battle of fundamental ideas as big arrogant egos and noses are being soundly put out of joint -scientific power cabals are being exposed - and the "Emperor is not wearing any clothes."
It is not everyone's cup of tea, that is why the great bulk of scientists, running safely with the herd, do not make important discoveries, nor bring about Paradigm Shifts.
It is likely to get a little hotter but I can see this shift being completed in the same time frame now of the Wegener/Continental Drift/Plate Tectonics change in understanding in the Geophysical Sciences shifts, about 2-5 years.
In my view "Extraordinary evidence requires a complete rethink and then requires an extraordinary explanation" - this reverses the oft used skeptical mantra " Extraordinary claims require extraordinary evidence". It needs reversal here because the extraordinary evidence now exists.
Here are just two examples from our paper, which are paradigm shifting (that is, pure nonsense under the dominant terrestrial neo-Darwinian paradigm):
1. The Murchison meteorite (landed in Murchison, Victoria in 1969 and was immediately recovered, and curated in the city museum in Melbourne). It has eukaryotic fossils, at > 4.5 billion years old - older than the Solar System. EM Scans of internal sliced structures independently assessed by highly reputable workers show distinct biological cells and microfossils (some look like fruiting bodies typical of slime molds). A critic must now give an explanation that avoids Panspermia for that finding. There are other carbonaceous meteorites with microfossils examined the same way. Contamination has been ruled out (Pflug and Heinz 1997, Hoover 2005, 2011, Miyake et al 2010). Thus eukayotic life is external to the Earth and at least >4.5 Billion years old.
2. The infra red extinction spectrum for interstellar cosmic dust in our Milky Way galaxy has the same signature as freeze dried E. coli (a common complex living cell). All our knowledge of the Universe, delivered by the scientific discipline of "Astronomy" has been built this way - get the spectrum (emission, absorption) in the laboratory on Earth- then focus the telescope on a cosmic source/object and ask - What is the spectrum or signature? Does it match that found in the Earth-based laboratory? All our chemical and physical knowledge of the Sun, other planets, comets, other stars etc. has been built up this way. Newton built his grand synthesis that way. As did Galileo and Kepler. Hoyle and Wickramasignhe predicted the match before they secured the astronomical observations (with Chandra's brother Dayal Wickramasinghe and DA Allen at the ANU in Canberra):
The same match is seen in cometary ejecta tails (Halleys). We cover all this in the review (see Fig 1 and associated text, Hoyle et al 1982, 1984, Wickramsinghe DT and Allen 1986). Again, a critic must provide a better explanation that avoids Panspermia, that is , better than that published by Hoyle, Wickramasinghe et al. In 40 years no astronomer or physicist has provided a better explanation, but many astronomers have observed the match. It is an exact match - you cannot get better than that in Science.
I got involved with Chandra and his colleagues because I knew that anyone calling themselves a "Scientist" and looking at the "extraordinary data" with a purely cool objective eye would draw the same conclusions as me. As a biologist am deeply immersed in RNA and DNA editing mechanisms, the Octopus RNA editing data reported last year ( I was at the GRC meeting and know the group) now place the Octopus in the class of "extraordinary genetic data"- so while some may want to pull their punches, I certainly won't. Now is not the time to be timid, as we have not published a timid paper. The prescience of the Russian space scientists detecting bacteria ( their DNA sequences) in the cosmic dust on the external surface of the ISS is another class of "extraordinary data" ( as is the Tardigrades).
I thought it important that at this moment you be aware of my views on this. Best and thanks.
Ted | Edward J Steele PhD | ASI, AIMS, ASCIA | CYO Foundation, Piara Waters, 6112 | Perth, AUSTRALIA
It is possible to find non biological explanations for almost all aspects of astronomical data relating to interstellar dust when looked at in isolation. This is manly because we only have remote spectroscopic /extinction observations to play with. We have acknowledged this in our paper.
The question then is are the non-biological interpretations more plausible? We have discussed some of these and their short comings in our paper. In assessing the relevance of the biological interpretation we have to draw on the many arguments put forward by HW over the decades. The "recent" discovery of large numbers of "Earth type" planets in habitable zones makes the Copernican argument very strong.
The question then boils down to how much of the stuff out there COULD be of biological origin. If we bring in the detritus of biology into the picture (and the missing dust issue) plausibly a good proportion of it. It is hard to tell. Then comes the million dollar question - what is the source of this material assuming it exists? In our paper we discuss Proto-planetary systems with comets as the major sites of replication. The studies of comets, starting with Haley, have provided some support for this hypothesis.
We need a smoking gun. Could come from in situ cometary studies or of studies of dust falling on Earth. It may even come from studies of evolutionary biology on Earth as discussed in the Steele et al. paper. ...Cheers, Dayal
So my point is "life anywhere means the same life everywhere", and life must be a galactic/cosmic phenomenon with a deeply connected biosphere.
But of course we must all work within the constraints of the sociology of science. The "band wagon" has a momentum that takes much effort and persuasion to stop....
That said, I agree, the gentler tone will not weaken the case. Thanks, all.
Analysis of images from Mars rovers shows insect- and reptile-like fossils, creatures according to Ohio University entomologist
Polly Cooper | received 26 Aug 1996 | posted 22 Jul 2019
