Now the huge surprise of HGT is no surprise. Now life's early start on Earth / punctuated equilibrium / convergent evolution / the ubiquity of unfamiliar and de novo genes / the huge store of unknown genes in viruses / genes that seem to precede their earthly deployment all make more sense. A theory of evolution that easily accounts for and even anticipates these things is worth considering.

Replies to Cosmic Ancestry, 2020-2022

from Adam S. Wilkins, Institute of Theoretical Biology, Humboldt University, Berlin | Sep - Nov 2022
This exchange omits almost all of Wilkins' words -- his requirememnt.

from Wilkins, 19 Sep 2022: ...As I understand it, you want "panspermia" to include "genetic programs" being carried into organisms that did not have them before by means of LGT, presumably by viruses. Is that right? And, if so, you are not bothered by the fact that those "genetic programs" had to originate somewhere before their transmission by LGT? Is that right? If so, I think that this is the same "kicking the can down the road" as a way of avoiding the problem of origination, in this case of new traits (whereas for conventional "panspermia" it concerns ignoring how life originated by natural processes elsewhere in the cosmos).

Well, let us substitute "genetic regulatory networks" or GRN for "genetic program" since it is the difference between contemporary language and 1960s or '70s-type talk. The problem is that for many complex traits, either physiological/biochemical or morphological, the GRNs are big, dozens (at minimum) to hundreds of genes. This is way too many genes to be carried by viruses. Perhaps you say, what about photosynthesis (your example)? Well, yes, even that: "photosynthesis" does not mean "chlorophyll" alone but a much larger biochemical system based on many genes.

A second problem is that LGT has been effectively disproved to be an agent of evolution in eukaryotes. Eukaryotes have proper sexual reproduction, with meiosis, and that is where new genetic properties and capacities form. There is a paper in PNAS in the August issue (Nick Lane and Andrew Pomiankowski and one other author whom I do not know) that makes the case, from a modelling perspective, agains LGT as an efficient agent of genetic change in eukaryotes. But there is a lot of comparative genomics that rules it out also.

As I say, I may indeed be completely misunderstanding your view of evolution. But if I am not too far off in that, then, for the reasons discussed above, I think that there are big problems with your point of view. To give you an idea of how I view genetic change in evolution, I attach two papers. I see as largely a matter of making new regulatory links in GRNs. Of course, new genes, which can evolve in different ways, must play some part but my bet is on the restructuring of GRNs by genetic changes that alter the regulatory connections as the main engine of genetic "innovation".

I hope that the above is of interest. ...With best wishes, Adam

"Recasting developmental evolution in terms of genetic pathway and network evolution . . . and the implications for comparative biology," by Adam S. Wilkins, Brain Research Bulletin [local pdf], 18 Apr 2005.
"Between 'design" and 'bricolage': Genetic networks, levels of selection, and adaptive evolution," by Adam S. Wilkins, PNAS [local pdf], 15 May 2007.

20 Sep 20 2022 | from Brig Klyce: Dear Adam Thank you for this thoughtful reply. You have spoken bluntly, and I will be blunt also. Still, we can retain good will. I think the issues are important, and communication is needed for exploring the issues. I have spent some time reading your attachments, and I thank you for them.

...you have correctly understood evolution by panspermia, which I promote. But I recognize that my central beliefs are provisional, and can be easily disproven by experiment. I _may_ be wrong, as I often acknowledge. Meanwhile, until experiments [sustaining any form of Darwinism] succeed, I believe evolution by panspermia deserves a committed advocate and a full hearing.

Why? First because there is so much lacking in the mainstream theory of evolution. (I offended Jim Shapiro by conflating his version with EES and Neo-Darwinism, but actually I classify Dawkins, Jerry Coyne, EES, NGE, GRN, etc. all as mainstream, because you are apparently convinced that life can make macroevolutionary progress on an initially lifeless and quarantined body. Please don't be offended.)

What's lacking?
1: Experimental proof. A demonstration that would show that ongoing macroevolutionary progress is possible in a quarantined system. I can't be blunt enough this is a huge problem. How can you ignore it? Shapiro seems to think Lenski has made the demonstration. That's an example where discussion should be thorough, not cut off.
2: A demonstration in a computer model. This was the Holy Grail of artificial intelligence for decades. Nothing. I've looked.
3: (Definitely third best) A convincing reconstruction from genomics. A tracing of the evolution of ...something, by a plausible path without magic or magical unlikelihood. You specifically mention photosynthesis. I think the case for HGT from sources including viruses is very strong. Yes, it needs to be properly networked, as you point out. That's where NGE, or GRNs, or my "robust software management" would come in. This would be as dumb as computer software, with features analogous to defrag, syntax check, backup, shutdown, save, delete, optimize, puzzle-solve, anti-viral software, low-power mode, ...a lot of tools. But none of this writes "new" programming, such as lengthy special enzymes for photosynthesis. If you think it does ...see Lacks 1 and 2.

BTW, "way too many genes to be carried by viruses...?" Viruses carry orders of magnitude more genes than the rest of life. The human genome has several times as many viral genes as "human" genes and that's just the ones that we still recognize. I saw the paper you mentioned, Marco Colnaghi et al., doi:10.1073/pnas.2205041119. It says that repeat sequences slow down LGT, not that they halt it. Evidence that humans have many "de novo" genes from _somewhere_ is abundant. For example: Ruiz-Orera et al., doi:10.1371/journal.pgen.1005721, 2015, or my comments [link].

In general, evolution by panspermia deserves a hearing also because it has a lot of positive evidence. But no need to go on. It's a still-provisional theory. I think it's time to admit that mainstream theory (all-inclusive as defined above) is also provisional. When you say, "my bet is on the restructuring of GRNs...," you seem to acknowledge that.

Thank you. I welcome your thoughts. Best regards, Brig

[...] Wilkins sends: "The Evolution of Meiosis From Mitosis," by Adam S. Wilkins and Robin Holliday, Genetics [local pdf], Jan 2009.

Klyce: Just a link to suggest viruses can do more than you have said:
Can Viruses Make Us Human?, re: Luis P. Villarreal, posted 28 Feb 2006.

from Wilkins: [omitted]

22 Sep | from Klyce: Dear Adam, I thought that list would get your attention. Thanks for looking at it. FYI, Luis P. Villarreal is Professor Emeritus, Molecular Biology and Biochemistry, School of Biological Sciences, University of California, Irvine. He is the author of "DNA Virus Contribution to Host Evolution," Chapter 15 in _The Origin and Evolution of Viruses_, Esteban Domingo, Robert Webster and John Holland, eds., Academic Press, 1999, a medical reference/text book. He is a listed member of Shapiro's group, The Third Way.

I will be glad to hear from you when you have time. Meanwhile, I will quickly reply to some of your questions that I highlighted earlier, in case it improves our understanding for future discussion. I understand that you may not reply soon.

Macroevolution: I thought there was some consensus that this is big changes like the emergence of photosynthesis, eukaryotes, nervous systems, eyes, ears, a very long list. It would usually require new enzymes. Of course these need to be networked properly. It is different from microevolution, such as when a single amino acid changes the optimum [visual] color range for migrating fish. Speciation may be unrelated, because reproductive isolation need not include macroevolutionary innovation.

Quarantine: Like Lenski's experiments. Like Pasteur's experiments. Like Earth was thought to be, before panspermia was acknowledged.

Mixes up the Question: I think the origin-of-life and evolutionary progress are not separate problems. Sure, once we have eukaryotic life, then the "hardware" is basically established. But the "software" - neeeded at every step - is the more difficult and interesting part anyway. Enough. Thanks again for the time you have taken. I appreciate your efforts. Best regards, Brig [...]

16 Oct | from Wilkins: [omitted]

17 Oct | from Klyce: ...But for HGT affecting eukaryotic evolution, there's a lot of evidence. ...My main concern is the lack of direct evidence for any mechanism producing sustained macroevolutionary advance in quarantine. [...]
...My main motivation is skepticism. I have actively looked for evidence that would sustain some version of later-day neo-darwinism (which, in my thought, includes Shapiro, you, Dawkins, etc.) I sponsored research, tried to establish a prize, etc. But, as with Shapiro, we may interpret the same evidence in different ways.

21 Oct | from Wilkins: Dear Brig, ...I would never classify myself as a Neodarwinian; that is a belief system of the 1930s through the 1960s, which I feel has been superseded by a far more complex view of evolutionary reality. Yes, I believe in the importance of natural selection (see next paragraph) in shaping new adaptive traits in populations but that, in my view, does not amount to being a "NeoDarwinian".

Second, I was really surprised at your statement that there is "no evidence" for natural selection. You and I must live in different universes since, to my eye, there is abundant evidence for it -- not "proof" (a standard too high for mere biology) but abundant strong evidence -- both in the popular literature and in the scholarly, scientific literature. One cannot think about the COVID-19 pandemic, or the success of invasive species, or microbial multi-resistance, or all sorts of newly described adaptations in various populations of various animals and plants, without invoking natural selection. Do you read the columns of Carl Zimmer in the NYT? His articles are loaded with examples. The evidence for natural selection in microbes, from experiments, both bacterial and eukaryotic, is overwhelming but there are plenty from plants and animals too.
PS: ...Just to illustrate how easy it is to find examples of natural selection, please take a look at the link below, which arrived in my in-box today, sent by a friend.
https://www.science.org/content/article/some-wolves-black-coat-isn-t-just-fashionable-it-s-lifesaver

from Klyce: Dear Adam ...I understand that there are conflicting schools of thought within the theory of evolution. Many people, like you, think the modern synthesis is inadequate or wrong, but they disagree on how to fix it. I'm with Jerry Fodor. He said, think the central story of the theory of evolution is wrong in a way that can't be repaired....
https://www.huffpost.com/entry/jerry-fodor-held-high-ground-to-evolutions-militant_b_5a3ec86ae4b0d86c803c722f
I regret not knowing him earlier and better. Anyway, I need a term for all the modern schools. I am wide open to suggestions. I certainly don't want to insult you.

Second, what I would have said about Natural Selection is this: There is no evidence that it can invent anything. Let me be even more drastic: There is no evidence that anything gets invented in quarantine. Stay with me for a minute....

I can understand your unhappiness if you thought I wanted more examples like the black wolves (which I welcome and will enjoy reading.) No, I gave you a pointer to a very brief essay presented at NASA, 2000, that explains the kind of evidence I amd seeking. https://www.panspermia.org/astrobio01.htm. It might come from something like Lenski's experiments with bacteria. Even an experiment in silico could establish the logical possibility. Of course, interpreting a potentially crucial experiment requires careful collaborative scrutiny like quantum physicists undertook following Bell's Inequality. In biology this is lacking. I was slightly miffed by your suggestion that I was not "familiar with the literature." If I'm opposed to a powerful majority, I'm damn sure going to find out what they think. My offer of references about HGT from viruses was a snippy retort.

You say "proof" is a standard too high for mere biology. I'm pausing over that one. (But, admittedly, my strongest assertion faces the same issue. I say that invention in quarantine is impossible, and you can't prove an impossibility.) Then you mention "abundant strong evidence." I have also cited abundant strong evidence in support of cosmic ancestry. I wish we could admit that both are provisional. Then we might agree on experiments that would discriminate. I've long been on a Quixotic quest for them it seems. I would advocate this topic for our agenda.

I find it a very welcome challenge to try to be clear to you. I welcome your thoughts. Thanks, very best regards, Brig

22 Oct: ...my last concluded with a plea for experiments to "discriminate" between the two theories we promote, as if there were no other possibilities. Usually that's an unsafe assumption. But in this case, I think it's safe, because the choice is between two mutually exclusive possibilities that leave out nothing:
1) Life can generate its own genetic coding for macroevolutionary advances, or 2) it can't.

Wilkins: [omitted].

from Klyce | 24 Oct: Adam, thanks for taking so much time with this. We are having a hard time with some basic concepts. The difficulty is much more basic than natural selection vs. invention, or GRNs vs. NGE vs. other variants. All of those variants begin with the conviction that life can - somehow - generate its own genetic coding for macroevolutionary advances, right? (I am sufficiently "familiar with the literature" that supports that range of views. I'm sure your version has some details I haven't learned, but I understand the overall conviction.) ...

To show that life can generate its own coding, one must show that the programming was not - somehow - supplied. I promise, I will accept convincing evidence, such as from quarantined experiments. I would even accept a computer model for establishing that something can generate its own coding for macroevolutionary advances. But if you think the case is already closed, we're gridlocked. I don't want to degenerate into condescension or talking past each other. We are both smart enough to do better. I welcome your considered thoughts.

In any case, we are on the record from here on. I will unblock the prior postings again for you to view and approve-or-not.

... from Klyce: ... Adam, I'm going to talk tough. Please don't be offended.
You referred to my "a priori convictions." Actually, you are the guilty party. Stay with me.
You promote your GRNs. I grant that they might be the answer. But I do not concede that the case is settled. I frustrate you with objections. You get insulted, and ...insulting.
But there is a basic, unaddressed issue: "All of those variants begin with the Conviction that life can - somehow - generate its own genetic coding for macroevolutionary advances, right?" Meanwhile, very many smart scientists doubt it. Half of educated adults doubt it, although they wouldn't state it that way.
Quarantined experiments don't succeed.
Computer models that might prove the principle don't succeed.
Third-best, historical reconstructions are gappy and unconvincing. Because historical evolution is unquarantined, the Conviction is not supported. I say it is time for a fresh look at the question.
What is the question? I suggest, "Where does the programming come from?"
It may well "originate" as you believe. But if it ever "originates," by GRNs or any other means, experiments should prove that. Yes, Prove. I know you have said that's too much to ask. I think it is not. In any case, I think you should acknowledge that the case [for the Conviction behind all variants] is not closed. ...Best regards, Brig
[...]
Adam, I think we have a chance to reach understanding. Thanks for this thoughtful reply. But --
Please, state what I say in my own words. I wrote, "There is no evidence that it can invent anything. Let me be even more drastic: There is no evidence that anything gets invented in quarantine." Not your "...no evidence for change in GRNs that first initially creates phenotypic...." There is an extremely basic point here. The logic is not difficult. The key word is "invent." When you restate it your way, you misrepresent me, glide past the basic issue, and reach an unjustified conclusion.

When prokaryotes turn into people, a lot has apparently been invented. A lot of genetic programming has certainly come from somewhere. You are convinced that you can explain where it comes from. You can do an historical reconstruction that you accept. Of course, others have competing reconstructions. Most of the public think that all of that is implausible. Very many smart experts doubt all of it because there is no proof.

"Quarantine" is not a hard concept. Twenty years ago, when I was promoting a challenge for a computer model, I stated it this way: "A system is genetically closed if, after the experiment begins, no additional instructions in any form -- viruses, bacteria, plasmids; or computer viruses, subroutines, patches, etc. -- are admitted." https://longbets.org/44/. A large fraction of my website is about this challenge / question / issue.

"...not one single jot of evidence for the idea that life on Earth was seeded by microbes from abroad?" Wrong. There is a world of evidence. Once I, eventually, accepted the possibility of panspermia, my eyes were opened. But that topic is premature just now.
"...it does seem a plenty strong conviction...." Right. My bet is on panspermia. When you say to me that my thinking is implausible, or there is no evidence for panspermia, I rebut you with plausibility and evidence. And I cite counterarguments against mainstream evolutionary biology (including yours), to establish a need for a radical alternative. I advocate for my hunch and I know I might be wrong. [...]
Thanks for your time and thoughtfulness. I truly appreciate you. Very best regards, Brig

Wilkins: [...][...] [he notices an article that I have also noticed:]
30 Oct: Science writers for Quanta take a wide look at HGT....

Klyce: Dear Adam, [you wrote] "...there is a core belief in all versions of the importance of natural selection as a major (though not sole) engine of evolutionary change." Whatever those other "engines" are, aren't they all supposed to operate in a quarantined system? And the genes you allow from LGT, they still had to "originate" somewhere in the quarantined system, right? There is a basic point that you can understand. But you revert to saying that cosmic ancestry is implausible. Please remember that many experts and half the population find the whole "core belief" implausible.

Of course natural selection works. Animal- and plant- breeding adequately demonstrate that. Lenski's experiments prove it. The range is severely limited. If you think NS "invents" anything, what's needed is proof-by-example (quarantined biology) or proof-of-principle (digitally quarantined computer models). [...]

Thanks for staying with me on this. Best regards, Brig
[...] I do not doubt that GRNs are very important. I make a similar point, using the term "Robust Software Management."
[You wrote] "The quantitative argument, which you dismiss, is serious." I may not remember your argument, but a germ population can double in as little as half an hour. Over time, this can get ...serious. Origin-of-life theorists love this fact.
DNA is devoid of meaning? What? Sure, random DNA has no meaning, but the DNA of life means Life. The genes for photosynthesis mean Photosynthesis, etc.

I see that you think cosmic ancestry is preposterous. But let's drop that subject altogether (3rd request), until you see why the "core belief" is inadequate. Let's focus on the glaring lack of proof-by-example in biology or proof-of-principle in a computer model. The very many experts who doubt the core belief are not all stupid or uninformed. I have made a concentrated effort to understand what the other side thinks. (I may not be able to explain the details of your specific system, but I know what the "core belief" is.) You seem to shut out the possibility of understanding.

I suggest that a scientific way to proceed would be to look for proof.

We may be at an impasse. Best regards, Brig [...]
18 Nov 2022: ...what's needed is proof....

The Black Cloud by Fred Hoyle
review by James Powers | posted 06 Oct 2022

A few weeks ago, I viewed a Robert Lawrence Kuhn interview and program on his philosophy TV program, Closer to Truth." (https://www.closertotruth.com/). He has aired a two-part interview with one of my heroes, Freeman Dyson (1923-2020). The interview was done in 2007 before his death. (https://www.youtube.com/watch?v=Glt7bFVyb8Y). In the interview Freeman Dyson was discussing how intelligence would survive in the Far Future, perhaps 1 trillion years from now when stars and galaxies will no longer exist. To explain, he recommended a science fiction work by Fred Hoyle, "The Black Cloud" (1957). Within the interview Freeman Dyson says, "One of the best ways to look at this is through science fiction. And one of the best is "The Black Cloud" (TBC) by Fred Hoyle....it is a story about a form of life, which is simply a cloud of dust grains which floats around space. The dust grains are in communication through electromagnetic fields. Instead of nerves, muscles and a brain it has patterns of electric and magnetic fields... Fred Hoyle wrote a story about a creature that came into our solar system and began wreaking havoc and sucking energy from the sun. Life could be radically different in its embodiment and still have the same kind of mental processes that we would recognize."

I was surprised because I had never heard of TBC. Of course, when he wrote this I was only 8 years old and I did not have the reading skills to understand the story nor the money to purchase it. However, a decade later and to this day I am an avid but choosy SF fan. How did I miss this gem for so many decades? During the 1950's the world was enchanted with SF, Flying Saucers, little green men, etc. Perhaps a smart cloud of dust was too radical. Remarkably, Freeman Dyson remembers the story 50 years after it was published! Fred Hoyle (1915-2001) was a famous astronomer. SF author and Panspermia enthusiast. He is famous for inventing the term, "Big Bang." The Big Bang was meant as a pejorative, but became the standard jargon for the astrophysicist's modern paradigm. He took a jab or two at the Big Banger's in "The Black Cloud," but that is not what the book is about. TBC is a thrilling exploration of the interaction between an intelligent interstellar creature made of dust and the Earth's primitive technological civilization. I cannot spoil the story. However, if you were the astronomer in 1957 who discovered a black spot that was growing larger in the constellation Lepus the Rabbit and the spot did not move against the background stars and it measurably affected the orbits of the outer planes of the solar system, you would be most alarmed! TBC takes us to a fascinating conclusion.

What I found most entertaining and ironic about TBC is how the scientists, engineers and politicians address the existential problem with a very primitive 1957 technology and contentious political environment of the early Cold War. It is amazing how much technology and progress we humans have made since 1957. We are like fish swimming not in a sea of water but in a sea of technology. The story could easily be rewritten today.

Freeman Dyson uses TBC to demonstrate the possibility or certainty that intelligent life could exist in a high entropy, cold, mostly disorganized environment. I think that a Type 3 Civilization may be embodied in a dust cloud such as the one envisioned by Fred Hoyle. This form of life avoids the centuries of multigenerational interstellar space travel that limit Homo sapiens. It also explains the Fermi Paradox. Perhaps some observing time on the James Webb Telescope could be devoted to searching for intelligent interstellar dust cloud life. Dust to dust.

The Black Cloud by Fred Hoyle, 1957.

06 Aug 2022, from Brig Klyce: [...] Dear Raju Your page on the 3d Way website engages my deep interest, and I see where you are coming from, a perspective like mine. However, I am suggesting a solution that may seem radical even to you. I am promoting it not because I am sure it's correct, but because I believe it needs to be under consideration. The variety of solutions admitted for discussion already all lack experimental proof, even in computer models.
Raju Pookottil: brief bio on The Third Way website.

My website shows my outlook. I understand that origin of life is not the 3d Way's interest, and I will not violate that. My major interest is in exploring the question "How Does Evolution Work?" I think the importance of HGT is that it tells us something fundamental. I would love to join you in trying to understand evolution. Thank you for your consideration. Best regards, Brig

15 Sep 2022, from Pookottil: Dear Brig, Thank you for the email and a huge apology that I haven't been able to reply to you sooner. ...As James has already expressed in his emails to you, TheThirdWay of evolution website is solely dedicated to act as a directory where we list people and their work related to evolution, where the criteria is that they do not agree with the current theory (the modern synthesis). Evolution working purely by random mutations/natural selection doesn't seem to offer a satisfactory explanation. The group now represents a wide range of people. Some think that the modern synthesis needs small additions and tweaks while others call for it to be totally replaced. However, what is common is that none of us in the group question the origin of life. From what I know, every member is satisfied with the explanation that life originated on earth and evolution is purely an earthly phenomenon. The actual details may not be yet agreed on - whether first it was a replicator such as DNA/RNA or whether it was a protein complex or just simply a soup of chemicals that started off first and they built up complexity over time.

From reading the materials on your website, you say that life should have existed forever. You say that life can only come from life. You are claiming that life should have existed even before the Big Bang happened and that intelligent life should have always existed. Nobody can completely disregard these as totally impossible. But our current knowledge of the universe and its beginnings do not seem to allow for such claims. That of course doesn't mean that is an established fact. There is very little we know about the universe and its beginnings and much of it is speculation. Even if life existed in some form before our known universe started its life from the big bang, it is difficult to see how any such life from an earlier universe or a parallel universe (or whatever you call it) would have made its way into our own universe. Life in our universe should have originated in our universe and there was none before the big bang. At least the big bang as the explanation of our universe seems to be the most sensible one so far and we have to go by it unless something better comes by in future.

You also seem to claim that new genetic material cannot arise from mutations and as such any genetic material preexisted and are delivered to our planet via comets.

On your website you say - "But this is not the same as macroevolutionary progress requiring whole new genes that differ from known predecessors by dozens to hundreds of essential nucleotides. In strong panspermia, those new genes must be supplied from elsewhere."

You seem to say that novel complex functional genes cannot keep developing in the organism itself. Basically you are saying that all the complex genes that we find in all complex organisms including us, came from some pre-existing life form somewhere in space. It is difficult to comprehend such an occurrence. Most functional genes present in most animals serve very specific functions, or more accurately, such genes are used in the production of proteins that serve very specific functions. For instance, spiders have genes that allow them to produce the silk usen to create their webs. For a human being or a dog, such a gene is useless. So the genes used to create spider webs should have come from a very similar, web weaving creature that existed/exists in space somewhere. Now even if such a gene it delivered to an earth residing early precursor to a spider, that creature needs to first create the glands that produce the silk (close to their rear end), the cells dedicated to silk production have to be lined along this gland. These cells have to be differentiated and epigenetic markers are added at the start and end of the genes that are needed for silk production, thus defining them as cells specialised for silk production only and nothing else. Then the spider needs all the mechanism needed to squirt out the silk. An even more complex set of instinctive knowledge and skill set which allows it to weave a perfectly designed web is also needed.

Just receiving a piece of gene from space, which is then passed on to the spider via HGT wouldn't help much. Unless there exists spiders that weave webs (in this distant planet), it is difficult to see where such a gene came from. For all the millions of proteins that we see in millions of species on earth, we will need the same or very similar creatures on another planet. And a gene for the web material could only be useful not just if it gets to a spider, but also during the right time of its evolutionary journey. A gene used by dinosaurs is only useful on earth during the period the earth had dinosaurs. Not a few millions years before or after they have existed and gone extinct. For each species, thus, comets should be bringing in regular supplies of new genes that would be useful to them during that phase of their evolution. A comet can only bring in genes from what exists in a distant planet at that time of its own evolutionary state.

If you say that genes cannot evolve from mutations and that they have to come from pre-existing genes and organisms that exists/existed on another planet or universe, how did those millions of genes evolve or take form on that planet? I am not saying that your theory is unworkable. I am just finding it difficult to understand how it would all come together.

But all that apart, Panspermia is mostly an origin of life theory. You do bring in HGT as a possible tool which serves a purpose in that theory. But the theory in itself is one that deals with origins and not on how evolution works on earth. As I mentioned at the start, The Third Way doesn't deal with that part, just how evolution happens on our planet. Regards, Raju

15 Sep, from Klyce: Dear Raju Thank you, truly, for taking the time to learn what cosmic ancestry is about. Good job for digging in. Let me quickly add a few comments, with no thought of changing your mind.

"...our current knowledge of the universe and its beginnings do not seem to allow for such claims...." One of my points is that the big bang theory (our "current knowledge") has too many problems of its own, and does not deserve to overrule other sciences.

"Just receiving a piece of gene from space, ...wouldn't help much." It has to be easier to take the next macroevolutionary step if the programming is available, vs if it has to be written from scratch.

"...that creature needs to first create the glands...." All of the difficulties you subsequently list are compounded if the programs are not available already. If they are available, something like Shapiro's NGE can get them working.

"...how did those millions of genes evolve...?" I'm not claiming they ever "evolved" in your sense. It's the monkeys writing Shakespeare, it's absurdly unlikely. But we never witness them originating anyway. (Mutating slightly, okay.) "Where do those millions of genes come from?" is my question.

BTW "millions of genes" is grossly understating what has been observed, so far, among bacteria and viruses on this planet. They're here already.

"I am just finding it difficult to understand how it would all come together." Yes, it's very radical. Similarly, when Earth was claimed to be round instead of flat, It was difficult to understand how the Chinese could be standing upside down.

I think the facts fit together well in cosmic ancestry, especially if the right questions are asked -- ones without hidden assumptions.

But Raju, thank you. You understand cosmic ancestry. Good job. I wish you well. And I would like to post yours and mine, for future science to see if they want. Thank you. Best regards, Brig


01 Jun 2022 from Brig Klyce: May I humbly request a copy of your subject article for study and possible review on my website about evolution and panspermia?
BTW, In 2012, I reviewed Evolution: A View from the 21st Century - www.panspermia.org/whatsnew71.htm#20121220
Thank you. Best regards, Brig

from Shapiro: A .pdf file of the paper you wish is attached. In case you aren't aware, my 2011 book went out of print, and I just published a 2nd edition with lots of additional material: Evolution: A View from the 21st Century. Fortified. You may find it worthy of a follow-up review.
Best wishes, Jim Shapiro
Engines of innovation: biological origins of genome evolution by James A. Shapiro, Biological Journal of the Linnean Society, accepted for publication 24 March 2022.

04 Jun: Jim, thanks! I have read this paper with close attention, and I see much to admire. However, I am not sure about something. Many of the genetic programs that produce the macroevolutionary advances you cite, like photosynthesis, are carried by viruses. Viruses likely provided them to eukaryotes. That leaves them unaccounted for, if you ask how the programs originated. Is this a matter of any concern to you?

If I ask where the programs come from, I enter a different path. It leads me eventually to a conclusion too radical for almost everybody, even some panspermia allies! I welcome any guidance or comments. If you have other writing along these lines, please point me there. BTW, I cited you briefly back in 1998: https://www.panspermia.org/whatsne4.htm#%20980812txt
Thanks, again. Very best regards, Brig

04 Jun - 17 Aug: Shapiro's emails are not shown, at his request.

Klyce: Dear Jim, thank you, truly, for your thoughtful response. You say, "...it often takes the invention of something new for the assemblage to succeed. How that can happen is the real question." Boy, do I agree!!! But the happening of the invention is not an observed phenomenon. This is not a small point. Stay with me, please.

Say the something new is 100 or 1,000 properly sequenced nucleotides. It is, okay, easily acquired. How? Some form of HGT, permissively defined. Okay. From where? Well, often it can be traced a good ways back, as you well know. (Sometimes not, as with de novo genes.) But seldom (ever?) does the tracing make a good case for the neo-darwinian gradual evolution of the something new. The trails just point, parallel, toward the dark past.

The "happening" of the invention is an assumption. Based ultimately on the big bang. A pretty loose theory. Not good enough! Could we please admit the possibility that the something new is not actually new? Just that admission lets the facts tumble together more easily. If any of this catches your interest, I will be very pleased.
Best regards, Brig

06 Jun | Klyce: Jim, my deconstructionist wording didn't help. Lemme start anew.

Your examples, bricks, bridges and computers, were all invented and made by somebody. That is well-enough understood. But the process of invention for genetic programs is seldom if ever understood. Yes, exons may get combined and make a new gene (if you will allow that word.) But the exon already has some programmatic content. And regulatory sequences must find existing programs to turn off or on.

I make this analogy: Imagine the Declaration of Independence is scrambled into a dozen or so fragments, with some typos. A smart word processing application, with syntax- and spell-check, could probably reassemble it correctly enough. But no word processor could produce it de novo.

You say, "We know mechanisms that can produce the novelty...." I suspect they are piecing together existing programs, like the smart word processor. I claim that quarantined experiments, in biology or computers, never produce novelty. I have followed Lenski fairly closely.

Actually, my doubts are like those of the creationists. But my resolution is different. Darwinists and creationists both ask how life, and genetic programs for higher life, originate. And both have unsatisfactory answers, I think. I ask where they come from. I see lots of HGT, and I never see actual invention. I will pay close attention to any examples you may offer.

I don't expect to convince you, but I would be tickled if you came to understand cosmic ancestry as a theory. It puts new light on things like the jillions of viral genes whose functions are completely unknown, life's early start on Earth, punctuated equilibrium, the importance of HGT, organics in space, chiral amino acids in meteorites, methane on Mars, etc, etc.

Thanks. Best regards, Brig

PS – Do you teach students?

07 Jun | Klyce: Jim, thanks for taking an interest. And thanks for summing up the issue: "How was a functional structure generated amongst the vastly much larger number of possible nonfunctional combinations?" I agree that that is the issue for darwinism (broadly defined). And as a skeptical outsider, I observe that there has been no real progress on that issue for far too long now. I appreciate your offer to dig out some well-documented examples.

I actually have attempted that myself, and turned up nothing. One study that I especially noticed was this one: "Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment," by Tin Yau Pang and Martin J. Lercher, doi:10.1073/pnas.1718997115, PNAS, online 18 Dec 2018. [See https://www.panspermia.org/whatsnew94.htm#20181218.] In it they comment, "...we found no evidence for the contribution of selectively neutral processes...." I think that means exploring sequence space was not fruitful. (This is bacteria, your field, right?)

Back to my deconstructionism: Functional structure can be acquired, as we observe all the time. But can it be generated on a virtually blank slate? In my skeptical opinion, examples are rare and weak, at best. A different approach deserves to be considered. If I could I could convince you of that much, it would be wonderful.

Thanks. Best regards, Brig

Klyce: Thanks. I think that the denovo ones were also originally acquired by transfer, but so long ago that those clues have disappeared.

I'm glad if we agree about the inadequacy of gradual accumulation of mutations. But I do not share your apparent optimism that some other mechanism will be found to generate novelties (invent new genetic programs). I think evidence for it would be already apparent, and I think computer modelers would have already demonstrated it.

Here's where I come to my huge leap: there are no novelties. New genetic programs are not actually new, they are as old as life. What we call evolution is actually the development on Earth of pre-existing life. It's very hard – it was for me – to get one's mind turned around this way, yes. But meanwhile, the evidence makes much more sense. I'm of course not the first with this idea. William Bateson, in 1914, for example: https://www.panspermia.org/whatsnew68.htm#12020319

Is this a concept you would ever consider?

Klyce: Dear Jim, Thanks, truly, for the MS. It was very helpful in clarifying your thinking. And it was / will be educational for me. Thanks also for your simple declaration (in email) "...I do believe novelty is produced de novo in the course of evolution." But let me ask something I'm not sure about. Do you believe that you and your like-minded allies are on the right track, not far from closing the gaps in the theory of evolution?

You see that mobile genetic elements are active and important. You know that stress can speed things up. You have some reservations about directed mutation, but I think it, too, will prove out. You have a lot to say about CRMs and other "noncoding elements." All that confirms and expands my thinking.

But you comment, "It is very difficult to imagine how random mutations and phyletic gradualism could generate functionally significant numbers of shared CRMs [that] could evolve at unlinked genetic loci encoding different proteins." To me, it's difficult to generate even one, by any means. This would be an example of a small gap that remains. A bigger one would be the software management you mention that gets the insertions to the right places. You acknowledged in earlier email that there are gaps.

To me these gaps are unfathomable with any Darwinian logic, because the things need to originate. But in "Purposeful Evolution" you do not claim to know the origin of any of them. In fact, you conclude by asking, "...whether the capacity for actively and purposefully generating hereditary variation is an essential feature of life." I am so ready to agree. If for generating you had said exploring, I would be with you 100%.

If exploring is what life does, the reservoir of genes (forgive the term) in viruses in the ocean, for example, looks like a huge resource. All those ORFs have never, far as we know, been tested. And viruses can transform whole populations in a generation (Ohno).
Susumu Ohno, Evolution by Gene Duplication, Springer-Verlag Publishing Company, 1970. p 55.

Meanwhile, your purposefully I happily endorse! It would require me to think longer before I could fully explain my own reasoning. But consider: Cyanobacteria oxygenate the planet. Genetic programming for oxygen metabolism is ready and waiting (https://www.panspermia.org/genesborn.htm#textbox). It looks ...purposeful.

You said my website links were helpful. Thanks. Here's one that touches on purpose. It would pertain to not only Dawkins, but EES as well: https://www.panspermia.org/whatsnew74.htm#20130913

Thanks for staying with me. I welcome your thoughts. Best regards, Brig

Klyce: Dear Jim, thanks. My comment about directed mutation arises from reading about point mutations that occur preferentially at certain positions, especially, diversity-generating-retroelements (DGRs). See for example Paul G. Blaire et al, 2015, https://www.nature.com/articles/ncomms7585. Stress-induced activity among the right controlling elements also seems in a sense directed. But maybe that use is imprecise or incorrect.

I'm still unsure where you are on my broader question. Genomic novelty (lengthy new programming made evident by new features) has not been demonstrated to originate in any quarantined experiment, not even in computer models. The transition from point mutations to block transpositions does not rescue the situation – computer modelers have tried it. This lack of experimental support in any medium is a serious problem.

This leaves only genomic archaeology for a source of evidence. That needs to be better than it is now, to be blunt, because even the sequences that you point to don't have much of an origin you can pin down. How confident are you that good enough evidence will emerge? Confident or not, I hope you would be willing to entertain the possibility of cosmic ancestry, or anything like it, that does not need for the programming to originate.

[...] Thanks again. I hope we will keep talking. Very best regards, Brig

Klyce: [...]Thanks ever so much for getting back to me so quickly and so cordially. ...At this point, no harm in responding to your points, I suppose.

1) My website is about evolution and the origin of life [OOL] on Earth. As for OOL, I observe that it looks virtually impossible on Earth in the time available. If so, panspermia should be admitted as a possibility. NASA apparently agrees. I was strongly influenced by Thomas Kuhn, who says that no theory ever falls under its, own weight -- there must be an alternative. I cite evidence supporting panspermia because I think its viability needs upholding. I do not simply assume that it is true, and I remain wide open to any evidence for OOL. ...I never brought it up in my exchanges with you.

2) Of course evolutionary variability can come from mutation, recombination, regulatory changes, etc., with a big role for the environment. My position is that many macroevolutionary advances come following transfer, from somewhere, at some time. This is unquestionably true. For bacteria, a consensus is building that HGT is "all there is," to quote Ernst Mayr. See this web entry: https://www.panspermia.org/whatsnew103.htm#20210310. Eukaryotic life seems to be heading in the same direction (for one example see Keeling and Palmer, 2008, discussed here: https://www.panspermia.org/whatsne51.htm.) If the transferred genetic programs come from species that can't use them, Darwinism in all variants should be especially puzzled.

2) b) Mechanistic issues would be a very fruitful thing to discuss, I would think.

2) c) [My] position would mean that the future path of evolutionary change is limited only by the genetic programming that is available. As you know, every newly sequenced genome discovers genes (forgive the term) that had never been seen before. When pandora viruses with 1,900 or 2,500 genes were sequenced in 2013, only 7% had recognizable homologs (https://www.panspermia.org/whatsnew74.htm#20130720.) Venter thinks the bacterial pangenome has infinitely many genes. Meaningful biological input looks like a virtually unlimited resource already.

I think there's still a crisis, and the needed paradigm shift is bigger than many evolutionary biologists are willing to consider 4 years ago. ... Thanks again for your patience forbearance and cordiality. Best regards, Brig

Klyce: Dear Jim - Thanks for staying with me. I gather that you emailed [Recognized expert] soon after you received mine of June 7th, in which I had said, "Functional structure can be acquired, as we observe all the time. But can it be generated on a virtually blank slate? In my skeptical opinion, examples are rare and weak, at best."

[Recognized expert] is well aware of de novo genes. He soon says, "...the dominant majority of these works lack evidence for the existence of noncoding ancestral sequences...." This is already a problem for darwinism, because in darwinian evolution (all variants) the genes must originate. They would have earlier versions from which a history could be plausibly reconstructed. I wish I could convince you that this issue is critical. If genes can originate, quarantined experiments should easily demonstrate it. They don't. Or at least a computer model should demonstrate the analogous phenomenon. They don't. What about evidence from historical reconstructions? ...most of them don't either.

He lists some remaining possibilities: "...these reported genes may also have alternative sources from non- de novo origination processes, e.g. lateral gene transfer...." (Like I been sayin'.)

"... from a rapidly evolving donor such as bacteria or virus...." So the process was not trial and error toward the eukaryotic function, and the evidence has been erased?

"...or loss of outgroup sequences." So the leftovers happen to have the functional programming?

Finally he cites a review in Nature, 2019. I commented on it when it was current, quoting this part, ...genes do not always evolve from existing ones, as biologists long supposed. Instead, some are fashioned from desolate stretches of the genome that do not code for any functional molecules. Desolate stretches that happen to have functional programming, with no darwinian provenance? Jim, to quote you, "The emperor has no clothes. Somebody has to say it."

I know you don't like the term "gene." I notice that you had asked him about "domain origination." I like the term "genetic programming" or "programs" - lengthy sequences with programmatic meaning. How this originates is a premature and not fruitful question, I believe. If you ask only where the programming comes from, you make better progress. To me, that question logically follows the question that we both ask, How does life evolve?

In 2004 I wrote an essay partly in response to an article by Manyuan Long et al. that might interest you.
https://www.panspermia.org/wordcount.htm.

Thanks again. I hope you and I may stay engaged. The issues are important. Very best regards, Brig

Klyce: Thanks for a quick response! I'm still online, so I'll quickly answer. You say, "Not everything is acquired by horizontal transfer from outside." A lot is, we see. This is already a shift for darwinism. But you're saying some isn't. I think the evidence for that claim is so weak that it's a crisis. It can't be convincingly demonstrated in experiments. I'm not the only one saying this:

"Most people accept evolution; even creationists accept microevolution. If we start getting macroevolution in the lab, then they'll accept the macroevolution.... The scientists should be saying, Prove it. Do it in the lab." – Harvard Medical School Professor of Genetics George Church, 2007, Life, John Brockman, ed., Harper Perennial, 2016 (p 140, emphasis in source text).

And historical reconstructions are also unconvincing. ...I think we understand each other. I would love to engage with your other renegades to see if there's common ground to work from. I think a truly 3rd way should get a look! Thanks. Very best regards, Brig

Klyce: Jim, we may be talking past each other. Your focus seems to be speciation, hybridization, adaptation, fitness, diversity. I think these have little to do with the big question about evolution: how ongoing macroevolutionary advance is possible. But you may think they can ultimately explain it. Do you?

I understand that natural selection can kill the things that don't work. But the things that do work, and are apparent inventions, that's what's interesting. Okay, "new domains" can supply new programming. But the sequence of the new domain - how did it get composed, in darwinian evolution? It seems to just turn up. That it ever got composed. somehow, is an assumption that lacks evidence. We don't see it. But it can get installed by other genetic capabilities that you understand better than anybody.

Speciation can create reproductive isolation, which may be helpful. Hybridization is HGT, wholesale. Adaptation is microevolution - optimizing and tinkering with what's available. Fitness ... ability to get selected? Diversity? Fine.

But your system needs to supply the invention, and I think it doesn't. Rearranging of domains, we both need that. But where they come from is an unsolved problem for darwinism. Do you think you and your allies are making adequate progress on this one? Do you even agree that it's a problem? If we could agree on the same question, what are we trying to solve, we might not talk past each other.

Don't we both begin: How does evolution work? Here I mean Evolution as the public understands it - prokaryotes to people. Photosynthesis. Lungs, wings. We know a lot more about genetic programming now. So, where does the programming come from? If we agree so far, let's pursue that question?

You may not like any of this reasoning. You may ask an entirely different question. Any reply will be welcome. Thanks. Brig

No genome is an island: toward a 21st century agenda by James A. Shapiro, Annals of the New York Academy of Sciences, 2019.

23 Jun | Klyce: Dear Jim - Many thanks for the pdf. I have read it closely, once, with lively thoughts along the way. I also watched the YouTube video of your presentation at the American Society for Microbiology, Jan 19, 2017. I can learn a great deal from you, obviously. In comparison, my own knowledge must look to you ...undergraduate. My website is largely a chronicle of my own education, obviously. Please forgive my shortcomings as I comment.

Language: I admire your precision WRT the word "gene," the primary example. I wish you would observe the same caution with "evolution" (all variants.) You say, "...'Asgard' group of archaea that have evolved many proteins previously thought to be unique to eukaryotic cells." An ordinary reader will assume (as you appear to assume) that Asgard -- by some internal, local process -- invented the proteins via composing the DNA sequence that encodes them. But this is the very process you are questioning, I thought. If you had said only that they acquired them, or they have them, no problem.

Same issue with "origin" (all variants.) The word appears throughout the paper. "...and membrane structures that document their common cyanobacterial origins." What's wrong with source? Same complaint about this phrase: "...protists and animal guts constitute evolutionary 'melting pots,' where new adaptations can arise ...." Meaning they didn't already exist? All you really know is that they "turn up" like a forgotten relative at a family reunion. I think the words matter.

"Adaptation" is another one. If a point mutation changes the color range of an opsin for a new environment, fine, microevolution. That process has a narrow range. But the word is used to mean other evolutionary steps where DNA transfer did the work. Caveat emptor, I guess.

I notice that the term de novo is absent from the paper. Instead, "novel"? "For example, symbiosis, hybridization, and infection can simultaneously modify survival, trigger rapid genome change, and add DNA to novel genome configurations...." Okay, they may be "novel" in the sense of not having been put together on Earth before. But if they fit together and work like machine parts or sense-making text, the word "novel" implies more than that. (Slippery and possibly trivial issue here.) Meanwhile, de novo DNA, as I understand it, has no apparent provenance that would include a process of trial and error. It just works.

Testing: I am very pleased that you agree - testing is needed. This is a point that I have made for years on my website. But I want to test an assumption that you already make! I have promoted 2 lines of testing. In computer models: http://www.panspermia.org/proof5.htm. (This page also includes comments about Richard Lenski's closed E.coli experiments.) Later I tried to sponsor a prize for a computer model: https://www.panspermia.org/eprize.htm.

And I sponsored a research project in historical reconstruction: https://www.panspermia.org/tomray01.htm. Tom Ray was a computer modeler who wanted to explore with his computing savvy the newly available genomic sequences. But he misrepresented to me his level of interest. Also https://www.panspermia.org/graphspaper.htm. This was my way of explaining the project to NASA's Astrobiology group. You will see that the question is posed in a naive way. But I still think the question is sound, and the approach is not misguided.

Conclusion: You wrote, "In addition, we should never forget that asking outrageous questions and designing experiments to answer them has always been one important way we make significant scientific progress." I couldn't agree more. What about letting some of your students engage with my website. We might learn from each other. (I'm still hopeful to interest you and your like-minded colleagues.)

Jim, I wish you success in your quest. And I wish you would agree, it's time to include for consideration something even as radical as "cosmic ancestry".

Let's keep at it! Best regards, Brig

...15 Jul: Jim, I'm getting the message that you've heard enough from me. Two things:

Here's an essay from 19 years ago wherein Chandra and I say that Darwinism (all variants that promise ...macroevolutionary advance without a source) must be challenged to produce evidence. It dawns upon me (although maybe Popper said) that the theory, as it stands, cannot be falsified. Anyway, what we wrote then, for an ID compendium, makes the point adequately.
https://www.panspermia.org/thirdalt.htm

May I publish extracts from our [these] emails in my Replies section, with a pointer from What'sNEW? I think it could be instructive for future history of science - to see how we tried to communicate across very different paradigms.

Thanks for your kindness and patience. Very best regards, Brig

04 Aug: Dear Jim - Maybe I'm too radical.... Maybe not for a seminar or course about, or including, the most radical amendments to evolutionary theory? Dialog with informed, challenging students might prove fruitful all around. Even if cosmic ancestry is wrong, discussion might reveal where EES needs work? Serious suggestion.
Thanks, Brig

Klyce: Dear Jim
...I say a hearty Yes! to pursuing engagement with your like-minded colleagues. So glad you consider me not to be too radical. As for committed, yes I really believe what I promote on the website. However, I remain entirely open to contrary evidence. I have actively promoted research projects that could upend me. I do follow mainstream research closely. My goal is advocating for an entirely scientific and legitimate alternative to the current paradigm. As I recall, Thomas Kuhn said this about Galileo: he ultimately succeeded not with evidence, but with marketing and persistence. Merely establishing a legitimate alternative would be success for me.

Not sure what's not open to empirical study. Popper said something similar about darwinian evolution, I think. Anyway, this is the kind of subject I would like to discuss, with civility, good intentions and optimism. [...]

I say EES without knowing what it is, obviously. And I carelessly refer to Neo-Darwinism and Darwinism with little distinction. In my philosophy there are two categories for theories of evolution:

1) Theories in which true invention - new genetic programs - come from within a closed biosphere/ecosphere, like Earth was formerly thought to be. I've been calling all of it Darwinism. I obviously need another term.

2) Theories in which true invention - new genetic programs - cannot simply (or complicatedly) come from within. They can't because the entropy law is firm. If not, they must be somehow supplied, as by panspermia with HGT. Deciding in favor of one or the other was the purpose of research projects mentioned above. In either category [just above], microevolution - adaptation, optimization, etc., is possible within narrow parameters, as computer models readily demonstrate.

Not sure what you mean by biological intervention. I would love to read your forthcoming writing. Thanks, truly, for kind comments about the website. [...] My whole issue is "How Does Evolution Work?" I think I make a good case for a different way. [You seem] to agree that a different way is needed. My piece of twenty years ago offered a naive outline of ways to investigate -
https://www.panspermia.org/threetests.htm
But any way you can suggest for going forward is welcome.[...]

Being realistic, evolutionary biologists are almost entirely within category 1) above. I'm asking them to look at category 2). This is asking a lot. [...]

Best regards, Brig

Klyce: Jim, many thanks for your thoughts, and for the opportunity to dialog with you about them.

1. I admit to having read only some, and not enough about EES. I will go back to your earlier emails for references. I want to increase my knowledge.

2-3. I am fairly well-informed about Darwinism and Neo-Darwinism. However I have wrongly labelled some of the "non-Darwinian" programs in the former categories - an unnecessary confusion that I will not repeat. I am aware of HGT, adaptive and directed mutation, and other related phenomena, some just coming to light. However, I think your assertion, "...they are fully equipped to generate new genomic content without those inputs" is open to challenge. The possible pan-genome for eukaryotes is enormous, and unfamiliar genes are found everywhere, without apparent limit. How do you know outside inputs are dispensable, without quarantined experiments that keep inputs out? (Lenski's instance of aerobic citrose metabolizing was likely achieved with cryptic genes, as he admits.) The input may come long before it gets expressed. I welcome your thoughts about this.

4. Like you I see no "energetic limit to the biological creation of genomic inventions." But I see lots of confusion on this subject. Thermodynamic entropy and logical entropy are not the same. But I believe Logical Entropy lives under the analogous prohibition - It cannot decrease. So my limit is logical. Of course, this may be wrong. Still, invoking energy to create genomic inventions is certainly undemonstrated. I have considered this subject carefully:
https://www.panspermia.org/seconlaw.htm

5. I am extremely grateful to you for your patience and your listening. Our paradigms are so different that it is not easy. I believe we can at least understand each other. I am honored to have this conversation with you..

Klyce: Dear Jim - Thanks for your comment here. The example from Lenski is a good one to discuss. I have quickly read the reference linked in yours: D. J. Van Hofwegen, C. J. Hovde and S. A. Minnich, "Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA", J Bacteriol 198 (2016), no. 7, 1022-1034. https://doi.org/10.1128/jb.00831-15.
The issue for Van Hofwegen et al. should be how the bacteria acquired the programming for aerobic metabolism of citrose. The sequencing by Lenski et al. revealed that it was already present in their population as "cryptic genes". I believe other mechanisms, your Natural Genetic Engineering, activated the programming. NGE is capable of exploring the full potential of the resident programming - all there is in Lenski's quarantined system.

I think I already mentioned this study which found, "HGT can potentiate adaptation to future environmental change."
"Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation" by Laura C. Woods, Rebecca J. Gorrell et al, W. Ford Doolittle, ed., doi:10.1073/pnas.2005331117, PNAS, 14 Oct 2020.

NGE also would be capable of accepting, assembling, puzzle-piecing together, properly inserting, regulating, testing, optimising (or even "mothballing"?) additional programming acquired by some form of HGT. NGE is truly fabulous, something to marvel at. I hope you are recognized for highlighting it.

What has not been shown is that NGE, or anything like it, can compose new genetic progamming. Several times in our correspondence you have mentioned the need for decisive experiments. I couldn't agree more. But until the phenomenon is demonstrated in decisive experiments, I think it remains hypothetical, not ready to rule out alternative hypotheses. I welcome your thoughts.
Thanks again. Best regards, Brig

Klyce: You say, "Whenever there is domain shuffling in proteins or connection of new transcriptional control signals to a coding sequence, 'new genetic programming' has been created...." I believe this is not necessarily so. "New genetic programming" might actually be existing programming reassembled. You remember my analogy -- a computer with syntax- and spell-check and related features could reassemble the Declaration of Independence from a dozen or so pieces. Natural Genetic Engineering could perform a similar function on protein domains and transcriptional controls. (This would be pretty wonderful already.) I imagine that this sounds strange to you, but at least it's possible. If so, HGT will be rampant. Evidence supports this, convincingly among prokaryotes.

Other times you have talked about the need for decisive experiments. I am curious to know where you are on that. What would the experiments ask, or seek? What medium would you use? What are your thoughts on experiments?
Very best regards, Brig

Klyce: Dear Jim – ...The immediate issue, I thought, was whether citrate utilization was invented, or acquired. I don't believe that either experiment ruled out the latter – acquired, possibly long earlier. With NGE, which you understand best, handling the implementation. Okay, my text analogy was distracting.

...I am still interested in evidence from the decisive experiments you have mentioned. I welcome any words from you.
Best regards, Brig

14 Aug | Klyce: Dear Jim – Thanks again for your kindness and patience in our recent emails. ...I see your position even more clearly now. I especially congratulate you for understanding and explaining Natural Genetic Engineering (NGE) in your other writings. I think I should adopt that term instead of "Robust Software Management".

NGE works for both of us in the same way really. I only pause when you add that the NGE toolkit enables living organisms "to evolve actively and cognitively." To me this is a leap into uncharted territory, with language more ambiguous than you would normally allow. I guess this is where the experiments that you often mention could be decisive. Until they are, I wish you would keep the door open to alternatives like cosmic ancestry.

Your comments about the passivity of Neo-Darwinism prompt me to acknowledge something. If we come from cosmic ancestry, life is still subject to happenstance. Evolution is able to advance because the programming, including that underlying NGE, is available. But it still takes very long to arrive at a stage like ours on Earth, and each step is still hit-or-miss.

As an aside - I promote cosmic ancestry from two directions. First, positive evidence like HGT, fossils in meteorites, organics in space, etc., etc. Second, skepticism about alternatives that don't need pre-existing programs. If I can raise "reasonable doubt," then "conviction" is premature, and alternatives should not be excluded. My skepticism was annoying to you, but you have stayed engaged, for which I am grateful. [...] Very best regards, Brig [...]

18 Aug 2022 from Shapiro:

Brig, I have ...decided not to authorize publication of our exchanges. ...I concluded the emails do not illustrate the appropriate kind of empirically based scientific exchange that will help the readers understand evolution. Jim
14 Aug 2022: James A. Shapiro is a biochemist and molecular biologist....

19 Aug 2022 from Klyce: Dear Jim – Thank you for your kindness and patience during our summer-long exchange. ...I am sorry that we did not further pursue discussion of the citrose utilization in Lenski's experiment. You believe it exemplifies invention. I suspect it demonstrates puzzle assembly -- still impressive. We did not reach agreement there. Similarly with new domains. You believe they are easy to find. I agree. But finding one does not show its origin – that's simply assumed.

I am advocating a paradigm shift. Maybe it's wrong. But paradigm shifts are part of the history of science. Science would do better if conflicting paradigms did not ignore each other or cut off communication. Our correspondence illustrated a good-faith attempt by both of us to reach agreement. We didn't. Still, someone might see what we foundered on and see a lesson there. Maybe our definitions were incompatible. Something.

Thank you again for your patience and wisdom. I will continue to follow your publications, and I ask you to alert me when you post or publish anything you think I should see. I still hope to interest you in a truly third way. Very best regards, Brig

PS: I would be very pleased to continue our discussion, but only for the record, please. Thanks. Brig

19 Aug 2022 from Klyce: ...I think we agree that NGE can do the installing, testing, puzzle-solving, optimizing, etc. Right?
I would add that we disagree about how much it has been shown to "write." Because the process of writing – a new domain of >100 nucleotides for example –
1) has not been demonstrated in quarantined experiments, and
2) cannot be plausibly reconstructed from genomics. New domains just suddenly show up.
...Very Best Regards, Brig

20 Aug from Shapiro: Brig, You attribute too much agency to NGE. NGE does the installation of novel sequences. It is the cell that uses NGE functions to restructure or rewrite DNA sequences. So testing, puzzle-solving, optimizing etc. constitute a whole-cell series of a actions that engage the cell's cognitive abilities. How that all happens is part of today's research agenda. NGE functions can generate domains of >100 bp by some combination of chimeric template joining and template-free polymerization. Jim

20 Aug from Klyce:
Dear Jim – Thanks for your clarification on NGE. I think the "Robust Software Management" that I refer to is probably, basically the same thing. ...I think you're the one attributing too much agency!
The "cell's cognitive abilities" is an invitation to a philosophical tangent that I would like to bypass.
But your last sentence, including, "...some combination of chimeric template joining and template-free polymerization" -- may we please stay on that one? My reaction:

Chimeric template joining would exemplify the puzzle-solving capability that we seem to agree about. It can easily be modelled in computers.

Template-free polymerization is a different animal. If the polymer is long enough to have any "new" function or unique enzymatic role, how long is that? If it's 30 a-as, 90 nucleotides, the possibilities are too numerous to explore in any reasonable time. Allowing amino acid substitutions doesn't fix the problem. It might reduce the exponent by ~10% (see Ramsey et al.), so only 4^80 possibilities would probably include a functional one? Too many.

Duncan C. Ramsey et al., "The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution" doi:10.1534/genetics.111.128025, Genetics, 2011. In real proteins, it may well be that at one site 3 amino acids are preferred and 17 unpreferred, while at a different site 5 are preferred and 15 unpreferred. ...At any given site, only a small number of amino acids are actually permissible.

Jim, it could work as you suppose. But given the theoretical difficulties and the lack of direct evidence, the internal inventive capability you advocate remains hypothetical, I believe. I welcome your thoughts. Very best regards, Brig

PS, I welcome your thoughts, for the record. You got my last-previous email, with that proviso? This is exactly the kind of discussion I would like to continue. I think there is a real chance for progress....
Robust Software Management in Genomes begins to outline the topic.

from Shapiro:
Brig, The chimeric joining and untemplated sequences are based on experiments results -
N. T. Umbreit, C. Z. Zhang, L. D. Lynch, L. J. Blaine, A. M. Cheng, R. Tourdot, L. Sun, H. F. Almubarak, K. Judge, T. J. Mitchell, A. Spektor and D. Pellman, "Mechanisms generating cancer genome complexity from a single cell division error," Science 368 (2020), no. 6488. https://doi.org/10.1126/science.aba0712.

from Klyce:
Dear Jim – Thanks for this reference. Yes, it does demonstrate that cellular mechanisms, call it NGE, can create lots of activity. This, I understand, is an example of "chimeric template joining and template-free polymerization." I was not aware of the BFB cycle or its reach. I'm glad to learn about it. I continue to learn from our exchanges and am grateful for them.

I understand that you think this process can produce useful, functional, new sequences - what I thought was "too much agency." My view is that if so, there would indications in many articles. This article described only negative consequences.

I interpret the results of Umbreit et al., first reaction, this way. "The chromosome breakage-fusion-bridge (BFB) cycle" is an example of Robust Software Management (RSM) responding to a problem that qualifies as Very Serious. If there's a chance to save the system, hit it with everything we've got. However, when it's this serious, recovery - a return to normal health - is rare. And no invention is even "contemplated."

Invention comes after HGT supplies the needed coding and RSM does its busywork. That begins when HGT first arrives. It may result in immediate installation, activation and testing. It may result in failure. HGT may also be followed by mothballing. Later, prompted by changed circumstances, RSM may retrieve a mothballed program for re-testing.

I recognize that your version of a third way includes much more than standard Neo-Darwinism (and EES?). But to me it has the same problems as they have. Implausibility (based on US opinion polls, if nothing else), and missing evidence (as discussed above.) If so, I suggest that evolution by different means should not be excluded outright. Still trying! ...I welcome your thoughts. Best regards, Brig

addendum, 05 Sep | Klyce to Shapiro:
Dear Jim – I have just ordered (the Kindle version) of the ...Fortified edition (2022) of your book. I also read the review [of the 1st edition] by Adam S. Wilkins. I thought it was even-handed and well done, given the obvious depth of the disagreement between you. It helped me understand better some of your earlier words to me – "living organisms have the natural genetic engineering toolkit to evolve actively and cognitively...."

Review of Shapiro's Evolution..., by Adam S. Wilkins, Genome Biol Evol., 2012.

Wilkins quotes you, "Innovation, not selection, is the critical issue in evolutionary change." He disagrees. I agree with you. In popular thought, innovation is exemplified by the first appearance, in the history of life on Earth, of things like photosynthesis, cell specialization, ...a very long list of things. (So far, so good.) Where do they come from? The DNA that codes for them. (One step at a time....) Where does that come from? Vertical inheritance. Before that? HGT. It may go back to viruses, bacterial genes, old stuff, or it "seems to have come from nowhere." Okay, but how does the coding originate? (Wait a minute. We haven't clearly observed that phenomenon.) But agreed, Innovation is the issue.

"...the ability of cells to alter their genomes in response to environmental challenge.... what does the engineering? ...The cell is thus its own agent." I assume Wilkins has not mischaracterized you here. I'm with you, but with a limited definition of the cell's agency. He mentions that a lot of your changes are somatic only, but certainly enough are inherited. More important, environmental stimulus can provoke genetic change, I agree. Adaptive and even directed mutation, and yes, it's heritable. Stress can even accelerate HGT, I think we agree. You know all this better than I, better than anyone.

"This scattershot generation of new variants.... there are (as yet) no cases of 'precisely targeted' evoked genetic variation...." I'm with Wilkins now. Your last example to me of the BFB cycle (N. T. Umbreit et al, 2020) created only negative consequences. Lenski's citrose utilization can be explained by silent programming reactivated. A sure example of what you are advocating remains missing, or at least unconvincing. At this late stage, a serious problem.

"Selection operates as a purifying but not creative force." Wilkins disagrees. I'm with you again. This seems to be the issue behind, "...evolutionary biology is increasingly separating into two camps.... The two contemporary groups, divided over this point, are not so much talking past each another as ignoring one another. This cannot be a constructive situation though whether it has the makings of a full-fledged Kuhnian paradigm crisis is too soon to tell." I was pleased that you and I were not talking past or ignoring each other.

"... the only alternative for the origination of these capabilities, if one discards natural selection as the generative agent, is some supranatural force, a position that I am certain is not being advocated here." Here I'm with Wilkins, although I don't see how natural selection rescues him. But the point is irrelevant. No one has yet shown that these capabilities can originate. Once you recognize the nakedness of that assumption, you can see evolution another way – as grand-scale, long-term development.

Oddly, I think "evolution" is less creative than you do. Less creative than Wilkins thinks, too. If programs don't have to originate, now, natural selection (with installed software management) is sufficient for the rest. Now the process can be easily modelled in computers. Now the huge surprise of HGT is no surprise. Now life's early start on Earth / punctuated equilibrium / convergent evolution / the ubiquity of unfamiliar and de novo genes / the huge store of unknown genes in viruses / genes that seem to precede their earthly deployment — all make more sense. A theory of evolution that easily accounts for and even anticipates these things is worth considering.
Thanks. Brig Fortified edition

10 Sep: Dear Jim -- I have now spent a few hours with the Fortified edition of your book. My earlier positive comments about the first edition still stand, and there's even more to admire now. It's clear that you know the tools that genomes use to manage their contents. I congratulate you and I thank you for sharing your knowledge. As you know, I see the same system of tools as essential for unlocking and deploying existing genetic programming, as in cosmic ancestry.
30 Dec 2012: review of Evolution: A View from the 21st Century - 1st edition.

Thanks, also, for admitting that some "experimental and conceptual gaps need to be filled." But do you mean to include the gaps between
(a) the theory of evolution as taught in school -- neo-darwinism, EES, your version, A.S. Wilkins's etc. -- in which evolution makes ongoing macroevolutionary advances in quarantine, and
(b) the doubts of the general public -- as evident in opinion polls?

Those gaps are not trivial. Many smart scientists share those doubts. Proponents of ID, of course (Michael Behe, e.g.), but so do very many others (Lynn Margulis, George Church, e.g.). Most of them steer clear of the fray, because it's unproductive and uncivil. Darwinists of all stripes (you, too) are confident that conclusive proof is forthcoming, and, meanwhile, serious alternatives can be summarily excluded.

Think with me for a moment about quantum theory. It began by creating a canyon-size gap in physics. But Bohr and Einstein never quit talking. Crucial experiments (Bell's Inequality) seemed to leave the old philosophy unworkable, yet questions remained unsettled until every possible alternative explanation had been explored. Turns out, yes, the old philosophy is unworkable. A new philosophy must replace it. And no one thinks this philosophy is complete. Dialog was fruitful and continues to be.

Now think about today's theory of evolution. There are profound disagreements, but each side talks only with itself. Experiments (Lenski et al.) are interpreted in conflicting ways, without collaborative scrutiny. In my opinion, scientific principles and practice are being ignored. If science is abandoned, you "hand the victory" to your anti-science opponents, to paraphrase Fred Hoyle.

In 2012, you said, Given the exemplary status of biological evolution, we can anticipate that a paradigm shift in our understanding of that subject will have repercussions far outside the life sciences.... I agree with these words. Could we somehow find common ground after all?

Evolution: A View from the 21st Century. Fortified. by James A. Shapiro, Cognition Press, 2022.



Brig, thank you for the heads up on the paper "The Origin of Life: What Is the Question?" I read it through. For me at least, it was heavy going and didn't seem to go anywhere on the question of how life on Earth is here. I respect philosophy and (most) philosophers although I agree with Richard Feynman who basically argued that they have contributed nothing permanent or anything of real value to answering scientific questions. That's the scientist in me talking, of course.

My subject heading "How?" refers to how is it possible to write a paper that lists over 300 authors in the References and NOT once explicitly reference Chandra Wickramasinghe, Fred Hoyle, Richard Hoover, Gilbert Levin and a host of others who have directly addressed all the relevant issues about life on Earth in published refereed journals articles, monographs, and books--people who have created and made the very question of life appearing on Earth. They seem trapped just like Ptolemy and others were for centuries--that Earth was the be-all and end-all of the physical arrangement of the universe. This exactly parallel geocentrism continues to plague the life on Earth question despite a very large and persuasive body of evidence for it being a cosmic phenomenon, which your Panspermia website has so extensively and thoroughly documented.

But worst of all, as you point out, is how they proceed with absolutely no evidence on pure faith that life is magically generated by non-living entities and processes happening on Earth despite nobody ever witnessing any such process. That they left out those who have created modern panspermia indicts them for persisting in this worn-out paradigm that must go away.
George

25 May 2022: Philosophical evolutionary biologists give the Origin of Life problem a wide-ranging review.

endogenous retrovirus may have rewired the gene regulatory network...
from Klyce to Kotaro Sasaki et al. | 17 May 2022

Dear Dr. Sasaki, et al. - On my website about evolution and panspermia, I have briefly commented on your subject article. (Please alert me if I have misunderstood anything.) I believe the paradigm shift that is needed to understand evolution is bigger than most scientists are willing to entertain: All the programming already exists, but still it takes billions of years to sort itself out, and still it usually fails. But that's where the evidence points, I think.

Thanks for your excellent, open-minded research. Best regards, Brig
16 May 2022: The gene regulatory network....

Human Accelerated Regions [HARs] | from George Nickas | 15 Apr 2022

Brig, in reference to the April 15 What's New, how long will it take for the smart people to stop saying life began on Earth out of nothing when conditions were right and to replace that falsehood with something like 'life was arriving on Earth from the universe well before Earth had cooled enough for it to survive until finally Earth had cooled off enough for life to gain a foothold and take off.'
George
15 Apr 2022: This means life could have begun as little as 300 million years after Earth formed.

Human Accelerated Regions [HARs] | from George Nickas | 13 Feb 2022

Brig, thanks to your recent posts on panspermia I have been reading up on HARs--fascinating stuff. There are 49 HAR genes, right? And they mainly are what make us different than chimps, for example, right? If 98.5% of the human genome is non-coding, what part of that large percentage I wonder is regulatory genes. I get that the big issue is how the regulatory genes decide which coding genes to turn on and off. Is that right?
George=

from Brig: George, as a generalist, I am light on the details in most areas! I do not know how many HAR genes there are. The report I reference looked at 202 HARs, but ...how many were genes? Among the five listed in the table I reproduce, all are short, intron- or intergenic segments except maybe HAR1. "5' region" is in a gene I guess.

What part of the 98.5% is regulatory? Transcription factors are regulatory, right? So maybe even more regulatory than coding? I need to study this.

How do they decide? If the installed choices are few, maybe it's entirely by chance, letting natural selection sort it out!? I think that could work. I think there are some "birth defects" which might actually be the right choice in another world. For example, would dwarfism be better if it were a 2g world? Just throwing out ideas. ...

30 Jan 2022: HARs -- Segments that underwent recent, rapid mutation, analysed in 2006.

Social media platforms can serve as effective science communication if research summaries, outcome measures, and expert advice are sourced from and linked to peer-reviewed journals, scientific magazines, and websites of reputable research organizations. — Ming-Ju Amy Lyu, Chinese Academy of Sciences, Shanghai, China

Wood-Ljungdahl Pathway | from James Powers | 19 Jan 2022

Hello Brig, ...Thank you for the postings on Jan [17] about atmospheric bacteria.

You may recall our conversation from several years ago about the Wood-Ljungdahl anaerobic pathway. I have attached a review from 2008. My belief is that the clouds of Venus may harbor life utilizing the W-Lj pathway for survival. I also believe that this was how Hadean Earth was terraformed by the panspermic inoculation of aerial microbes into the molten Earth's superhot and supercritical dense CO2 and Nitrogen atmosphere. I think that you were skeptical at the time. In light of your postings, any change in your opinion?

Jim Powers | Napa, CA 94558
"Enzymology of the Wood-Ljungdahl Pathway of Acetogenesis" by Stephen W. Ragsdale, Ann N Y Acad Sci., March 2008 [
Local PDF].
17 Jan 2022: Trace gases ...could potentially support life.

re: AOPI - Webb Telescope | from James Powers | 09 Dec 2021
Hello Brig,
Nice article. I think it is set for launch on the 22nd. I agree with this comment. "Webb has such transformative capabilities that – to me – it's going to be the 'before' times and the 'after' times," says Jane Rigby, an astrophysicist at NASA's Goddard Space Flight Center in Greenbelt, Maryland, who serves as Webb's operations project scientist. Me Too!
"The $11-billion Webb telescope aims to probe the early Universe"
Nature, 08 Dec 2021.

This reminds me that I need to follow up with a comment about why there is dust and atomic "metals", etc. present in the early Universe. I think JWST will show evidence of dust as far back as it can see. Coming soon.

from Brig: ...What does the inflationary big bang predict (retrodict?) for dust?

from James: The BB nucleosynthesis theory predicts and calculates that only Hydrogen, Deuterium, Helium and a little Lithium and perhaps some Beryllium were produced in the very first few moments after the BB when conditions were correct. Population 3 stars could only be composed of these atoms. All other atoms were produced later inside stars and supernova. The atomic composition of the Universe matches the theory well.

I don't think the pre-galactic dust etc. is from the BB. It shows up later from an unexpected source.

Initial Star Formation is primarily driven by the magnetocaloric engine that separates and cycles paramagnetic atomic Hydrogen from diamagnetic molecular Hydrogen. (I am working out the details of this line of thought.)
Jim

crinoids | from George Nickas | 30 Nov 2021
Brig, thanks for the update on the crinoid story re Mars. I watched the Hoover interview. If he can't find a good reason for NASA to grind up the crinoids after finding them, nobody can. I don't think it is possible to overestimate how conservative NASA is in all this Mars exploration business. Since the discovery on Mars, they seem to have gone into a mode where they don't want to be surprised. It's like as if Nature does not give them what they want to find on Mars then they will ignore it or hide it. Like you decide in advance what is an acceptable find, and look only for it. Definitely not science. As Hoover said, water on Mars is a known fact for fifty years. Why keep looking for it unless you have the mindset that you will only accept life on Mars if it exists now and for that you need water, but its already there! Very strange.
27 Nov: crinoids update. 25 Nov: Hoover interview.

13 Dec:
...thoughts I had today after reading the posting on the website about NASA's wanting to check on Europa to see if it is 'inhabitable'. Europa inhabitable?? Of course it has water and is inhabitable. When will NASA get over its lust to find out if solar system objects are 'inhabitable' and start looking to see if places like Europa are INHABITED? Of course Europa has water! Wake up NASA! Go there and search for life for heaven's sake and not water! Search for inhabited, not inhabitable.
George
Are Water Plumes Spraying from Europa? by Lonnie Shekhtman, NASA, Goddard, 30 Nov 2021.
28 Oct: NASA's search for life.

dark matter | from George Nickas | 17 Jul 2021
...something is exerting gravitational forces in galaxies making them spin too fast as you pointed out. We have no other way to explain the spin rates of galaxies without using gravity as we know it. I apologize if I gave the impression that the gravity we see acting but cannot explain does not exist. My objection has been wholly that astronomers have dismissed known forms of matter as producing that gravity. They are basically claiming that we have observed everything through our telescopes that could possibly produce the extra gravity, so we should stop looking for unseen (so far) ordinary matter. If the Big Bang is a correct theory, then I might agree with them, but matter exists within a cosmological framework. That framework can limit and bound -- i.e. not permit ordinary matter in some form to be the 'dark matter'. Or it can open the door to ordinary matter being plentiful enough to produce the gravitational effects seen.
I'm on that side. When you go into a cornfield you only see the corn growing in that field this year. You cannot claim that corn did not grow in that field last year or the year before or the year before that.
George

from Brig: ...this leaves the door open for black holes or rogue planets to contribute?

...Yes it leaves the door open for black holes or rogue planets, but the door is even wider open for dead stars. Remember one dead star has the mass of tens to hundreds of thousands of rogue planets. I don't favor black holes because they possess extreme gravity which we know requires extreme mass and extreme mass at least among stellar corpses is quite rare. Dead stars on the other hand could be very plentiful and virtually impossible to detect through telescopes. When I submit my work to a refereed journal, it will be rejected, because in it I will reject the Big Bang as a preface. But I am retired and the only tenure I have is in marriage to my wife of 50 years, so I can't be fired except by her. Nevertheless, rejecting the Big Bang effectively as have Hoyle et al is the path to being called a kook or worse in the halls of modern cosmology. Yet we know that there is absolutely nothing refutable in the claim that the universe has existed for much longer than a mere 13.8 billion years which in a very real sense is not that long a time. Cosmologists of the present fail to appreciate what the Big Bang really is; a backwards in time extrapolation of observations massaged and manipulated in totally an ad hoc manner to produce a single creation event with no physically causal basis.. It just did is what they say. It is physics and astronomy by proclamation, not by deduction. As you know, Hoyle et al utterly reject the religious impulse that is behind this creationist theory and have said clearly that it has no place in science. And of course Hoyle and Wickramasinghe over and over have shown that a universe that is constrained by a Big Bang is a grossly insufficient time for life to somehow magically arise from dead atoms and molecules. Wickramasinghe is blessed in not being a Christian in the sense that he can accept that living things may have existed since forever. Still the need for a creation event runs so deeply the cosmologists (and biologists!) violate their own science to make it happen. Brig, I don't know what your religious orientation is, but you will forgive me if I say the worst thing that every happened to cosmology is that it fell into the hands of Christian scientists. End of tirade!

The End and the Big Bang has more.

Reductionism vs Emergence | from John Hughes | 03 Jun 2021
[excerpt only] ...Robert Laughlin, also a condensed matter physicist, wrote a book called A Different Universe, in which he argued that attempts to apply the fundamental equations of quantum mechanics to any system with more than 100 particles leaves you with something that can only be solved with God's computer (i.e., it can't really be solved). Based on this, he argued that you really can't derive the higher levels of structure from the lower levels and that there do exist higher order, emergent principles that are required to understand the world.

from Klyce: My favorite example of emergence comes from Conway's Game of Life. Played on an infinite grid of squares. The squares are either filled or empty. At step two, a square is filled or empty depending on its state [and the state of the 8 neighboring squares] on step one. Then step 3, 4, etc. From these simple rules, all kinds of phenomena emerge - moving objects that deserve to be named. Blinkers and gliders are the simplest, but even great big things that seem to flap wings and move along. "Flying busses" and whatever. They may collide and send new entities off in other directions.

Simple rules, complicated resulting phenomena. Emergence.

The human genome is an instruction set that would fill a [small] library. The emergent phenomena are bound to be surprising. Language, music, consciousness, on and on....

Believing this does not discourage me. For one thing, I'm not alone. I have friends and family and loved ones like you!

Our article published | from Ted Steele | 02 Jun 2021
Our short summary on all our critical work and analysis of evidence published last year is now formally published and accessible online as a short invited 'Commentary'....
"Cometary Origin of COVID-19,"
Infectious Diseases and Therapeutics | local pdf, 18 May 2021.

cyclic model | from Dr George Nickas | 05-08 Nov 2020

to Paul Steinhardt: Prof Steinhardt: Have you read the 1993 paper by Hoyle et al -- the Quasi-Steady-State-Cosmology -- an expanding model which oscillates cyclically and has no creation event? Your recent paper nowhere gives any credit to Hoyle et al for their priority in inventing this model. I have attached it....
Sincerely, George Nickas, Emeritus Professor of Physics and Astronomy Corpus Christi, TX

A Quasi Steady State Model with Creation of Matter, ApJ 410: 437-457, 20 Jun 1993.
31 Oct 2020: ...a cosmos that has no beginning, no end...., our notice about Steinhardt.
+ Paul Steinhardt sent George Nickas a friendly and conciliatory reply, thanking him for the alert. I asked Nickas to ask Steinhardt if I could post that reply here. Steinhardt said no.

06 Nov, Klyce to Nickas: George, thanks! I have an issue with his expression, "To simply conflate ideas...." My overall point is that the whole story has to be consistent -- have no internal contradictions. The origin-of-life from nonbiological chemicals seems entirely impossible to me. But if life always existed, that impossibility is not fatal -- it's irrelevant. However, if cosmology precludes life from the eternal past, the whole story doesn't fit together. The standard big bang would apparently preclude life from the eternal past. Steinhardt's model, and others, don't. I never say that he endorses cosmic ancestry. He just now heard of it, probably. Thanks again. Best regards, Brig

06 Nov, from Nickas: Brig, of course you hit all the marks on the issue internal consistency. Cosmology must be consistent with biology. Your phrase 'eternal past' is the key. Finite cosmologies in both space and time, by definition, have no eternal past! Thus not only do space and time have to be created out of nothing, but life itself has to come out of unknown and perhaps unknowable chemistry in less time than 13.8 billion years, the present 'age' of all things since the infamous Big Bang. This is a deadly restriction--no pun intended!.. We know Hoyle and Wickramasinghe repeatedly emphasized with quantitative models how utterly impossible it was to produce the complexity and order in even the simplest enzyme through random processes--the still prevailing paradigm. Thus, the problem of the origin of life becomes less important in the sense that no special ad hoc initial conditions are necessary leading naturally a universe with eternal past. As H+W emphasized the 'game' is how living organisms fill and travel through the universe--aka Panspermia!. ...

08 Nov, from Nickas: Brig, looked further into [Steinhardt's] model--it is essentially a series of big bounces that concentrates matter to Planckian conditions which preclude the survival of any form of life in each bounce--the last bounce was 13.8 billion years ago fitted to the Big Bang. In other words he gets his cake and eats it--bounces aka bangs but not just a single one. Bottom line is that no life exists in the present universe earlier than 13.8 billion years ago because life is destroyed in that last bounce. Presumably Steinhardt would argue that life is re-created every 13.8 billion years after each bounce, but the issue of life appears absolutely nowhere in the model. He played with the equations and got what he wanted as do the Big Bangers. He contributes nothing new--still a cosmic background microwave fine tuned to dark energy generated by repeated bangs--dark energy is an essential component of the model. It's a cosmology that cares not at all about life filling the universe. When asked, Hoyle denied trying to make the QSSC model compatible with his other work on panspermia, but the QSSC model accommodates life over much longer time than 13.8 billion years without postulating a beginning. Had the QSSC theory made life impossible to survive over its cycles, Hoyle and Wickramasinghe would most certainly not have done panspermia incompatible with QSSC in the years after QSSC was published. That's the advantage of inventing independent theories which can be justifiably conflated. ...George

Fred Hoyle Interviewed, 05 Jul 1996. The End and the Big Bang.

Venusian spores | from Dr George Nickas | 18 Sep 2020
Brig, as we know, priority in science is important especially in the case of the work on panspermia of Hoyle and Wickramasinghe who have been continually overlooked or ignored as being first on any number of matters in panspermia.. I refer to the piece on the discovery of phosphine in the Venusian atmosphere by Charles Q. Choi who suggests looking for spores there. He does not mention that Hoyle and Wickramasinghe in their 1988 book Cosmic Life Force wrote about spores that might exist in the upper Venusian atmosphere, I quote from page 42;

"The repeated variations of temperature caused by a circulating cloud system, however, tend to favour bacteria capable of forming spherical spores which are still more hardy than the bacteria giving rise to them. The upper clouds of Venus produce a rainbow indicating that the cloud particles are mainly spherical and that they have sizes in the region of 1 micrometer. Measurement of the refractive indices of these particles are fully consistent with the properties of bacterial spores. The populations of cloud bacteria are expected to be periodically topped by fresh cometary injections. Such injections could also supply the Venusian atmosphere with a steady input of inorganic nutrients to replace what must inevitably fall into the atmosphere below"

Hoyle and Wickramasinghe as usual way ahead of everybody else on matters of panspermia--in this case by 32 years!

George Nickas          
14 Sep 2020: our related posting about possible life in Venus' atmosphere.

The Conversation | from Dr Predrag Slijepcevic | 22 Jul 2020
The widely read portal The Conversation published my short essay...
Bacteria and viruses are travelling the world on highways in the sky, 21 Jul 2020.

somatic RNA ...passed on to embryos | from James Powers | 16 May 2020
...Thanks for the posting on the transport of RNA to germ lines in your What's New 12 May 2020. Here is the cited preceding companion paper that I had saved in my "Weird Biology Class 1" file [link below]. I wonder what Charles Darwin would think? The RNA paper continues to confirm my belief that epigenetic teleology is indeed a part of New Biology and supersedes Neo-Darwin evolution. What could be a better Science Fiction story about how I could use an RNA brain booster to determine the genotype and phenotype of my child – just by thinking?

By the way, the more that I think about star formation, the more I believe that we are missing a major building block of the universe. Stars are impossible with our (or my) current knowledge of astrophysics. This is reminiscent when Lord Kelvin calculated the age of the sun by calculating how much energy that the sun generated by the combustion of coal. He had no idea about nuclear fusion and the strong nuclear force. I believe that modern science is laboring under a similar condition of ignorance.

Stay safe! ...Jim Powers | Napa, CA

Parental olfactory experience influences behavior and neural structure in subsequent generations by Brian G Dias and Kerry J Ressler, Nature Neuroscience, 01 Dec 2013.
Somatic RNA can be passed on to embryos: the referenced What'sNEW article.

Additional thoughts re Italian data.... | from Reg Gorczynski | 24 Apr 2020
Coronavirus has been detected on particles of air pollution by scientists investigating whether this could enable it to be carried over longer distances and increase the number of people infected. The work is preliminary and it is not yet known if the virus remains viable on pollution particles and in sufficient quantity to cause disease.

The Italian scientists used standard techniques to collect outdoor air pollution samples at one urban and one industrial site in Bergamo province and identified a gene highly specific to Covid-19 in multiple samples. The detection was confirmed by blind testing at an independent laboratory. Leonardo Setti at the University of Bologna in Italy, who led the work [https://www.medrxiv.org/content/10.1101/2020.04.15.20065995v1], said it was important to investigate if the virus could be carried more widely by air pollution. "I am a scientist and I am worried when I don't know," he said. "If we know, we can find a solution. But if we don't know, we can only suffer the consequences."

Two other research groups have suggested air pollution particles [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151372/] could help coronavirus travel further in the air [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7156797/]. A statistical analysis [https://www.medrxiv.org/content/10.1101/2020.04.11.20061713v1] by Setti's team suggests higher levels of particle pollution could explain higher rates of infection in parts of northern Italy before a lockdown was imposed, an idea supported by another preliminary analysis [https://www.medrxiv.org/content/10.1101/2020.04.06.20055657v1]. The region is one of the most polluted in Europe.


Chandra Wickramasinghe re: Airborne transmission | Ted Steele re: sequence testing
Reg Gorczynski re: widespread exposure | Brig Klyce re: mutations | 17-19 Apr 2020

Wickramasinghe: ...we have to take account of the KD spread data and the mid latitude jet stream that fits the 30-60 degree latitude belt, but goes from west to east. It could go through a whole circuit without deposition to the ground so the temporal connections may be dealt with that way? Atmospheric transmission

Steele: ...I have no problem with swabbing the environment for viral RNA and protein- I am sure that can be done. At present the focus is on detecting the RNA sequence in infected subjects - I have no problem with that either (in every infection cycle "empty" virions get released- e.g. those without a genome). The assay as I think I understand it is usually set up to "dissolve away the protein" or to release the RNA so the RT -PCR assay can get going. This is the same as releasing genomic DNA from cells in sequencing assays of all sorts..

The RNA sequence is crucial as that indicates the source and the stage of infection in a person-to-person chain (because in every infection a healthy person will attempt to cripple the replicating virus by introducing APOBEC/ADAR deaminase-mediated mutations (broadly C-to-U and A-to-I(G)) on either the top (+) or bottom (-) strand of the double stranded replicating form (RF) of the virus. We can tell from the sequence motif which APOBECs (C-sites) are active- there are two A-site ADARs (1/2) and their motifs are hard two separate (both are WA, where W = A or U).

What happened in central China Nov -Dec 2019? The behaviour of the Chinese government is all we can go on. They quarantined almost all of central China on about Jan 14 and shuffled 500-700 people in a lock down. They then had spray teams in protected suites out dousing roads, machinery etc - graphic movies on our evening news TV. That says logically they had some idea of the extent of the environmental viral contamination (whether they assayed viral protein, or viral RNA). I think the Chinese government knew by then that the contamination was immense in their vital industrial heartland – and if they sampled vegetation as well as wild and domestic animals they would have found the virus RNA signature everywhere, I think at high dose. Wuhan itself from all the rumours of deaths was hit with a high dose. I high dose of this common cold virus, can kill a lot of people. At lower doses less so, and then the elderly co-morbid are clearly at risk (people in their 70s like me with asthma). I think New York City from all reports we see got a very high dose- and everything points to a Wuhan scenario in that city. But all the numbers are suspect- COVID-19 positivity will be very high in New York City- so everyone who dies there is likely to be positive for COVID-19. Same in Lombardy region of Italy that displayed all the same signs of a high dose in-fall (and this will apply to Spain, and Tehran/Qom). The extend of antibody positivity for COVID-19 coat proteins will be a very important epidemiological number, as Reg keeps pointing out. That should have been instituted very early in the peace....

Gorzinski: ...In a startling finding, new Stanford research reveals between 48,000 and 81,000 people in Santa Clara County alone may already have been infected by the coronavirus by early April — that's 50 to 85 times more than the number of official cases at that date. The estimate comes from a first-in-the-nation community study of newly available antibody tests that suggest how widespread the invisible — and perhaps benign — companion has been in the Bay Area's hardest-hit county. Not only do the numbers show how the U.S.'s severe shortage of testing led to a profound undercount of COVID-19 cases, they indicate the virus is far less deadly than believed. Just how much of an undercount? Stanford's low-end estimate of Santa Clara County cases is nearly double the confirmed total — 28,000 — for the entire state of California. The study estimated 2.5% to 4.2% of residents here carry antibodies to the pathogen, a marker of past infection that suggests it may be safe for them to go back to work and school. "The most important implication is that the number of infections is much greater than the reported number of cases," concludes the research paper, published Friday morning in the online journal medRxiv.

Santa Clara County, home to Stanford University and 1.9 million residents, was one of the first hot spots for the coronavirus in the country. As of Friday, it officially had recorded 1,833 cases and 69 deaths related to coronavirus. The new Stanford study comes at a time when health experts and elected officials look to immunity as one way to blunt the impact of the pandemic. It is not yet known if antibodies prevent future infection. If so, antibody protection could offer people a safe route out of strict "sheltering." The research also implies that the death rate is far lower than believed. At the time of research, 39 county residents had died — a fatality rate, based on estimated infections, of only 0.12 to 0.2%. California's assumed death rate, based only on confirmed cases, is 3%. The study also showed how Santa Clara County's hospitals appeared to have dodged the long-feared surge of patients: Unlike New York, Santa Clara County's hospitals have yet to be overwhelmed. Fewer than 600 people are being treated for the virus at hospitals throughout the Bay Area. The Stanford study, led by Dr. Eran Bendavid, an infectious disease specialist and professor of medicine with Stanford Health Policy, shows whether someone has been infected by the virus in the past. They recruited participants by placing targeted advertisements aimed at Santa Clara County on Facebook. They used Facebook because it allows for targeting by zip code and sociodemographic characteristics. In contrast, COVID-19 virus testing only tests people with significant symptoms. It does not measure the true number of people who have been infected by the virus, many of whom have no symptoms or very mild symptoms. Several other teams worldwide also have started testing population samples. Like Stanford, they've found that there's a large underestimate of infections. Reports from the town of Robbio, Italy, where the entire population was tested, suggest at least 10% rate of infections. A survey in the western Germany municipality of Gangelt, highly affected by illness, found a 14% positive rate.

Klyce: ...Here is a cropped screengrab from a figure linked from [ "Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States," by J.R. Fauver, M. E. Petrone, E. B. Hodcroft et al., doi:10.1016/j.cell.2020.04.021, 11 Mar 2020]. If "mutations" means single-nucleotide mutations, then, all of these sequences are 99.967% identical?

phylogeny of virus

our message re: Coronavirus | with Ted Steele | 26 Mar 2020

Dear Ted – I would like to advocate a gentler and less strident tone for our message. We are suggesting that the virus came from space – very hard for most people to swallow. We are not denying, I hope, that people-to-people transmission is real, or that the severity of the disease looks to be dosage dependent. If so, some of the currently proposed practices make sense. We will do much better if we do not sound like fanatics. I think it is a gross tactical error, for example, to disparage Anthony Fauci. May we please tone it down?... from Brig Klyce

from Graham Steele: ...you guys need to provide me - if we want the media to follow and report this potential alternative narrative - with a 'one page' brief that outlines in layman's terms;

  1. what is your finding.?
  2. why do your findings matter now - given that the situation is Changing so Rapidly and the United States will be an absolute shit show any moment now as the economy falls apart (pitch fork economics.!)
  3. How can your findings be beneficial to the public??? Should we be focusing on spraying bleach all over town?????
  4. what steps, based on your findings should we be doing.??

from Chandra Wickramasinghe: This is my response on the trot...

  1. The prevailing idea is of a new virus arising from an animal and passing on to the human population, first in Wuhan, and thereafter spreading elsewhere in the world mainly along a 40-60 degree N latitude belt. The spread is assumed to be only possible by person-to-person contact. This model is difficult to reconcile fully with all the available data.
  2. We suggest that the virus originated in a comet a fragment which broke up in the stratosphere above Wuhan. A fast-growing body of evidence now supports the once ridiculed idea of panspermia - that the Earth's biosphere in effect extends out to the remotest parts of the galaxy. Furthermore, the origin and evolution of life took place against the backdrop of a gigantic connected cosmic biosphere. In this context a virus like COVID-19 that can interact with humans is not impossible to comprehend.
  3. A correct understanding of the origin of the new virus could have an immediate impact on how we deal with the virus. There was certainly a catastrophic fall-out of the virus in China sometime towards the end of October 2019. Fall out appears to be the primary mode of transfer of the virus to humans, with secondary transmission occuring by close contact. The fall out in China appears to have been followed by a sequence of other fall out events in Iran, Italy, perhaps New York. In each case fall-out seems to have been followed by some degree of person-to-person transfer. If this is accepted the it is obvious that social distancing strategies should be combined with monitoring suspected environments, and environmental sampling and deep cleansing could well be an additional measure that may help to prevent spread. Community spreading that has often been mentioned may well be a feature of environmental contamination by an infalling virus.
  4. In a matter of such profound importance to humanity and to the entire world economy, discovering the truest cause of this disaster should be accorded the highest priority. Knowing where one's enemy comes from could be half the battle. ...Sincerely, Chandra

from Reg Gorczynski: I support that response Chandra....I am really concerned that everyone's response to this "social distancing" having any effect on curtailment on incidence will be presumed to reflect a validity to the prior hypothesis (person-to-person spread). It is importantly also what we would predict if you lock people up and have zero exposure to a community environment with foamite spread (after infall of virus from the stratosphere...but no-one except us has proffered that explanation!) Also the key issue (scientifically) is that there is data supporting the latter hypothesis which the former cannot, and it also offers an approach to preemptive testing for newer infections (atmospheric origin). ...Reg

from Ted Steele: Dear Brig: Many thanks for your advice. ...In a War, as we are now in, there is no time to behave like nervous nellies. When I joined with Chandra, you and the others in 2016 it became clear to me we were in a major War of Ideas- in a scientific war your bullets are critical thinking and raw evidence, and you take no prisoners. ... Thus I do not think this is going to cool down anytime soon, therefore all of us have to decide whether we are going to fight or run.

If I took the second alternative - on reverse transcriptase and Lamarck in 1978 - I would have run for the hills. Science is not actually a garden party with high tea and cucumber sandwiches. It is populated by power mongers like Anthony Fauci, big egos with stupid ideas and ruthless and often wrong decision making. If I had taken that attitude I would not have survived to continue publishing these past 40 or so years.

I am happy to debate scientific facts in the open scientific arena- but no one except Sir Peter Medawar and Sir John Maddox - has been willing to get into the ring and join the battle directly. I am happy to take on all comers, and I await someone with courage to get into the ring. While I took some lethal hits from Medawar and Maddox, I have survived and we are actually winning the War for reverse transcription and Lamarck. While we are still fighting on those fronts (reverse transcription and Lamarck) these are now mopping up operations.

....while I may be more selective in my email lists, I will not back down. ...Thanks for the advice- nice to know I am thought as a 'fanatic'. Ted


hemolithin protein isolated from a meteorite | James Powers | 07 Mar 2020

...By the way, the article on the hemolithin protein isolated from a meteorite is interesting. Unfortunately, the described protein is composed of only glycine amino acids. Glycine has no chirality. If the amino acid was alanine, for example, we could determine if the protein was due to a chemical process or a biological origin. If it has equal numbers of left-handed and right handed amino acids, then this would indicate a chemical process. If the protein was a result of biology, then there would be a predominance of left- or right-handed amino acids. Keep on. ...Jim Powers | Napa, CA

Brig Klyce – Good work! ...You are aware that amino acids racemize over time, probably faster if agitated, as by radiation in space.

Powers – Amino acids will racemize in time. However amino acids in proteins cannot racemize without destroying the protein.

Klyce – ...Wasn't there also alanine in this one? Was its chirality noted?

Powers – I took a closer look at this paper. They did find Alanine in some of the peptide fragments. The peptides are listed in the table. However, they did not account for this in the structure. They did not mention alanine in the discussion or conclusions. I looked at the structure again. The hydroxy of hydroxyglycine in the structure is not bound to the amine nitrogen, which is how commercial Hydroxyglycine is described. The hydroxy is bound to the alpha-Carbon in the chain. I don't know what to make of all this. Mass spec cannot determine chirality.

03 Mar 2020: our posting about the protein in a meteorite.

Corona virus and cosmic life | facebook chat with Greg Irwin | 29 Feb 2020

Greg Irwin – Does the original concentration in Wuhan work with that hypothesis? ( 27 Feb 2020)

Brig Klyce – Wuhan is right there, yes. But also noteworthy -- a meteor fell Oct 11 North of Wuhan. It would have penetrated deep into the atmosphere (see https://vixra.org/pdf/2002.0118v1.pdf). Entirely possible that the meteor and cometary dust that landed higher were all fragments of the same comet and therefore encountered at the same time. [On second thought, this makes sense only if the meteor arrived after the dust had reached the jetstream.]

Irwin – ...My doubts regarding panspermic explanations are founded where they've always been. Let me paste in two excerpts from the article.

"The support for the alternative view that life is a cosmic phenomenon stems mainly from the fact that the information content of life at a genetic and molecular level is super-astronomical; and this needs at least an astronomical or cosmological setting."

And: "The panorama of life on Earth is the result of the assembly of such bacterial and viral genes that has come to be assembled like pieces of a gigantic jig-saw puzzle over some 4.2 billion years."

How is complexity developing (from scratch) over 4.2 billion years incredible ("super-astronomical"), while that complexity developing over 13.8 billion years — and shipped around the cosmos for further assembly — is credible? You know I don't see that one.

Klyce – I don't either. I thought you knew that. I will email you a paper, "Some Things Are Simply Given". I can't put it online yet, because it's to be published in a forthcoming book. Basically, I think life must have always existed (and so the standard big bang needs tweaking.) Then I run into the coalition of Darwinists and creationists, both of whom love the standard, one-time-only big bang.

Irwin – Do send it to me. I knew that Wickramasinghe and Hoyle remained skeptical about the big bang. I know that you struggled for years against just-so stories being used to fill gaps in science, but 'life must have always existed' sounds like a just-so capitulation. Where will you look for such life? Or for its seepage or transmission from that place or non-place to our cosmos?

I don't think Darwinists love the big bang; they have had to struggle to adapt to it as a given (as Christians have had to adapt (or fail to adapt) to Darwinism). It is those very Darwinian difficulties that set you out toward Panspermia, I believe.

Creationists of the inerrantist and young earth mindset can't go for the big bang either. We creationists who are more agnostic about God's how do find ourselves buoyed by the discovery that matter is not eternal — but that, as it were, came to us; we did not seek it or expect it any more than the rest of the world did. The big bang was delivered to us (all) in about 1965 as surely as the evolution of our species was in 1859.

Klyce – Dude -- you are undoubtedly my best correspondent for this (loosely specified) issue. Comments to consider with the paper --
Preface: to rephrase Goedel: mathematics has no inconsistencies, but cannot provide its own grounding. ...Anyway, likewise with science (no inconsistencies, but cannot provide its own grounding).

I think the creationists want to show that science is inconsistent for relying on material causes, because these don't work for the origin of life and evolution. I agree they don't work. But if life always existed they don't have to work. That way, science can remain fully consistent. And creationists have [everyone has] to give up only the standard, one-time-only/in-the-finite-past big bang. Can't creationists see that life from eternity is a miracle!

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