Evolution: A View from the 21st Century
with James Shapiro | Jun-Aug + Sep 2022
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: James, thanks, truly. I have looked at your references. Khalturin et al. comment, "...every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species." Milde et al. say "We have identified nematocyte-specific genes by suppression subtractive hybridization and find that a considerable portion has no homologues to any sequences in animals outside Hydra." Van Oss and Carvunis is one I have studied and commented on (link below).
I think we are still not fully understanding each other. I am aware that predecessors to genes are sometimes – often found de novo. The trouble with them is that they have no neo-darwinian provenance – no history of formation by trial and error. I discuss this at length on the website. The following 4 brief entries are especially relevant. I hope you have time to look at them.
https://www.panspermia.org/whatsnew84.htm#20160104
https://www.panspermia.org/whatsnew86.htm#20160821
https://www.panspermia.org/whatsnew96.htm#20190527
https://www.panspermia.org/whatsnew99.htm#20201220
I appreciate your patience! I believe the problems with neo-darwinism are too big to fix, to paraphrase Jerry Fodor.
I welcome your thoughts. 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
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, as Fred Hoyle remarked.
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.
How? | from George Nickas | 25 May 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.
https://thebulletin.org/2023/10/black-swans-from-mars/
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.
