Back to Shapiro (Evolution)

by dhw, Wednesday, March 25, 2020, 11:31 (1464 days ago)

Since we have long since abandoned Davies and returned to Shapiro, I'm transferring this discussion.


DAVID: Shapiro showed bacteria can modify their DNA, nothing more and we all accept it as a great contribution to evolutionary research. You use your individual bias to stretch the concept to suit what you would like to believe. Still 50/50 odds.

dhw: “You use your individual bias” to pretend that I am stretching Shapiro’s theory. You force me to quote what you quoted in your book: “Living cells and organisms are cognitive (sentient) entities that act and interact purposefully…They possess sensory, communication, information-processing and decision-making capabilities….Evolutionary innovation arises from the production of new cells and multicellular structures as a result of cellular self-modification functions and cell fusions.” (James A Shapiro). Now please tell me how I have stretched his concept. And if the odds are 50/50, it would be totally irrational to reject the theory.

DAVID: I don't reject his theory but his interpretation of what he observed.

Then you reject his theory in favour of your own, as below:

DAVID: All he saw could just as easily be intelligent instructions onboard, provided by God. That is the ID view of him. And I would note my books never rejected God on the basis of quoting Shapiro, whom I admire.

Just as easily = 50%. Shapiro’s theory does not reject God, and nor do I. It covers cellular intelligence, not the source of cellular intelligence.

DAVID: Please reread Shapiro from 2017 at Royal Society:
David's theory of evolution: James A. Shapiro's view 2017 (Evolution)
by David Turell @, Tuesday, January 07, 2020, 20:31 (77 days ago) @ David Turell

Not exactly what you think about him. His book has hyperbole which sells books, not his scientific thoughtful presentation.

Are you saying that the quotes in your book are a lie and he doesn’t believe that cells are cognitive beings whose intelligence creates evolutionary innovations? The lecture was delivered to a specialist audience, but there is nothing in what you quoted to contradict what he said earlier. I will bold the relevant references, since you seem to think he has changed his mind.

QUOTE: These examples show us that core biological capacities for self-modification in response to ecological challenge have been integral to the history of life on earth. That conclusion should not surprise us since extant organisms are descendants of multiple evolutionary episodes. Considering potential interactions between dynamic ecological conditions and the biological engines of cell and genome variation raises important questions about control and specificity in evolutionary innovation. The years to come likely hold surprising lessons about how cell fusions, genome doublings, and natural genetic engineering may operate non-randomly to enhance the probabilities of evolutionary success."

Please explain how core biological capacities for self-modification contradict the theory of the intelligent cell, and how non-random “natural genetic engineering” contradicts his theory of "natural genetic engineering" as explained in the earlier quotes. Did his lecture offer a new definition of "natural genetic engineering”? And you still haven’t told me how I have stretched his theory to suit my own bias.

Back to Shapiro

by David Turell @, Wednesday, March 25, 2020, 19:04 (1464 days ago) @ dhw

Since we have long since abandoned Davies and returned to Shapiro, I'm transferring this discussion.

DAVID: I don't reject his theory but his interpretation of what he observed.

dhw: Then you reject his theory in favour of your own, as below:

DAVID: All he saw could just as easily be intelligent instructions onboard, provided by God. That is the ID view of him. And I would note my books never rejected God on the basis of quoting Shapiro, whom I admire.

dhw: Just as easily = 50%. Shapiro’s theory does not reject God, and nor do I. It covers cellular intelligence, not the source of cellular intelligence.

I know that. He was president of his Temple.


DAVID: Please reread Shapiro from 2017 at Royal Society:
David's theory of evolution: James A. Shapiro's view 2017 (Evolution)
by David Turell @, Tuesday, January 07, 2020, 20:31 (77 days ago) @ David Turell

Not exactly what you think about him. His book has hyperbole which sells books, not his scientific thoughtful presentation.

dhw: Are you saying that the quotes in your book are a lie and he doesn’t believe that cells are cognitive beings whose intelligence creates evolutionary innovations? The lecture was delivered to a specialist audience, but there is nothing in what you quoted to contradict what he said earlier. I will bold the relevant references, since you seem to think he has changed his mind.

QUOTE: These examples show us that core biological capacities for self-modification in response to ecological challenge have been integral to the history of life on earth. That conclusion should not surprise us since extant organisms are descendants of multiple evolutionary episodes. Considering potential interactions between dynamic ecological conditions and the biological engines of cell and genome variation raises important questions about control and specificity in evolutionary innovation. The years to come likely hold surprising lessons about how cell fusions, genome doublings, and natural genetic engineering may operate non-randomly to enhance the probabilities of evolutionary success."

My book quotes are exact and correct. What lies? My bold just above simply notes his exact meaning is a future hope that his volume work will show how speciation works. The quote is simply hopeful and an extension of his findings which form a basis for future research, nothing more..

dhw: Please explain how core biological capacities for self-modification contradict the theory of the intelligent cell, and how non-random “natural genetic engineering” contradicts his theory of "natural genetic engineering" as explained in the earlier quotes. Did his lecture offer a new definition of "natural genetic engineering”? And you still haven’t told me how I have stretched his theory to suit my own bias.

Once again, work in bacteria, which may have carried over to future evolved forms, not proven. It is obvious free-living bacteria had to have the abilities to survive until now, especially since they are shown to be vital to current life's various functions. You are not misusing him to support your theory of cellular intelligence, but trying to apply his DNA modifications to intelligent cell functions that already have modified their DNA to produce certain rigid automatic necessary functions as part of a complex multicellular organism. In other words you apply his hope to solve evolution to what is already evolved. Reminder: my view is ID view of him.

See a new entry on squid and DNA modification

Back to Shapiro

by dhw, Thursday, March 26, 2020, 15:54 (1463 days ago) @ David Turell

DAVID: I don't reject his theory but his interpretation of what he observed.

dhw: Then you reject his theory in favour of your own, as below:

DAVID: All he saw could just as easily be intelligent instructions onboard, provided by God. That is the ID view of him. And I would note my books never rejected God on the basis of quoting Shapiro, whom I admire.

dhw: Just as easily = 50%. Shapiro’s theory does not reject God, and nor do I. It covers cellular intelligence, not the source of cellular intelligence.

DAVID: I know that. He was president of his Temple.

So what was your point in telling us you never rejected God? Nor did Shapiro.

DAVID: Please reread Shapiro from 2017 at Royal Society:
David's theory of evolution: James A. Shapiro's view 2017 (Evolution)
by David Turell @, Tuesday, January 07, 2020, 20:31 (77 days ago) @ David Turell
Not exactly what you think about him. His book has hyperbole which sells books, not his scientific thoughtful presentation.

dhw: Are you saying that the quotes in your book are a lie and he doesn’t believe that cells are cognitive beings whose intelligence creates evolutionary innovations? The lecture was delivered to a specialist audience, but there is nothing in what you quoted to contradict what he said earlier.

DAVID: My book quotes are exact and correct. What lies? My bold just above [dhw: whole quote omitted for brevity] simply notes his exact meaning is a future hope that his volume work will show how speciation works. The quote is simply hopeful and an extension of his findings which form a basis for future research, nothing more.

Of course he acknowledges that it is a theory, and not yet proven, but he hopes it will be. But what on earth was the point in your telling me: “Not exactly what you think about him. His book has hyperbole which sells books, not his scientific thoughtful presentation.” My quotes were not hyperbole, and his lecture in no way contradicts those quotes. You also accused me of stretching his theory to fit my bias. There is no stretching and there is no hyperbole. Please stop pretending that Shapiro does not propose cellular intelligence as the driving force behind evolutionary innovation. The rest of your post merely reiterates that his theory is not proven. Of course not. Otherwise it would be a fact. You go on to refer me to the article on squid and octopus:

"The octopus has a very large genome and can edit their own genomes, altering their RNA. They “ do not always follow their genetic instructions to the letter:'”
https://mindmatters.ai/2018/09/is-the-octopus-a-second-genesis-of-intelligence/

DAVID: So we see Shapiro's bacterial work passed on in evolution, but not speciation so far. The authors are surprised how much is done outside the nucleus itself. Note the title reference to 'genetic information'.

Again, it is a theory, and he does not attempt to pass it off as a fact. I have no objection to the word “information”! See Paul Davies post.

David (under “bilaterians and ediacarans”): I do not think an autonomous intelligence from God exists to allow evolutionary changes or daily adaptive changes beyond the epigenetic changes which we know about. For new species, God speciates.

I know! I’m simply surprised that you should state your beliefs as if they were a fact. You do the same when defending your whole theory of evolution – you say you do not question “God’s choices”, when you mean you do not question your personal interpretation of God’s choices.

DAVID: The 50/50 possibility is my honest observation of the odds of truth. I believe 100% that so-called cellular intelligence is cells following God-provided instructions.

Yes, you are honest in your 50/50 assessment of the odds. That is why it is illogical to dismiss a 50/50 chance that you are wrong.

Back to Shapiro

by David Turell @, Thursday, March 26, 2020, 22:32 (1463 days ago) @ dhw

DAVID: Please reread Shapiro from 2017 at Royal Society:
David's theory of evolution: James A. Shapiro's view 2017 (Evolution)
by David Turell @, Tuesday, January 07, 2020, 20:31 (77 days ago) @ David Turell
Not exactly what you think about him. His book has hyperbole which sells books, not his scientific thoughtful presentation.

dhw: Are you saying that the quotes in your book are a lie and he doesn’t believe that cells are cognitive beings whose intelligence creates evolutionary innovations? The lecture was delivered to a specialist audience, but there is nothing in what you quoted to contradict what he said earlier.

DAVID: My book quotes are exact and correct. What lies? My bold just above [dhw: whole quote omitted for brevity] simply notes his exact meaning is a future hope that his volume work will show how speciation works. The quote is simply hopeful and an extension of his findings which form a basis for future research, nothing more.

Of course he acknowledges that it is a theory, and not yet proven, but he hopes it will be. But what on earth was the point in your telling me: “Not exactly what you think about him. His book has hyperbole which sells books, not his scientific thoughtful presentation.” My quotes were not hyperbole, and his lecture in no way contradicts those quotes. You also accused me of stretching his theory to fit my bias. There is no stretching and there is no hyperbole. Please stop pretending that Shapiro does not propose cellular intelligence as the driving force behind evolutionary innovation. The rest of your post merely reiterates that his theory is not proven. Of course not. Otherwise it would be a fact. You go on to refer me to the article on squid and octopus:

"The octopus has a very large genome and can edit their own genomes, altering their RNA. They “ do not always follow their genetic instructions to the letter:'”
https://mindmatters.ai/2018/09/is-the-octopus-a-second-genesis-of-intelligence/

DAVID: So we see Shapiro's bacterial work passed on in evolution, but not speciation so far. The authors are surprised how much is done outside the nucleus itself. Note the title reference to 'genetic information'.

dhw: Again, it is a theory, and he does not attempt to pass it off as a fact. I have no objection to the word “information”! See Paul Davies post.

David (under “bilaterians and ediacarans”): I do not think an autonomous intelligence from God exists to allow evolutionary changes or daily adaptive changes beyond the epigenetic changes which we know about. For new species, God speciates.

dhw: I know! I’m simply surprised that you should state your beliefs as if they were a fact. You do the same when defending your whole theory of evolution – you say you do not question “God’s choices”, when you mean you do not question your personal interpretation of God’s choices.

Why should I question what I believe to be the truth?


DAVID: The 50/50 possibility is my honest observation of the odds of truth. I believe 100% that so-called cellular intelligence is cells following God-provided instructions.

dhw: Yes, you are honest in your 50/50 assessment of the odds. That is why it is illogical to dismiss a 50/50 chance that you are wrong.

Please remember you are the agnostic. I am not.

Back to Shapiro

by dhw, Friday, March 27, 2020, 12:05 (1462 days ago) @ David Turell

Dhw: Of course he [Shapiro] acknowledges that it is a theory, and not yet proven, but he hopes it will be. But what on earth was the point in your telling me: “Not exactly what you think about him. His book has hyperbole which sells books, not his scientific thoughtful presentation.” My quotes were not hyperbole, and his lecture in no way contradicts those quotes. You also accused me of stretching his theory to fit my bias. There is no stretching and there is no hyperbole. Please stop pretending that Shapiro does not propose cellular intelligence as the driving force behind evolutionary innovation.

You have not commented on this, and so I hope it will mark the end of this unproductive thread of discussion.

David (under “bilaterians and ediacarans”): I do not think an autonomous intelligence from God exists to allow evolutionary changes or daily adaptive changes beyond the epigenetic changes which we know about. For new species, God speciates.

dhw: I know! I’m simply surprised that you should state your beliefs as if they were a fact. You do the same when defending your whole theory of evolution – you say you do not question “God’s choices”, when you mean you do not question your personal interpretation of God’s choices.

DAVID: Why should I question what I believe to be the truth?

Because you are trying to proselytize, and you haven’t a hope of doing so if you cannot find a logical argument to support your fixed beliefs. (I am referring to your overall theory of evolution, not to your belief in God or even in his purpose - though that is what leads to many of your illogicalities).

DAVID: The 50/50 possibility is my honest observation of the odds of truth. I believe 100% that so-called cellular intelligence is cells following God-provided instructions.

dhw: Yes, you are honest in your 50/50 assessment of the odds. That is why it is illogical to dismiss a 50/50 chance that you are wrong.

DAVID: Please remember you are the agnostic. I am not.

I think you will be on safer ground, then, if you say outright that those fixed beliefs which you cannot explain are based on irrational faith and not on reason. I would say the same to any atheist who places his faith in the theory that all the complexities of life have arisen by sheer chance (e.g. chance origin of life, evolution governed by random mutations).

Back to Shapiro

by David Turell @, Friday, March 27, 2020, 20:52 (1462 days ago) @ dhw

Dhw: Of course he [Shapiro] acknowledges that it is a theory, and not yet proven, but he hopes it will be. But what on earth was the point in your telling me: “Not exactly what you think about him. His book has hyperbole which sells books, not his scientific thoughtful presentation.” My quotes were not hyperbole, and his lecture in no way contradicts those quotes. You also accused me of stretching his theory to fit my bias. There is no stretching and there is no hyperbole. Please stop pretending that Shapiro does not propose cellular intelligence as the driving force behind evolutionary innovation.

dhw: You have not commented on this, and so I hope it will mark the end of this unproductive thread of discussion.

The hyperbole is in his book, not you,, since he is pointedly convinced his theory will advance the research in evolution. I fully agree with him. He has done amazing work, but in reality, it tells us nothing more that live-on-their-own bacteria can self-edit their DNA more than epigenetics in multicellular organisms. It is obvious to me bacteria had to have this ability, since in recent years, it is obvious bacteria were meant to survive to form helpful biomes for all larger animals. When this discussion site started that was not known, and I can remember we wondered why they survived from the beginning. Advances in science then and now will show us obvious purposes to interpret.

But your stretch to believe our cells act intelligently is not supported by his work. Nothing is more clear to me. Bacteria are not our cells.


David (under “bilaterians and ediacarans”): I do not think an autonomous intelligence from God exists to allow evolutionary changes or daily adaptive changes beyond the epigenetic changes which we know about. For new species, God speciates.

dhw: I know! I’m simply surprised that you should state your beliefs as if they were a fact. You do the same when defending your whole theory of evolution – you say you do not question “God’s choices”, when you mean you do not question your personal interpretation of God’s choices.

DAVID: Why should I question what I believe to be the truth?

dhw: Because you are trying to proselytize, and you haven’t a hope of doing so if you cannot find a logical argument to support your fixed beliefs. (I am referring to your overall theory of evolution, not to your belief in God or even in his purpose - though that is what leads to many of your illogicalities).

They are illogical to you because you humanize God when you theorize about Him. My God is nothing like what you imagine about God.


DAVID: The 50/50 possibility is my honest observation of the odds of truth. I believe 100% that so-called cellular intelligence is cells following God-provided instructions.

dhw: Yes, you are honest in your 50/50 assessment of the odds. That is why it is illogical to dismiss a 50/50 chance that you are wrong.

DAVID: Please remember you are the agnostic. I am not.

dhw: I think you will be on safer ground, then, if you say outright that those fixed beliefs which you cannot explain are based on irrational faith and not on reason. I would say the same to any atheist who places his faith in the theory that all the complexities of life have arisen by sheer chance (e.g. chance origin of life, evolution governed by random mutations).

As you know I was an agnostic and came to believe because of the reading I did, and, as Adler writes, I came to believe 'beyond a reasonable doubt'. You are stuck with my position; are not an atheist because of the complexity of the design of life; you cannot move beyond the recognition of the need for a designer by deciding to stop at that point. Our only difference really is that I have given the designer a name and believe He existed and exists.

Back to Shapiro

by dhw, Saturday, March 28, 2020, 13:15 (1461 days ago) @ David Turell

dhw: Of course he [Shapiro] acknowledges that it is a theory, and not yet proven, but he hopes it will be. But what on earth was the point in your telling me: “Not exactly what you think about him. His book has hyperbole which sells books, not his scientific thoughtful presentation.” My quotes were not hyperbole, and his lecture in no way contradicts those quotes. You also accused me of stretching his theory to fit my bias. There is no stretching and there is no hyperbole. Please stop pretending that Shapiro does not propose cellular intelligence as the driving force behind evolutionary innovation.

dhw: You have not commented on this, and so I hope it will mark the end of this unproductive thread of discussion.

DAVID: The hyperbole is in his book, not you…

What hyperbole? He advances cellular intelligence and natural genetic engineering as a theory, just as you advance your logical designer God theory and your illogical theory of evolution. Both hyperbole?

DAVID: …..but in reality, it tells us nothing more that live-on-their-own bacteria can self-edit their DNA more than epigenetics in multicellular organisms.

Why do you insist on restricting the discussion to bacteria, just because that is his special field? He is building on the work of other specialists who are also convinced that cells are intelligent, sentient, cognitive beings. Should we dismiss your theories about God and evolution just because you are not a theologian cum biochemist cum palaeontologist cum microbiologist cum physicist cum archangel?

DAVID: But your stretch to believe our cells act intelligently is not supported by his work. Nothing is more clear to me. Bacteria are not our cells.

It is not my stretch. You yourself have quoted the theory, and the theory is not confined to bacteria! Do you really believe that Shapiro is unaware of all the research done by McClintock and Margulis and others who have drawn the same conclusions as himself about cellular intelligence?

DAVID: The 50/50 possibility is my honest observation of the odds of truth. I believe 100% that so-called cellular intelligence is cells following God-provided instructions.

dhw: Yes, you are honest in your 50/50 assessment of the odds. That is why it is illogical to dismiss a 50/50 chance that you are wrong.

DAVID: Please remember you are the agnostic. I am not.

dhw: I think you will be on safer ground, then, if you say outright that those fixed beliefs which you cannot explain are based on irrational faith and not on reason. I would say the same to any atheist who places his faith in the theory that all the complexities of life have arisen by sheer chance (e.g. chance origin of life, evolution governed by random mutations).

DAVID: As you know I was an agnostic and came to believe because of the reading I did, and, as Adler writes, I came to believe 'beyond a reasonable doubt'. You are […] not an atheist because of the complexity of the design of life. […] Our only difference really is that I have given the designer a name and believe He existed and exists.

I know your position and mine. I am just pointing out to you that your position is no more and no less “beyond a reasonable doubt” than that of the convinced atheist, and since you keep emphasizing that there is no point in using human reason to answer all the awkward questions, quite clearly you can’t answer them, which means your fixed beliefs are based on faith and not on reason.

DAVID (under “trading mitochondria"): Mitochondrias are as free-ranging as Margulis might have imagined when she proposed her theory. They must play some sort of a role in speciation. This article is actually about using them in therapy.

It is worth pointing out that Margulis was another staunch believer in cellular intelligence.

Back to Shapiro

by David Turell @, Saturday, March 28, 2020, 21:06 (1461 days ago) @ dhw

dhw: You have not commented on this, and so I hope it will mark the end of this unproductive thread of discussion.

DAVID: The hyperbole is in his book, not you…

dhw: What hyperbole? He advances cellular intelligence and natural genetic engineering as a theory, just as you advance your logical designer God theory and your illogical theory of evolution. Both hyperbole?

Shapiro is now retired and all his work was on how bacteria can edit and modify their DNA. His theory implies that this ability was passed on in evolution and might imply how cells became so intelligent looking, with no proof they are really intelligent. And the ability might lead somehow to a means of speciation.


DAVID: …..but in reality, it tells us nothing more that live-on-their-own bacteria can self-edit their DNA more than epigenetics in multicellular organisms.

dhw: Why do you insist on restricting the discussion to bacteria, just because that is his special field? He is building on the work of other specialists who are also convinced that cells are intelligent, sentient, cognitive beings. Should we dismiss your theories about God and evolution just because you are not a theologian cum biochemist cum palaeontologist cum microbiologist cum physicist cum archangel?

Answered above with a fuller discussion of his apparent thoughts, as I interpret his book and his paper to the Royal Society in 2017.


DAVID: But your stretch to believe our cells act intelligently is not supported by his work. Nothing is more clear to me. Bacteria are not our cells.

dhw: It is not my stretch. You yourself have quoted the theory, and the theory is not confined to bacteria! Do you really believe that Shapiro is unaware of all the research done by McClintock and Margulis and others who have drawn the same conclusions as himself about cellular intelligence?

I quoted his theory to recognize his contribution to the current status of research in how evolution works. Of course he knows previous work and opinion, and whether cells are intelligent or simply act intelligently by following instruction is a matter of opinion.

DAVID: Please remember you are the agnostic. I am not.


dhw: I think you will be on safer ground, then, if you say outright that those fixed beliefs which you cannot explain are based on irrational faith and not on reason. I would say the same to any atheist who places his faith in the theory that all the complexities of life have arisen by sheer chance (e.g. chance origin of life, evolution governed by random mutations).

DAVID: As you know I was an agnostic and came to believe because of the reading I did, and, as Adler writes, I came to believe 'beyond a reasonable doubt'. You are […] not an atheist because of the complexity of the design of life. […] Our only difference really is that I have given the designer a name and believe He existed and exists.

dhw: I know your position and mine. I am just pointing out to you that your position is no more and no less “beyond a reasonable doubt” than that of the convinced atheist, and since you keep emphasizing that there is no point in using human reason to answer all the awkward questions, quite clearly you can’t answer them, which means your fixed beliefs are based on faith and not on reason.

The bold is the your usual twisted version of my views. I have politely given you 'guesses' about God's reasoning in the past and you have quoted them to argue against my views. I really can guess as much as you do, but it is difficult not to humanize God if you and I use human reasoning to guess why He chose to do what He did and how He seemed to accomplish His purposes. Logically, if my view of God is accepted that He is fully in charge, and capable of doing all He wishes when He wishes, then simply studying history tells us His actions, without questioning His decisions, as if He were human in thought, making decisions on the fly. My fixed belief is God exists and runs the show with clear purposes in mind. Purposes on the way to a goal: 1) start life and keep bacteria around for larger help with more complex organisms (biomes); 2) create a huge bush of life with proper econiches to supply food for life to have the energy it constantly needs; 3) to use evolution to create humans with their most unusual mental capacity, whose existence or survival is not required as part of the previous bush of life.


DAVID (under “trading mitochondria"): Mitochondrias are as free-ranging as Margulis might have imagined when she proposed her theory. They must play some sort of a role in speciation. This article is actually about using them in therapy.

dhw: It is worth pointing out that Margulis was another staunch believer in cellular intelligence.

Yes. Belief, nothing more. We still await proof.

Back to Shapiro

by dhw, Sunday, March 29, 2020, 13:25 (1460 days ago) @ David Turell

DAVID: The hyperbole is in his book, not you…

dhw: What hyperbole? He advances cellular intelligence and natural genetic engineering as a theory, just as you advance your logical designer God theory and your illogical theory of evolution. Both hyperbole?

DAVID: Shapiro is now retired and all his work was on how bacteria can edit and modify their DNA. His theory implies that this ability was passed on in evolution and might imply how cells became so intelligent looking, with no proof they are really intelligent. And the ability might lead somehow to a means of speciation.

Over and over again you emphasize that his theory is not proven. If it was, it would be a fact. If his theory is hyperbolic because it hasn’t been proven, where does this leave your God theory and your theory of evolution?

DAVID: …..but in reality, it tells us nothing more that live-on-their-own bacteria can self-edit their DNA more than epigenetics in multicellular organisms.

dhw: Why do you insist on restricting the discussion to bacteria, just because that is his special field? He is building on the work of other specialists who are also convinced that cells are intelligent, sentient, cognitive beings. Should we dismiss your theories about God and evolution just because you are not a theologian cum biochemist cum palaeontologist cum microbiologist cum physicist cum archangel?

DAVID: Answered above with a fuller discussion of his apparent thoughts, as I interpret his book and his paper to the Royal Society in 2017.

I have shown you that the quotes from the lecture do not in any way contradict the theory as outlined in the passages you quote in your book.

DAVID: Of course he knows previous work and opinion, and whether cells are intelligent or simply act intelligently by following instruction is a matter of opinion.

So please stop pretending that he only knows about bacteria, please stop calling his theory hyperbolic, please stop pretending that I stretch his theory, and please recognize that any unproven theory – just like the God theory – can only be a matter of opinion until it is established as a fact.

Back to Shapiro: supported by cheese making study

by David Turell @, Saturday, October 17, 2020, 20:44 (1258 days ago) @ dhw

The involved fungi can cause the bacteria to modify:

https://phys.org/news/2020-10-funky-cheese-microbes.html

"Many microbes produce airborne chemical compounds called volatile organic compounds, or VOCs, as they interact with their environment. A widely recognized microbial VOC is geosmin, which is emitted by soil microbes and can often be smelled after a heavy rain in forests. As bacteria and fungi grow on ripening cheeses, they secrete enzymes that break down amino acids to produce acids, alcohols, aldehydes, amines, and various sulfur compounds, while other enzymes break down fatty acids to produce esters, methyl ketones, and secondary alcohols. All of those biological products contribute to the flavor and aroma of cheese and they are the reason why Camembert, Blue cheese and Limburger have their signature smells.

"The Tufts researchers found that VOCs don't just contribute to the sensory experience of cheese, but also provide a way for fungi to communicate with and "feed" bacteria in the cheese microbiome. By pairing 16 different common cheese bacteria with 5 common cheese rind fungi, the researchers found that the fungi caused responses in the bacteria ranging from strong stimulation to strong inhibition. One bacteria species, Vibrio casei, responded by growing rapidly in the presence of VOCs emitted by all five of the fungi. Other bacteria, such as Psychrobacter, only grew in response to one of the fungi (Galactomyces), and two common cheese bacteria decreased significantly in number when exposed to VOCs produced by Galactomyces.

"The researchers found that the VOCs altered the expression of many genes in the bacteria, including genes that affect the way they metabolize nutrients. One metabolic mechanism that was enhanced, called the glyoxylate shunt, allows the bacteria to utilize more simple compounds as "food" when more complex sources such as glucose are unavailable. In effect, they enabled the bacteria to better "eat" some of the VOCs and use them as sources for energy and growth. (my bold)

"'The bacteria are able to actually eat what we perceive as smells," said Casey Cosetta, post-doctoral scholar in the department of biology at Tufts University and first author of the study. "That's important because the cheese itself provides little in the way of easily metabolized sugars such as glucose. With VOCs, the fungi are really providing a useful assist to the bacteria to help them thrive.'"

Comment: Note the bold. I would state it differently. The fungi stimulated the bacteria to change gene expression, as Shapiro would accept.

Back to Shapiro: editing DNA fights off viruses

by David Turell @, Thursday, November 12, 2020, 15:08 (1232 days ago) @ David Turell

Some bacteria self-destruct to save the colony:

https://www.sciencemag.org/news/2020/11/microbes-mystery-dna-helps-defeat-viruses-and-h...

"For several years, researchers have been adapting retrons—mysterious complexes of DNA, RNA, and protein found in some bacteria—into a potentially powerful way to alter genomes of single cell organisms. Now, biology is catching up, as two groups report evidence that, like CRISPR, retrons are part of the bacterial immune arsenal, protecting the microbes from viruses called phages.

"Last week in Cell, one team described how a specific retron defends bacteria, triggering newly infected cells to self-destruct so the virus can’t replicate and spread to others. The Cell paper “is the first to concretely determine a natural function for retrons,” says Anna Simon, a synthetic biologist at Strand Therapeutics who has studied the bacterial oddities. Another paper, which so far has appeared only as a preprint, reports a similar finding.

***

"In the 1980s, researchers studying a soil bacterium were puzzled to find many copies of short sequences of single-stranded DNA littering the cells. The mystery deepened when they learned each bit of DNA was attached to an RNA with a complementary base sequence. Eventually they realized an enzyme called reverse transcriptase had made that DNA from the attached RNA, and that all three molecules—RNA, DNA, and enzyme—formed a complex.

"Similar constructs, dubbed retrons for the reverse transcriptase, were found in many bacteria.

***

"The team then noticed that the DNA encoding retron components often accompanied a protein-coding gene, and the protein varied from retron to retron. The team decided to test its hunch that the cluster of sequences represented a new phage defense. They went on to show that bacteria needed all three components—reverse transcriptase, the DNA-RNA hybrid, and the second protein—to defeat a variety of viruses.

***

"The researchers concluded that the retron somehow “guards” another molecular complex that is the bacterium’s first line of antiviral defense. Some phages deactivate the complex, which triggers the retron to unleash the membrane-destroying protein and kill the infected cell,

***

"the group realized that next to the genes coding for a retron in a Salmonella bacterium was a gene for a protein toxic to Salmonella. The team discovered the retron normally keeps the toxin under wraps, but activates it in the presence of phage proteins."

Comment: To repeat: Bacteria edit their DNA to self-destruct and save the colony. I would ask how did this developed? Did bacteria learn this on their own or did it happen by design?

Back to Shapiro: an editing bacterium

by David Turell @, Monday, November 23, 2020, 17:28 (1221 days ago) @ David Turell

A giant bacterium alters DNA:

https://www.sciencedaily.com/releases/2020/11/201119141705.htm

The largest freshwater bacterium, Achromatium oxaliferum, is highly flexible in its requirements, as researchers have now discovered: It lives in places that differ extremely in environmental conditions such as hot springs and ice water. The adaptation is probably achieved by a process which is unique to these bacteria: only relevant genes are enriched in the genomes and transcribed, while others are archived in cell compartments.

***

Achromatium is special in many respects: It is 30,000 times larger than its "normal" counterparts that live in water and owing to its calcite deposits it is visible to the naked eye. It has several hundred chromosomes, which are most likely not identical. This makes Achromatium the only known bacterium with several different genomes.

***

"We suggest environmental adaptation in Achromatium occurs by increasing the copy number of relevant genes across the cell's hundreds of chromosomes. This is in stark contrast to other bacteria which eventually lose irrelevant genes. So the high number of genomes makes the versatility possible," explains Dr. Danny Ionescu, leader of the study from IGB.

Achromatium is full of calcium carbonate crystals that are located between the outer and cytoplasmic membranes. These crystals fold the cytoplasmic membrane forming pockets of cytoplasm which the researchers suggest to hold clusters of chromosomes. They hypothesize that these clusters enable Achromatium to "archive" genes of no immediate use.

"The functional versatility of Achromatium and its genomic features contradict what we know for other bacteria, for example the concept of bacterial species and the driving forces of bacterial speciation. In Achromatium, mother and daughter cells are likely not identical and each cell is unique holding a multitude of genes, some of which are not essential for life in a particular habitat. Therefore, each cell keeps the potential to rapidly adapt to changing or new environmental conditions," concludes Professor Hans-Peter Grossart, co-author of the study and head of the aquatic microbial ecology group at IGB.

Comment: This a very specialized bacterium. But it fits Shapiro to a 'T'.

Back to Shapiro: an editing bacterium

by David Turell @, Monday, September 19, 2022, 20:06 (556 days ago) @ David Turell

Another fit to Shapiro, Klebsiella:

https://phys.org/news/2022-09-silent-mutations-bacteria-evade-antibiotics.html

"Researchers have discovered a new way hospital-acquired infections resist antibiotics, through a "silent" genetic mutation.

***

"The researchers looked at the bacterium Klebsiella pneumoniae, which causes infections in the lungs, blood and wounds of those in hospitals, with patients that have compromised immune systems, such as those in intensive care units, being especially vulnerable.

***

"In order to be effective, antibiotics need to get inside bacteria, and in K. pneumoniae this happens via a channel in the bacterium's outer membrane, formed by a protein called OmpK36. The team discovered a genetic mutation that makes the bacteria produce less of the protein, effectively shutting some of these channels and keeping carbapenem antibiotics out.

***

"This mutation, however, works differently to standard mutations that result in antibiotic resistance. Usually, mutations change the genetic code so that when it is "read" by ribosomes and converted into a protein, it produces a different chain of amino acids with different functions.

"This mutation still produces the same amino acid chain, but alters the structure of an important mRNA intermediate, preventing ribosomes reading the code and producing protein from it.

"When looking for mutations, genomic techniques are usually searching for changes to the amino acid sequence. However, since this mutation alters a structure, rather than the sequence itself, it could be thought of as a "silent" mutation.

"First author Dr. Joshua Wong, from the Department of Life Sciences at Imperial, said, "In the age of big data and genomics, mutations such as we have discovered may be considered 'silent' as the genetic code results in the same protein sequence.

***

"Using data from resistant bacteria samples collected globally, the team showed that the mutation had arisen several times independently. This suggests it is not random, and is instead driven by the need of the bacteria to defend itself again the antibiotics.

"Lead researcher Professor Gad Frankel, from the Department of Life Sciences at Imperial, said, "The mutation evolved on several occasions independently, and this tells us that this novel mechanism is not a one-off fluke, but instead driven by antibiotic consumption. This suggests that the mutation occurs under antibiotic pressure and highlights the side effects of excessive antibiotic usage in hospitals and other settings.'"

Comment: fits Shapiro to a 'T'. DNA had to be edited to have this happen. This is a minor modification of a protein pathway, not speciation as dhw would hope for in his extrapolated theorizing.

Back to Shapiro: how some bacteria handle DNA

by David Turell @, Wednesday, February 08, 2023, 15:53 (414 days ago) @ David Turell
edited by David Turell, Wednesday, February 08, 2023, 15:59

Very differently using Histones:

https://www.nature.com/articles/d41586-023-00334-4

"A startling discovery in bacteria suggests that some species have a bizarre way of packaging chromosomes and regulating gene expression — using proteins that, until recently, weren’t thought to exist in bacteria at all.

"In a preprint posted on bioRxiv on 26 January, researchers report the characterization of proteins called histones that, in two bacterial species, seem to bind together to coat regions of the bacterial chromosome1. This is completely different from the arrangement of histones seen in other organisms. For example, in organisms called eukaryotes, whose cells have a membrane-bounded nucleus, DNA winds around histones, rather than being encased by them.

"Although histones are vital tools for maintaining chromosome structure and controlling gene activity in eukaryotes and microorganisms called archaea, for years it was widely assumed that they did not exist in bacteria.

***

"Eukaryotic histones are remarkably uniform in their structure and function — a consistency that can be frustrating for researchers who want to study histone evolution, says biochemist Karolin Luger at the University of Colorado Boulder. “If you want to get at the evolutionary origin, you can’t go to a ‘primitive’ eukaryote,” she says. “It already has everything.”

"The lack of diversity also raises questions for synthetic biologists in search of new ways to control gene expression, says Tobias Warnecke, a molecular evolutionary biologist at Imperial College London. “The fundamental composition of the chromatin and how gene expression works is very similar across eukaryotes and then you start wondering, ‘is that a frozen accident?’” he says. “Is there something special about histones that makes them unique, or can we build systems in a different way?”

***

"When the researchers isolated the histone protein from B. bacteriovorus and analysed its structure, both on its own and while it was interacting with DNA, they were surprised to find that it did not behave like any known histones from archaea or eukaryotes. The bacterial histones came together in pairs that surrounded the DNA strand. Long chains of these could act as a shield around the DNA, a marked difference from their function in eukaryotes, in which histones group together to form a spool around which the DNA winds. “I was blown away,” says Luger.

***

"As part of their study, the researchers surveyed thousands of bacterial genomes. They found histone-like proteins in about 2% of the genomes, which suggests that there will be many other systems to study. “People got excited and said ‘oh, bacteria weren’t supposed to have histones’,” says Warnecke. “But if you work on microbial evolution, you know that if you look hard enough, you’ll find some.'”

Comment: the theory that eukaryotes and Archaea are directly related in early evolution now has to accept that bacteria may be more directly related than thought. Note that the article does not mention Shapiro's work. It depends upon how much he did with histones, if at all. At least we now know how active histones are in editing.

Back to Shapiro: how some bacteria handle DNA

by David Turell @, Friday, May 12, 2023, 20:39 (321 days ago) @ David Turell

A new finding that bacteria have histones to manage their DNA:

https://www.the-scientist.com/news-opinion/bacteria-have-histones-after-all-study-70951...

"Warnecke and colleagues are challenging the idea that these space-saving proteins are not commonplace in bacteria. In a preprint uploaded to bioRxiv this January that has yet to undergo peer review, the team describes hundreds of potential histone proteins in bacteria, including one that they predict interacts with DNA in an unusual way.

***

"Hocher sifted through over 18,000 bacterial genomes using shorter histone-related proteins from archaea as references. With this strategy, he discovered over 400 bacterial proteins that contain a signature 3D histone structure called a histone fold, suggesting histones could be scattered across many bacterial species.

"With so many candidates to choose from, the researchers homed in on a histone in the species Bdellovirbio bacteriovorus, a bacterium that preys upon other bacteria. The team thought it might be a good candidate for finding histones because the bacterium changes size throughout its lifecycle and thus would need to carefully time DNA compression and unwinding. As a small predatory cell, it invades a prey bacterium, expands in size, and divides into multiple small predators, continuing the cycle.

"The team detected a histone fold in an uncharacterized B. bacteriovorus’ protein called Bd0055 and wondered if this protein could help orchestrate DNA packaging. By observing that, in the presence of the protein, DNA moved much slower through pores in a gel, they confirmed that Bd0055 binds DNA. Deleting the gene turned out to be lethal in B. bacteriovorus cells both inside and outside prey bacteria, indicating that the protein is essential throughout the lifecycle.

"With all evidence thus far suggesting Bd0055 could be a typical histone protein, the team set out to determine if Bd0055 forms spools for DNA to wrap around. Computer simulations carried out by Shawn Laursen at the University of Colorado Boulder revealed that the protein-protein interactions that are needed to form spools would be unstable for this protein. Instead, the simulations revealed that Bd0055 might bind to the outer edges of DNA strands. Warnecke has never seen other histones behave this way. “There’s really nothing like the edge-on binding,” he says.

"Rather than packaging the DNA to occupy less space, the authors argue that the edge-on binding could straighten the strands and protect the DNA from over-compression during division into smaller cells. Indeed, straightened DNA spirals have been observed in this bacterium. Nessa Carey, a molecular biologist who works on histones and was not involved with the study, agrees, noting that “it’s a possible interpretation” but also wonders if the protein may have a shielding action against bacteriophages or arsenal in the prey bacterium. The protein could be “making DNA harder to get at and attack.”

***

"B. bacteriovorus is known to have exchanged genes with a distant relative, Leptospira interrogans, in the past, and the researchers found a similar histone protein in this species. Laursen says he plans to investigate this histone next. His supervisor, Karolin Luger, tells The Scientist in an email that because Leptospira histones share many features with Bd0055, the team suspects they might bind DNA “in the same unorthodox manner,” but there are also “intriguing differences.”

“'We currently have a ‘beer bet’ in the lab on the outcome,” Luger says. “At any rate, it will be exciting to see whether this DNA binding mode is a general phenomenon for bacterial histones.'”

Comment: This adds to Shapiro's bacterial DNA studies but does not further advance his theory of evolution. We know that bacterial DNA floats around in the bacterial body, but it is hard to imagine it is totally uncontrolled. A bacterium, living on its own, must run its life by protecting itself, and so it is more complex in many ways than some multicellular cells doing a repetitive job in some organ.

Back to Shapiro: how phages modify DNA

by David Turell @, Tuesday, December 05, 2023, 17:27 (114 days ago) @ David Turell

In the fight with bacteria:

https://communities.springernature.com/posts/unlocking-the-puzzle-of-phage-proteins-bui...


"...bacterial viruses – phages - have a remarkable propensity to shuffle fragments of their genes which can help phages overcome bacterial resistance mechanisms. These findings suggest that viral evolution may sometimes be better understood from the point of view of protein domains rather than entire proteins.

"Both phages and bacteria are known to frequently pick up new genes during interactions with other microbes or mobile genetic elements like viruses and plasmids. This phenomenon is known as horizontal gene transfer (HGT), and it's responsible for the astonishing diversity seen in prokaryote genomes.

"Does such horizontal transfer work only at the level of entire genes? There are some known examples of proteins that have modular structures i.e. are composed of fragments that potentially can be used in multiple combinations. They include proteins involved in recognizing bacterial hosts (receptor binding proteins, RBPs) and enzymes responsible for breaking down the bacterial cell wall (endolysins).

"This phenomenon has practical implications. It has been harnessed in biotechnology, such as the search for new endolysins with antibacterial properties and the design of synthetic phages with altered host ranges.

***

"When we examined thousands of phage genomes, we found that domain mosaicism is widespread in phage proteins of various functions, not limited to RBPs or endolysins. Moreover, it is not only present within proteins that have the same function. Similar fragments are also shared by proteins that perform different biological functions.

"When we compared the extend of mosaicism between various phage proteins we found that the ones that are most mosaic apart from RBPs (i.e. tail fibers and tail spikes) and endolysins, are DNA polymerases.

***

"...having their own DNA polymerases gives phages an edge in the evolutionary arms race, as it allows for more specific replication of their DNA and competition with the host's DNA polymerase. Finally, it allows to overcome multiple bacterial mechanisms that defend against phages.

"In fact, the most mosaic proteins identified in this study are heavily involved in the ongoing battle between bacteria and phages and are often targeted by bacterial defense mechanisms. Therefore, they are under intense evolutionary pressure to diversify while maintaining their functions, and domain mosaicism is a key strategy to achieve this.

"What is even more interesting, we found that the phenomenon of reshuffling domains within phage proteins is an on-going process and we showed a number of examples of such recent reshuffling within: tail fibres, endolysins but also DNA polymerases, replication initiation proteins, ribonucleotide reductases and neck passage proteins.

***

"...the discovery of recent diversification via domain shuffling opens up possibilities for directed evolution experiments, which could lead to the creation of new phages with custom functionalities and host ranges." (my bold)

Comment: the ongoing warfare between phages and bacteria is an ancient battle from the beginning of life. It demonstrates why bacteria must have the ability to edit their DNA to create new anti-phage tools. Note my bold. I worry about tinkering with phages which might result in a form that might attack us!

Back to Shapiro: organisms remove DNA in fetuses

by David Turell @, Tuesday, December 05, 2023, 19:29 (114 days ago) @ David Turell

A common event:

https://www.the-scientist.com/features/downsizing-dna-71512?utm_campaign=TS_eTOC_2023&a...

"Marie Delattre, a biologist...has studied the nematode Mesorhabditis belari for nearly a decade now. The microscopic worm first caught her attention for its unconventional approach to reproduction, where only a small fraction of offspring keep their male parent’s DNA.

***

"During this brief point in the worms’ development, part of their genomes appeared to vanish.

***

"Even after more than a century of research, there are still many unanswered questions about programmed DNA elimination.

***

"Recent technologies such as DNA sequencing have bolstered researchers’ efforts to probe this process. By comparing sequences of the genomes of germ cells and somatic cells from the same organism, researchers can look for long stretches in the germline genome that are absent from the somatic genome. These studies have shown that species can eliminate anywhere between 0.5 percent and 90 percent of their genomes.

***

"...regardless of species, the eliminated regions include large stretches of repeated DNA sequences, which typically do not encode the instructions for proteins.

***

"Programmed DNA elimination pops up on almost every branch of the tree of life, but the processes are as diverse as the flora and fauna that use them. The nematodes and unicellular ciliates seem to slice their genomes into small pieces and remove a subset. Vertebrates seem to be more likely to remove full chromosomes.

"These different approaches involve the same set of core steps: part of the genome is marked for elimination, and as the cell divides, this DNA is shunted out of the nucleus and ultimately removed from the cell. In ciliates and worms, the cell also needs to slice up the DNA into fragments. How this happens in cells is still largely unknown. But studies from Wang, Delattre, and others are starting to piece together the process.

***

"Researchers still don’t know how the lagging chromosomes or discarded DNA fragments are chosen. In worms, Delattre uses detailed maps of the genome and RNA measurements to figure out how the cell knows where to fragment the DNA and what proteins make the cuts.

***

"Another explanation is that eliminated genes might play a role in germ cells during reproduction, where they may need to make an arsenal of proteins that are unnecessary in other cells of the body. Studies in Ascaris and in zebra finches revealed that their eliminated genes have functions in sex organs like the testes, where germ cells originate.

***

"It’s also possible that programmed DNA elimination could play diverse r oles in different species. “I would say, at this point, that they’re different processes,” Suh said. Smith agreed and noted that the evolutionary history of DNA elimination is still hazy. He speculated that each major branch of life may have independently developed the ability to eliminate DNA. “They’re doing similar things, but they got there through very different evolutionary trajectories,” he said.

***

"For now, many scientists agree that the next step is to study programmed DNA elimination in more species. “We probably don’t know the majority of species that actually do this,” Smith said.

***

"Every songbird eliminates at least one chromosome, but in some cases it’s the biggest chromosome; in other species it’s the smallest one. The genes on the eliminated chromosomes can be completely different between species but they have one thing in common: Some of the gene sequences are very similar to those found on retained chromosomes, a trend that hasn’t yet been observed in other types of animals.9

“'It gets more and more confusing with every species,” Suh said."

Comment: yes, the whole of all genomes is a mystery, yet to unravel. Here we see purposeful editing for elimination, while in bacteria we see editing only for improvement, an opposite event.

Back to Shapiro

by David Turell @, Thursday, April 08, 2021, 15:41 (1085 days ago) @ dhw

A new study shows how bacteria can revive pseudogenes when necessary:

https://sciencenews.dk/en/scientists-use-evolution-to-revive-zombie-genes

"The Technical University of Denmark has developed a method that speeds up evolution by pressuring bacteria and fungi to develop at a furious pace.

"Researchers have now discovered that this method – adaptive laboratory evolution – can also revive pseudogenes.

"The discovery is interesting because it indicates why evolution has retained these zombie genes that could otherwise easily have been discarded. The pseudogenes probably function like spare parts that keep an old car working so it can be used when the new one has broken down.

***

"A pseudogene is a gene that no longer functions and has shared ancestry with a functioning gene. For example, in evolutionary terms a bacterium may no longer require a specific protein coded by a specific gene and because this protein is not required for the organism to survive, the gene does not need to be repaired.

"The pseudogenes are a legacy in the genome from a time when the bacteria functioned differently. Bacteria have up to 10,000 genes and also between 100 and 1000 pseudogenes that have no function and appear not to have any purpose.

"The pseudogenes might be expected to disappear over time, but bacteria seem to retain them, which has long puzzled researchers.

"They finally have an idea why the bacteria do not discard the pseudogenes.

***

"The researchers investigated what happens to Escherichia coli if they gradually remove parts of the genes the bacterium uses to make proteins that draw iron into the bacterial cells.

"When bacteria enter a host, they need iron to divide and proliferate, and they absorb the iron from their surroundings using specific proteins. When these proteins no longer function, the bacteria stop growing and dividing.

***

"However, the researchers were also surprised to see that one of the bacterial cultures suddenly began to grow again, as if it still had fully functional versions of the genes the researchers had removed.

"The researchers analysed the genome of the bacteria and discovered that the bacteria still lacked the gene that had been removed. Instead the bacteria had repaired a pseudogene, which caused the bacteria to produce a different protein that could enable the cells to absorb iron.

“'The bacteria repaired a pseudogene that they were not using anymore. It was a minor repair. The bacteria needed to either remove two nucleotides from the DNA or insert four to activate the gene.

***

"After the researchers discovered the repaired pseudogenes, they returned to their database of 300,000 bacterial genomes to see whether any of the bacteria with which they previously had worked had also recreated lost functions by repairing pseudogenes. Here they found several other examples of bacteria that had taken old genes into use to survive.

“'This provides fascinating insight into how evolution works. Organisms do not seem to discard pseudogenes because they provide opportunities to survive. This is a genetic reservoir that they can use if needed."

Comment: Shapiro did excellent work and this study is further proof of his point that bacteria edit their DNA.

Back to Shapiro: reviews rethinking genome research

by David Turell @, Wednesday, May 26, 2021, 23:04 (1037 days ago) @ David Turell

An interesting book review:

https://inference-review.com/article/from-genes-to-genomes

"Genome Chaos is a book of no small ambition. Based on his experience in cancer cytogenetics, Henry Heng invites readers to rethink the role of the genome in determining the hereditary properties of cells and organisms. He distinguishes between gene-centric and genome-based views of heredity and argues that the physical organization of the genome incorporates a higher systems level of information beyond its genes or coding sequences. For Heng, genes are rather like a parts list capable of encoding proteins and RNA that can be assembled and used in many different ways to produce cells and organisms with quite distinct properties. In making his argument, Heng challenges a number of notions about the genotype–phenotype relationship. (my bold)

"According to Heng’s genome-based perspective, evolution can be broken down into two modes. Microevolutionary change operates within species much as Charles Darwin envisaged, by “numerous, successive, slight modifications.”1 Macroevolutionary change rapidly restructures the genome to establish a new architecture, leading to new species and new phenotypes without changing the basic gene content. The transition from microevolutionary to macroevolutionary change—the period Heng labels genome chaos—occurs when there is great stress on either somatic cells, as in cancer chemotherapy, or independent organisms, as in episodes of drastic ecological change and mass extinctions.

***

"In Heng’s concept, it is the genome system properties of novel chromosome organizations and not specific gene content that drives the major steps in the evolution of all but a few exceptional cancers.

"A chapter of Genome Chaos is devoted to applying these conclusions to organismal evolution. A similar model, Heng claims, fits the punctuated nature of the fossil record and cytological observations of chromosomal differences within groups of closely related species.4 Chimpanzee and hominid gene sequences match to within 98%, but they differ with respect to a chromosome fusion and several inversions. The result is that chimpanzees (2n = 48) have a karyotype with two more chromosomes than hominids (2n = 46).

***
"Heng’s idea that genome system information is critical in taxonomic divergence has some interesting implications, notably the counter-conventional notion that the normal evolutionary function of sexual reproduction is to suppress, rather than enhance, major phenotypic variation within species. The need for meiotic chromosome pairing in the formation of gametes at each generation prevents individuals carrying germline chromosome changes from producing progeny who can pass on those changes. (my bold)

"The most controversial aspect of Heng’s argument in Genome Chaos is the claim that specific gene-based changes play a minor role in the macroevolutionary process.

***

"At numerous points throughout Genome Chaos, Heng urges researchers to reorient their thinking about basic evolutionary processes. He argues persuasively for a shift from a gene-based to a genome-based approach, a transition he describes as moving from a one-dimensional to a four-dimensional view of genomic information and function.

***

"...there is no comprehensive theory that accounts for how a given genome architecture facilitates the expression of particular phenotypes using the parts list specified by its coding sequences.

***

"Despite our current relative ignorance, we can reasonably expect that patterns will be discerned in the whole genome sequence data that will provide greater mechanistic insight into how chromosome restructuring episodes occur, with important implications both for cancer therapy and evolutionary biology.

"The case Heng makes for thinking about genomes rather than just genes is strong and convincing. By alerting the genomics community to a new scientific frontier, Genome Chaos accomplishes two important and complementary goals. It clearly demonstrates that a great deal of fundamental evolutionary biology and genetics research still needs to be done before newly acquired genomics and genome-editing technologies can be used to maximum advantage.

Comment: No gene editing noted. Instead a positive discussion to discern the 3-D interrelationships of genes to each other and to gene transcription modifiers. Note the references to how information relates to the 3-D interrelationships (in my bolds). The 3-D interrelationships themselves may actually carry information in the specific arrangement of genome parts.

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