Back to Shapiro (Evolution)

by dhw, Wednesday, March 25, 2020, 11:31 (301 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 (301 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 (300 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 (300 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 (299 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 (299 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 (298 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 (298 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 (297 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 (95 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 (69 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 (58 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'.

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