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Excellent presentation by Bruce Damer and Dave Deamer
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MarkE
Sep 26, 2023, 10:10:49 AM9/26/23
to talk-o...@moderators.isc.org
The title is “A new model for the origin of life: A new model for the origin of life: Coupled phases and combinatorial selection in fluctuating hydrothermal pools.”
https://youtu.be/nk_R55O24t4?feature=shared
Summary: “Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution and selection in a dehydrated surface phase followed by encapsulation and combinatorial selection in a hydrated phase. This model is partly supported by recent science, and lies partly in the realm of speculation including a hypothesized pathway for the parallel evolution of the functional machinery of life. Complex models like this present challenges for science in the 21st century and we will describe a new technology to enable the simulation of such models.”
I say “excellent presentation” because it is a well-explained overview of a model these leading OoL researchers have collaborated extensively on. Commendably, their approach attempts to resolve the “water paradox” with cycles of hydration and dehydration, the salt problem using freshwater hydrothermal pools, it seeks a systems chemistry approach moving reactions away from equilibrium, and urges getting out of glasswear and into prebiotically plausible natural environments.
THIS I BELIEVE IS ONE OF THE MOST RECENT AND BEST HOLISTIC OOL MODELS ON OFFER, FROM LEADERS IN THE FIELD.
Some observations and comments.
* 3:51 Off the bat Damer asked the question, “Why does the community need a new model for the origin of life?”
He then answers in a way remarkably similar to criticisms by James Tour and William Bains.
* 6:51 “Freeman Dyson who I confer with what about once a year on this project, and he kind of gives us a thumbs up, in general had this idea that life began with little bags of garbage and these are lipid bags in solution the garbage is the dirty water that is the random chemical compound components, and that somehow this dirty water started to do metabolism and that it could replicate its contents and then the bags would grow and split in two, and if they split in two now quickly enough and reliably enough, you'd have life, but that's a you know it sounds a little kind of flippant, but in fact this is a very profound insight as to how life may have started…”
See: https://groups.google.com/g/talk.origins/c/Ki5fLxziHos/m/QeqGRxj2AQAJ
* 11:54 “so here we have a sort of putative environment for what we're talking about. You'll notice that there's sort of this slurry here that sort of represents the fact that perhaps this pool dried down many times and it's rehydrated many times and it turns out when this happens that things are deposited on the edge of the pool think of them like think of this like a bathtub ring in your bathtub…”
Displayed is a photo of pool with chemical deposits visible from changing water levels. Kudos for proposing a process and locating it in prebiotically plausible natural environment.
How/where from the supply of free lipids and nucleotides and/or amino acids?
Dilution of these monomers in the pool a problem, despite the drying-concentrating effect.
No mention of a mechanism for chirality necessity.
But an interesting and innovative scenario all the same. It does offer a stepwise pathway for pre-biotic evolution.
* 19:54 “I think there's two dozen volcanoes on Kamchatka; I think there's several hundred hydrothermal systems the size of Yellowstone on Kamchatka, it's just an enormous system so on the early Earth the hydrothermal field attached you know on a volcanic island would have been one of the most chemically rich and dynamic environments.”
Arguing against myself for a moment: it would be easy to under-appreciate that you get to roll the dice an incomprehensibly large number of times.
* 23:48 “let's look at here's our a primitive protocell on the way to life in our system that has as we mentioned before pores it has a membrane of course it has something that's stabilizing the membrane something like a primitive cytoskeleton it has the beginnings of a metabolic system it has the beginnings of replicator and in all of this it has to have some kind of emergent feedback mechanism that controls the rates of everything because as soon as you get a chemical reaction that goes around and generates products it can get out of control you need to have a regulatory mechanism that controls those rates…”
All that from recycled little bags of garbage. But I accept it’s a hypothesis ready for testing. Let the empirical verification begin.
* 27:29 “…when the proto cell is able to do the trick of dividing its contents dividing itself and creating daughter cells”
Usefully accurate and repeatable cell division that duplicates and separates the protocell’s polymers prior to pinching and splitting? Wow.
* 49:16 “with one of our instruments here's how we test the hypothesis. we're going to make an anaerobic condition we just chose carbon dioxide we could use others if we wished such as nitrogen for example but we cannot have oxygen there that these temperatures oxygen begins to attack the molecules we want to have an anaerobic environment…”
Credit for the experimental commitment. Let’s see what emerges.
https://youtu.be/nk_R55O24t4?feature=shared
Summary: “Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution and selection in a dehydrated surface phase followed by encapsulation and combinatorial selection in a hydrated phase. This model is partly supported by recent science, and lies partly in the realm of speculation including a hypothesized pathway for the parallel evolution of the functional machinery of life. Complex models like this present challenges for science in the 21st century and we will describe a new technology to enable the simulation of such models.”
I say “excellent presentation” because it is a well-explained overview of a model these leading OoL researchers have collaborated extensively on. Commendably, their approach attempts to resolve the “water paradox” with cycles of hydration and dehydration, the salt problem using freshwater hydrothermal pools, it seeks a systems chemistry approach moving reactions away from equilibrium, and urges getting out of glasswear and into prebiotically plausible natural environments.
THIS I BELIEVE IS ONE OF THE MOST RECENT AND BEST HOLISTIC OOL MODELS ON OFFER, FROM LEADERS IN THE FIELD.
Some observations and comments.
* 3:51 Off the bat Damer asked the question, “Why does the community need a new model for the origin of life?”
He then answers in a way remarkably similar to criticisms by James Tour and William Bains.
* 6:51 “Freeman Dyson who I confer with what about once a year on this project, and he kind of gives us a thumbs up, in general had this idea that life began with little bags of garbage and these are lipid bags in solution the garbage is the dirty water that is the random chemical compound components, and that somehow this dirty water started to do metabolism and that it could replicate its contents and then the bags would grow and split in two, and if they split in two now quickly enough and reliably enough, you'd have life, but that's a you know it sounds a little kind of flippant, but in fact this is a very profound insight as to how life may have started…”
See: https://groups.google.com/g/talk.origins/c/Ki5fLxziHos/m/QeqGRxj2AQAJ
* 11:54 “so here we have a sort of putative environment for what we're talking about. You'll notice that there's sort of this slurry here that sort of represents the fact that perhaps this pool dried down many times and it's rehydrated many times and it turns out when this happens that things are deposited on the edge of the pool think of them like think of this like a bathtub ring in your bathtub…”
Displayed is a photo of pool with chemical deposits visible from changing water levels. Kudos for proposing a process and locating it in prebiotically plausible natural environment.
How/where from the supply of free lipids and nucleotides and/or amino acids?
Dilution of these monomers in the pool a problem, despite the drying-concentrating effect.
No mention of a mechanism for chirality necessity.
But an interesting and innovative scenario all the same. It does offer a stepwise pathway for pre-biotic evolution.
* 19:54 “I think there's two dozen volcanoes on Kamchatka; I think there's several hundred hydrothermal systems the size of Yellowstone on Kamchatka, it's just an enormous system so on the early Earth the hydrothermal field attached you know on a volcanic island would have been one of the most chemically rich and dynamic environments.”
Arguing against myself for a moment: it would be easy to under-appreciate that you get to roll the dice an incomprehensibly large number of times.
* 23:48 “let's look at here's our a primitive protocell on the way to life in our system that has as we mentioned before pores it has a membrane of course it has something that's stabilizing the membrane something like a primitive cytoskeleton it has the beginnings of a metabolic system it has the beginnings of replicator and in all of this it has to have some kind of emergent feedback mechanism that controls the rates of everything because as soon as you get a chemical reaction that goes around and generates products it can get out of control you need to have a regulatory mechanism that controls those rates…”
All that from recycled little bags of garbage. But I accept it’s a hypothesis ready for testing. Let the empirical verification begin.
* 27:29 “…when the proto cell is able to do the trick of dividing its contents dividing itself and creating daughter cells”
Usefully accurate and repeatable cell division that duplicates and separates the protocell’s polymers prior to pinching and splitting? Wow.
* 49:16 “with one of our instruments here's how we test the hypothesis. we're going to make an anaerobic condition we just chose carbon dioxide we could use others if we wished such as nitrogen for example but we cannot have oxygen there that these temperatures oxygen begins to attack the molecules we want to have an anaerobic environment…”
Credit for the experimental commitment. Let’s see what emerges.
MarkE
Sep 26, 2023, 7:30:49 PM9/26/23
to talk-o...@moderators.isc.org
4:29 “[OoL research has] been mainly focused on individual solution chemistry experiments where they want to show polymerization over here, or they want to show metabolism over here, and Dave and I believe that it's time for the field to go from incremental progress to substantial progress. So, these are the four points we've come up with to make substantial progress in the origin of life, and the first one is to employ something called system chemistry, having sufficient complexity so instead of one experiment say about proteins, now you have an experiment about the encapsulation of proteins for example, and informational molecules built from nucleotides in an environment that would say be like an analog of the early Earth, build a complex experiment. Something we're calling sufficient complexity, and all of these experiments have to move the reactions away from equilibrium. And what do we mean by that? Well, in in your high school chemistry experiments, something starts foaming something changes color and then the experiment winds down and stops. Well, life didn't get started that way. Life got started by a continuous run-up of complexity and building upon in a sense nature as a ratchet. So we have to figure out how to build experiments that move will move away from equilibrium…”
6:31 “You can't sit in a laboratory just using glassware. You have to go to the field. You have to go to hot springs, you have to go to […] Iceland and come check and sit down and see what the natural environment is like, rather than being in the ethereal world of pure reactants and things like that…”
Gary Hurd
Sep 27, 2023, 10:45:50 PM9/27/23
to talk-o...@moderators.isc.org
MarkE
Sep 28, 2023, 12:50:50 AM9/28/23
to talk-o...@moderators.isc.org
peter2...@gmail.com
Dec 8, 2023, 6:42:03 PM12/8/23
to talk-o...@moderators.isc.org
I had starred this when it first appeared, then forgot about it so
completely that I didn't recognize it first.
MarkE was badgered by Bill Rogers to read Deamer and Damer's take
on OOL (Origin of Life), and by doing so, he has called Bill's bluff...
Oh, wait, he calls it an "excellent presentation", heedless of my warning that it is to be found,
AT BEST, below the 20th floor of the 100 floor metaphoric "OOL skyscraper" at the roof
of which is the first free-living prokaryote. The lipid bag puts it possibly that high. The
contents are somewhere on the way to the second floor.
On Tuesday, September 26, 2023 at 10:10:49 AM UTC-4, MarkE wrote:
> The title is “A new model for the origin of life: A new model for the origin of life: Coupled phases and combinatorial selection in fluctuating hydrothermal pools.”
Heck, this was old hat when I was a teen-ager half a century ago. Or maybe I am
recalling a "well, du-uh" speculation of mine that the way to OOL was
repeated drying/concentration of probiotic "soup" followed by dilution.
Fox had already succeeded in producing "microspheres" in one such cycle,
and it seemed natural to move on.
Little did I suspect back then how incredibly intricate the simplest bacteria are.
> https://youtu.be/nk_R55O24t4?feature=shared
>
> Summary: “Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution and selection in a dehydrated surface phase followed by encapsulation and combinatorial selection in a hydrated phase. This model is partly supported by recent science, and lies partly in the realm of speculation including a hypothesized pathway for the parallel evolution of the functional machinery of life.
Huge understatement, that "speculation."
>Complex models like this present challenges for science in the 21st century and we will describe a new technology to enable the simulation of such models.”
Sounds like a sentence out of a grant proposal which could get anything between a "poor" and "very good" rating,
depending almost totally on how the rest of the proposal goes. Proposals rated "excellent," at least in my
area of pure mathematics, make more modest statements.
On that basis, I rate Deamer and Damer's "proposal" as "fair," IF the rest is much better than what
MarkE quotes below.
Even so, one such rating is usually enough to kill a proposal. Even one "good" needs to be balanced
by at least one "excellent" to have a snowball's chance in the hell of these days of "grade inflation."
>
> I say “excellent presentation” because it is a well-explained overview of a model these leading OoL researchers have collaborated extensively on. Commendably, their approach attempts to resolve the “water paradox” with cycles of hydration and dehydration, the salt problem using freshwater hydrothermal pools, it seeks a systems chemistry approach moving reactions away from equilibrium, and urges getting out of glasswear and into prebiotically plausible natural environments.
So one might think if one believed that such environments still exist. But any products would be gobbled up
by the living things in the environment. One simply does not have the wherewithal for spontaneous generation of life
in the modern day environment. The best you can hope for is to substitute enormous tanks for "glassware", maybe
on the scale of the vast cyclotrons [or whatever] that seem to have successfully produced a Higgs boson.
>
> THIS I BELIEVE IS ONE OF THE MOST RECENT AND BEST HOLISTIC OOL MODELS ON OFFER, FROM LEADERS IN THE FIELD.
If that's true, so much the worse for less fine models, and for the others in the field of OOL.
> Some observations and comments.
>
> * 3:51 Off the bat Damer asked the question, “Why does the community need a new model for the origin of life?”
>
> He then answers in a way remarkably similar to criticisms by James Tour and William Bains.
>
> * 6:51 “Freeman Dyson who I confer with what about once a year on this project, and he kind of gives us a thumbs up, in general had this idea that life began with little bags of garbage and these are lipid bags in solution the garbage is the dirty water that is the random chemical compound components, and that somehow this dirty water started to do metabolism and that it could replicate its contents and then the bags would grow and split in two, and if they split in two now quickly enough and reliably enough, you'd have life, but that's a you know it sounds a little kind of flippant, but in fact this is a very profound insight as to how life may have started…”
Dream on, Deamer and Damer.
> See: https://groups.google.com/g/talk.origins/c/Ki5fLxziHos/m/QeqGRxj2AQAJ
>
> * 11:54 “so here we have a sort of putative environment for what we're talking about. You'll notice that there's sort of this slurry here that sort of represents the fact that perhaps this pool dried down many times and it's rehydrated many times and it turns out when this happens that things are deposited on the edge of the pool think of them like think of this like a bathtub ring in your bathtub…”
>
> Displayed is a photo of pool with chemical deposits visible from changing water levels. Kudos for proposing a process and locating it in prebiotically plausible natural environment.
> How/where from the supply of free lipids and nucleotides and/or amino acids?
> Dilution of these monomers in the pool a problem, despite the drying-concentrating effect.
> No mention of a mechanism for chirality necessity.
>
> But an interesting and innovative scenario all the same. It does offer a stepwise pathway for pre-biotic evolution.
MarkE is infatuated with a bunch of gobbledygook, tending towards a "poor" rating.
>
> * 19:54 “I think there's two dozen volcanoes on Kamchatka; I think there's several hundred hydrothermal systems the size of Yellowstone on Kamchatka, it's just an enormous system so on the early Earth the hydrothermal field attached you know on a volcanic island would have been one of the most chemically rich and dynamic environments.”
>
> Arguing against myself for a moment: it would be easy to under-appreciate that you get to roll the dice an incomprehensibly large number of times.
MarkE should make that arguing permanent.
>
> * 23:48 “let's look at here's our a primitive protocell on the way to life in our system that has as we mentioned before pores it has a membrane of course it has something that's stabilizing the membrane something like a primitive cytoskeleton it has the beginnings of a metabolic system it has the beginnings of replicator
WHAT REPLICATOR? Fox's protocells "replicated" but they are universally conceded to be a dead end.
"and in all of this it has to have some kind of emergent feedback mechanism that controls the rates of everything because as soon as you get a chemical reaction that goes around and generates products it can get out of control you need to have a regulatory mechanism that controls those rates…”
>
> All that from recycled little bags of garbage. But I accept it’s a hypothesis ready for testing. Let the empirical verification begin.
MarkE isn't even waiting for a regulatory mechanism. He's head over heels in love
with the scenario.
>
> * 27:29 “…when the proto cell is able to do the trick of dividing its contents dividing itself and creating daughter cells”
>
> Usefully accurate and repeatable cell division that duplicates and separates the protocell’s polymers prior to pinching and splitting? Wow.
It occurs to me that MarkE may be sarcastic here, and perhaps that goes back
to ALL his laudatory comments.
>
> * 49:16 “with one of our instruments here's how we test the hypothesis. we're going to make an anaerobic condition we just chose carbon dioxide we could use others if we wished such as nitrogen for example but we cannot have oxygen there that these temperatures oxygen begins to attack the molecules we want to have an anaerobic environment…”
>
> Credit for the experimental commitment. Let’s see what emerges.
Prediction: nothing but glorified tar.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
https://people.math.sc.edu/nyikos
completely that I didn't recognize it first.
MarkE was badgered by Bill Rogers to read Deamer and Damer's take
on OOL (Origin of Life), and by doing so, he has called Bill's bluff...
Oh, wait, he calls it an "excellent presentation", heedless of my warning that it is to be found,
AT BEST, below the 20th floor of the 100 floor metaphoric "OOL skyscraper" at the roof
of which is the first free-living prokaryote. The lipid bag puts it possibly that high. The
contents are somewhere on the way to the second floor.
On Tuesday, September 26, 2023 at 10:10:49 AM UTC-4, MarkE wrote:
> The title is “A new model for the origin of life: A new model for the origin of life: Coupled phases and combinatorial selection in fluctuating hydrothermal pools.”
recalling a "well, du-uh" speculation of mine that the way to OOL was
repeated drying/concentration of probiotic "soup" followed by dilution.
Fox had already succeeded in producing "microspheres" in one such cycle,
and it seemed natural to move on.
Little did I suspect back then how incredibly intricate the simplest bacteria are.
> https://youtu.be/nk_R55O24t4?feature=shared
>
> Summary: “Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution and selection in a dehydrated surface phase followed by encapsulation and combinatorial selection in a hydrated phase. This model is partly supported by recent science, and lies partly in the realm of speculation including a hypothesized pathway for the parallel evolution of the functional machinery of life.
>Complex models like this present challenges for science in the 21st century and we will describe a new technology to enable the simulation of such models.”
depending almost totally on how the rest of the proposal goes. Proposals rated "excellent," at least in my
area of pure mathematics, make more modest statements.
On that basis, I rate Deamer and Damer's "proposal" as "fair," IF the rest is much better than what
MarkE quotes below.
Even so, one such rating is usually enough to kill a proposal. Even one "good" needs to be balanced
by at least one "excellent" to have a snowball's chance in the hell of these days of "grade inflation."
>
> I say “excellent presentation” because it is a well-explained overview of a model these leading OoL researchers have collaborated extensively on. Commendably, their approach attempts to resolve the “water paradox” with cycles of hydration and dehydration, the salt problem using freshwater hydrothermal pools, it seeks a systems chemistry approach moving reactions away from equilibrium, and urges getting out of glasswear and into prebiotically plausible natural environments.
by the living things in the environment. One simply does not have the wherewithal for spontaneous generation of life
in the modern day environment. The best you can hope for is to substitute enormous tanks for "glassware", maybe
on the scale of the vast cyclotrons [or whatever] that seem to have successfully produced a Higgs boson.
>
> THIS I BELIEVE IS ONE OF THE MOST RECENT AND BEST HOLISTIC OOL MODELS ON OFFER, FROM LEADERS IN THE FIELD.
> Some observations and comments.
>
> * 3:51 Off the bat Damer asked the question, “Why does the community need a new model for the origin of life?”
>
> He then answers in a way remarkably similar to criticisms by James Tour and William Bains.
>
> * 6:51 “Freeman Dyson who I confer with what about once a year on this project, and he kind of gives us a thumbs up, in general had this idea that life began with little bags of garbage and these are lipid bags in solution the garbage is the dirty water that is the random chemical compound components, and that somehow this dirty water started to do metabolism and that it could replicate its contents and then the bags would grow and split in two, and if they split in two now quickly enough and reliably enough, you'd have life, but that's a you know it sounds a little kind of flippant, but in fact this is a very profound insight as to how life may have started…”
> See: https://groups.google.com/g/talk.origins/c/Ki5fLxziHos/m/QeqGRxj2AQAJ
>
> * 11:54 “so here we have a sort of putative environment for what we're talking about. You'll notice that there's sort of this slurry here that sort of represents the fact that perhaps this pool dried down many times and it's rehydrated many times and it turns out when this happens that things are deposited on the edge of the pool think of them like think of this like a bathtub ring in your bathtub…”
>
> Displayed is a photo of pool with chemical deposits visible from changing water levels. Kudos for proposing a process and locating it in prebiotically plausible natural environment.
> How/where from the supply of free lipids and nucleotides and/or amino acids?
> Dilution of these monomers in the pool a problem, despite the drying-concentrating effect.
> No mention of a mechanism for chirality necessity.
>
> But an interesting and innovative scenario all the same. It does offer a stepwise pathway for pre-biotic evolution.
>
> * 19:54 “I think there's two dozen volcanoes on Kamchatka; I think there's several hundred hydrothermal systems the size of Yellowstone on Kamchatka, it's just an enormous system so on the early Earth the hydrothermal field attached you know on a volcanic island would have been one of the most chemically rich and dynamic environments.”
>
> Arguing against myself for a moment: it would be easy to under-appreciate that you get to roll the dice an incomprehensibly large number of times.
>
> * 23:48 “let's look at here's our a primitive protocell on the way to life in our system that has as we mentioned before pores it has a membrane of course it has something that's stabilizing the membrane something like a primitive cytoskeleton it has the beginnings of a metabolic system it has the beginnings of replicator
"and in all of this it has to have some kind of emergent feedback mechanism that controls the rates of everything because as soon as you get a chemical reaction that goes around and generates products it can get out of control you need to have a regulatory mechanism that controls those rates…”
>
> All that from recycled little bags of garbage. But I accept it’s a hypothesis ready for testing. Let the empirical verification begin.
with the scenario.
>
> * 27:29 “…when the proto cell is able to do the trick of dividing its contents dividing itself and creating daughter cells”
>
> Usefully accurate and repeatable cell division that duplicates and separates the protocell’s polymers prior to pinching and splitting? Wow.
to ALL his laudatory comments.
>
> * 49:16 “with one of our instruments here's how we test the hypothesis. we're going to make an anaerobic condition we just chose carbon dioxide we could use others if we wished such as nitrogen for example but we cannot have oxygen there that these temperatures oxygen begins to attack the molecules we want to have an anaerobic environment…”
>
> Credit for the experimental commitment. Let’s see what emerges.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
https://people.math.sc.edu/nyikos
erik simpson
Dec 8, 2023, 7:17:03 PM12/8/23
to talk-o...@moderators.isc.org
more comprehensive treatment of this subject (with references) than a Youtube presentation.
You have a history of belittling progress in this field, but many researchers aren't dismayed.
The "100 story building" is a fairy castle.
peter2...@gmail.com
Dec 8, 2023, 9:37:03 PM12/8/23
to talk-o...@moderators.isc.org
> The Wikipedia entry on abiogenisis https://en.wikipedia.org/wiki/Abiogenesis is a much
> more comprehensive treatment of this subject (with references) than a Youtube presentation.
Detailed, sure. But if it is "comprehensive," then that is a dramatic sign that we are
> more comprehensive treatment of this subject (with references) than a Youtube presentation.
no further along than what I've been saying for years.
BTW, the level of exposition, when combined with Deamer and Damer's breathless prose, rises to "fair"
as far as grant proposals are concerned. See comments about that in the text preserved above.
> You have a history of belittling progress in this field, but many researchers aren't dismayed.
ridiculous claims of "first lab-produced cell in the next decade" which should be a huge embarrassment
to the researchers who claimed it independently of each other and at widely varied times.
James Tour put these people in their place between 34 minutes and 55 minutes of the following video:
"Dr. Lee Cronin & Dr. James Tour on Science and the Origin of Life, Cambridge Faculty Roundtable"
https://www.youtube.com/watch?v=6GDv4f2zUus
It's over 3 hours long, and even if one skips the preliminaries prior to the introduction, it's about two
and three quarter hours long.
> The "100 story building" is a fairy castle.
and you are indulging in evasive polemic to avoid seriously thinking about it.
Just look at your performance on the thread, "Re: JAMES TOUR VICTORIOUS?!"
One ad hominem after another, with no documentation whatsoever to support it.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
http://people.math.sc.edu/nyikos
MarkE
Dec 8, 2023, 11:37:03 PM12/8/23
to talk-o...@moderators.isc.org
On Saturday, December 9, 2023 at 10:42:03 AM UTC+11, peter2...@gmail.com wrote:
> I had starred this when it first appeared, then forgot about it so
> completely that I didn't recognize it first.
>
> MarkE was badgered by Bill Rogers to read Deamer and Damer's take
> on OOL (Origin of Life), and by doing so, he has called Bill's bluff...
>
> Oh, wait, he calls it an "excellent presentation", heedless of my warning that it is to be found,
> AT BEST, below the 20th floor of the 100 floor metaphoric "OOL skyscraper" at the roof
> of which is the first free-living prokaryote. The lipid bag puts it possibly that high. The
> contents are somewhere on the way to the second floor.
My characterisation as "excellent" is not sarcastic inasmuch as I applaud them for them bluntly calling out their own field:
> I had starred this when it first appeared, then forgot about it so
> completely that I didn't recognize it first.
>
> MarkE was badgered by Bill Rogers to read Deamer and Damer's take
> on OOL (Origin of Life), and by doing so, he has called Bill's bluff...
>
> Oh, wait, he calls it an "excellent presentation", heedless of my warning that it is to be found,
> AT BEST, below the 20th floor of the 100 floor metaphoric "OOL skyscraper" at the roof
> of which is the first free-living prokaryote. The lipid bag puts it possibly that high. The
> contents are somewhere on the way to the second floor.
“[OoL research has] been mainly focused on individual solution chemistry experiments where they want to show polymerization over here, or they want to show metabolism over here, and Dave and I believe that it's time for the field to go from incremental progress to substantial progress. So, these are the four points we've come up with to make substantial progress in the origin of life, and the first one is to employ something called system chemistry, having sufficient complexity so instead of one experiment say about proteins, now you have an experiment about the encapsulation of proteins for example, and informational molecules built from nucleotides in an environment that would say be like an analog of the early Earth, build a complex experiment. Something we're calling sufficient complexity, and all of these experiments have to move the reactions away from equilibrium. And what do we mean by that? Well, in in your high school chemistry experiments, something starts foaming something changes color and then the experiment winds down and stops. Well, life didn't get started that way. Life got started by a continuous run-up of complexity and building upon in a sense nature as a ratchet. So we have to figure out how to build experiments that move will move away from equilibrium…You can't sit in a laboratory just using glassware. You have to go to the field. You have to go to hot springs, you have to go to […] Iceland and come check and sit down and see what the natural environment is like, rather than being in the ethereal world of pure reactants and things like that…”
Far from being "head over heels in love with the scenario", read this as my recognition of their unintended tying a noose around the current OoL program.
“...with one of our instruments here's how we test the hypothesis. we're going to make an anaerobic condition we just chose carbon dioxide we could use others if we wished such as nitrogen for example but we cannot have oxygen there that these temperatures oxygen begins to attack the molecules we want to have an anaerobic environment…”
My affirming response of "Credit for the experimental commitment. Let’s see what emerges" is genuine in that I appreciate their willingness for experimental accountability. But I concur with you on this at least: "Prediction: nothing but glorified tar."
erik simpson
Dec 9, 2023, 11:47:04 AM12/9/23
to talk-o...@moderators.isc.org
but I'm used to your style of argument. Tour himself provides sufficient documentation, which you reject
as either "ad hominim" or "cherry picking". The cherries are low-handing fruit in his expression of "child-like faith"
(your terminology, probably unintentionally insulting) .
erik simpson
Dec 9, 2023, 6:02:04 PM12/9/23
to talk-o...@moderators.isc.org
argument "James Tour Victorious?" on the the same subject. James Tour and his admirers
(are you one of them?) are of no interest, and I regret having involved myself in this exercise.
peter2...@gmail.com
Dec 12, 2023, 6:07:07 PM12/12/23
to talk-o...@moderators.isc.org
It's good to see that you are still paying attention to what goes on in some of the
threads you started, Mark. Unfortunately, I have had very little time for posting
in the last two months, and this month promises to be similar.
By the time I send in the letter grades for the students in my classes, a family reunion will
begin that lasts until after Christmas, and I do not want to overthrow the perfect record that I have set:
one of taking a break from Usenet for at least three weeks in the holiday season and a bit beyond.
I hope you will still be around when I return early in January.
[In 2021, I stretched it to almost six months,but that won't happen this time.]
But I will still be very sparse with my posts until the second week in February.
On Friday, December 8, 2023 at 11:37:03 PM UTC-5, MarkE wrote:
> On Saturday, December 9, 2023 at 10:42:03 AM UTC+11, peter2...@gmail.com wrote:
> > I had starred this when it first appeared, then forgot about it so
> > completely that I didn't recognize it first.
> >
> > MarkE was badgered by Bill Rogers to read Deamer and Damer's take
> > on OOL (Origin of Life), and by doing so, he has called Bill's bluff...
> >
> > Oh, wait, he calls it an "excellent presentation", heedless of my warning that it is to be found,
> > AT BEST, below the 20th floor of the 100 floor metaphoric "OOL skyscraper" at the roof
> > of which is the first free-living prokaryote. The lipid bag puts it possibly that high. The
> > contents are somewhere on the way to the second floor.
> My characterisation as "excellent" is not sarcastic inasmuch as I applaud them for them bluntly calling out their own field:
Are they correct, though? Their proposal seems to be such a no-brainer
that it's hard to believe there aren't researchers doing it.
The only reason I can think of is that the outside funding for grants
puts a premium on not "diluting" experiments by aiming for more than
one very specific goal.
The wisest professor I ever had once told me: "Things will get worse before
they get better, because we have sold ourselves to the devil of external funding."
> “[OoL research has] been mainly focused on individual solution chemistry experiments where they want to show polymerization over here, or they want to show metabolism over here, and Dave and I believe that it's time for the field to go from incremental progress to substantial progress. So, these are the four points we've come up with to make substantial progress in the origin of life, and the first one is to employ something called system chemistry, having sufficient complexity so instead of one experiment say about proteins, now you have an experiment about the encapsulation of proteins for example, and informational molecules built from nucleotides in an environment that would say be like an analog of the early Earth, build a complex experiment.
One of the articles in the Talk.Origins Archive talks about an "ur-cell" which is minuscule compared
to the smallest bacterium, yet has cell membrane, a strand of nucleotides for self-replication, and protein.
The trouble is, the reproduction of such things is so slow without enzymes, that it cannot
be part of an avenue to life as we know it in a mere 200 million years.
>"Something we're calling sufficient complexity, and all of these experiments have to move the reactions away from equilibrium. And what do we mean by that? Well, in in your high school chemistry experiments, something starts foaming something changes color and then the experiment winds down and stops. Well, life didn't get started that way. Life got started by a continuous run-up of complexity and building upon in a sense nature as a ratchet. So we have to figure out how to build experiments that move will move away from equilibrium…You can't sit in a laboratory just using glassware. You have to go to the field. You have to go to hot springs, you have to go to […] Iceland and come check and sit down and see what the natural environment is like, rather than being in the ethereal world of pure reactants and things like that…”
>
> Far from being "head over heels in love with the scenario", read this as my recognition of their unintended tying a noose around the current OoL program.
IMO, they are just moving to a slightly bigger noose.
> “...with one of our instruments here's how we test the hypothesis. we're going to make an anaerobic condition we just chose carbon dioxide we could use others if we wished such as nitrogen for example but we cannot have oxygen there that these temperatures oxygen begins to attack the molecules we want to have an anaerobic environment…”
>
> My affirming response of "Credit for the experimental commitment. Let’s see what emerges" is genuine in that I appreciate their willingness for experimental accountability. But I concur with you on this at least: "Prediction: nothing but glorified tar."
Thanks for clarifying what you originally wrote. I should have read more carefully between the lines.
I point out below what I'm referring to here.
I now see that the following is meant to be criticism:
> > > How/where from the supply of free lipids and nucleotides and/or amino acids?
> > > Dilution of these monomers in the pool a problem, despite the drying-concentrating effect.
> > > No mention of a mechanism for chirality necessity.
> > >
> > > But an interesting and innovative scenario all the same. It does offer a stepwise pathway for pre-biotic evolution.
One destined to remain pre-biotic unless your questions are answered.
Hence I withdraw the following comment:
> > MarkE is infatuated with a bunch of gobbledygook, tending towards a "poor" rating.
> > >
> > > * 19:54 “I think there's two dozen volcanoes on Kamchatka; I think there's several hundred hydrothermal systems the size of Yellowstone on Kamchatka, it's just an enormous system so on the early Earth the hydrothermal field attached you know on a volcanic island would have been one of the most chemically rich and dynamic environments.”
> > >
> > > Arguing against myself for a moment: it would be easy to under-appreciate that you get to roll the dice an incomprehensibly large number of times.
> > MarkE should make that arguing permanent.
And it looks like you will, unless Bill Rogers gets up the courage to say that you really should
read *everything* Deamer and Damer have published.
> > >
> > > * 23:48 “let's look at here's our a primitive protocell on the way to life in our system that has as we mentioned before pores it has a membrane of course it has something that's stabilizing the membrane something like a primitive cytoskeleton it has the beginnings of a metabolic system it has the beginnings of replicator
> > WHAT REPLICATOR? Fox's protocells "replicated" but they are universally conceded to be a dead end.
> > "and in all of this it has to have some kind of emergent feedback mechanism that controls the rates of everything because as soon as you get a chemical reaction that goes around and generates products it can get out of control you need to have a regulatory mechanism that controls those rates…”
> > >
> > > All that from recycled little bags of garbage. But I accept it’s a hypothesis ready for testing. Let the empirical verification begin.
I also withdraw the following comment:
> > MarkE isn't even waiting for a regulatory mechanism. He's head over heels in love
> > with the scenario.
> > >
> > > * 27:29 “…when the proto cell is able to do the trick of dividing its contents dividing itself and creating daughter cells”
> > >
> > > Usefully accurate and repeatable cell division that duplicates and separates the protocell’s polymers prior to pinching and splitting? Wow.
What you are talking about here is clearly on their "wish list,"
and I believe it will remain there for decades.
> > > * 49:16 “with one of our instruments here's how we test the hypothesis. we're going to make an anaerobic condition we just chose carbon dioxide we could use others if we wished such as nitrogen for example but we cannot have oxygen there that these temperatures oxygen begins to attack the molecules we want to have an anaerobic environment…”
"Anaerobic" is very well known to be necessary to have any chance of succeeding.
> > >
> > > Credit for the experimental commitment. Let’s see what emerges.
> > Prediction: nothing but glorified tar.
Erik Simpson had nothing intelligent to say about all anything you or I
have said on this thread.. His is a perfect case of "sour grapes" and off-topic innuendo.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
threads you started, Mark. Unfortunately, I have had very little time for posting
in the last two months, and this month promises to be similar.
By the time I send in the letter grades for the students in my classes, a family reunion will
begin that lasts until after Christmas, and I do not want to overthrow the perfect record that I have set:
one of taking a break from Usenet for at least three weeks in the holiday season and a bit beyond.
I hope you will still be around when I return early in January.
[In 2021, I stretched it to almost six months,but that won't happen this time.]
But I will still be very sparse with my posts until the second week in February.
On Friday, December 8, 2023 at 11:37:03 PM UTC-5, MarkE wrote:
> On Saturday, December 9, 2023 at 10:42:03 AM UTC+11, peter2...@gmail.com wrote:
> > I had starred this when it first appeared, then forgot about it so
> > completely that I didn't recognize it first.
> >
> > MarkE was badgered by Bill Rogers to read Deamer and Damer's take
> > on OOL (Origin of Life), and by doing so, he has called Bill's bluff...
> >
> > Oh, wait, he calls it an "excellent presentation", heedless of my warning that it is to be found,
> > AT BEST, below the 20th floor of the 100 floor metaphoric "OOL skyscraper" at the roof
> > of which is the first free-living prokaryote. The lipid bag puts it possibly that high. The
> > contents are somewhere on the way to the second floor.
> My characterisation as "excellent" is not sarcastic inasmuch as I applaud them for them bluntly calling out their own field:
that it's hard to believe there aren't researchers doing it.
The only reason I can think of is that the outside funding for grants
puts a premium on not "diluting" experiments by aiming for more than
one very specific goal.
The wisest professor I ever had once told me: "Things will get worse before
they get better, because we have sold ourselves to the devil of external funding."
> “[OoL research has] been mainly focused on individual solution chemistry experiments where they want to show polymerization over here, or they want to show metabolism over here, and Dave and I believe that it's time for the field to go from incremental progress to substantial progress. So, these are the four points we've come up with to make substantial progress in the origin of life, and the first one is to employ something called system chemistry, having sufficient complexity so instead of one experiment say about proteins, now you have an experiment about the encapsulation of proteins for example, and informational molecules built from nucleotides in an environment that would say be like an analog of the early Earth, build a complex experiment.
to the smallest bacterium, yet has cell membrane, a strand of nucleotides for self-replication, and protein.
The trouble is, the reproduction of such things is so slow without enzymes, that it cannot
be part of an avenue to life as we know it in a mere 200 million years.
>"Something we're calling sufficient complexity, and all of these experiments have to move the reactions away from equilibrium. And what do we mean by that? Well, in in your high school chemistry experiments, something starts foaming something changes color and then the experiment winds down and stops. Well, life didn't get started that way. Life got started by a continuous run-up of complexity and building upon in a sense nature as a ratchet. So we have to figure out how to build experiments that move will move away from equilibrium…You can't sit in a laboratory just using glassware. You have to go to the field. You have to go to hot springs, you have to go to […] Iceland and come check and sit down and see what the natural environment is like, rather than being in the ethereal world of pure reactants and things like that…”
>
> Far from being "head over heels in love with the scenario", read this as my recognition of their unintended tying a noose around the current OoL program.
> “...with one of our instruments here's how we test the hypothesis. we're going to make an anaerobic condition we just chose carbon dioxide we could use others if we wished such as nitrogen for example but we cannot have oxygen there that these temperatures oxygen begins to attack the molecules we want to have an anaerobic environment…”
>
> My affirming response of "Credit for the experimental commitment. Let’s see what emerges" is genuine in that I appreciate their willingness for experimental accountability. But I concur with you on this at least: "Prediction: nothing but glorified tar."
I point out below what I'm referring to here.
> > > How/where from the supply of free lipids and nucleotides and/or amino acids?
> > > Dilution of these monomers in the pool a problem, despite the drying-concentrating effect.
> > > No mention of a mechanism for chirality necessity.
> > >
> > > But an interesting and innovative scenario all the same. It does offer a stepwise pathway for pre-biotic evolution.
Hence I withdraw the following comment:
> > MarkE is infatuated with a bunch of gobbledygook, tending towards a "poor" rating.
> > >
> > > * 19:54 “I think there's two dozen volcanoes on Kamchatka; I think there's several hundred hydrothermal systems the size of Yellowstone on Kamchatka, it's just an enormous system so on the early Earth the hydrothermal field attached you know on a volcanic island would have been one of the most chemically rich and dynamic environments.”
> > >
> > > Arguing against myself for a moment: it would be easy to under-appreciate that you get to roll the dice an incomprehensibly large number of times.
> > MarkE should make that arguing permanent.
read *everything* Deamer and Damer have published.
> > >
> > > * 23:48 “let's look at here's our a primitive protocell on the way to life in our system that has as we mentioned before pores it has a membrane of course it has something that's stabilizing the membrane something like a primitive cytoskeleton it has the beginnings of a metabolic system it has the beginnings of replicator
> > WHAT REPLICATOR? Fox's protocells "replicated" but they are universally conceded to be a dead end.
> > "and in all of this it has to have some kind of emergent feedback mechanism that controls the rates of everything because as soon as you get a chemical reaction that goes around and generates products it can get out of control you need to have a regulatory mechanism that controls those rates…”
> > >
> > > All that from recycled little bags of garbage. But I accept it’s a hypothesis ready for testing. Let the empirical verification begin.
> > MarkE isn't even waiting for a regulatory mechanism. He's head over heels in love
> > with the scenario.
> > >
> > > * 27:29 “…when the proto cell is able to do the trick of dividing its contents dividing itself and creating daughter cells”
> > >
> > > Usefully accurate and repeatable cell division that duplicates and separates the protocell’s polymers prior to pinching and splitting? Wow.
and I believe it will remain there for decades.
> > > * 49:16 “with one of our instruments here's how we test the hypothesis. we're going to make an anaerobic condition we just chose carbon dioxide we could use others if we wished such as nitrogen for example but we cannot have oxygen there that these temperatures oxygen begins to attack the molecules we want to have an anaerobic environment…”
> > >
> > > Credit for the experimental commitment. Let’s see what emerges.
> > Prediction: nothing but glorified tar.
have said on this thread.. His is a perfect case of "sour grapes" and off-topic innuendo.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
MarkE
Dec 16, 2023, 8:37:10 AM12/16/23
to talk-o...@moderators.isc.org
S - stabilizing factors for membrane integrity
P - pore forming for controlled nutrient and waste transfer
M - metabolism, capable of catalyzing growth
F - controlled by feedback networks
R - self-replication
"This system triggers a polymer mechanism D that can duplicate minimally viable sets of these polymers and deliver them by division into daughter cells. If these daughter cells contain fully functional polymer systems and are able to grow and divide again, they form the first lines of living cells."
If the average polymer length is say 100 units, that is 500 units assembled _before_ Darwinian evolution starts. That seems like a real problem.
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