Theory of the Origin of Life on Earth

[A.T. Murray]

In Stage One, Mentifex and others suggest that biological life started from a two-dimensional film of amino acids in a tidal pool. With evaporation and concentration, myriad combinations of not-yet-living molecules could flap around and form complex structures akin to rudimentary living cells. If one structure replicates itself by bonding endlessly with similar or identical structures but is not yet living, the stage is set for lightning to strike the primordial soup and break off molecular clusters that float about freely and attract replicator material in such a way that each cluster elongates itself to a certain point and then breaks apart into "offspring" clusters in what we might call Stage Two of evolution.

In Stage Two the amino clusters are not yet replicating genetically. They are simply growing longitudinally to a point where they break apart but continue replicating.

In Stage Three, a strip on the elongated surface bonds with amniotic chemicals which toggle under sunlight between two pulsing states which cause locomotion of the parent clusters and therefore also of the child clusters.

In Stage Four, moving clusters which chance to become longitudinally hollow replicate faster than the merely solid clusters, and soon the hollow beasties, still self-replicating by splitting apart, consume all the resources in each tidal pool.

In Stage Five, some of the locomotive hollow clusters mutate at the forward-moving end into a primordial mouth structure and at each "caboose" end by default into a primordial anus structure. As the little beasties move about in the tidal pool, the mouth orifice swallows quasi-nutrients that make the longitudinal cluster not only grow fatter but also replicate as fatter beasties when they break apart. Thus we see larger and larger beasties filling the tidal pool.

In Stage Six, a filament of non-identical amino acids -- some combination of adenine, thymine, guanine and cytosine -- chances to form longitudinally in each beastie in such a way that the breaking of the chain causes two different kinds of child beasties to result from each successive splitting, since the rupture will not always occur between the same two amino acids, and each terminal amino acid will bond differently with nearby molecules, causing diversity to evolve among the child beasties. The same genetic chain of amino acids remains in each child beastie, but a kind of molecular counter stipulates that different kinds of beasties will result after a certain number of splittings apart and only a maximum number of splittings will be permitted as governed by the primordial equivalent of telomeres.

In Stage Seven, different kinds of child beasties will adhere or tend to stick together in a conglomerate or globule of beasties which all contain the same genetic filament of amino acids, but which form a globule or primordial organism that survives and replicates only if the constituent child-cells cooperate beneficially for the survival of the fittest organisms.

https://www.mail-archive.com/a...@agi.topicbox.com/msg08662.html -- archive.
http://cyborg.blogspot.com/2022/02/origin-of-life.html

[Bob Casanova]

On Fri, 11 Feb 2022 21:30:48 -0800 (PST), the following
appeared in talk.origins, posted by "A.T. Murray"
<menti...@gmail.com>:

Ummm...OK. Since both your cites say exactly the same thing,
and since the author ("Mentifex"?) is apparently an "AI
coder" and not a biologist, perhaps you'd care to give your
take on it?
>
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[A.T. Murray]

Yesterday Mentifex here was trying to write "Mentifex and the Parallel Civilization of Intelligent Robots," about how the creation of true AI initiates a new civilization alongside our own human civilization. It seemed like a good idea to go back to the very origins of life on earth as a forward to http://ai.neocities.org/AiEvolution.html or the current situation.

https://freesoftwarefoundation.org/read/prog/1644530906 -- is the same message as above, posted on a rather disreputable website, but one which strives to avoid all censorship of odd ideas. "Mentifex" (mindmaker) here is trying to be a self-appointed "Prog" columnist on that site.

Yesterday, imagining a primordial soup of amino acids led to a frenzied working-out of successive stages in how life could originate. Although yours truly Mentifex is not a biologist, we are talking about a barren Earth devoid of all biology.

In the New York Times we read now and then about efforts to assemble the right "soup" and then to "spark" the origin of life.

The above post is simply some ideas for the professional biologists to react to -- especially Stage Six on the possible origin of DNA and the genetic code.

Thank you for reading, and thanks especially to the Moderator for allowing the strange ideas.

Arthur T. Murray (Mentifex)

[Zen Cycle]

oy vey....

[broger...@gmail.com]

On Saturday, February 12, 2022 at 12:35:41 AM UTC-5, menti...@gmail.com wrote:
<snip>
>
> In Stage Three, a strip on the elongated surface bonds with amniotic chemicals .......
"amniotic chemicals"???
>
<snip>
> In Stage Six, a filament of non-identical amino acids -- some combination of adenine, thymine, guanine and cytosine -- ........ same genetic filament of amino acids, <snip>

given him time and he'll fix the Standard Model of physics, too.

[jillery]

Don't worry about the moderators. He and it are very tolerant of
strange ideas. But you might have some problems with a few posters.

--
You're entitled to your own opinions.
You're not entitled to your own facts.

[Bob Casanova]

On Fri, 11 Feb 2022 22:38:15 -0800 (PST), the following

appeared in talk.origins, posted by "A.T. Murray"
<menti...@gmail.com>:

>On Friday, February 11, 2022 at 10:10:40 PM UTC-8, Bob Casanova wrote:
>> On Fri, 11 Feb 2022 21:30:48 -0800 (PST), the following
>> appeared in talk.origins, posted by "A.T. Murray"
>> <menti...@gmail.com>:
>> >In Stage One, Mentifex and others suggest that biological life started from a two-dimensional film of amino acids in a tidal pool. With evaporation and concentration, myriad combinations of not-yet-living molecules could flap around and form complex structures akin to rudimentary living cells. If one structure replicates itself by bonding endlessly with similar or identical structures but is not yet living, the stage is set for lightning to strike the primordial soup and break off molecular clusters that float about freely and attract replicator material in such a way that each cluster elongates itself to a certain point and then breaks apart into "offspring" clusters in what we might call Stage Two of evolution.
>> >
>> >In Stage Two the amino clusters are not yet replicating genetically. They are simply growing longitudinally to a point where they break apart but continue replicating.
>> >
>> >In Stage Three, a strip on the elongated surface bonds with amniotic chemicals which toggle under sunlight between two pulsing states which cause locomotion of the parent clusters and therefore also of the child clusters.
>> >
>> >In Stage Four, moving clusters which chance to become longitudinally hollow replicate faster than the merely solid clusters, and soon the hollow beasties, still self-replicating by splitting apart, consume all the resources in each tidal pool.
>> >
>> >In Stage Five, some of the locomotive hollow clusters mutate at the forward-moving end into a primordial mouth structure and at each "caboose" end by default into a primordial anus structure. As the little beasties move about in the tidal pool, the mouth orifice swallows quasi-nutrients that make the longitudinal cluster not only grow fatter but also replicate as fatter beasties when they break apart. Thus we see larger and larger beasties filling the tidal pool.
>> >
>> >In Stage Six, a filament of non-identical amino acids -- some combination of adenine, thymine, guanine and cytosine -- chances to form longitudinally in each beastie in such a way that the breaking of the chain causes two different kinds of child beasties to result from each successive splitting, since the rupture will not always occur between the same two amino acids, and each terminal amino acid will bond differently with nearby molecules, causing diversity to evolve among the child beasties. The same genetic chain of amino acids remains in each child beastie, but a kind of molecular counter stipulates that different kinds of beasties will result after a certain number of splittings apart and only a maximum number of splittings will be permitted as governed by the primordial equivalent of telomeres.
>> >
>> >In Stage Seven, different kinds of child beasties will adhere or tend to stick together in a conglomerate or globule of beasties which all contain the same genetic filament of amino acids, but which form a globule or primordial organism that survives and replicates only if the constituent child-cells cooperate beneficially for the survival of the fittest organisms.
>> >
>> >https://www.mail-archive.com/a...@agi.topicbox.com/msg08662.html -- archive.
>> >http://cyborg.blogspot.com/2022/02/origin-of-life.html
>> >
>> Ummm...OK. Since both your cites say exactly the same thing,
>> and since the author ("Mentifex"?) is apparently an "AI
>> coder" and not a biologist, perhaps you'd care to give your
>> take on it?
>> >

>Yesterday Mentifex here was trying to write "Mentifex and the Parallel Civilization of Intelligent Robots," about how the creation of true AI initiates a new civilization alongside our own human civilization. It seemed like a good idea to go back to the very origins of life on earth as a forward to http://ai.neocities.org/AiEvolution.html or the current situation.
>
>https://freesoftwarefoundation.org/read/prog/1644530906 -- is the same message as above, posted on a rather disreputable website, but one which strives to avoid all censorship of odd ideas. "Mentifex" (mindmaker) here is trying to be a self-appointed "Prog" columnist on that site.
>
>Yesterday, imagining a primordial soup of amino acids led to a frenzied working-out of successive stages in how life could originate. Although yours truly Mentifex is not a biologist, we are talking about a barren Earth devoid of all biology.
>
>In the New York Times we read now and then about efforts to assemble the right "soup" and then to "spark" the origin of life.
>
>The above post is simply some ideas for the professional biologists to react to -- especially Stage Six on the possible origin of DNA and the genetic code.
>
>Thank you for reading, and thanks especially to the Moderator for allowing the strange ideas.
>

Asked and answered; thanks. I'd point out a couple of
things...

The fact that the Earth was barren of life at the time life
started (sort of obvious), the formation of life involved
the beginnings of biological processes, not computer
programs and algorithms, and thus is in the realm of
biology, not comp sci. And although there may be analogies,
analogies prove nothing, and can bite you on the butt if you
rely on them absent actual evidence. And NYT articles are
not evidence, either. I suspect there will be a few
professional biologists who will have better and more
detailed responses (I'm a retired EE, not a biologist or an
actual scientist of any sort).

And the moderator basically allows anything from anyone not
a proven abusive troll (and yes, there have been a few); the
"moderation" consists of a filter which rejects any post
with more than 4 groups in the distro, along with a set of
*specific* individuals, some banned for excessive
nymshifting to avoid killfiles.

[Ernest Major]

It's rather confused, bordering on "not even wrong". The confusion
between nucleobases (moieties of DNA monomers) and amino acids (used to
construct proteins) stands out, and doesn't inspire confidence, but
perhaps that is a minor problem that could be charitably ascribed to a
brainfart. (And I assume that "amniotic" is meant to be "abiotic".)

It's also rather zoocentric - the life it describes originating has a
lot of the characteristics of animals, which are a small part of life on
earth, and relatively late arrivals on the scene. (Life has been around
for 3 or some billion years; animals evolved less than a billion years ago.)

When we refer to the origin of life we are thinking of the origin of
something like a simplified bacterium. The urorganism would have a cell
membrane, a genetic system, a metabolism, a means of absorbing nutrients
from the environment, and a method of cell division - we're looking for
a way to get to that, not for an explanation of locomotion,
multicellularity, or a through gut.

--
alias Ernest Major

[jillery]

On Sat, 12 Feb 2022 09:47:49 -0700, Bob Casanova <nos...@buzz.off>

A.T. Murray aka Mentifex didn't say or imply that computer programs
and algorithms had anything to do with the formation of life, or that
analogies proved anything. Mentifex describes above a plausible
hypothesis similar to those of other OOL researchers, one which could
be, and perhap is being, modeled using AI. My understanding is AI is
a tool becoming more common in molecular biology, ex. protein folding.

Also, Mentifex's use of English and technical terms suggest Mentifex
is unfamiliar with their use, ex. "amniotic chemicals" to refer to
molecules made from amino acids. There are several posters to T.O.
who appear to be non-native English speakers. Perhaps Mentifex could
be shown equivalent tolerance, at least initially.

>And the moderator basically allows anything from anyone not
>a proven abusive troll (and yes, there have been a few); the
>"moderation" consists of a filter which rejects any post
>with more than 4 groups in the distro, along with a set of
>*specific* individuals, some banned for excessive
>nymshifting to avoid killfiles.
>>

--

[Athel Cornish-Bowden]

I'm reminded of what someone once wrote about a paper that they were
asked to review (sorry: I can't locate the original): "this paper has
parts that are correct and parts that are original. Unfortunately the
parts that are correct are not original, and the parts that are
original are not correct."

So far as the the parts that are correct but not original, Mentifex
needs to take a look at M. Eigen and P. Schuster (1978b) “The
hypercycle: a principle of natural self-organization. Part C: The
realistic hypercycle” Die Naturwissenschaften 65, 341–369.


--
Athel -- French and British, living mainly in England until 1987.

[Ernest Major]

In the process of writing the above I discovered a couple of lacunae in
my understanding.

Could the urorganism have handled absorption and excretion solely by
diffusion across the cell membrane? (Metabolising diffusible nutrients
into other non-diffusible compounds would maintain an incoming flow of
nutrients; but there's trade off between having mechanisms to import
non-diffusible compounds had have mechanisms to synthesise
non-diffusible compounds - which add more complexity to the urorganism?
And there is the issue of whether compounds in use would have the
necessary diffusibility.)

And do bacteria in general have endocytosis mechanisms like eukaryotes
or do they rely on just diffusion and transport channels? And if not do
any bacteria in particular? A web search gives me an answer to this one
- the first indentification of an endocytosis-like mechanism in
prokaryotes was discovered in 2010, in Gemmata obscuriglobus
(Planctomycetes).

--
alias Ernest Major

[Gary Hurd]

I'll recommend some reading on OOL

For intro level books on origin of life, see;

Hazen, RM 2005 "Gen-e-sis" Washington DC: Joseph Henry Press

Deamer, David W. 2011 “First Life: Discovering the Connections between Stars, Cells, and How Life Began” University of California Press

If you have had a good background, First year college; Introduction to Chemistry, Second year; Organic Chemistry and at least one biochem or genetics course see;

Deamer, David W. 2019 "Assembling Life: How can life begin on Earth and other habitable planets?" Oxford University Press.

Hazen, RM 2019 "Symphony in C: Carbon and the Evolution of (Almost) Everything" Norton and Co.

Nick Lane 2015 "The Vital Question" W. W. Norton & Company

Note: Bob Hazen thinks his 2019 book can be read by non-scientists. I doubt it.

Nick Lane spent some pages on the differences between Archaea and Bacteria cell boundary chemistry, and mitochondria chemistry. That could hint at a single RNA/DNA life that diverged very early, and then hybridized.

[Bob Casanova]

On Sat, 12 Feb 2022 14:28:09 -0500, the following appeared
in talk.origins, posted by jillery <69jp...@gmail.com>:

I did, which is why I asked my initial question and why I
thanked him for his response. My reply to that response
implicitly invited clarification.

>
>>And the moderator basically allows anything from anyone not
>>a proven abusive troll (and yes, there have been a few); the
>>"moderation" consists of a filter which rejects any post
>>with more than 4 groups in the distro, along with a set of
>>*specific* individuals, some banned for excessive
>>nymshifting to avoid killfiles.
>>>
--

[A.T. Murray]

Thanks, everybody, for the astute responses.
I especially enjoyed the "not even wrong" allusion, which I think comes from Richard Feynman.
In my frenzied eagerness I used "amniotic" even though it pertains only to the womb.
Just now on the Medium publishing platform I have tried to post the same seven steps with a
"blockquote" elaboration of each step, such as for Stage Six:
Expansion of idea
"The evolution of DNA needs to be worked out in greater detail. One possibility is that a strand of primordial mono-filament DNA attracts the complementary amino acids which would form a persistent double strand, but which instead cause the primordial cell to split into two daughter cells, where the fusion and fission repeat themselves ad infinitum. Seen in this light, the whole process of the origin of life is just a mechanism by which the DNA replicates itself forever while undergoing chance mutations which cause the evolution of species. "
but Medium is not letting me sign in with Google.
I really need to stick to my lifelong AI project and not dabble in biology.
To admit to you all how phony "Mentifex " often is, consider the following.
On LinkedIn and elsewhere I often claim Berkeley graduate school,
but in my first week at Berkeley I was drafted into the U.S. Army.
Once I sneakily got published in the premier science magazine Nature --
by placing a "position wanted" ad describing my work in AI. (15 responses)
In sum, two days ago I got all excited about the origin of life ,
but today I realize that mother nature probably tried millions of solutions
and I can not possibly guess what the successful ones were.

You are all a very congenial group, by the way -- not what i call "Mentifex-bashers."
Bye for now,
Arthur T. Murray (independent AI scholar Mentifex)

[jillery]

On Sat, 12 Feb 2022 18:26:19 -0700, Bob Casanova <nos...@buzz.off>

So when you reply that computer programs and algorithms have nothing
to do with the formation of life and analogies don't prove anything,
that's your idea of tolerance? Perhaps you could also "point out" so
many other things that have nothing to do with the formation of life
and proofs and Mentifex's comments.

>>>And the moderator basically allows anything from anyone not
>>>a proven abusive troll (and yes, there have been a few); the
>>>"moderation" consists of a filter which rejects any post
>>>with more than 4 groups in the distro, along with a set of
>>>*specific* individuals, some banned for excessive
>>>nymshifting to avoid killfiles.
>>>>

--

[jillery]

On Sat, 12 Feb 2022 15:14:40 -0800 (PST), Gary Hurd <gary...@cox.net>
wrote:

I was hoping you would post your recommendations here.

[jillery]

On Sun, 13 Feb 2022 00:13:54 -0800 (PST), "A.T. Murray"
<menti...@gmail.com> wrote:

>Thanks, everybody, for the astute responses.
>I especially enjoyed the "not even wrong" allusion, which I think comes from Richard Feynman.
>In my frenzied eagerness I used "amniotic" even though it pertains only to the womb.
>Just now on the Medium publishing platform I have tried to post the same seven steps with a
>"blockquote" elaboration of each step, such as for Stage Six:
>Expansion of idea
>"The evolution of DNA needs to be worked out in greater detail. One possibility is that a strand of primordial mono-filament DNA attracts the complementary amino acids which would form a persistent double strand, but which instead cause the primordial cell to split into two daughter cells, where the fusion and fission repeat themselves ad infinitum. Seen in this light, the whole process of the origin of life is just a mechanism by which the DNA replicates itself forever while undergoing chance mutations which cause the evolution of species. "
>but Medium is not letting me sign in with Google.
>I really need to stick to my lifelong AI project and not dabble in biology.
>To admit to you all how phony "Mentifex " often is, consider the following.
>On LinkedIn and elsewhere I often claim Berkeley graduate school,
>but in my first week at Berkeley I was drafted into the U.S. Army.
>Once I sneakily got published in the premier science magazine Nature --
>by placing a "position wanted" ad describing my work in AI. (15 responses)
>In sum, two days ago I got all excited about the origin of life ,
>but today I realize that mother nature probably tried millions of solutions
>and I can not possibly guess what the successful ones were.
>
>You are all a very congenial group, by the way -- not what i call "Mentifex-bashers."
>Bye for now,
>Arthur T. Murray (independent AI scholar Mentifex)

Your OP included several technical faux pas, which show your
unfamiliarity with molecular biology, which IMO is forgivable given
your expressed interest is in AI. After all, the only people who
don't make mistakes are those who are dead.

And since you mention it, the thrust of OOL is not to find out how
Mother Nature actually did it, as that's impossible to know for
certain. Instead it is to identify plausible pathways and plausible
environments, with which AI can help. So I hope you continue to learn
more about OOL and apply your AI talents to it.

[Bob Casanova]

On Sun, 13 Feb 2022 06:19:46 -0500, the following appeared

I suspected that the only reason you posted a comment to me
was to start an argument, on any excuse or none; good to see
I was correct.

>
>>>>And the moderator basically allows anything from anyone not
>>>>a proven abusive troll (and yes, there have been a few); the
>>>>"moderation" consists of a filter which rejects any post
>>>>with more than 4 groups in the distro, along with a set of
>>>>*specific* individuals, some banned for excessive
>>>>nymshifting to avoid killfiles.
>>>>>
--

[Ernest Major]

On 13/02/2022 08:13, A.T. Murray wrote:
> I especially enjoyed the "not even wrong" allusion, which I think comes from Richard Feynman.

The "not even wrong" phrasing originates with Pauli.

--
alias Ernest Major

[Gary Hurd]

You are most welcome.

I have not seen a lot of new work in reviews, and the current professionals are very focused on extra-terrestrial projects. I am hoping Jack W. Szostak will crank out a book.

[jillery]

On Sun, 13 Feb 2022 10:06:12 -0800 (PST), Gary Hurd <gary...@cox.net>

>You are most welcome.
>
>I have not seen a lot of new work in reviews, and the current professionals are very focused on extra-terrestrial projects. I am hoping Jack W. Szostak will crank out a book.

OOL and identfying extraterrestrial life inform each other. But
research on extraterrestrial life has the advantage of being funded,
and has the potential to be about extant environments, as opposed to
OOL being substantially historical guesswork.

[jillery]

On Sun, 13 Feb 2022 08:56:17 -0700, Bob Casanova <nos...@buzz.off>

Breaking news, sparky, it's not about you. Unlike you, I post to
emphasize points that IMO need making. I couldn't care less if you
replied, and whether you reply or not doesn't inform my posts. In
fact, I'm still hoping that someday you will grow up, follow your own
advice and ignore posts to which you can't reply intelligently. Get
over yourself.

>>>>>And the moderator basically allows anything from anyone not
>>>>>a proven abusive troll (and yes, there have been a few); the
>>>>>"moderation" consists of a filter which rejects any post
>>>>>with more than 4 groups in the distro, along with a set of
>>>>>*specific* individuals, some banned for excessive
>>>>>nymshifting to avoid killfiles.
>>>>>>

--