Evolution 2.0 Prize - $10 million

[Evgenii Rudnyi]

"How do you get from chemicals to code? How do you get a code without
designing one?"

"What You Must Do to Win The Prize

You must arrange for a digital communication system to emerge or
self-evolve without "cheating." The diagram below describes the system.
Without explicitly designing the system, your experiment must generate
an encoder that sends digital code to a decoder. Your system needs to
transmit at least five bits of information. (In other words it has to be
able to represent 32 states. The genetic code supports 64.) "

https://www.herox.com/evolution2.0

[Lawrence Crowell]

There are molecules that already do this. DNA and polypeptides are sequences that are in effect codes.

LC

[Evgenii Rudnyi]

Am 18.01.2021 um 01:01 schrieb Lawrence Crowell:
> There are molecules that already do this. DNA and polypeptides are
> sequences that are in effect codes.

Yes, this is exactly the point by the prize. The question is to show how
something like this could happen spontaneously.

Evgeny

[smitra]

On 18-01-2021 18:03, Evgenii Rudnyi wrote:
> Am 18.01.2021 um 01:01 schrieb Lawrence Crowell:
>> There are molecules that already do this. DNA and polypeptides are
>> sequences that are in effect codes.
>
> Yes, this is exactly the point by the prize. The question is to show
> how something like this could happen spontaneously.
>
> Evgeny
>

It requires violating local thermodynamic equilibrium. I'm working on an
article and a few presentations for upcoming conferences where I explain
this in detail. This then proves that none of the current models for
prebiotic chemistry can explain the origin of life. A viable scenario is
to get to a large random organic structure forged in an interstellar ice
grain, where organic molecules at low temperatures under UV irradiation
will only interact with nearest neighbors. Thermodynamic equilibrium is
never reached, the system moves farther and farther away from this as
the reactions under UV radiation continue. This way one gets to large
so-called percolation clusters of organic molecules that have a random
structure.

Such random organic structures look totally useless to explain the
origin of life, because what you want are the very specific molecules
that are involved in the biochemical processes in living organisms.
However, the structure of these random organic molecules is such that it
has interior structures with compartments containing large random
polymers and random interior surface structures. These can then serve as
micro-environments within which prebiotic chemistry under normal local
thermodynamic equilibrium conditions can work. With a finite number of N
structures in a compartment one will break symmetries such as chiral
symmetry at a level of 1/sqrt(N). Small molecules can escape the
compartments via pores in the random structure while large molecules get
trapped inside.

Saibal

[Brent Meeker]

On 1/18/2021 3:58 PM, smitra wrote:
> On 18-01-2021 18:03, Evgenii Rudnyi wrote:
>> Am 18.01.2021 um 01:01 schrieb Lawrence Crowell:
>>> There are molecules that already do this. DNA and polypeptides are
>>> sequences that are in effect codes.
>>
>> Yes, this is exactly the point by the prize. The question is to show
>> how something like this could happen spontaneously.
>>
>> Evgeny
>>
>
> It requires violating local thermodynamic equilibrium. I'm working on
> an article and a few presentations for upcoming conferences where I
> explain this in detail. This then proves that none of the current
> models for prebiotic chemistry can explain the origin of life.

There are not models that assume thermodynamic equilibrium. Biologists
aren't stupid.  They all know that abiogenesis requires a source of
energy as low entropy.  Urey showed that lightning can create organic
molecules.  Nick Lane has a theory based on alkaline vents on the ocean
floor.  He bases this on the ubiquity of ADP->ATP as the energy carrier
for all living organisms.  These vents form complex mineral structures
which provide the kind of micro-environments you mention.

Brent

[smitra]

On 19-01-2021 05:44, 'Brent Meeker' via Everything List wrote:
> On 1/18/2021 3:58 PM, smitra wrote:
>> On 18-01-2021 18:03, Evgenii Rudnyi wrote:
>>> Am 18.01.2021 um 01:01 schrieb Lawrence Crowell:
>>>> There are molecules that already do this. DNA and polypeptides are
>>>> sequences that are in effect codes.
>>>
>>> Yes, this is exactly the point by the prize. The question is to show
>>> how something like this could happen spontaneously.
>>>
>>> Evgeny
>>>
>>
>> It requires violating local thermodynamic equilibrium. I'm working on
>> an article and a few presentations for upcoming conferences where I
>> explain this in detail. This then proves that none of the current
>> models for prebiotic chemistry can explain the origin of life.
>
> There are not models that assume thermodynamic equilibrium. Biologists
> aren't stupid.  They all know that abiogenesis requires a source of
> energy as low entropy.  Urey showed that lightning can create organic
> molecules.  Nick Lane has a theory based on alkaline vents on the
> ocean floor.  He bases this on the ubiquity of ADP->ATP as the energy
> carrier for all living organisms.  These vents form complex mineral
> structures which provide the kind of micro-environments you mention.
>
> Brent

Of course they don't assume thermodynamic equilibrium, but they do all
assume local thermodynamic equilibrium (LTE). Out of equilibrium means
that the system is not described by a single temperature and a single
set of chemical potentials, there are instead temperature gradients and
chemical potential gradients. Locally in a small enough volumes, you do
have approximate thermal equilibrium, the departure from
Maxwell-Boltzmann distribution will be very small locally (the deviation
is not exactly zero otherwise you could not have heat conduction and
diffusion).

In contrast, a violation of LTE means that LTE breaks down completely.
I.e. you cannot describe the thermodynamic state of the system using
chemical potentials and a temperature that depend on position and time.
The deviation of the distribution function of molecules from
Maxwell-Boltzmann form is then very large.

A violation of LTE is impossible under Earth-like conditions.
Apparently, even in the interior of stars, LTE is still an extremely
good approximation, according to my astronomy professor who lectured
about stellar physics. Thing is that under LTE you cannot get to the
sort of micro-environments with random structures on the molecular scale
that are required for the origin of life.

Saibal

[Brent Meeker]

And those deviations are the whole point of driving the entropy
decreasing processes of life.

>
> In contrast, a violation of LTE means that LTE breaks down completely.
> I.e. you cannot describe the thermodynamic state of the system using
> chemical potentials and a temperature that depend on position and
> time. The deviation of the distribution function of molecules from
> Maxwell-Boltzmann form is then very large.

Which I might expect where molten lave meets cold sea water.

>
> A violation of LTE is impossible under Earth-like conditions.
> Apparently, even in the interior of stars, LTE is still an extremely
> good approximation, according to my astronomy professor who lectured
> about stellar physics. Thing is that under LTE you cannot get to the
> sort of micro-environments with random structures on the molecular
> scale that are required for the origin of life.

So you're telling me that photon absorbtion in photosynthesis is LTE.
That those sparks in Urey's experiment were  in LTE?

Brent

[smitra]

In these processes where LTA is briefly violated the molecules will soon
find themselves elsewhere where LTE is again valid. In general, you
can't build something on the molecular scale at some point without
molecules farther away interfering with what is going on (unless you
have sophisticated machinery already present to exploit the process,
like in case of photosynthesis). So, a process that initially breaks
chiral symmetry in one way will soon undergo interactions with other
nearby molecules that will cause the process to go in the other
direction. On the long term such effects will then get averaged out.

The fundamental problem you then have is that with only simple molecules
you are subject to the Eigen limit. All you can do is to get to polymers
that can contain information that can copy themselves using template
copying. But the error rate per copied part then defines the maximum
amount of information that can be contained, for realistic systems this
is way too small to code for a sophisticated error correction system.
Without such systems the error rate will thus remain high and you can
never get to the biological world.

If instead you already have forged very large molecules in
micro-environments (that are themselves also made out of organics), you
can circumvent the Eigen limit due to the size of the molecules.
Information can also be present in the larger scale properties of
molecules that can be copied far more accurately. This possibility is
not directly available in conventional prebiotic models, because of the
small size of the molecules one starts out with. They have to resort to
very complex models involving such things as autocatalytic sets to evade
this problem but that brings in a whole host of other problems.

Saibal

[Evgenii Rudnyi]

I do not know if you have seen this paper:

Molecular Codes in Biological and Chemical Reaction Networks
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054694

They claim that in random chemical networks one can find some semantic:

"High semantic capacity was found in the studied biochemical systems and
in random reaction networks where the number of second order reactions
is twice the number of species."

I guess that they should apply for the prize.

Evgeny

[smitra]

That's an interesting paper! Note that the theoretical physicist Paul
Davies is the one who took the initiative to set up this prize and he is
strong skeptic against all current approaches in prebiotic chemistry.
I've read the work of his research group (Paul Davies and Sara Walker),
their no-go arguments are quite strong, but they don't propose solutions
that I find all that attractive. That led me to do my own work in this
field.

Saibal

[Philip Benjamin]

[Philip Benjamin]
Molecular code? In an Evolution qua Trans-speciation model? A code is a very highly 'organized' informational system with a definite purpose. That is not random evolution. A code needs a CODER? Anything to do with any system of real existence, be it alive or dead, has to necessarily address the questions of aseity, causality, infinte regress, meaning, morals, telos etc. There is no such thing a s random chemical reaction networks!! All chemistry is 'directed' via various chemical bonds which are spin governed (not uncontrolled) predetermined particle configurations of duets and octets as in the stable (nonreactive, or inert) rare gases 9Noble Gases) of the Periodic Table. Physicists either stay with physics and the Lawa of Logic or have some basic understanding of the Laws of Chemistry before coming to such 'chemical' conclusions.
Philip Benjamin

-----Original Message----- : everyth...@googlegroups.com <everyth...@googlegroups.com> On Behalf Of Evgenii Rudnyi
Sent: Tuesday, January 19, 2021 11:01 AM Subject: Re: Evolution 2.0 Prize - $10 million

I do not know if you have seen this paper:

Molecular Codes in Biological and Chemical Reaction Networks

https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjournals.plos.org%2Fplosone%2Farticle%3Fid%3D10.1371%2Fjournal.pone.0054694&amp;data=04%7C01%7C%7C381780709c934f913ca808d8bc9bcf1b%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637466724671099313%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=K5VbtINZFak2ljnxBYPQYhrF0Cl7VLyquzYyAExHuGE%3D&amp;reserved=0

They claim that in random chemical networks one can find some semantic:

"High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species."

I guess that they should apply for the prize.

Evgeny

.

[spudb...@aol.com]

For Chemistry, specifically biochemistry, we still cannot after 70 years(?) go beyond the Stanley Miller-Harold Urey experiment to see if the can run a chemical process that starts with elements and leads to even simple life. I am not asserting religion here, but what have we missed? This is worse than nuclear fusion's time-lag, or Waiting for Godot. 

-----Original Message-----
From: smitra <smi...@zonnet.nl>
To: everyth...@googlegroups.com
Sent: Wed, Jan 20, 2021 12:32 am
Subject: Re: Evolution 2.0 Prize - $10 million

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[Brent Meeker]

Read Nick Lane's book, "The Vital Question"  and  listen to his address to the Royal Society.  It's online.

Brent

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[Telmo Menezes]

Am Mi, 20. Jan 2021, um 23:52, schrieb spudboy100 via Everything List:

For Chemistry, specifically biochemistry, we still cannot after 70 years(?) go beyond the Stanley Miller-Harold Urey experiment to see if the can run a chemical process that starts with elements and leads to even simple life. I am not asserting religion here, but what have we missed? This is worse than nuclear fusion's time-lag, or Waiting for Godot. 

I find it plausible that life requires some extremely unlikely chemical configuration to randomly happen. From our human lifespan, such an event appears almost impossible to happen by chance, but in very large timescales it's not so unlikely anymore.

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[spudb...@aol.com]

Ah! Much thanks.

To view this discussion on the web visit https://groups.google.com/d/msgid/everything-list/ce6ad7be-8ef2-2213-f8e5-1b2c91290c3e%40verizon.net.

[spudb...@aol.com]

Interesting 2013 paper. I didn't get from the paper whether the authors concluded that this coding is constituted from an emergent feature of the cosmos, given the right conditions? Is it a feature of embedded an emergent program, based on physics that acts on the chemicals, panspermia, Ufo's, God? (you know He doesn't like to be called that! -BG2)

Unanswerables....

-----Original Message-----
From: Evgenii Rudnyi <use...@rudnyi.ru>
To: everyth...@googlegroups.com
Sent: Tue, Jan 19, 2021 12:01 pm
Subject: Re: Evolution 2.0 Prize - $10 million

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[smitra]

People working in this field wrongly think that a primitive form of
biology can work with only simple chemical compounds and that you can
extend biology this way to the very beginning. This idea has been
rigorously disproved theoretically and also the lack of experimental and
observational evidence for a more primitive biology demonstrates this.
Why are people pursuing this if it doesn't work? This is because of the
argument that that sufficiently early in the universe there were only
simple molecules and it is (wrongly) thought that the only way one can
get to very large and complex organic molecules is via biological
processes.

Saibal

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[Lawrence Crowell]

On Monday, January 18, 2021 at 11:03:38 AM UTC-6 use...@rudnyi.ru wrote:

Am 18.01.2021 um 01:01 schrieb Lawrence Crowell:
> There are molecules that already do this. DNA and polypeptides are
> sequences that are in effect codes.

Yes, this is exactly the point by the prize. The question is to show how
something like this could happen spontaneously.

Evgeny

I think it does involve something to do with the contact between the quantum and macroscopic world. Quantum mechanics is purely Markovian, in that fluctuations do not communicate information that is stored. Biology and by extension chemistry in an open thermodynamic setting are subMarkovian, which means that memory of the state of a system is possible. In some manner this occurs in some einselection of quantum states as large N unit of quantum action systems that are stable against environmental decoherence.

LC