Re: A chat with AI on OoL

On Wed, 11 Dec 2024 08:29:08 -0800, erik simpson
<eastside.erik@gmail.com> wrote:

On 12/10/24 9:46 PM, MarkE wrote:

Q1. WHAT ARE THE PROBLEMS WITH PREBIOTIC NUCLEOTIDE SYNTHESIS?
 
ChatGPT: The synthesis of prebiotic nucleotides—the building blocks of
RNA and DNA—is a key question in understanding the origins of life.
Several challenges make it difficult to explain how nucleotides could
have formed naturally under prebiotic conditions. These challenges include:
 
1. Complexity of Nucleotide Synthesis
 
Nucleotides are composed of three components:
 
     •    A nitrogenous base (e.g., adenine, guanine, cytosine, thymine,
or uracil)
 
     •    A five-carbon sugar (ribose in RNA or deoxyribose in DNA)
 
     •    One or more phosphate groups
 
The formation of these components, and their subsequent assembly into
nucleotides, is chemically complex and unlikely under simple prebiotic
conditions.
 
2. Stability of Ribose
 
     •    Ribose, the sugar component of RNA, is chemically unstable,
especially under the conditions thought to exist on early Earth (e.g.,
high temperatures or in the presence of water).
 
     •    Ribose is also challenging to produce selectively in prebiotic
conditions; it tends to degrade into other sugars or break down entirely.
 
3. Formation of Nitrogenous Bases
 
     •    Nitrogenous bases like adenine can form under prebiotic
conditions (e.g., through polymerization of hydrogen cyanide), but these
reactions typically require specific conditions (e.g., concentrated
hydrogen cyanide solutions) that may not have been widespread on early
Earth.
 
     •    Other bases, like cytosine, are more difficult to synthesize
and are less stable.
 
4. Coupling of Ribose and Nitrogenous Bases
 
     •    Attaching a nitrogenous base to ribose to form a nucleoside
(e.g., adenosine) is a thermodynamically unfavorable reaction in aqueous
solutions. This step requires precise conditions and catalysts that may
not have been available prebiotically.
 
5. Phosphorylation
 
     •    Adding a phosphate group to form a complete nucleotide is
another chemically challenging step. Prebiotic phosphate sources are
limited, and phosphorylation typically requires high energy, specific
catalysts, or activating agents.
 
6. Chirality Problem
 
     •    Ribose and other sugars exist as a mixture of left-handed and
right-handed forms (chirality). However, RNA and DNA require exclusively
right-handed ribose (D-ribose). Prebiotic processes do not naturally
favor one chiral form over the other, making this selectivity difficult
to explain.
 
7. Dilution and Competition
 
     •    On early Earth, chemical reactions likely occurred in vast
oceans or other dilute environments. In such settings, precursors of
nucleotides would be diluted and might interact with competing
substances, leading to non-nucleotide byproducts.
 
8. UV Sensitivity
 
     •    Many of the components of nucleotides, such as ribose and
nitrogenous bases, degrade rapidly under ultraviolet (UV) light, which
was abundant on early Earth. This raises questions about how these
components could accumulate in sufficient quantities for nucleotide
synthesis.
 
Proposed Solutions and Partial Successes
 
Scientists have proposed various scenarios to address these challenges:
 
     •    Mineral Catalysis: Certain clays or metal ions may have
facilitated the coupling of sugars, bases, and phosphates.
 
     •    Alternative Pathways: Non-enzymatic pathways for nucleotide
synthesis have been proposed, such as the formamide pathway or pathways
involving cyclic intermediates.
 
     •    Localized Environments: Hydrothermal vents, dry-wet cycling in
tidal pools, or evaporating ponds may have concentrated reactants and
created favorable conditions.
 
     •    Role of RNA Precursors: Some researchers suggest simpler
precursors to RNA (e.g., nucleotide-like molecules) could have emerged
first, bypassing the need for fully-formed nucleotides initially.
 
Despite these efforts, the prebiotic synthesis of nucleotides remains
one of the most significant challenges in origin-of-life research.
 
 
Q2. HOW LONG FOR A SELF-REPLICATING RNA TO FORM?
 
ChatGPT: The time required for a self-replicating RNA molecule to form
is highly uncertain and depends on various assumptions about the
conditions on prebiotic Earth. Current estimates vary widely because
they are based on a combination of theoretical calculations,
experimental results, and speculative scenarios. Here are some factors
to consider:
 
Key Variables
 
     1.    Chemical Environment
 
     •    The concentration of RNA precursors (e.g., nucleotides) plays
a crucial role. High concentrations are needed for RNA to polymerize,
but achieving this in a prebiotic setting is challenging due to dilution
in oceans or other large water bodies.
 
     2.    Catalysts and Conditions
 
     •    The presence of catalysts, such as mineral surfaces, could
accelerate the formation of RNA. Dry-wet cycles, geothermal activity, or
UV light might also have provided the energy needed for polymerization.
 
     3.    Randomness of Sequence Assembly
 
     •    Self-replicating RNA likely requires a specific sequence to
function. The odds of forming such a sequence randomly depend on its
length:
 
     •    A short RNA molecule with self-replicating ability might be
30-60 nucleotides long.
 
     •    The probability of assembling such a sequence randomly is
astronomically low unless specific conditions concentrate and guide the
process.
 
     4.    Evolutionary Precursor Molecules
 
     •    It’s unlikely that the first self-replicator appeared in its
fully functional form. Simpler molecules or partial replicators may have
existed, which evolved into more efficient self-replicators over time.
 
     5.    Timescale of Early Earth
 
     •    Prebiotic chemistry likely occurred over millions of years,
providing vast amounts of time for rare events to happen.
 
Theoretical Estimates
 
     1.    Random Assembly
 
     •    If a self-replicating RNA requires a specific sequence of 40
nucleotides, and each position can be one of four bases (A, U, G, C),
the odds of assembling it randomly are or approximately . Even with high
concentrations of nucleotides and rapid assembly rates, the time
required for such an event is extraordinarily long in a completely
random system.
 
     2.    Catalyzed or Facilitated Assembly
 
     •    Experiments suggest that chemical environments, such as
hydrothermal vents or mineral surfaces, can greatly accelerate the
assembly of RNA-like molecules. In such conditions, the formation of
self-replicating RNA might occur in thousands to millions of years,
depending on local conditions.
 
Experimental Insights
 
     •    Laboratory experiments have demonstrated that short RNA
strands can self-replicate under controlled conditions, but these
conditions are often unrealistic for prebiotic Earth.
 
     •    Researchers have developed RNA molecules with self-replicating
capabilities, but these are typically engineered in the lab and are
longer and more complex than what could plausibly form spontaneously.
 
Best Guess
 
Based on current understanding, the formation of a self-replicating RNA
molecule could take anywhere from:
 
     •    Millions to hundreds of millions of years under favorable
prebiotic conditions, assuming significant environmental facilitation
and a robust supply of precursors.
 
     •    Billions of years or longer without specific facilitating
mechanisms, given the improbability of random sequence formation.
 
Conclusion
 
The emergence of self-replicating RNA likely required specific
environmental niches, prebiotic evolutionary processes, and immense
spans of time. While precise timing remains speculative, it is clear
that the conditions needed for this process were rare and required a
combination of chance and favorable chemistry.
 
 
Q3. SO, WE NEED FAVOURABLE PREBIOTIC CONDITIONS, SIGNIFICANT
ENVIRONMENTAL FACILITATION, AND A ROBUST SUPPLY OF PRECURSORS, I.E. FAR
FROM EQUILIBRIUM DYNAMIC SYSTEM, TO BE MAINTAINED FOR MILLIONS OR
HUNDREDS OF MILLIONS OF YEARS? ISN’T THE PROBABILITY OF THAT VANISHINGLY
SMALL?
 
ChatGPT: Yes, the probability of all these conditions aligning and
persisting for millions or hundreds of millions of years is indeed
extraordinarily low. This challenge has led many researchers to describe
the origin of life as one of the most difficult problems in science.
Here’s why the scenario is so improbable, and how some researchers
attempt to address these issues:
 
Why the Probability Is Vanishingly Small
 
     1.    Prebiotic Conditions
 
     •    Fragility of Conditions: The precise environmental conditions
(e.g., localized concentrations of nucleotides, optimal temperatures,
and pH levels) necessary for nucleotide synthesis and polymerization
would need to be sustained long enough to enable the assembly and
replication of RNA molecules.
 
     •    Dynamic Instability: Natural systems on early Earth were far
from static. Localized environments could be disrupted by catastrophic
events (e.g., meteor impacts, volcanic eruptions, or ocean mixing),
resetting or destroying any nascent chemical complexity.
 
     2.    Far-from-Equilibrium Dynamics
 
     •    Maintaining a far-from-equilibrium system (e.g., one with
continuous energy flow and chemical cycling) requires an ongoing energy
source. However, such systems are inherently unstable and prone to
reverting to equilibrium (e.g., dissipation of concentration gradients
or thermal energy).
 
     3.    Precursor Supply
 
     •    The availability of nucleotide precursors is a major
bottleneck. Ribose, nitrogenous bases, and phosphates would need to
accumulate locally in significant concentrations and remain chemically
stable, despite the presence of competing reactions or degradation
pathways.
 
     4.    Time Constraint
 
     •    While millions of years seem like an immense amount of time,
the number of possible molecular interactions occurring in even the most
favorable prebiotic environments may still fall short of the required
conditions for a self-replicating RNA molecule to emerge.
 
Attempts to Address the Improbability
 
Researchers propose several mechanisms to mitigate the improbability of
these conditions:
 
     1.    Localized Environments
 
     •    Hydrothermal Vents: These provide continuous energy (e.g.,
heat and chemical gradients) that could drive far-from-equilibrium
chemical reactions.
 
     •    Tidal Pools or Evaporating Ponds: Cycles of wetting and drying
may have concentrated reactants and facilitated polymerization.
 
     •    Mineral Surfaces: Minerals like clays or metal sulfides can
adsorb organic molecules, concentrate them, and catalyze reactions.
 
     2.    Iterative Processes
 
     •    The origin of life may have involved many failed chemical
pathways, with only rare pockets of progress. Evolutionary processes
could have gradually selected for molecules or systems that were
slightly more stable or replicable, eventually leading to
self-replicating RNA.
 
     3.    Simpler Prebiotic Systems
 
     •    Some researchers suggest that RNA may not have been the first
replicator. Simpler molecules or “proto-RNA” systems might have formed
first, with RNA emerging later as a more efficient replicator.
 
     4.    Exogenous Sources
 
     •    Organic compounds from meteorites, comets, or interstellar
dust might have supplemented Earth’s prebiotic chemistry, providing an
additional source of precursors.
 
     5.    Autocatalytic Networks
 
     •    Rather than requiring a single, self-replicating RNA molecule,
life may have started with a network of simpler, mutually reinforcing
chemical reactions (an autocatalytic set), which eventually gave rise to
RNA-based replication.
 
Probabilistic Perspective
 
While the probability of these conditions aligning is vanishingly small
on a single planet, the sheer scale of the universe increases the odds:
 
     •    The early Earth had millions of microenvironments, each
presenting a slightly different set of conditions.
 
     •    The universe contains billions of planets, each with
potentially unique prebiotic chemistries.
 
The low probability of any single instance of abiogenesis might be
outweighed by the vast number of opportunities for it to occur across
time and space.
 
Philosophical Implications
 
The improbability of life’s origin raises questions about:
 
     •    Anthropic Principles: Are we observing the universe from a
biased perspective because we exist in the rare case where these
conditions were met?
 
     •    Alternative Scenarios: Could life have originated elsewhere in
the universe and been delivered to Earth via panspermia?
 
In summary, while the likelihood of all these factors aligning seems
vanishingly small, researchers explore the possibility that life emerged
through incremental, iterative steps over vast spans of time and across
numerous microenvironments. The search for more plausible pathways,
whether on Earth or elsewhere, continues to challenge our understanding
of the origins of life.
 

ChatGPT produces no information.  It rephrases what it's been told,
which sometimes makes it clearer.  In particular, the chirality problem
isn't a problem at all. 

That's an example of what I have just posted about in another thread.
No matter what the scientists say, AI has decided that chirality *is*
a problem so expect to see more and more output based on that
assumption.

Natural selection acted on the organisms nad
produced the winner (what we see).  The loser was eaten.  Different
chiralitis are still edible.