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From: MarkE <me22over7@gmail.com>
Newsgroups: talk.origins
Subject: Re: Paradoxes
Date: Sun, 12 Jan 2025 14:47:21 +1100
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On 12/01/2025 1:48 am, RonO wrote:
> On 1/11/2025 2:04 AM, MarkE wrote:
>> Potential paradoxes are of particular interest because if unresolved, 
>> they may indicate not just difficultly but impossibility.
>>
>> Benner's framing remark is noteworthy: "Discussed here is an 
>> alternative approach to guide research into the origins of life, one 
>> that focuses on 'paradoxes', pairs of statements, both grounded in 
>> theory and observation, that (taken together) suggest that the 
>> 'origins problem' cannot be solved."
>>
>> The examples below no doubt have debated degrees of resolution. 
>> Provided FYI.
>>
>> _____________________
>>
>> *Paradoxes in the Origin of Life*
>> Steven A. Benner, 2015
>> https://link.springer.com/article/10.1007/s11084-014-9379-0
>>
>> ...
>>
>> We now can play the game. Here, the task is to write out pairs of 
>> propositions reasonably grounded in existing theories, where these 
>> pairs (if compared) create a paradox (Benner 2009). This focus on 
>> paradoxes directs us towards questions that must be resolved before 
>> any solution to the origins problem can emerge. Is also directs us 
>> away from spending time researching simple “puzzles”.Footnote3 Its 
>> greatest value, however, is to force us to address the content of the 
>> theory itself, even those parts of the content that are normally 
>> assumed without articulation.
>>
>> We illustrate this game by mentioning five examples of paradoxes 
>> within the origins problem. We stipulate that “replication involving 
>> replicable imperfections” (RIRI) evolution requires a linear 
>> biopolymer, perhaps RNA, or organized collections of molecules. All of 
>> the paradoxes below must be resolved before the origins question 
>> easily lends itself to hypothesis-directed “normal” research:
>>
>> (a)The Asphalt Paradox (Neveu et al. 2013)
>> An enormous amount of empirical data have established, as a rule, that 
>> organic systems, given energy and left to themselves, devolve to give 
>> uselessly complex mixtures, “asphalts”. Theory that enumerates small 
>> molecule space, as well as Structure Theory in chemistry, can be 
>> construed to regard this devolution a necessary consequence of theory. 
>> Conversely, the literature reports (to our knowledge) exactly zero 
>> confirmed observations where RIRI evolution emerged spontaneously from 
>> a devolving chemical system. Further, chemical theories, including the 
>> second law of thermodynamics, bonding theory that describes the 
>> “space” accessible to sets of atoms, and structure theory requiring 
>> that replication systems occupy only tiny fractions of that space, 
>> suggest that it is impossible for any non-living chemical system to 
>> escape devolution to enter into the Darwinian  world of the “living”.
>>
>> Such statements of impossibility apply even to macromolecules not 
>> assumed to be necessary for RIRI evolution. Again richly supported by 
>> empirical observation, material escapes from known metabolic cycles 
>> that might be viewed as models for a “metabolism first” origin of 
>> life, making such cycles short-lived. Lipids that provide tidy 
>> compartments under the close supervision of a graduate student 
>> (supporting a protocell-first model for origins) are quite non-robust 
>> with respect to small environmental perturbations, such as a change in 
>> the salt concentration, the introduction of organic solvents, or a 
>> change in temperature.
>>
>> (b) The Water Paradox
>> Water is commonly viewed as essential for life, and theories of water 
>> are well known to support this as a requirement. So are biopolymers, 
>> like RNA, DNA, and proteins. However, these biopolymers are corroded 
>> by water. For example, the hydrolytic deamination of DNA and RNA 
>> nucleobases is rapid and irreversible, as is the base-catalyzed 
>> cleavage of RNA in water. This allows us to construct a paradox: RNA 
>> requires water to function, but RNA cannot emerge in water, and does 
>> not persist in water without repair. Any solution to the “origins 
>> problem” must manage the paradox forced by pairing this theory and 
>> this observation; life seems to need a substance (water) that is 
>> inherently toxic to polymers (e.g. RNA) necessary for life.
>>
>> (c) The Information-Need Paradox
>> Theory can estimate the amount of information required for a chemical 
>> system to gain access to replication with imperfections that are 
>> themselves replicable. These estimates vary widely. However, by any 
>> current theory, biopolymers that might plausibly support RIRI 
>> evolution are too long to have arisen spontaneously from the amounts 
>> of building blocks that might plausibly (again by theory) have escaped 
>> asphaltic devolution in water. If a biopolymer is assumed to be 
>> necessary for RIRI evolution, we must resolve the paradox arising 
>> because implausibly high concentrations of building blocks generate 
>> biopolymers having inadequate amounts of information. These 
>> propositions from theory and observation also force the conclusion 
>> that the emergence of (in this case, biopolymer-based) life is 
>> impossible.
>>
>> (d) The Single Biopolymer Paradox
>> Even if we can make biopolymers prebiotically, it is hard to imagine 
>> making two or three (DNA, RNA, proteins) at the same time. For several 
>> decades, this simple observation has driven the search for a single 
>> biopolymer that “does” both genetics and catalysis. RNA might be such 
>> a biopolymer. However, genetics versus catalysis place very different 
>> demands on the behavior of a biopolymer. According to theory, 
>> catalytic biopolymers should fold; genetic biopolymers should not 
>> fold. Catalytic biopolymers should contain many building blocks; 
>> genetic biopolymers should contain few (Szathmary 1992). Perhaps most 
>> importantly, catalytic biopolymers must be able to catalyze reactions, 
>> while genetic biopolymers should not be able to catalyze reactions 
>> and, in particular, reactions that destroy the genetic biopolymer. Any 
>> “biopolymer first” model for origins must resolve these paradoxes, 
>> giving us a polymer that both folds and does not fold, has many 
>> building blocks at the same time as having few, and has the potential 
>> to catalyze hard-but-desired reactions without the potential to 
>> catalyze easy-but-undesired reactions.
>>
>> (e) The Probability Paradox
>> Some biopolymers, like RNA, strike a reasonable compromise between the 
>> needs of genetics and the needs of catalysis. Further, no theory 
>> creates a paradox that excludes the possibility that some RNA might 
>> catalyze the replication of RNA, with imperfections, where the 
>> imperfections are replicable. However, experiments show that RNA 
>> molecules that catalyze the destruction of RNA are more likely to 
>> arise in a pool of random (with respect to fitness) sequences than RNA 
>> molecules that catalyze the replication of RNA, with or without 
>> imperfections. Chemical theory expects this to be the case, as the 
>> base catalyzed cleavage of RNA is an “easy” reaction 
>> (stereoelectronically), while the SN2 reaction that synthesizes a 
>> phosphodiester bond is a “difficult” reaction. Thus, even if we solve 
>> the asphalt paradox, the water paradox, the information need paradox, 
>> and the single biopolymer paradox, we still must mitigate or set aside 
>> chemical theory that makes destruction, not biology, the natural 
>> outcome of are already magical chemical system.
>>
>> ...
>>
>> _____________________
>>
>> *What are existing paradoxes with abiogenesis?*
>>
>> ChatGPT: Abiogenesis, the natural process by which life arises from 
>> non- living matter, faces several paradoxes and challenges that have 
>> been discussed extensively in the scientific community. Below are some 
>> of the key paradoxes:
>>
>> 1. Eigen’s Paradox
>> Description: It highlights the challenge of maintaining genetic 
>> fidelity in early replicators. For replication to occur with 
>> sufficient accuracy, a complex enzyme (like a polymerase) is needed. 
>> However, to code for such an enzyme, a relatively long genetic 
>> sequence is required, which in turn cannot be reliably replicated 
>> without the enzyme.
>> Implication: This creates a chicken-and-egg problem between the 
>> emergence of information-carrying molecules and the machinery required 
>> for their accurate replication.
>> - Proposed Resolutions:
>> Hypercycles: Cooperative networks of replicating molecules.
>> Compartmentalization: Protection of genetic material in vesicles.
>> Short RNA worlds: Early life may have started with very short RNA 
>> molecules.
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