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From: RonO <rokimoto557@gmail.com>
Newsgroups: talk.origins
Subject: Re: Paradoxes
Date: Sat, 11 Jan 2025 08:48:06 -0600
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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 
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