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Path: news.eternal-september.org!eternal-september.org!news.eternal-september.org!feeder3.eternal-september.org!nntp-feed.chiark.greenend.org.uk!ewrotcd!news.eyrie.org!beagle.ediacara.org!.POSTED.beagle.ediacara.org!not-for-mail From: Martin Harran <martinharran@gmail.com> Newsgroups: talk.origins Subject: Re: A chat with AI on OoL Date: Thu, 12 Dec 2024 14:21:46 +0000 Organization: A noiseless patient Spider Lines: 344 Sender: to%beagle.ediacara.org Approved: moderator@beagle.ediacara.org Message-ID: <c5sllj1tlq2elvft491flb18v3k0qade80@4ax.com> References: <vjb8v7$1dedq$1@dont-email.me> <3ec92c64-9b0d-4505-8fb8-30979892a718@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Injection-Info: beagle.ediacara.org; posting-host="beagle.ediacara.org:3.132.105.89"; logging-data="91073"; mail-complaints-to="usenet@beagle.ediacara.org" User-Agent: ForteAgent/8.00.32.1272 To: talk-origins@moderators.isc.org Cancel-Lock: sha1:LOlkKvga7TdOXKD+wntHGjnDsrI= Return-Path: <news@eternal-september.org> X-Original-To: talk-origins@ediacara.org Delivered-To: talk-origins@ediacara.org id 7CC36229782; Thu, 12 Dec 2024 09:21:55 -0500 (EST) by beagle.ediacara.org (Postfix) with ESMTPS id 30F3C229765 for <talk-origins@ediacara.org>; Thu, 12 Dec 2024 09:21:53 -0500 (EST) by pi-dach.dorfdsl.de (8.18.1/8.18.1/Debian-6~bpo12+1) with ESMTPS id 4BCELngX385203 (version=TLSv1.3 cipher=TLS_AES_256_GCM_SHA384 bits=256 verify=NOT) for <talk-origins@moderators.isc.org>; Thu, 12 Dec 2024 15:21:49 +0100 (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature ECDSA (P-256) server-digest SHA256) (No client certificate requested) by smtp.eternal-september.org (Postfix) with ESMTPS id 982C35F8FA for <talk-origins@moderators.isc.org>; Thu, 12 Dec 2024 14:21:47 +0000 (UTC) Authentication-Results: name/982C35F8FA; dmarc=fail (p=none dis=none) header.from=gmail.com id 248F5DC01A9; Thu, 12 Dec 2024 15:21:47 +0100 (CET) X-Injection-Date: Thu, 12 Dec 2024 15:21:47 +0100 (CET) X-Auth-Sender: U2FsdGVkX19d2wbROQf65rIR2LTKudBskxZ405ihk9g= HEADER_FROM_DIFFERENT_DOMAINS,NML_ADSP_CUSTOM_MED, RCVD_IN_DNSWL_BLOCKED,RCVD_IN_VALIDITY_CERTIFIED_BLOCKED, RCVD_IN_VALIDITY_RPBL_BLOCKED,SPF_HELO_NONE,SPF_PASS, USER_IN_WELCOMELIST,USER_IN_WHITELIST autolearn=ham autolearn_force=no version=3.4.6 smtp.eternal-september.org 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 >> ========== REMAINDER OF ARTICLE TRUNCATED ==========