Some thoughts on the Origin of Life
Hello everyone.
I spent some time working on a partial submission for the Evolution 2.0 Origin of Life Prize and had some insights that could be of value to the community, and are very cool. It was not eligible, so I retracted the submission and figured I'd provide some of the insights here.
As I see it, the question comes down to 2 things: Explain prebiotic life to RNA, then RNA to DNA.
Both are easy to conceptualize with the correct framing, so I built the model and rationale. Essentially the core insight for the first part is that cell metabolism fundamentally runs on nucleotides and/or derivatives. Outlined in more detail below. Not just ATP/GTP, but NAD/FAD, SAM, etc. This couples the function to the physical association with the genetic material.
The second part is easier than expected to explain with the correct framing. This question becomes, how can the cell productively write its environment into the genome? My research has afforded some insights here and the paper goes into more detail.
This comes down to the writers of the code that can write dinucleotides, trinucleotides, etc. Their activity is context dependent, therefore the conditions of the writing are dependent on that context. And they do not just write sequence, they write structural capacity. Thinking of DNA/RNA outside of structural context is akin to only looking at the primary sequence of a protein.
The second frame for part 2 is from the immune system. The pathology focus removed, it looks like the immune system can be thought of as productive integration of environmental conditions into the genome/epigenome. The capacity is established in the extant system.
Here is the final section of the paper with more detail if anyone has an interest. I am not saying this is a complete picture, but I think it is really cool.
- Conclusion
One system, written in nucleotides. [Interpretation] The genetic material is nucleic acid, and the same nucleotides that spell it out are, pervasively, the carriers that run metabolism. The cell’s energy currency is the ribonucleoside triphosphates (ATP, GTP, CTP, UTP); its redox currency is nucleotide-based (NAD+/NADH, NADP+/NADPH, FAD); its acyl carrier is coenzyme A; its methyl donor is S-adenosylmethionine; its sugars are handed off as nucleotide-sugars for glycosylation and glycogen (UDP-glucose, UDP-GlcNAc, GDP-mannose, CMP-sialic acid); its phospholipids are assembled through CDP-choline and CDP-diacylglycerol; its sulfate is activated as the adenosine conjugate PAPS; and its second messengers are cyclic nucleotides (cAMP, cGMP, the cyclic di-nucleotides). Across energy, redox, acyl, methyl, sugar, lipid, sulfur, and signalling, the carrier is a nucleotide — most often built on the same adenosine handle a nucleotide-binding maker would have recognised (§3.2). The genome’s alphabet and the cell’s metabolic currency are one chemical inventory, not two.
The integration is a flow, not a wiring diagram. The ribonucleotides are at once the monomers of the labile running layer (RNA: catalysis, regulation, metabolite contact) and the stock from which the stable archive is cut: ribonucleotide reductase is the single de-novo gate that draws from the shared pool and commits it, one way, into DNA (§3.1). Building or marking the genome therefore debits the same pool that runs the metabolism, and the conversion between the two is a metabolic branch point, not a side reaction. Code, currency, and archive are three states of one nucleotide flow.
The origin question follows from the chemistry. There is no moment at which a static dictionary self-assembles, because writing was condition-dependent nucleotide addition from the first templated step, in the same nucleotide stock that ran the proto-metabolism. Neither half of the code was authored: the mapping from triplet to amino acid was found rather than assigned (§3.4), and metabolism supplied the inputs and the first writes — the abundance of an activated nucleotide standing in for the state of the cell (§3.6). What changes across that history is only what fixes the sequence — a nucleic-acid template early, a folded protein later — never the condition-instructed character of the writing itself. So the genetic code is the durable record of one metabolism-embedded writing process, written in the molecules that also run the cell, in the currency it spends to write: each write records a condition and, by spending the metabolite, alters it. That is the literal sense in which this information records and alters its own conditions.
https://aixiv.science/abs/aixiv.260627.000003
If you have questions, please let me know. There is a lot more going on.