Checkpoint, 12 Nov 2026: cells, RNA, amino acids, immunity and "living = motion"

Settled facts

• When one organism absorbs another, the smaller genome stays a separate molecule. Fragments get inserted at scattered sites in the host's chromosomes, and most of the smaller genome is lost.
• The only shared protein core is the protein-making machinery, with roughly 350 protein families in the last common ancestor. No protein is shared by all viruses.
• RNA is the programmable messenger, aimed by sequence. Proteins are the strong actors, aimed by shape.

Positions held, with my verdict

Position	Verdict
RNA predates proteins but became a viable genetic code only once its bases were tied to amino acid links	Holds as a claim about the code (the stereochemical theory). Lab RNA can copy itself a little without peptides, so it fails as a claim about heredity. The binding evidence covers about 8 amino acids, and the transfer RNA adapter is still needed for assembly.
Once the minimal set-up exists it can be extended easily	True at the edges (selenocysteine, pyrrolysine, lab-added amino acids), but the core 20 are frozen.
The replication system is an immune function and the instigator of gene transfer	Not supported. Parts of the copying machinery are parasite-derived, and mobile elements are the main instigators. Defence is a leading reason transfer stays open, and it also filters it.
Every gene was born of an immune or replication need	Only in a narrow form. Many genes come from parasite DNA (syncytin, RAG, Arc), but metabolic and structural genes trace to chemistry and energy.
Ageing is gene termination	True for salmon, octopus and annual plants. For most animals ageing is selection neglecting the late years.
Amino acids are central, ubiquitous and immutable	Central and ubiquitous yes. Immutable only after the code froze, since they are modified chemically after construction.
Living = motion	Better as organised, self-maintaining motion that can reproduce. A dormant seed is the same machinery switched off.

Where we ended up agreeing

• Parasite pressure explains why replication comes with variety built in.
• Immunity holds the top claim on cell resources when the threat is real, and loses it when the cell can't afford it.
• Stress and defence share wiring in cells.
• Much of life's motion is done by proxy, as with seeds, viruses and plasmids.

Open for the next chapter

1. When did the amino acid and RNA loop close, meaning when a system first made its own amino acids?
2. What share of genes trace to parasite or defence material? That could test the narrow form of the every-gene claim.
3. A tighter wording of "living" that handles dormancy.