Origin of life checkpoint 2: immune system, ribosome, viroids and viruses

Date: 13 November 2026 (Sydney). Follows origin_of_life_sequence_checkpoint_2026-11-13.md.

1. Where we landed

• FUCA = the ribosome. FUCA is the first universal common ancestor. Andrew's decision, with Claude's amendment: it is the ribosome at the point it starts joining amino acids in an order set by a copyable RNA.
• Definition of "alive" (Claude's commitment). A thing is alive when it both works (uses energy to build and maintain itself) and inherits (copies information that can vary).
  • Ribosome alone: works, does not inherit. A motor.
  • Viroid alone: inherits, does not work. A message.
  • Life starts at the coupling of the two.
• The ladder of small agents: viroid, then virusoid, then virus.
• Proteins attached later. Bare replicators came first; shell proteins were recruited afterwards from cell proteins.

2. The names, sorted

Name	What it is	Shell?	Genes?
Prion	Infectious misfolded protein, no nucleic acid	No	No
Viroid	Bare circle of non-coding RNA, 246 to 401 units, plants	No	No
Virusoid (satellite RNA)	Viroid-like RNA circle that travels in a helper virus's shell	Borrowed	No
Hepatitis delta	Viroid-like RNA circle, borrows hepatitis B's shell	Borrowed	One
Obelisk	Viroid-like RNA circle in bacteria (reported 2024), about 1,000 units	No	One or two
Virus	Genome that carries the gene for its own shell	Own	Yes
Virion	Not a separate agent: the packaged travel form of a virus	n/a	n/a
Plasmid	Independent DNA circle in a cell, moves only by cell contact	No	Yes

Shell, coat and capsid all mean the same thing.

3. Points established along the way

Immune system

• No physical boundary; it is defined by telling self from non-self.
• Self is read as short peptides displayed on MHC molecules (major histocompatibility complex). The peptides are ordinary protein fragments; the display and the training are what is special.
• The oldest known defences are built on nucleic acid: CRISPR in bacteria and archaea, RNA interference in plants and insects. Which defence came first cannot be established.

RNA, tRNA and the ribosome

• Genomic tag hypothesis (Weiner and Maizels, 1987): a tRNA-shaped fold first served as the "start copying here" marker on RNA genomes.
• The ribosome's working core is RNA alone. It is a symmetrical pocket of two tRNA-sized pieces; Ada Yonath's group proposed this pair as the proto-ribosome.
• Most of the roughly one hundred genes shared by all life concern the ribosome. Bacteria and archaea share the ribosome but differ in membranes and DNA-copying enzymes, which supports "ribosome before the cell".
• DNA is derived from RNA: its building blocks are made from RNA's, and DNA copying needs an RNA primer.

Viroids

• Single-stranded, circular, non-coding RNA. Not messenger, transfer or ribosomal RNA; its own class (infectious non-coding RNA).
• Copied by host enzymes by rolling circle. One family lives in the chloroplast, which is a captured bacterium.
• Origin unsettled: relic of an RNA world (Diener, 1989) or a later arrival.

Plasmids and viruses

• A plasmid is transcribed by the host's RNA polymerase into linear RNA, gene by gene.
• Plasmids exchange because the transfer genes sit on the plasmid; it spreads itself.
• Plasmids and viruses overlap: gain shell genes and a plasmid becomes a virus; lose them and a virus becomes a plasmid.

Energy before mitochondria

• The cell membrane charged like a battery, with a rotary turbine (ATP synthase) making ATP. LUCA (last universal common ancestor) already had it.
• Before that, the leading proposal: natural gradients at alkaline deep-sea vents, hydrogen plus carbon dioxide as the reaction, iron-sulphur minerals as catalysts, phosphate as the currency, lipids as the insulation.
• Methane was the exhaust of that chemistry in archaea. Lipids became a major fuel only after oxygen arrived.

Us

• Not algae. An animal cell is an archaeon-derived host plus one captured bacterium (the mitochondrion). Algae and plants added a second (the chloroplast).

4. Ideas tested that did not hold

• A viroid as "a double tRNA fused to a prion": a viroid has no protein and is not built from tRNA.
• The early machinery as DNA: it is RNA plus peptide.
• "Amino acid replicator": peptides do not template-copy; the machine joins amino acids. "Peptide maker" fits.
• The chromosome as that machine: the chromosome stores instructions.
• The ribosome using viroids as protein carriers: tRNA is the carrier.
• A "life force": every ribosome step is ordinary chemistry paid for with fuel.
• Plasmids transcribed to circular RNA: the transcript is linear.
• Plants as early: land plants are about 470 million years old; bacteria and archaea at least 3.5 billion.

5. Still open

• Are viroids relics or latecomers?
• Did life start at vents or in surface ponds?
• Was FUCA enclosed in a membrane or not?
• Did viruses invent DNA (Patrick Forterre's hypothesis)?

6. Names not yet met, so they are no surprise next time

• Transposon ("jumping gene"): a DNA segment that moves around inside one genome. The antibody-shuffling enzymes descend from one.
• Retrovirus and endogenous retrovirus: an RNA virus that writes itself into host DNA; "endogenous" means an old copy now inherited in the genome.
• Satellite virus: has its own shell gene but needs a helper virus to be copied.
• Virophage: a small virus that parasitises a giant virus.
• Giant virus: a virus with a genome larger than some bacteria.