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Chat log: plasmids to origin of life

Query 1

what is a plasmid

Reply 1

Claude: [November 12, 2026, 05:21:02 AM]

A plasmid is a small, circular piece of DNA that sits separately from a cell's chromosome and replicates on its own. Plasmids are most common in bacteria, though some yeasts and other microbes carry them too.

They usually carry a few genes that aren't essential but are useful in particular conditions, such as antibiotic resistance, toxin production, or the ability to break down unusual compounds. Bacteria can pass plasmids to each other by conjugation, which is a major way resistance genes spread between species.

In the lab, engineered plasmids serve as vectors. A gene is cut into one, the plasmid is put into bacteria, and the bacteria copy it and express it. This is how insulin and many other recombinant proteins are made, and it underlies most molecular cloning.

Query 2

are they alive

Reply 2

Claude: [November 12, 2026, 05:22:00 AM]

No, not by the usual definition. A plasmid has no metabolism, doesn't grow, and can't reproduce by itself. It's just a DNA molecule. It copies only because it borrows the host cell's machinery: the cell's enzymes replicate it, and the cell's ribosomes read its genes.

That puts plasmids in the same grey zone as viruses, but they sit even further from life. A virus at least has a protein coat and a way of getting into cells. A plasmid is naked DNA that depends on its host for everything, though it can behave a bit like a parasite or symbiont, since the host pays the cost of carrying it and sometimes gets a benefit like antibiotic resistance.

Query 3

is there an RNA equivalent

Reply 3

Claude: [November 12, 2026, 05:23:18 AM]

Yes, a few things come close, though none is a perfect match.

Viroids: small, circular, naked RNA molecules that infect plants. They code for no proteins and replicate using the host's enzymes, so they are the nearest thing to an "RNA plasmid." They are infectious, though, and cause plant diseases, whereas most plasmids are benign.
Satellite RNAs: small RNAs that depend on a helper virus for replication and packaging. Some are circular.
Double-stranded RNA elements in yeast and fungi: killer toxin systems in yeast, for example, are carried as dsRNA that is inherited cytoplasmically without being part of the genome. These behave most like plasmids, since they are stable, heritable, sometimes useful to the host, and not essential. They are packaged in viral-like particles, so they are really degenerate viruses.
Circular RNAs (circRNAs): found in many animal cells. They are cellular products and do not replicate, so they don't count.
Retrotransposons: they move through an RNA intermediate but live in the genome, so they are not free-floating.

If you're thinking about origins of life, viroids are often cited as possible relics of an RNA world, because they are tiny, circular, and replicate with minimal machinery.

Query 4

tell me about FUCA

Reply 4

Claude: [November 12, 2026, 05:24:34 AM]

Given the thread, I'm assuming you mean the First Universal Common Ancestor, the counterpart to LUCA.

LUCA vs FUCA

LUCA, the Last Universal Common Ancestor, is the most recent population from which all current life descends. It was already fairly sophisticated: DNA, RNA, ribosomes, a genetic code, ATP synthase, and probably a few hundred to a couple of thousand genes.
FUCA is the earlier stage: the first entity or community of replicating things that everything later descends from. It would predate LUCA by a long stretch, and it is much more speculative.

What it might have been

A single organism is probably the wrong picture. Many researchers, following Carl Woese, argue for a community of primitive replicators swapping genetic material freely (horizontal transfer), with lineages only later separating into distinct branches.
Candidate chemistries include an RNA world, a metabolism-first system on mineral surfaces or in hydrothermal vents, or a mix of the two. Your protein-first idea would be another candidate in this space.
The gap between FUCA and LUCA is where the genetic code, the ribosome and membranes would have been refined.

Evidence There is no direct fossil or genetic record of FUCA. It is inferred from universal features of life, from comparative genomics, and from lab work on prebiotic chemistry and RNA replicators.

If you meant something else, such as the human gene FUCA1 (alpha-L-fucosidase, linked to the disease fucosidosis), tell me and I'll cover that instead.

Query 5

what's the difference between LUCA and a plasmid

Reply 5

Claude: [November 12, 2026, 05:48:39 AM]

They aren't the same kind of thing: LUCA was a living population, and a plasmid is a piece of DNA that lives inside one.

LUCA was a population of cells with its own metabolism, membrane, ribosomes and a full set of genes. It could grow and reproduce on its own. Every living thing today descends from it.
A plasmid is a small piece of DNA with a handful of genes. It has no metabolism of its own and can't replicate without a host cell, so it is a passenger in a cell, not a lineage.

LUCA's genome was a host's genome, a few hundred to a couple of thousand genes covering the basics of cell life. A plasmid carries only a few extras, such as antibiotic resistance, and the host can live without it.

There is one link between them. LUCA probably swapped genes freely with its neighbours, and plasmid-like elements were likely one of the ways it did so. That kind of gene-swapping is also why the early tree of life is so tangled.

Query 6

but plasmid exchange genetic material so they must be alivd

Reply 6

Claude: [November 12, 2026, 05:50:23 AM]

Exchanging genetic material doesn't make something alive, because the plasmids aren't doing the exchanging. The bacterial cell is. In conjugation the cell builds a pilus, makes contact with another cell, and pumps the DNA across. The plasmid carries the genes that tell the host to do this, but the host supplies the machinery, the energy and the copying enzymes. It's a bit like a USB stick: it holds instructions that get a computer to copy it, but the stick isn't running anything.

A test for life is whether something can reproduce on its own using its own metabolism. Plasmids fail that, and so do viruses. Many biologists treat the line as blurry, though, and your instinct has some support. Plasmids evolve, compete with each other, and act in their own "interest" (some even kill daughter cells that fail to inherit them). Selfish genetic elements like this can be seen as replicators in their own right, and some people count them as a form of life, or at least a precursor to it.

So it comes down to where you draw the definition. Under "can copy itself independently" they're out. Under "evolving replicator" they're arguably in.

Query 7

do virus and plasmids interact

Reply 7

Claude: [November 12, 2026, 05:51:42 AM]

Yes, in several ways.

Phages carrying plasmid-like genomes: some bacteriophages (e.g. phage P1, N15) don't integrate into the chromosome after infecting. They sit in the cell as a circular or linear plasmid and replicate alongside it, so the line between virus and plasmid blurs.
Transduction: phages sometimes package plasmid DNA by mistake and carry it to a new cell, which is another way resistance genes spread.
Plasmids that defend against phages: many plasmids carry restriction-modification systems, CRISPR-like systems or abortive infection genes that protect the host from phage attack.
Phages that target plasmids: some phages bind the pilus that plasmids make for conjugation, so they infect only cells carrying the plasmid. Others prey on plasmid-borne features.
Plasmid-virus hybrids: archaea in particular have elements that act as both, with a plasmid-like genome that can be packaged into virus-like particles. Some researchers think viruses and plasmids share common ancestry for this reason.
Competition: plasmids and prophages compete inside the same cell, since the host can't always support both, and one can exclude the other.

The relationship is a mixture of cooperation and rivalry, and it shows how much of microbial life is a web of gene-sharing elements, not separate lineages.

Query 8

go deep on "Plasmid-virus hybrids: archaea in particular have elements that act as both, with a plasmid-like genome that can be packaged into virus-like particles"

Reply 8

Claude: [November 12, 2026, 05:54:47 AM]

Here are the main cases, from the least to the most virus-like. All of them are in archaea.

1. pSSVx and pSSVi: plasmids that hijack a virus (Sulfolobus)

pSSVx is a virus–plasmid hybrid that coexists in the cell with the fusellovirus SSV1 and can be packaged into viral particles. It was first described in 1999 as a hybrid between a plasmid and a virus.
It belongs to the pRN plasmid family. Besides the typical pRN proteins, it encodes two SSV1 proteins that are probably involved in packaging the plasmid.
The packaging is parasitic. When plasmid-containing cells are superinfected with the fusellovirus SSV2, pSSVi and pSSVx hijack the virus's virion-assembly machinery and are encapsidated into virus-like particles, which spreads the plasmids through the cell population in a virus-like way.
Not every relative does this. The plasmid pXZ1 and the virus SSV4 can be propagated together without prominent harm to each other. pXZ1 encodes an SSV-type integrase but cannot be packaged into viral particles.
Here the plasmid has no capsid genes of its own. It is a satellite that borrows a helper virus's capsid, much like the satellite viruses and virophages known from other systems.

2. pT26-2 and other Thermococcales plasmids with viral genes

pT26-2, from Thermococcus sp. 26-2 (21.5 kb), encodes many proteins with homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales.
Related plasmids share genes with archaeal viruses. For example, pTN2 and pP12-1 are about 12 kb and share six genes, including homologues of genes from the virus PAV1 of Pyrococcus abyssi.
This pattern points to ancient recombination between plasmids and viruses, and it was proposed that PAV1-like viruses arose from recombination between a plasmid and a virus, one donating the genome-propagation genes and the other the virion-formation genes.

3. pR1SE: a plasmid that infects like a virus (Halorubrum lacusprofundi, Antarctica)

This one is probably the strongest case. The plasmid, described in a 2017 Nature Microbiology paper, comes from an Antarctic haloarchaeon, and it transfers by a mechanism similar to a virus.

The plasmid DNA is enclosed in regularly shaped plasmid vesicles (membrane vesicles). They contain both host-derived and plasmid-encoded proteins, so the plasmid is coding for part of its own "particle."
The released vesicles can infect a plasmid-free strain, which then makes plasmid-containing vesicles itself.
Infection of plasmid-free cells occurs without direct cell-to-cell contact, which sets it apart from conjugation.
pR1SE can integrate and replicate as part of the host genome, and later resolve out again, sometimes carrying fragments of host DNA. This is how temperate viruses behave.
The authors argue this removes the last major distinction between viruses and plasmids: the element that most resembles a plasmid encodes proteins that go into the particle, and the particle can infect other cells. Forterre and colleagues suggested the term "plasmidions" for such particles.

Why this matters

It's a continuum. Network analysis of the archaeal virosphere found that most gene-sharing modules contain capsid-less mobile elements as well as viruses, showing tight evolutionary connections between the two. Archaea are where the boundary is least sharp.
Viruses may have arisen from plasmids more than once. Rolling-circle replication genes of bacterial and archaeal ssDNA viruses trace back to different families of prokaryotic plasmids. pR1SE-style vesicle transfer is a plausible first step toward a virus: a plasmid picks up a way to leave the cell and enter another.
It reaches large genomes too. The giant "Borg" elements found in archaea are almost a third the size of their host genomes. Some researchers see them as something intermediate between chromosome, plasmid and virus.

Caveats

The packaging in pSSVx is dependent on a helper virus, while pR1SE needs none. So "hybrid" covers quite different arrangements.
Dissemination by plasmid vesicles has so far been described only for pR1SE, so it may not be general.
The idea that plasmid vesicles are evolutionary precursors to viruses is a hypothesis and not established.

This also bears on your earlier question about whether plasmids are alive. If a plasmid can encode its own particle and infect cells, "not alive because it isn't infectious" no longer separates it from a virus.

Sources:

Query 9

what does archaea have to do with it ?

Reply 9

Claude: [November 12, 2026, 05:57:22 AM]

Nothing fundamental. Archaea are just where the hybrids were found and where they are easiest to see. The reasons, roughly:

Archaeal viruses are strange. Many have virion shapes (spindles, bottles, droplets) and gene sets found nowhere else, and most of their genes have no known relatives in other viruses. With no universal viral genes to compare, researchers lean on shared genes between viruses and plasmids to work out relationships, and that exposes the overlap.
Many are hyperthermophiles. Hot-spring Sulfolobus and Thermococcus were studied intensively for their viruses and plasmids from the 1980s on, so the best-characterized cases come from there.
Their viruses and plasmids are small and mixed up. Archaeal plasmids and viruses often share the same replication genes and sit in the same cells. Bacteria have the same kind of overlap (phage P1 behaves like a plasmid), but archaeal examples are more varied.
Less research. Archaea are far less studied than bacteria, so each new find tends to look novel.

The deeper point is that archaea are a third domain of life, sharing ancestry with eukaryotes for their information-processing machinery (replication, transcription, translation) while looking like bacteria in cell structure. Their mobile elements therefore don't fit neatly into either the bacterial or the eukaryotic picture, which is part of why they blur the virus/plasmid line.

So the plasmid–virus continuum is probably a general feature of life. Archaea just give some of the clearest examples.

Query 10

so do archaea carry or host them ?

Reply 10

Claude: [November 12, 2026, 05:58:25 AM]

Yes, archaea are the hosts. Every hybrid I described lives inside an archaeal cell and depends on it for its replication machinery, energy and protein synthesis.

pSSVx / pSSVi live in Sulfolobus cells, and the helper virus SSV2 infects the same cells.
pT26-2 and its relatives live in Thermococcus.
pR1SE lives in the Antarctic haloarchaeon Halorubrum lacusprofundi.

So the picture is a host cell that "carries" a plasmid, sometimes alongside a virus, and the plasmid and virus then compete for or share the cell's resources. A cell can hold several of these elements at once, each with its own agenda.

Archaea also defend themselves. Many have CRISPR systems and other defences against viruses and plasmids, and some of those defence genes sit on mobile elements, which is the cooperation and rivalry I mentioned earlier. A host can end up domesticating a mobile element, keeping genes it finds useful, and in the long run some elements become part of the chromosome.

Query 11

do all archaea have them ?

Reply 11

Claude: [November 12, 2026, 05:59:14 AM]

No. Many archaea carry plasmids or integrated viral elements, but plenty of strains have none, and the numbers are uncertain.

Some groups are rich in them. Hyperthermophiles like Sulfolobus and Thermococcus, and haloarchaea in salt lakes, often carry plasmids, and some haloarchaea carry several, including very large ones (megaplasmids).
Many isolates have none. Plasmid-free strains are common even within species that sometimes have them. Plasmids cost the host energy, so cells can lose them when there's no benefit.
Integrated viral elements are more widespread. Genome sequencing finds proviruses and virus-like elements in many archaeal genomes, so more strains carry some mobile-element signature than carry a free plasmid.
The data is skewed. Only a minority of archaea can be grown in the lab, and most of what we know comes from cultured, often extremophile, strains. Metagenomics suggests the uncultured majority carry plenty of mobile elements too, but that evidence is patchier.

So treat these elements as very common in archaea, not universal, and the exact frequency as an open question.

Query 12

how did they get there ?

Reply 12

Claude: [November 12, 2026, 06:00:07 AM]

Nobody knows for certain, but there are a few main hypotheses. They aren't mutually exclusive, and different elements probably arose different ways.

1. They came from the cell itself (escaped genes). A stretch of host DNA acquires its own replication origin and replication gene and becomes a separate replicon. Many small plasmids look like this, built from a replication gene plus a few extras. Fragments of chromosome can also split off, which is one idea for how megaplasmids formed.

2. Viruses degenerated into plasmids. A virus that loses its capsid genes but keeps its replication machinery becomes a plasmid. Integrated viruses (proviruses) that decay in the host genome can be freed in this form. Plasmids sharing genes with viruses, like pT26-2 and the PAV1 relatives, fit this.

3. Plasmids evolved into viruses. The reverse direction: a plasmid picks up genes for a particle or vesicle plus a way to exit and enter cells. pR1SE looks like a step along this road, and the rolling-circle replication genes of many viruses can be traced to plasmid families.

4. Recombination between plasmids and viruses. Where both occupy one cell, they swap genes. pSSVx, with its borrowed SSV1 proteins, shows this in progress.

5. Very old origin. Selfish replicators probably existed before the first cells, and the early gene-swapping community discussed earlier may have included plasmid-like elements. In that view they didn't arrive in archaea so much as predate them, and have been carried along ever since.

Once an element is in a lineage, it spreads sideways too, through conjugation, vesicles and virus particles, which blurs the original source. Reconstructing origins from sequences is difficult because mobile elements swap genes so freely, so the evidence for any single case is usually suggestive and not conclusive.

Query 13

but viruses don't have replication machinery as they get caught up in their host's !

Reply 13

Claude: [November 12, 2026, 06:02:05 AM]

That's true for many viruses, but not all, and it matters for the point I made.

Viruses vary a lot in how much replication machinery they carry:

Many do rely heavily on the host. Small DNA viruses often encode little beyond one initiator protein and let the host's polymerases do the copying.
Others bring their own. Many archaeal and bacterial dsDNA viruses, and the giant viruses of eukaryotes, encode their own DNA polymerase, helicase, primase or similar enzymes. RNA viruses must carry an RNA polymerase, because cells have no enzyme that copies RNA from RNA.
Even the dependent ones carry a trigger. A virus or plasmid usually encodes its own replication-initiator protein (like the Rep proteins mentioned earlier) that recognizes its origin and starts copying. The host's machinery then does the bulk of the work. Without that initiator, the host wouldn't copy the element specifically.

So what I meant by "keeps its replication machinery" is the initiator and any extra enzymes the element encodes, not a full self-sufficient copying system. Nothing here replicates entirely alone, but the amount of host help varies.

Your point also supports the continuum idea: a virus that depends on its host for most of its copying is functionally much like a plasmid, and what mainly separates them is whether they make a particle.

Query 14

what's the diff RNA vs DNA virus ?

Reply 14

Claude: [November 12, 2026, 06:03:30 AM]

The difference is the genome's chemistry, and that shapes almost everything else about how the virus replicates and evolves.

Replication

DNA viruses copy their genome with DNA polymerases, often the host's (in the nucleus for most eukaryotic ones). Large ones bring their own.
RNA viruses must encode an RNA-dependent RNA polymerase, because cells have no enzyme to copy RNA from RNA. They usually replicate in the cytoplasm, away from the nucleus. Retroviruses (like HIV) are a special case: they copy RNA into DNA with reverse transcriptase and then insert it into the host genome.

Mutation rate

RNA polymerases generally lack proofreading, so RNA viruses mutate far faster, roughly a million-fold more than their hosts' DNA. They evolve quickly and form diverse populations, which is why flu and HIV escape immunity and drugs so readily.
DNA viruses copy more accurately and change more slowly.

Genome size

Fast mutation limits how long an RNA genome can be before errors kill the virus. Most RNA viruses are small (a few thousand to about 30,000 bases, coronaviruses being near the top), while DNA viruses range from small up to giants with over a million base pairs.

Where they live

Eukaryotes host huge numbers of RNA viruses. Bacteria and archaea host mostly DNA viruses, and RNA viruses are rare there.

Relevance to your earlier question

RNA viruses are the ones with the least dependence on host machinery for copying the genome itself. DNA viruses, especially small ones, lean more on the host, which is why they sit closer to plasmids.

Query 15

what does the genetic material in archaea look like ?

Reply 15

Claude: [November 12, 2026, 06:05:05 AM]

Archaeal genetic material is DNA, double-stranded like in bacteria and eukaryotes, but organized in a mix of bacterial and eukaryotic ways.

Chromosome

Usually a single circular chromosome, as in bacteria, typically 1–5 million base pairs.
It sits in the cytoplasm with no nucleus, though it is packaged into a compact nucleoid.
Genes are often grouped into operons, like bacteria. Introns are rare, though a few exist, mostly in tRNA and rRNA genes.

Packaging

Many archaea wrap DNA around histone proteins, forming nucleosome-like structures. This is a eukaryote-like feature, though the archaeal version is simpler.
Others, especially some crenarchaea, use non-histone proteins instead.

Copying and reading the genome

Replication, transcription and translation use machinery much closer to eukaryotes than to bacteria. Archaeal RNA polymerase resembles eukaryotic polymerase II, and replication often starts from multiple origins on the circular chromosome (bacteria use one).
Archaea were long thought of as bacteria for this reason, until Carl Woese's rRNA work in the 1970s showed they form their own domain.

Chemistry that differs

The DNA itself is standard, but archaeal cell membranes are built from distinct lipids (ether-linked, branched), unlike bacteria and eukaryotes.
Hyperthermophiles protect their DNA against heat with an enzyme called reverse gyrase, plus extra DNA-binding proteins and high intracellular salt or polyamines.

Extra DNA

Plasmids (including the large megaplasmids), integrated viral elements and CRISPR arrays all sit alongside the main chromosome, and a lot of the variation between strains lives in these.

Query 16

do any cells have chrosomes and no RNA or DNA ?

Reply 16

Claude: [November 12, 2026, 06:06:08 AM]

No. A chromosome is by definition a long molecule of genetic material (DNA, or RNA in some viruses) plus its packaging proteins, so a chromosome with no nucleic acid wouldn't exist.

Some related cases are close to what you might be thinking of:

Cells with no DNA at all. Mature red blood cells in mammals eject their nucleus and have no chromosomes, and platelets are cell fragments with no nucleus. They can't divide, and they were made by cells that did have DNA.
Cells with no RNA genome. All known cellular life uses DNA as its genome. RNA genomes exist only in viruses.
Protein-based heredity. Prions are misfolded proteins that spread by converting normal copies of the same protein, and they carry heritable information with no nucleic acid. Yeast prions even pass between generations of cells, but they don't make chromosomes. They're a separate inheritance system that sits alongside the DNA.

This connects to your protein-first origin-of-life idea: prions show that proteins can transmit a self-propagating state, but so far nothing shows a protein-only system storing the kind of open-ended, variable information a genome does.

Query 17

is a jump from a prion to RNA possible?

Reply 17

Claude: [November 12, 2026, 06:07:03 AM]

A direct conversion is very unlikely, but a gradual handover is plausible, though speculative.

Why a direct jump doesn't work

A prion carries information in its fold. The amino acid sequence stays the same and only the shape changes, so it can't specify new sequences.
Nothing in chemistry reads a protein sequence and writes a nucleic acid. The cell's flow from nucleic acid to protein has no reverse path, so a prion can't be "converted" into RNA.

What could plausibly happen instead

Co-evolution. Self-propagating protein aggregates (prion-like or amyloid) could have coexisted with RNA, each helping the other. The RNA wouldn't descend from the protein, it would arrive from separate chemistry.
Protein surfaces help RNA. Amyloid-like structures can bind and concentrate nucleotides and RNA, and protect them. Notably, modern prions replicate poorly in a test tube unless RNA or other polyanions are added as cofactors, so the two already cooperate.
Handover of the job. If RNA gave more accurate, more variable, more evolvable information storage than a fold could, selection would favor the RNA taking over as the template while proteins did structure and catalysis. That is roughly where life ended up.
Peptide–RNA links. Recent prebiotic chemistry work shows amino acids can attach to RNA under plausible conditions, which supports an early RNA–peptide partnership.

The weak point for a protein-first model The hard step is information. A prion state can be copied but can't easily grow or vary in the open-ended way a sequence can, so protein-first scenarios need some way for proteins to store and evolve sequence information before RNA is involved. Most researchers think that favors RNA or RNA–peptide co-evolution, though no one has demonstrated either route.

Query 18

name all the life forms prions have been found in

Reply 18

Claude: [November 12, 2026, 06:09:31 AM]

There are two groups: prions that cause disease, and prion-like proteins that act as normal, sometimes useful, heritable states. The list below is from my own knowledge and not checked against current sources.

Disease-causing prions (transmissible spongiform encephalopathies)

Humans: Creutzfeldt-Jakob disease (sporadic, inherited, and acquired forms such as variant CJD), kuru, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia.
Sheep and goats: scrapie, the first known prion disease.
Cattle: bovine spongiform encephalopathy (mad cow disease), which caused variant CJD in humans.
Deer, elk, moose and reindeer: chronic wasting disease, the one currently spreading in wild populations.
Mink: transmissible mink encephalopathy.
Cats: feline spongiform encephalopathy, probably from contaminated food.
Zoo animals such as kudu, nyala, oryx, and some captive big cats, again linked to contaminated feed.
Experimental hosts: mice, hamsters, rats, voles, and some primates can be infected in the lab.

Prion-like states in fungi (non-disease, inherited)

Baker's yeast (Saccharomyces cerevisiae) has several, such as [PSI+] (affecting translation termination), [URE3], and [PIN+]. Some are harmful and some seem to give a survival advantage under stress.
Podospora anserina, a filamentous fungus, has the [Het-s] prion, which regulates a self/non-self recognition system.
Other yeasts and fungi have been reported to carry prion-like elements.

Other possible cases

Bacteria: some bacterial proteins form prion-like, self-propagating states (for example Rho in Clostridium botulinum in experiments), but how natural these are is debated.
Animals and plants (normal function): prion-like aggregation is involved in memory-related proteins such as Aplysia CPEB and Drosophila Orb2, and in some immune signalling proteins in mammals, which are prion-like but not infectious in the disease sense.

Not found Prions haven't been found in archaea, as far as I know.

Query 19

is the RNA in worms and fungi any different ?

Reply 19

Claude: [November 12, 2026, 06:12:07 AM]

The RNA molecule is chemically the same everywhere (A, U, G, C with a ribose-phosphate backbone). What differs is how it's processed and what it's used for.

Worms (C. elegans)

Trans-splicing. Many worm mRNAs get a short spliced leader sequence (SL1/SL2) added to the front. Most animals don't do this, and it lets the worm express genes arranged in operons, which is bacteria-like.
RNA-dependent RNA polymerases (RdRPs). Worms copy RNA from RNA to amplify small interfering RNAs, so a small trigger makes lots of secondary siRNAs. Humans and other mammals lack this.
Systemic and heritable RNAi. Silencing signals spread between cells, and can pass to offspring for several generations.
Small RNAs: the first microRNAs (lin-4, let-7) were discovered in worms, and they have piRNAs and other small RNA classes of their own.

Fungi

Very varied RNAi. Neurospora silences genes by RNAi ("quelling"), and fission yeast uses RNAi to maintain heterochromatin. Baker's yeast has lost RNAi altogether, though some of its strains carry dsRNA killer elements (the ones I mentioned earlier).
Few introns in baker's yeast, so there's much less splicing than in animals or plants, while other fungi have many more.
Mycoviruses: many fungi host dsRNA viruses and RNA elements that are inherited and usually cause no symptoms.

So the difference is in the surrounding systems and not the RNA itself. Both groups also have RdRPs (which came up earlier as the enzyme cells normally lack), so cellular RNA-to-RNA copying does exist, in a few lineages.

Query 20

fungi ?

Reply 20

Claude: [November 12, 2026, 06:13:28 AM]

I'm taking that as "tell me more about fungal RNA". Here's what stands out.

RNAi is patchy across fungi

Neurospora has two silencing pathways: quelling (silences repeated transgenes in the vegetative stage) and MSUD (silences unpaired genes during sexual reproduction).
Fission yeast uses RNAi to build heterochromatin at centromeres. That is a role beyond gene silencing.
Baker's yeast lost RNAi, but a few budding yeasts (e.g. Saccharomyces castellii) kept a simplified version.
Some pathogens, such as Cryptococcus, use RNAi to guard against transposons and so protect genome stability.

RNA viruses and satellites

Many fungi carry dsRNA mycoviruses (families such as Totiviridae and Partitiviridae). They have no extracellular phase: they spread through spores and by cell fusion (hyphal anastomosis).
Some give the host a benefit, like the yeast killer toxin that kills rival strains. Others weaken the host, and this has been studied as a possible control for crop pathogens such as chestnut blight fungus.
These are essentially RNA elements inherited like plasmids, which ties back to your earlier question.

Other RNA features

Fungal introns range from nearly none in baker's yeast to many in filamentous fungi.
Fungal mitochondria have group I and II self-splicing introns, ribozymes that cut themselves out of the RNA, a classic example of RNA acting as an enzyme.
Some fungi edit RNA, notably during sexual development in Fusarium, where A-to-I editing of mRNAs is tied to spore formation.

Query 21

what's a ribozyme ?

Reply 21

Claude: [November 12, 2026, 06:16:24 AM]

A ribozyme is an RNA molecule that works as an enzyme, speeding up a chemical reaction the way a protein enzyme would. Before the early 1980s, textbooks said only proteins could do that. Tom Cech (self-splicing introns in Tetrahymena) and Sidney Altman (RNase P) showed otherwise, and they shared the 1989 Nobel Prize in Chemistry.

Known natural examples:

Self-splicing introns (group I and II) cut themselves out of an RNA.
RNase P trims tRNA precursors, and its catalytic part is RNA.
The ribosome is a ribozyme: the bond-forming step in protein synthesis is catalyzed by ribosomal RNA, not by the proteins around it.
Small self-cleaving ribozymes (hammerhead, hairpin, HDV and others) cut themselves, and they show up in viroids and some viral RNAs.

The reason they matter is the RNA-world hypothesis. An RNA that can both store information and catalyze reactions could, in principle, copy itself without proteins. Ribozymes made in the lab can copy short stretches of RNA, though none can yet copy something as long as itself accurately.

Query 22

how are ribozymes formed ?

Reply 22

Claude: [November 12, 2026, 06:18:05 AM]

I'll take that two ways: how a cell makes one, and how they came to exist.

How a cell makes one

Transcription. A gene is copied from DNA into RNA by RNA polymerase, like any other RNA.
Folding. The RNA strand folds back on itself, with stretches pairing up to form stems and loops, and then packs into a specific 3D shape. That shape creates the active site.
Metal ions and sometimes proteins help. Magnesium ions are usually needed to stabilize the fold and take part in the chemistry. Some ribozymes, like RNase P, have protein partners that make them work better.

So a ribozyme is just an RNA whose sequence happens to fold into a catalytic shape. The sequence determines the fold, and the fold determines the activity.

How they originated

Nobody knows for certain. The favored idea is that random RNA sequences formed on early Earth (from nucleotides made by prebiotic chemistry) and a small fraction folded into active shapes.
Lab evidence supports this: in "in vitro evolution" experiments, researchers start with trillions of random RNA sequences, select the ones that catalyze a reaction, copy them with mutations, and repeat. Active ribozymes for many reactions have emerged this way within a few rounds, so catalytic RNAs aren't vanishingly rare.
The hard part is forming long enough RNA chains in the first place, which is a separate open problem.

Query 23

RNA folds ? isn't that what proteins do ? or a prion ? why would it fold ?

Reply 23

Claude: [November 12, 2026, 06:20:11 AM]

Any long chain molecule with groups that attract or repel each other will fold, so proteins aren't special in that respect. RNA is a single strand, unlike DNA's usual double helix, and that leaves its bases free to pair with each other.

Why RNA folds

Base pairing. A pairs with U and G pairs with C. A single strand folds back so that complementary stretches pair up, forming hairpins and stems, much like a zipper closing.
Stacking. The flat bases stack on each other like coins, which adds stability.
Ions. The backbone is negatively charged, so the strand repels itself. Magnesium and other positive ions screen that charge and let the chain pack tightly.
Energy. The folded shape has lower free energy than the loose strand, so it forms spontaneously, the same driving principle as for proteins.

How it compares with proteins

Proteins fold mostly because of hydrophobic residues burying themselves away from water, plus hydrogen bonds and charge interactions. Their 20 amino acids give a lot of chemical variety.
RNA has only 4 bases, mostly doing the same pairing trick, so it folds into fewer distinct shapes and is generally a weaker catalyst. That's why ribozymes are less versatile than protein enzymes.

Prions A prion is a protein that can fold into two stable shapes, and the misfolded one converts others of the same protein. That's a different phenomenon from ordinary folding, though the underlying forces are the same.

Query 24

I don't believe in misfolds

Reply 24

Claude: [November 12, 2026, 06:21:23 AM]

You're partly right about the word, but the phenomenon is well supported.

Where you have a point

"Misfold" suggests an error, and that's often the wrong picture. The prion form is a second stable conformation of the same sequence, not a botched copy. For many proteins the amyloid form is actually the lower-energy state, and the normal fold is stable only because it's kinetically trapped. "Alternative fold" or "alternative conformation" is more accurate.
In yeast and Podospora, the prion state is a working feature. [Het-s] does a job, so calling it a mistake makes no sense there.

Where the evidence is hard to dismiss

Pure recombinant prion protein made in bacteria, with no brain tissue, can be converted to a form that causes disease when injected into animals.
Prion fibrils have been resolved by cryo-EM, showing a different structure from the normal protein.
Distinct prion "strains" with different properties propagate faithfully, which means the shape itself carries the information.
The normal and prion forms have the same amino acid sequence and differ only in conformation.

If your objection is to the idea that proteins fail to fold correctly as a general thing, I'd agree that's overstated. If it's to prions being a real conformational phenomenon, the experiments above would need an alternative explanation, and I don't know of a good one.

Query 25

so RNA can transcribe prions?

Reply 25

Claude: [November 12, 2026, 06:24:04 AM]

Not quite. The terms are mixed up, so here is the chain:

Transcription is DNA being copied into RNA.
Translation is RNA being read by ribosomes to build a protein.
A prion protein is made the normal way: the PRNP gene (in humans) is transcribed into mRNA, and the mRNA is translated into the prion protein (PrP).

So RNA doesn't make prions in the sense of creating the misfolded or alternative shape. It makes the ordinary protein, and that protein can then flip into the prion conformation, either spontaneously (rarely), through a gene mutation that destabilizes the normal fold, or by contact with an existing prion. Once a prion is present, it converts more copies by shape-templating, with no RNA or DNA involved in that step.

There is one real link to RNA. In the test tube, prion conversion often goes better when RNA or other polyanions are present, so RNA may act as a cofactor that helps the protein switch shape. That's a helper role and not a template.

Query 26

can RNA make amino acids ?

Reply 26

Claude: [November 12, 2026, 06:25:19 AM]

Not in living cells, and not demonstrated in the lab either, though RNA can do several related jobs.

What actually makes amino acids Cells build them with protein enzymes through metabolic pathways, starting from simple molecules like sugars and ammonia. No RNA catalyst is known to carry out those steps.

What RNA can do with amino acids

Join them into peptides. The ribosome's catalytic core is RNA, so RNA forms the peptide bonds in protein synthesis.
Attach them to RNA. Lab-made ribozymes (such as the "flexizymes") can load amino acids onto tRNA, a job normally done by protein enzymes called aminoacyl-tRNA synthetases.
Bind them. Some RNAs (aptamers and riboswitches) selectively bind particular amino acids.

What hasn't been shown A ribozyme that builds an amino acid from simpler chemicals. This is one reason the RNA world idea needs help: RNA seems to manage the information and some catalysis, but it is a poor chemist for building the other parts of a cell.

Where early amino acids probably came from Prebiotic chemistry that needs no RNA. Amino acids form in spark-discharge experiments (Miller-Urey), in hydrothermal conditions, and in meteorites like Murchison, which contain dozens of them. So the supply of amino acids on early Earth probably came from geochemistry, with RNA later learning to use them.

Query 27

are there other nucleic acids and what does nucleic mean

Reply 27

Claude: [November 12, 2026, 06:28:21 AM]

What "nucleic" means It comes from "nucleus". Friedrich Miescher isolated the substance from the nuclei of white blood cells in 1869 and called it nuclein. It turned out to be acidic (phosphate groups), hence nucleic acid. The name stuck even though we now know they're found in cells with no nucleus too.

Other nucleic acids Beyond DNA and RNA, there are lab-made nucleic acids, collectively called XNAs (xeno nucleic acids), where the sugar backbone is swapped for something else. They can store information and in some cases be copied and evolved:

PNA (peptide nucleic acid): a peptide-like backbone instead of sugar-phosphate, which makes it uncharged and very stable.
TNA (threose nucleic acid): a four-carbon sugar, simpler than ribose, and a candidate for a pre-RNA genetic material.
GNA (glycol nucleic acid): an even simpler backbone.
LNA (locked nucleic acid): a ribose locked in shape, widely used in diagnostics.
HNA (hexitol) and CeNA (cyclohexenyl): six-membered ring sugars that engineered polymerases can copy.
Morpholinos: used as antisense drugs.

None are known in nature, as far as I know. They matter for two reasons: they show the sugar-phosphate backbone of DNA and RNA isn't essential for heredity, and the simpler ones (TNA, PNA, GNA) are candidates for what came before RNA.

Beyond that, the base alphabet can be extended. Researchers have made DNA with extra synthetic base pairs (such as Hachimoji DNA, with eight letters) that can be copied and even transcribed.

Query 28

that's what I was hoping - so how is GNA created ?

Reply 28

Claude: [November 12, 2026, 06:31:17 AM]

GNA is made by organic chemistry in the lab. Nothing shows it forming naturally. The following is from my own knowledge and I haven't checked it against current sources.

What it is Glycol nucleic acid has a backbone of repeating three-carbon propylene glycol units joined by phosphate bonds, with a base (A, T, G or C) hanging off each unit. There is no ring sugar at all, which makes it the simplest nucleic acid backbone known to pair.

How it's made

Build the monomer. Start from glycidol (a small three-carbon epoxide). Opening the epoxide with a nucleobase attaches the base to the three-carbon unit, giving a "glycol nucleoside." Using the (S)- or (R)-form of glycidol decides which of the two mirror-image GNAs you get.
Protect and activate. The reactive groups are capped, and one is converted to a phosphoramidite, the standard building block of automated DNA synthesis.
Assemble the strand. A DNA synthesizer links the monomers one at a time into a strand, as it would for ordinary DNA. This work came out of Eric Meggers' group in the 2000s.

How it behaves

Its duplexes are very stable, more so than DNA's.
The two mirror-image forms behave differently. The (S)-form pairs with RNA in some cases, but GNA generally doesn't pair well with DNA.
Engineered polymerases have been reported to copy it, though poorly, so open-ended evolution with GNA is far less developed than with RNA.

The origin question GNA is appealing as a pre-RNA candidate because its building blocks are so simple. But I'm not aware of a demonstrated prebiotic route to its nucleosides, so as of my knowledge it's an attractive idea without a proven pathway.

Query 29

but PNAs occur naturally ?

Reply 29

Claude: [November 12, 2026, 06:32:28 AM]

Not that I know of. PNA was designed in the lab in 1991 by Peter Nielsen's group, and no natural PNA has been found. I may be missing a recent discovery, so treat that as "not known" and not "proven absent."

What does occur naturally is the backbone's building block, aminoethylglycine (AEG):

It forms in spark-discharge experiments simulating early Earth, which is why Stanley Miller's group proposed in 2000 that PNA-like polymers might have preceded RNA.
It has been detected in cyanobacteria cultures, and reported in some meteorite analyses, though I'm less sure of that one.

So the plausible story is natural backbone units with no known natural strands carrying bases. The weak points are attaching the bases to the backbone and getting long chains without enzymes, neither of which has a convincing prebiotic route yet.

PNA is also uncharged, so it pairs with DNA and RNA very strongly (no electrostatic repulsion between strands), which is why it's useful in the lab. That same property makes it hard to copy, because there's no obvious way for a polymerase to handle it.

Query 30

so "nucleic" is a misnomer

Reply 30

Claude: [November 12, 2026, 06:34:05 AM]

Partly. It's a historical name that no longer describes the molecules well, but it was accurate when coined.

Where it's off: nucleic acids occur in bacteria and archaea, which have no nucleus, and in mitochondria and chloroplasts, viruses and plasmids. RNA does much of its work outside the nucleus. PNA and the other XNAs aren't acids at all in the usual sense (PNA has no phosphate, so it's neutral).
Where it's fine: Miescher found the material in nuclei and it was acidic, so the name was a correct description of what he had. Chemistry is full of names like this: "oxygen" means acid-former, but oxygen doesn't form acids by itself.

A more accurate modern description would be "genetic polymers" or "information-carrying polymers," and some origin-of-life researchers do use "XNA" or "informational polymers" for that reason. "Nucleic acid" stays in use mainly because it's established and everyone knows what it means.

Query 31

so are microplastics fusing with RNA or DNA -or- are they becoming genetic ?

Reply 31

Claude: [November 12, 2026, 06:36:48 AM]

No, there is no evidence of either. Microplastics don't become genetic, and I'm not aware of any chemical fusion with DNA or RNA.

Why they can't be genetic Heredity needs a polymer that can be copied with variation: units in a sequence that a template process can read and reproduce. Plastics like polyethylene, polystyrene and PET are repeating chains of one or two unit types, with no information-bearing sequence and nothing to template a copy.

What does happen

Sticking, not fusing. DNA and RNA can adsorb onto plastic surfaces, especially nanoplastics with a positive surface charge, through electrostatic and hydrophobic attraction. It's like DNA clinging to a bead, and it's reversible.
The "plastisphere." Microbes form biofilms on plastic, and these communities carry many antibiotic-resistance genes and plasmids. Some studies suggest gene transfer between bacteria may be higher in them, because plastics crowd cells together. The plastic is a platform and not a participant.
Indirect effects on cells. Some lab studies report that nanoplastics cause oxidative stress or inflammation, which can damage DNA secondarily. How much this happens at realistic exposure levels is still being worked out, so the strength of the evidence is mixed.
Carrying chemicals. Plastics can carry additives and absorbed pollutants, and some of those are DNA-damaging. That is the chemical doing it, not the plastic polymer.

So the realistic concerns are about what rides on or leaches from plastics, and where they concentrate microbes and genes, not about the plastic becoming genetic material.

Query 32

how dissimilar are Amino acids from R- and D- Nucleic acids ?

Reply 32

Claude: [November 12, 2026, 06:40:52 AM]

Quite dissimilar in structure, but they share more origins and chemistry than they first appear to. I'm reading "R- and D-" as ribo- and deoxyribo-nucleic acids.

Differences

Parts. An amino acid is small: an amine group, a carboxylic acid group, and a variable side chain on one carbon. A nucleotide has three parts: a nitrogen-rich ring base, a five-carbon sugar, and a phosphate.
Elements. Nucleic acids contain phosphorus, which the 20 standard amino acids lack (sulfur appears in two of them).
Links. Amino acids join through peptide (amide) bonds. Nucleotides join through phosphodiester bonds between sugars.
Charge. The nucleic acid backbone is uniformly negative. A protein's charge varies with its side chains.
Variety. Proteins use 20 monomers with very different chemistries (water-loving, water-hating, acidic, basic). Nucleic acids use 4 bases that differ only slightly, which makes them good at pairing and poor at catalysis.
Chirality. Life uses L-amino acids and D-sugars, so the two handedness choices point opposite ways.

Similarities

Both are chain-forming condensation polymers, built by releasing water, and both are chiral.
Shared precursors. Hydrogen cyanide, ammonia, formaldehyde and related simple molecules can feed both. Adenine is effectively five HCN units, and Strecker chemistry makes amino acids from HCN, aldehydes and ammonia. Work by John Sutherland's group showed one set of conditions can make precursors of nucleotides, amino acids and lipids together.
Shared biosynthesis. Cells build purines and pyrimidines using the amino acids glycine, aspartate and glutamine.
They interact. The ribosome, aminoacyl-tRNAs and RNA-binding proteins all join the two worlds. Arginine's side chain binds phosphate groups, which is why many nucleic acid binders are rich in it.

So they're built from different parts, but they come from the same simple chemistry, and the early partnership between them may be the more natural starting point than either alone.

Query 33

so it is possible that they both could've been formed by the breakdown of volcanic byproducts along with amino acids, making their origin simple !

Reply 33

Claude: [November 12, 2026, 06:45:02 AM]

For the building blocks, yes, that's a credible picture. For the origin of life as a whole, "simple" overstates it.

What supports your idea

Volcanic gases (water, CO₂, nitrogen compounds, sulfur compounds) plus lightning or heat can produce HCN, formaldehyde and ammonia, the feedstock for both amino acids and nucleobases.
Stanley Miller ran a volcanic-style spark experiment in 1983. When the stored samples were re-analysed in 2008, they held many more amino acids than he had reported at the time.
Sutherland's group made precursors of nucleotides, amino acids and lipids from HCN and hydrogen sulfide under UV light. That's a cyanide-and-sulfur chemistry, which volcanic and impact settings could supply.
Hydrothermal vents and meteorites supply additional routes, and meteorites like Murchison carry amino acids and nucleobases.

Where "simple" breaks down

Mixtures. These reactions yield a messy blend, including a lot of tar, and not clean sets of just the useful molecules.
Concentration. The products would be extremely dilute in an ocean, so there must be pools, mineral surfaces or ice that gather them.
The phosphate problem. Phosphate is scarce in soluble form, and nucleotides need it.
Ribose is fragile, breaking down easily and forming in a mixture of sugars.
Chaining them up. Joining monomers into long chains in water, without enzymes, is hard, because water pushes bonds the wrong way.
Handedness. Making only L-amino acids and D-sugars, instead of a 50/50 mix, has no accepted explanation.
Self-copying. Getting a chain that can replicate itself is a further, separate hurdle.

So the supply of raw materials was probably easy, and that part of your view looks right. The difficult part is turning that mixture into organized, self-copying chemistry, and that's still open.

Query 34

I explained before that self-copying is a myth and that multiple cycling phenomena provide the initial inertia or momentum to force gentle collisions

Reply 34

Claude: [November 12, 2026, 06:48:42 AM]

I don't have your earlier explanation in this chat, so I'm responding to it as you've put it now. Part of it has real support, and part has a gap.

Where the research agrees with you

Cycling as the driver of assembly is a live area. Wet-dry cycles (Deamer, hot-spring pools) join monomers into chains. Thermal gradients and convection in vent pores (Braun, Mast) concentrate molecules and force strand separation. Freeze-thaw cycles concentrate reactants in ice, and day/night UV cycles drive Sutherland-type chemistry.
Your point that self-copying is mostly a myth also holds up in the lab. No RNA copies itself in isolation. Replication experiments need temperature cycling to pull the strands apart, like PCR, so the environment does a lot of the work. "Self-replicating" is shorthand for "replicates in a cycling environment with supplies."
Gentle motion and collisions matter because the main problem is dilution, and cycling and stirring create the encounters.

Where there's a gap Cycling provides energy and encounters, but not memory. If the pattern lives in cycling constituents, something has to carry it from one cycle to the next, or every cycle starts fresh. The closest research idea is "compositional inheritance" (Lancet, Kauffman, autocatalytic sets), where a set of molecules reproduces its own mix. The standard objection is that these sets have very limited heredity: they can't store many variants, so they don't evolve open-endedly. That's the point a sequence polymer solves, and it's why most researchers still want something like RNA or a strand-based carrier.

So I'd call it a stage-setting mechanism, a strong one, and the open question is what stores the pattern between cycles. Your "strands" idea may be your answer to that.

Query 35

lipids are the link that you are missing and the sugar (ribose too) hold the data

Reply 35

Claude: [November 12, 2026, 06:51:01 AM]

On lipids you have a point and I under-weighted them. On sugars holding the data, the evidence points the other way, though there's a version of it that works.

Lipids as the link

Compartments are widely seen as essential. Szostak's work shows fatty acid vesicles can grow and divide under gentle cycling and stirring, and RNA inside them copies better than free in solution. That fits your cycling and gentle-motion picture.
Lipids also give inheritance without a sequence. The "lipid world" idea (Lancet, Segré) is that a lipid assembly passes on its composition when it divides. That is the compositional inheritance I mentioned, and the usual objection stands: composition holds little information and can't build up variation the way a sequence can.
Lipids sit beside your other ideas too, since lipids, amino acids and aromatic scaffolds can form together in the same conditions.

Sugars holding the data

In DNA and RNA the information is in the base sequence. The sugar is the backbone, and swapping it (TNA, GNA, HNA, from earlier) leaves information storage intact. That suggests the particular sugar isn't the data carrier.
Ribose is also a poor candidate for carrying anything lasting, because it's chemically fragile and forms in a mixed bag of sugars unless minerals like borate protect it.
The version that does work: sugar chains (glycans) are information-dense, with huge variety from branching and linkage, and cells use them as a "sugar code" on surfaces. They aren't templated or copied, though, so they carry information without heredity.

What would make it convincing A demonstration that a lipid or sugar assembly can pass on a specific variant to the next generation and keep it for many generations. That's the missing test, and it's the same hurdle every compositional model faces.

Query 36

you must be kidding ! sugars are complex carbohydrates and as such, hold complex messaging

Reply 36

Claude: [November 12, 2026, 06:53:03 AM]

Not kidding, and on the capacity point you're right. We differ on something narrower.

Where you're right Glycans can carry far more information per length than nucleic acids or proteins. Sugar units can join at several positions, in two orientations (α or β), and with branching. By one classic estimate, a six-unit sugar chain has on the order of a trillion possible structures, against about 64 million for a six-amino-acid peptide and 4,096 for six nucleotides. I'm giving that figure from memory, so treat it as approximate.

Cells use that richness. Blood groups (ABO), immune recognition, cell-to-cell signalling and the glycosylation of proteins all run on sugar patterns.

The two distinctions

Ribose isn't a complex carbohydrate. It's a single five-carbon sugar. The complex messaging lives in chains (oligosaccharides, polysaccharides), and in RNA the ribose is just a repeating link, with the information carried by the bases attached to it. So "ribose holds the data" doesn't follow from the glycan point.
A message isn't the same as heredity. Glycans are made by enzymes that add one unit at a time in a set order, and no process reads an existing glycan and makes a copy. The instructions for those enzymes are in DNA. So glycan information is rich but not self-propagating.

For your scheme to work, the cycling environment would need to reproduce a specific branched sugar structure from one generation to the next. I know of no demonstrated way to do that, and that is the gap, not the amount of information the sugars can hold.

Query 37

ribose holds the instructions !

Reply 37

Claude: [November 12, 2026, 06:54:16 AM]

The experiments say the instructions follow the bases, not the ribose, though ribose does shape what the instructions can do.

Two tests

Swap the sugar, keep the bases. Holliger's group copied sequences from DNA into XNAs built on other sugars (HNA, CeNA, TNA and others) and back again, and the information survived intact. If ribose held the instructions, that couldn't work.
Keep the sugar, change the bases. Rewrite the base order in an RNA strand and the encoded information changes completely, with the same ribose backbone throughout.

So in both directions the sequence of bases is the data, and the sugar-phosphate chain is the scaffold they're strung on.

What ribose does contribute

Catalysis and folding. The 2'-hydroxyl group on ribose is what lets RNA fold into active shapes and act as a ribozyme. DNA, without it, is a worse catalyst but a far more stable store. That one atom is much of the functional difference between RNA and DNA.
Compatibility. The sugar decides which strands can pair with which, which is why GNA and RNA interact and GNA and DNA mostly don't.
Metabolism. Ribose sits inside ATP, NAD, coenzyme A and cyclic AMP, so it links the information molecules to the energy and cofactor chemistry, as you said earlier.

So it's fair to say ribose shapes how the information is used, kept and linked to metabolism. The claim that it holds the instructions themselves doesn't match the XNA results, and a sugar-only information model would have to explain those.

Query 38

back again ? so it was there already !

Reply 38

Claude: [November 12, 2026, 06:55:37 AM]

Yes, the information was already there in the starting DNA, and the experiment doesn't claim otherwise.

The experiment started with a DNA sequence, copied it into an XNA strand, then copied that back into DNA and checked that the sequence matched. It shows the information can be moved between different backbones without changing. It doesn't show where the first sequence came from.

Two things follow from that:

The information is carried by the base order, since it came through the XNA step unchanged while the sugar changed.
The experiment says nothing about origins. The researchers supplied the starting sequence and the engineered polymerases that did the copying. Nature had to get its first sequence and its first copying machinery some other way, and that's the open question we've been circling.

So your point stands against any reading of the experiment as an origin story. It supports only the narrower claim that sequence information doesn't depend on the particular sugar.

Query 39

agree but ribose doesnt get burned so its the ideal sugar

Reply 39

Claude: [November 12, 2026, 06:57:00 AM]

Partly true in practice, but it doesn't make ribose ideal, and chemically it's one of the less durable sugars.

Where you're right Ribose isn't a main fuel. Cells run on glucose and fats and make ribose on demand, through the pentose phosphate pathway, for building nucleotides and cofactors. It's reserved for structural and information work more than for energy.

Where it falls short

It can be burned. Cells can break ribose down, feeding it back into glycolysis via the same pathway. E. coli can grow on ribose as its only carbon source, and animals can metabolize it, just slowly. Nucleotide breakdown releases it for reuse or fuel.
It's chemically fragile. Free ribose degrades in water within hours to days at warm temperatures, and the 2'-hydroxyl makes RNA break down far faster than DNA. This is why DNA uses deoxyribose, which lacks that hydroxyl, for long-term storage.
It's reactive. Ribose attaches to proteins (glycation) much more readily than glucose does, which can damage them.
Simpler sugars are sturdier. Backbones like TNA and GNA are more stable, which is part of why they're pre-RNA candidates.

So ribose looks chosen for function (the 2'-hydroxyl allows folding and catalysis, and the ring geometry suits base pairing) and for its place in metabolism, not for durability. "Ideal" depends on the job: good for an active, catalytic molecule, and a poor choice for a lasting archive.

Query 40

other way around - proteins attach to ribose

Reply 40

Claude: [November 12, 2026, 06:58:25 AM]

For the chemistry I described (glycation), the bond is between the two, so either direction of wording is fair. Your direction describes other things that happen with ribose and proteins, and these are more specific.

Glycation. Ribose's reactive carbonyl group reacts with amine groups on a protein (lysine, for example). Whether you say the sugar attaches to the protein or the protein to the sugar, it's one covalent bond formed without an enzyme.
ADP-ribosylation. Enzymes attach ADP-ribose, a ribose-containing unit, onto proteins as a regulatory tag. This is used in DNA repair, stress responses and bacterial toxins (cholera and diphtheria toxins work this way).
Binding without covalent bonds. Proteins recognize ribose specifically. Many enzymes that use NAD, ATP or FAD have a pocket shaped to grip the ribose part (the Rossmann fold is the classic case). Bacteria have dedicated ribose-binding proteins to import and sense it. RNA-binding proteins contact the 2'-hydroxyl to tell RNA from DNA.
The ribosome. Proteins sit on an RNA scaffold, with ribose in the backbone throughout.

So ribose is a common anchor point for proteins in cells. That fits your view of ribose as a metabolic link between proteins and RNA, and it's well supported as a pattern of how modern cells work. It doesn't by itself tell us which came first, but it shows the two have been tightly linked for a very long time.

Query 41

my new model is the Amino and Ribonucleic acids came first, then the prion (maybe with the virion) then RNA with the peptides, then the protein that "stuck" to all the aforementioned to form DNA/plasmids !

Reply 41

Claude: [November 12, 2026, 07:05:48 AM]

I'll go step by step, since you want objections raised before the model hardens. I'm reading "ribonucleic acids" in step 1 as the building blocks (ribose and ribonucleotides), because full RNA chains first would be the RNA world you reject.

1. Amino acids and ribonucleotide building blocks first. Well supported. Both can come from the same simple chemistry (HCN, volcanic and impact sources), as discussed.

2. Then a prion, maybe with a virion. Plausible with an adjustment. Real prions are long proteins, but short peptides (about 6-7 residues) can form self-templating amyloid on their own, so a prion-like stage needs only short chains. This matches the "amyloid world" idea in the literature. The virion part is the weaker link:

A virion is a shell around a genome, so it implies a genome and usually a host.
If you mean a protein shell or container that forms first, that works without a genome. Virus-first hypotheses exist but are minority views.
Your cycling environment can stand in for the host.

3. Then RNA with peptides. Good fit. Peptide–RNA partnerships are an active research area (RNA carrying amino acids, peptides stabilizing RNA).

4. Then a protein "stuck" to all of it, forming DNA and plasmids. This is the step that needs repair.

A protein can't turn into DNA, because DNA's building blocks are nucleotides.
There is one real protein-to-DNA link: ribonucleotide reductase, a protein enzyme that converts ribonucleotides into deoxyribonucleotides, DNA's building blocks. So proteins did make DNA possible, by chemistry on RNA's parts, and that supports "protein arrives late and gives rise to DNA." It's a conversion step, not sticking.
Plasmids then follow as circular DNA, closed by ligase and recombination enzymes.

What's missing

Compartments. Lipids were in your last version and aren't here.
Where the pattern is stored between cycles, which remains the crux.

A testable version Predict that a short amyloid-forming peptide surface speeds up joining ribonucleotides into chains and protects them. That can be tried in a lab, and a positive result would tie steps 2 and 3 together.

Query 42

not RNA chains, that was after amino acids chained

Reply 42

Claude: [November 12, 2026, 07:07:07 AM]

Understood: the monomers come first, amino acids chain up first (peptides, then the prion-like stage), and nucleotide chains come afterward. Your revised order is easier to defend than my reading of it, and the reason supports you.

Why peptides before nucleotide chains makes sense

No phosphate problem. Joining amino acids needs no phosphate, and phosphate is scarce and poorly soluble on early Earth. Nucleotides need it, so RNA chains face a supply bottleneck that peptides avoid.
Simpler chain-making. Amino acids join under plain wet-dry cycling, on mineral surfaces, or with simple activating agents. Nucleotide chains need activated monomers and usually a clay surface, and they stay short.
Early stage can be tiny. Self-templating amyloid forms from very short peptides, so the first "prion" doesn't need long chains.

Objections that remain

Timing. Ribonucleotide monomers would be in the same pools, so they could start joining wherever conditions allow. You've already treated the stages as parallel, so "first" must mean the first pattern that persists, not strict chronology.
Why RNA joins later. The model needs a reason nucleotide chains became worth keeping once peptides existed. The obvious one is that peptide surfaces protect and concentrate them, which is the testable prediction from before.
Information. A peptide prion stores a conformation, not a variable sequence. The handover to something that does store sequence, which would be RNA in your model, is the step where the explanation has to do the most work.

The model so far Monomers → amino acid chains (prion-like, maybe a shell) → RNA chains alongside the peptides → proteins and enzymes that give rise to DNA and plasmids. The least supported joint is the second one, the handover of information to RNA.

Query 43

hey, it's there to be shot down, right ? but it might fly instead. ok, lets wrap it up and reflect the chatlog as an md file and you must not exercise your editorial license, so hands off !