Then What Is DNA?
If a set of molecules can reproduce without a genome, what is the genome doing in a cell?
Some molecules can copy themselves without any DNA. In laboratory experiments, small groups of proteins or RNA keep making more of each other with no genome involved, and four of them are described below. So what is DNA for in a living cell? Two questions answer it. Does the cell make its own DNA? Yes: its enzymes copy it and repair it. Does the cell have to read its DNA to replace its own worn-out parts? Yes: every new protein is built from it. That makes DNA two things at once, a record the cell keeps and a record the cell cannot keep going without. The second half of that is a proposal this site has drafted and not yet adopted into its framework (see The proposal, below).
Related pages: Reading the Strand and Autocatalytic Sets.
Reproduction without a genome
Stuart Kauffman gathers four laboratory results in A World Beyond Physics (2019). Each is a set of molecules that makes more of itself from a supply of smaller pieces, and none of them uses DNA.
One peptide that copies itself. Reza Ghadiri's group built a peptide 32 amino acids long that joins a 15-amino-acid piece and a 17-amino-acid piece into a new copy of itself (Lee et al. 1996). The peptide holds the two pieces in place while they join, so it is a template. It is a template made of protein, which is the point Kauffman draws from it.
A network of peptides. Gonen Ashkenasy, working with Ghadiri, designed a set of 81 related peptides, each 32 amino acids long, and ran a network of nine of them, in which peptides speed the formation of themselves and of each other (Ashkenasy et al. 2004).
Two RNA enzymes that make each other. Tracey Lincoln and Gerald Joyce evolved a pair of RNA enzymes, each of which joins two pieces to build the other (Lincoln and Joyce 2009). Given a supply of pieces, the pair kept replicating indefinitely.
RNA networks that form on their own. Niles Lehman's group cut a ribozyme into fragments and mixed them. The fragments assembled into cycles of three and more members, and a three-member cycle grew faster than a single molecule that copied only itself (Vaidya et al. 2012).
The first result is a single molecule copying itself. The other three are collective: no member makes itself, and the set, taken whole, makes every member. Kauffman's conclusion is that “molecular reproduction by systems of small proteins is clearly possible,” and that it need not rest on DNA or RNA templates.
A set has no separate copy of its instructions
When a collective set makes more of itself, what does it pass on? Only its own mix of molecules. The molecules present now make the molecules present next time, and nothing else holds the information. To find out what the set is, you have to look at the set itself. (This site calls that kind of record an α-trace.)
A cell keeps something extra: a separate copy of its instructions, written in DNA, that can be copied, stored and read later.
What DNA does in a cell
Kauffman tells a history: molecules that made each other came first, and DNA came later. That may be how DNA arose, but it doesn't say what DNA does in a cell today. Two questions do.
Does the cell write it? Yes. The cell's own enzymes copy its DNA, then check and repair the copy. DNA is something the cell makes and maintains, a record the cell keeps.
Must the cell read it to rebuild itself? Yes. The cell's proteins wear out and have to be replaced, and every new one is built by reading a stretch of DNA. A cell that can't read its DNA can't replace its own machinery.
So DNA plays two parts. The cell writes it and keeps it in repair, which makes it a record. The cell also has to read it before it can rebuild itself, which makes it one of the parts the cell cannot do without.
What losing the reading looks like
A mature human red blood cell has no nucleus and no ribosomes, and it makes no new protein. It keeps working on the proteins it already has, and it circulates for up to about 120 days before it is removed (OpenStax, Anatomy and Physiology). It is a loop that can no longer read its record, and it runs down.
The example needs one caution. The red blood cell loses the whole reading apparatus along with the DNA, so it shows what happens when reading stops. It does not isolate the DNA alone.
Does this clash with the α-trace page?
The α-trace page says a record is made by a running process and never drives it. DNA fits that. DNA does nothing by itself: the cell's machinery reads it, and the reading is the cell's own work. The α-trace page even gives an example close to this one: genes that are being read, which it calls live α-trace because they shape what the cell does next.
The proposal
This page claims more than the α-trace page does: in a cell, reading DNA is not optional, because the cell cannot rebuild its own machinery without it. The sovereignty test already asks whether a structure can rebuild its own boundary from raw materials. It does not yet ask the same of the machinery a structure runs on. The proposal would make it ask. It is drafted and not adopted, so the claim that DNA is part of what keeps the cell going is a draft too. The question the proposal asks, whether a structure can rebuild the catalysts it depends on, comes from Robert Rosen.
What this page does not claim
It does not say how DNA arose, or when. It makes no claim about rates or durations. It does not say how Kauffman classifies DNA beyond what the pages cited here state; his wider argument in the book was not read for this page. And it does not treat the collective sets above as sovereign: every member is made by the set, but none of them makes a boundary around the set.
Sources
- Kauffman, S. A. (2019). A World Beyond Physics: The Emergence and Evolution of Life. Oxford University Press. The two sections read were “Peptide Collectively Autocatalytic Sets” and “RNA Collectively Autocatalytic Sets” (the RNA section begins on p. 49). Kauffman dates the Ghadiri peptide to 1995; the paper appeared in 1996.
- Lee, D. H., Granja, J. R., Martinez, J. A., Severin, K., and Ghadiri, M. R. (1996). A self-replicating peptide. Nature 382, 525–528. doi:10.1038/382525a0. Abstract read.
- Ashkenasy, G., Jagasia, R., Yadav, M., and Ghadiri, M. R. (2004). Design of a directed molecular network. PNAS 101(30), 10872–10877. doi:10.1073/pnas.0402674101. Abstract read.
- Lincoln, T. A., and Joyce, G. F. (2009). Self-sustained replication of an RNA enzyme. Science 323, 1229. doi:10.1126/science.1167856. Read through the Scripps Research news release of January 2009; the abstract could not be retrieved.
- Vaidya, N., Manapat, M. L., Chen, I. A., et al. (2012). Spontaneous network formation among cooperative RNA replicators. Nature 491, 72–77. doi:10.1038/nature11549. Abstract read.
- OpenStax. Anatomy and Physiology, “Erythrocytes.” Read 2026-09-21.
The α-trace is a persistence descriptor: a reading taken of a running structure, defined while its loop runs. The claim that DNA is both trace and member rests on a proposed revision to the sovereignty conditions that has not been adopted, and is developed here at draft status. This page coins no construct and modifies no canon.
← Back to Reading the Strand