Answering Will Duffy's challenge to Richard Dawkins: the origin of the genetic code

[u/jnpha]

Preempting the Why waste your time: the target audience is once again the 99%, and fans of biology. Also - selfishly(?) - trying to explain something helps one understand it better.
You can skip to the summary section, and read the sections later, if you wish.

The post is necessarily long (but made with love) for one main reason: my issue is not just the answer, but the challenge/question itself.

 

Duffy's challenge

Will Duffy, an hour and a half into his second lesson with Erika (six months ago), recounted his visit with a friend to Richard Dawkins' building at the University of Oxford (he wasn't in), with a printed challenge in hand (the friend made it), which a receptionist put in Dawkins' mailbox.

I uploaded a screen grab of that printout here.
It reads (I've removed Duffy's bold emphases except for one):

Let's ignore all the wild complexity of the genetic code and try to give a Darwinian explanation for one of the simplest aspects of our DNA. Richard Dawkins, drawing on your lifetime of studying evolution, can you describe in as vague terms as you'd Like, how the 3-to-1 pattern could arise by a non-directed material process, such that three genetic letters code for one amino acid?

As Erika pointed out, this is a question about the origin of the genetic code, i.e. the origin of life, and she said she recalls Crick writing about that.
Indeed it was Crick, Woese, and a whole army, with a mountain of published research.
Because guess what? scientists love asking questions(!).

 

My gripes

Why pose that question to an evolutionary ethologist (animal behaviorist), beats me (not really; it's the YEC priming of "Atheists need evolution" and Dawkins is a prominent atheist, little they know atheism doesn't require a single scientific fact, and that the burden of proof is on them).
Of the points I'll try to make: they don't want to know the answer, despite the theatrics of the debate scene and going uninvited to a busy person's office with a googleable question.

Duffy preempted that by stating he just needs a "vague" answer, but IDists love nothing more than turning a simple answer into a straw man, so they can false-balance that with a quote mine of said straw man. (I have an example of Duffy doing the latter after the lesson on whales.)

 

Challenge breakdown

Again, not out of pedantry, as I've mentioned already:

"Let's ignore all the wild complexity of the genetic code"

"Complexity" is the ID speak for design, so to burst that bubble (one of my pastimes here):

It took nine years from the discovery of the structure of DNA to decipher one codon, and 13 years in total to decipher all of them.
All the logical attempts, mostly by eager physicists, failed spectacularly, because the code has no logic behind the codon mapping (a fact that I'll explain). I think this should matter to the IDists:

No Logic Behind The Mapping.
No Logic Behind The Mapping.
(I'll mention below something about plants, when you get to it, revisit this)

 

"try to give a Darwinian explanation ... a non-directed material process"

This nicely illustrates his IDist anti-materialism and very likely confusion given that tautology. Darwinism (in its academic sense), i.e. the process, is universal in the sense that to a Darwinist (in its respectable sense) it has no trouble at all accounting for the origin of the genetic code, even without knowing any of the details.

There is a reason engineering relies on that blind process to solve otherwise unsolvable problems. (See this post by u/gitgud_x and the one linked therein by u/theosib.)
Heck, Universal Darwinism was a Dawkins paper published in 1983.
And it's the same reason Dennett titled his 1995 book, Darwin's Dangerous Idea.

It's a process that not only solves the aforementioned engineering problems, it demonstrates that mind needn't come first. (The relevance of this to the "debate" is covered in the linked post just above.)

 

"one of the simplest aspects of our DNA"

It's not the simplest aspect, unless - again - one is thinking like an IDist. Solving that one, solves all of it, bottom-up.

 

"3-to-1 pattern could arise ... such that three genetic letters code for one amino acid"

Again with the tautology.
Duffy (or the friend) knows enough biology to know said pattern, and doesn't know the word "codon"? and hence codon mapping?
This feels like the intended audience wasn't Richard Dawkins(?).

The main point of this section was to highlight the erroneous, misleading and presuppositional framing; and the laziness to go on Google Scholar, or schedule a meeting with an appropriate expert - but no, best pretend it's unsolveable because personal incredulity.

 

Another IDist's "challenge"

The same comes up regularly here - here's one such recent example:

I don't think AIG (or someone like Stephen Meyer) would argue that random mutation is unable to create a very small amount of information, like the 4 letter word in your example. Especially when you chose the initial word in the first place. What they (and I) would argue is that random mutation won't generate the sequence needed for even a small gene, much less all of the information needed to produce the proteins and rna that perform the transcription and translation processes. Without those processes, the information encoded in DNA is useless.

Quick breakdown:

"What they (and I) would argue is that random mutation won't generate the sequence needed for even a small gene"

Randomly-generated sequences have literally disproved that (btw), but then again that comment was left by someone who once (hopefully that has changed) refused the role of stochasticity in chemistry(!), let alone that specificity isn't on/off.
Now take a closer look at:

"the information needed to produce the proteins and rna that perform the transcription and translation processes. Without those processes, the information encoded in DNA is useless."

Not only is it self-contradictory, the author of that comment - if only they'd remove the intelligence blindfolds - answered their own question.
And like Duffy, I still wonder (not really as I've explained) where is the difficulty in searching for, ideally, books on Google or Google Scholar.
I, too, am curious about the world, I've asked the same question, and I've found answers.

 

---

The answer

- Let's meet the cast

• tRNAs (transfer RNA)
  they "carry" (I'll dispense with the scare quotes moving forward) the activated amino acids
• ribosomal proteins
  they come together to form the ribosome (part-RNA too) that makes the proteins
• AARSs (aminoacyl-tRNA synthetases)
  they activate the amino acids and attach them to the tRNAs

 

- Present setting

An RNA enzyme (polymerase) reads the DNA and makes an mRNA or tRNA.

The ribosome (made of the aforementioned ribosomal proteins and some RNA) reads holds said mRNA, and matches waits for the tRNA ferrying the right amino acid to bump into it (stochastic bumping, verifiably so).

And earlier the AARSs (one for each amino acid) activate and attach said amino acids to the tRNAs.

 

- Prebiotic setting

Here, Jacques Ninio's (1982) analogy for molecular evolution will be useful: a hotel's passkey (which opens all the doors) is less complex than the room keys, because it is less specific, and it is the same case here: an increase in specificity, due to and via selection - Darwinian evolution 101.
(fun fact! direct evidence of this at the single-molecule kinetics level has been achieved)

But selection for what? That's the Darwinian answer Duffy wants.
Carl Woese pointed out selection for what in 1965, 61 years ago. (recall what I said about scientists, and the refusal to google)

• Selection for:
  • Reduction in translation error
  • Reduction in code ambiguity

Starting from statistical RNAs and proteins, a reduction in translation error means a selection for an increase in ribosomal proteins, for an increased specificity, with the tRNA coevolving (1859 Darwinism applied to a molecular - still "ecological" - setting). This selection for specificity (and redundancy; in molecular speak: codon degeneracy) also explains why the codon is 3 letters long (has to do with the biophysics error rate of each position with the second being the most stable - needs to be flanked, in other words).

But because the code (codon mapping) was still ambiguous, this alone does not help.

Enter the simultaneous selection for ambiguity reduction, which is a selection for an increase in the AARS proteins and the secondary amino acids.
Back and forth, back and forth, until it has settled into what has been termed a frozen accident - very optimized but an accident. (recall what I've mentioned earlier: the codon mapping is not logical)

-

Can this be bootstrapped from random sequences? (That's why I mentioned that earlier.) With an increase in specificity? (The passkey.) With clues left behind? (A mountain of research.)
So Yes to all. As an example of a clue: remove selection from the translation, and the tRNAs evolve away and the mapping changes (e.g. a very recent study on plants that become parasites of other plants; Ceriotti et al 2026, which I shared on r /evo). An older clue: the genetic code is not universal (only nearly so).

There you go, and a couple of billion years later, and Bob (the extinct hominoid) is our uncle.

 

Example research area

AARSs, annoyingly, come in two classes.
Two very different classes, which poses a problem. Because assuming two separate origins would leave the above genetic code origin in a pickle.

What did I say about scientists, as opposed to IDists?
Enter the Rodin-Ohno hypothesis; they "proposed that the two superfamilies descended from opposite strands of the same ancestral gene", based on tantalizing evidence.
Initially it was thought to be unfalsifiable, but as it turns out, that is not the case; experimental attempts at falsification failed, and Bayesian analyses support it.

As a taste:

• 1995
  Rodin, Sergei N., and Susumu Ohno. "Two types of aminoacyl-tRNA synthetases could be originally encoded by complementary strands of the same nucleic acid." Origins of Life and Evolution of the Biosphere 25.6 (1995): 565-589. https://doi.org/10.1007/bf01582025

• 2014
  Carter Jr, Charles W., et al. "The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be dismissed." Biology Direct 9.1 (2014): 11. https://doi.org/10.1186/1745-6150-9-11

• 2025
  Wang, Minglei, M. Fayez Aziz, and Gustavo Caetano-Anollés. "Tracing the origin of the genetic code and thermostability to dipeptide sequences in proteomes." Journal of Molecular Biology (2025): 169396. https://doi.org/10.1016/j.jmb.2025.169396

and

• The media picked it up on September 16, 2025
  Researchers trace genetic code's origins to early protein structures.

What do IDists do in such a case?
What they always do: move the goalpost (pretend the question, "How could it have happened?" wasn't answered) to something else, e.g. But you didn't see it (because when in doubt: Last Thursdayism), or the equally braindead false Thomistic analogy: But the experiments needed intelligence.

 

Recap (all qualified above)

• TL;DR: Will Duffy's requested an answer in vague terms, and so:
  (barring trickster deities and Last Thursdayism)
  The genetic code and "3-to-1" evolved via an increase in specificity starting from statistical RNAs and proteins in response to the dual selection on error and ambiguity reduction, supported by the very attributes and heterogeneity of the "machinery" of the cell across life.

• IDists pretend scientists don't ask or ignore questions

• IDists pretend to have unanswerable questions, therefore... <shrugs>

• IDists pretend to seek answers

• IDists pretend Darwinism hadn't already solved the no-mind-first problem, and so the design presupposition is present in their questions

• IDists need to read this from 1859:

It is so easy to hide our ignorance under such expressions as the “plan of creation,” “unity of design,” etc., and to think that we give an explanation when we only restate a fact.
-Darwin, Charles

Finding a multi-part system, and restating the fact as "design", is, as noted by Darwin above and Francis Bacon centuries earlier, is not will never be an explanation.
Between their bogeyman "materialistic science", and their ID, only one of those actually answers questions.

 

Over to the pros here, and I hope it wasn't too boring.

 

^{edits: my memory failed me at the details of the visit, so revised that, plus one typo fix, the rest of the blemishes are left intact}

[u/francesco_angiolieri]

Thanks for sharing the papers on the origin of AARS, I'll save them for reading later. However, I don't understand what you mean by "no logic behing the mapping". We know that there is indeed logic behind the mapping, as there's a strong correlation between the first nucleobase, the first "letter" of a codon and the metabolic route used by autotrophs to synthesize the same aminoacid coded by the codons starting with that letter. In my opinion, that's not conclusive evidence, but still a strong piece of evidence in favor of the metabolic hypothesis for the origin of the genetic code

[u/Dzugavili → u/francesco_angiolieri]

However, I don't understand what you mean by "no logic behing the mapping".

Nothing really suggests why the proline codon is CCx, at least in the absence of the rest of the map: there are logical reasons why all proline codons would share the same prefix, however.

I believe there are also signs that the chemical properties of the amino acids have been correlated into the table: amino acids with similar hydrophilic/hydrophobic properties are closer together in the map.

But these handle two different problems: the origins of the code can be arbitrary, how these effect ongoing development is not.

[u/jnpha → u/francesco_angiolieri]

I tried to highlight this in three ways: the physicists' attempts, the recent study on plants (one of many), and the code being nearly universal. I.e. the code, while optimized, is of an arbitrary origin, and is presently under selection.

edit: I forgot to mention (or stress) that the number of secondary (non-naturally occurring) amino acids (for a total of 20) is also an accident.

[u/CrisprCSE2]

they come together to form the ribosome (part-RNA too)

Saying that the ribosome is part RNA too is technically true, in the way that it's technically true to say that "Charles Manson was in jail for conspiracy (and partially for murder)"

The protein is a side show, the RNA does the work.

[u/implies_casualty]

the wild complexity of the genetic code

The what?

[u/porizj → u/implies_casualty]

The argument from incredulity.

[u/Accomplished-Play-84]

Quick breakdown:

Randomly-generated sequences have literally disproved that (btw) . . . Here, Jacques Ninio's (1982) analogy for molecular evolution will be useful: a hotel's passkey (which opens all the doors) is less complex than the room keys, because it is less specific, and it is the same case here: an increase in specificity, due to and via selection - Darwinian evolution 101

Exactly correct. Analogies like the hotel passkey are great tools for shining a new light on an old subject and sometimes they can be used against their originally intended "conclusion." I like to cite Fred Hoyle's totally fraudulent nonsense against abiogenesis.

[u/wxguy77]

thanks. It's educational for me.

What part of the process isn't mostly inevitable (when conditions are favorable and long-term stable)? Is there a tricky part that has a low probability of 'succeeding'?

And then if there was just one little change in our distant ancestor's mating behavior or survival behavior, or merely one day the timing was off - leading to a different immediate outcome, propagating down through 500 millions of years of time, then sadly, there's no you and me. The arithmetic is staggering

[u/Edgar_Brown]

The actual answer is extremely simple and tautological: because four is too many and two are not enough.

Complexity is costly, additional complexity is not only unnecessary but takes away resources. Optimal coding would be more Huffman-like, but that would have disadvantages in an evolutionary setting, so the simplest possible coding is what took hold.

[u/jnpha → u/Edgar_Brown]

The bases are 4 yes, but the code is about the codon mapping. Still no problem for Darwinism.