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Lately I have been taking an interest in mathematical biology. While reading "Evolutionary dynamics" by Martin Nowak, I came across this reference, where the author describes in short how John von Neumann had described a self reproducing automata which increased in complexity over time; the structure of which was equivalent to the central dogma of biology.

This leads me to my question - what is the role of automata theory in today's biology ? Is it still relevant ? Was there any role that it played in the development of biology ? I couldn't find very comprehensive answers on the internet, so if you know of any sources, please do link them.

Thank you.

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  • $\begingroup$ There is no central dogma in biology. Over 60 years ago as molecular biology was emerging, Crick explained the working hypothesis of those at the forefront of the field of molecular informatics as that information in DNA could be expressed as protein but not vice versa. Experimental evidence has rendered this idea a trivial commonplace — neither central nor a dogma. Anyway, how could the structure of machine be equivalent to a *concept"? $\endgroup$
    – David
    Commented May 27 at 16:37
  • $\begingroup$ Can you explain what you mean by "the development of biology"? Louis Pasteur was certainly a biologist, and his work predated Nowak's by almost one hundred years, as did Gregor Mendel's. $\endgroup$
    – anongoodnurse
    Commented May 27 at 17:06
  • $\begingroup$ @David Thanks for your response. As far as I am aware the process of DNA coding information for how proteins are synthesized is referred to as central dogma. I was referring to the process by this name, and not saying that this a 'dogma' that is 'central' to molecular biology. I should perhaps clarify what I mean by structure of a machine, I didn't mean physical structure, but the logical structure of it. Basically the way the von Neumann's machine works, it's components, and the relationship they bear with one another, is equivalent to central dogma. I hope to have clarified your doubt. $\endgroup$
    – Srinidhi kabra
    Commented May 29 at 12:33
  • $\begingroup$ @anongoodnurse what I mean to ask is has the development of automata theory contributed to biology in some way? If so then could you give me an example ? For example, game theory is applied to understand evolution. $\endgroup$
    – Srinidhi kabra
    Commented May 29 at 12:36
  • $\begingroup$ You awareness was faulty. See this answer from me on this topic: biology.stackexchange.com/questions/49201/… and for confirmation check the Wikipedia article on the topic. It would seem that the analogy you want — good or bad — is with DNA replication, that the structure of DNA is such as to allow self-replication, although not without the participation of other components. This is quite different from the relationship between the information between DNA and proteins of Crick, which is essentially a dead end. $\endgroup$
    – David
    Commented May 29 at 21:35

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Interpretation of the question

From the responses of the poster to questions in comments and the revision of the question my understanding of the comparison it makes is as follows.

The the structure of DNA with its two complementary strands gives it the logical potential for self-replication (by each separated strand being able to serve as a template for a complement). This is formally similar to the von Neumann’s idea of a self-replicating automaton.

The main question would seem to be “whether the ideas of von Neumann (or similar ideas that preceded it) had any influence on the discovery of the potential of DNA for self-replication.”

Answer

No.

Biology, both cellular and molecular, is an experimental subject. Biologists of the traditional kind had long known from direct observation that simple cells could replicate, but their ideas on how this occurred were vague and made no contribution to the deciphering of the replication mechanism.

DNA was investigated by other scientists who had concluded that the evidence indicated that it was the genetic material (an idea that was still contested in the 1940s), and felt that it was important to determine its structure. Neither Watson nor Crick anticipated how the mechanism of self-replication would fall out so beautifully from the structure. There was no theory driving their work, just a desire to see things at the molecular level.

Conclusion

Automaton theory was never relevant to biology, so the question “is it still relevant” falls by the wayside. Computation has a role to play in biology, but more in analysis and technology. The ideas that are the context for the design of experiments emerge mainly from jigsaw puzzling together of previous experimental observations, rather from theoretical concepts divorced from practice.

Bibliography

I recently wrote an account of the history of the discovery of the structure of DNA in answer to a question on SE History of Science and Mathematics. Although the main focus of that question is not relevant, it includes an extensive bibliography.

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  • $\begingroup$ thank you very much for your answer! This was helpful. $\endgroup$
    – Srinidhi kabra
    Commented May 30 at 10:39

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