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Comment by ild | Hacker News Reader

That claim about DNA, mutations and quantum effects - well it makes the paper less credible. DNA and its replication and mutations are largely non-quantum and it is also not true at all that in DNA every matters; minor alterations of the do not produce invalid code.

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The pull quote from the article is indeed misleading.

McFadden's work is an attempt to provide a foundation for adaptive mutation.

Adaptive mutation is where only well adapted mutations occur at odds with a random explantion.

From (the OP's author) McFadden's and Khalili's 1999 paper: A quantum mechanical model of adaptive mutation

"The principle that mutations occur randomly with respect to the direction of evolutionary change has been challenged by the phenomenon of adaptive mutations. There is currently no entirely satisfactory theory to account for how a cell can selectively mutate certain genes in response to environmental signals. However, spontaneous mutations are initiated by quantum events such as the shift of a single proton (hydrogen atom) from one site to an adjacent one. We consider here the wave function describing the quantum state of the genome as being in a coherent linear superposition of states describing both the shifted and unshifted protons. Quantum coherence will be destroyed by the process of decoherence in which the quantum state of the genome becomes correlated (entangled) with its surroundings."

http://www.researchgate.net/profile/Johnjoe_Mcfadden/publica...

Protein folding is a quantum thing indeed. And folding matters no less than the amino acids sequence.

Folding has nothing to do with DNA.

DNA encodes the amino acid sequence. Quantum mechanics defines the folding. These two things combined determine the colour of your eyes, etc., etc. Encoding per se is meaningless without the folding.

Also, the way how RNA polymerase work (i.e., transcription) is of quite a quantum nature too.

DNA needs to be _unfolded_ during transcription. Anyway, the information stored in DNA in a very much non-quantum nature.

> Also, the way how RNA polymerase work (i.e., transcription) is of quite a quantum nature too.

Proof?

Yes, the DNA encoded information is classic (please do not consider my comments as any kind of an endorsment of the OP article). But, as I said, this is only a half of the information you need to get any sensible predictions of the results. The rest is defined by folding, and it is very much quantum (heuristics aside).

> Proof?

I never heard of any polymerase simulation which did not involve computational quantum chemistry methods. Cannot even think of any possible classic approximation (again, heuristics aside - they're just masking the quantum nature of the underlying physics).

EDIT: as for transcription, do not forget about the operons. Theirs molecular mechanics is also very quantum.

DNA and RNA both also fold.

This is an approximation:

http://mfold.rna.albany.edu/?q=mfold/dna-folding-form

The underlying quantum chemistry (which doesn't need to specifically invoke coherence or tunneling) is required to get truly accurate results. Classical approximations aren't sufficient to measure really subtle energy differences between folded forms.

I am not talking about RNA. I am talking strictly about. The way DNA stores information has nothing to do with the way it is folded. Proteins and some types of RNA require proper folding to function, DNA does not.

This is incorrect: DNA in the folded form of chromatin stores information. In particular, chromatin state is epigenetic and is used to deactivate many genes during the development process.

Further, even a duplex is a "fold" (coiled coils are a structural motif).

You're fixating on the A T G C base form of encoding; DNA contains a lot more information than just that, encoded in its quatenary structure.

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