A Propaedeutic for Quantum Genetics

I think if people try, they will find that Kant might be of service to quantum biologists seeking to work their fragmentary exemplars into the growth of biological thought.

“Bohr was quite categorical that quantum mechanics was complete; and the most valuable lesson it had taught us was that of complementarity. He was anxious to extend its application to other ¯Fields such as reason and instinct, heredity and environment, physics and biology. His debate with Einstein, begun in the 1927 Solvay Congress, continued for more than two decades, and he adhered to his point of view. In the 70’s however, Dirac had this to say, … the present form of quantum mechanics should not be considered as the final form. It is the best that one can do up till now. But one should not suppose that it will survive indefinitely into the future. And I think that it is quite likely that at some future time we may get an improved quantum mechanics in which there will be a return to determinism and which will, therefore, justify the Einstein point of view. One is left speculating on what Dirac actually had in mind.” Bohr and Dirac by N Mukunda

There is some conversation among those who study Kant over whether his work has any bearing at all on current biology. This debate is nonsense. I know it does. It does not matter that I am not a well known biologist or that I have not completed a PhD. If reading Kant helps anyone to understand biology that is all one needs to know. It helped me. I was able to think about viruses in new ways by reading Kant’s “Metaphysical Foundations of Natural Science”. There may come a time when reading him is no longer helpful, but for now, it definitely is. There is debate after all.

I am going to give a bit a stream of consciousness below — from which flows every now and then from this tapping into — this philosophical re-course or our common heritage — but because it is a mix of metaphysics, science and general understanding, I leave it to the reader to judge whether this is insania or vesania or whether it is sane afterall but as I leave my own post- Foucauldian example this time, I want to show how powerful the future will be if we can grasp that biology may do things in the present only because they existed in the past but are no longer materially extant in the current generation.

I have metaphysically associated true’ attraction (between physical points) with natural selection at and of a locus and thus decoupled the fundamental force of attraction from biologically evolved molecular cohesions. This allows me to work within Kant’s transition project of the Opus Postumum on the forces in classifications and the classification of the forces per body, to provide chemistry with properties of physics and also to present a generationally based infinity between the mechanics of evolution and the forces of evolution that is coincident with cellular reproducibility without necessarily introducing purposiveness to the same biology of cell cycle physiological genetics. Going further through a specific idea on electron ordinality, biological chemicals are distinguished from chemical chemicals of(re-produced) educed ordertypes while all chemicals that were made, were made from the same atoms.

Chirality due to the existence of both RNA and DNA biologically separates aggregation from without as in chemistry and from within as in biology because it establishes inheritance of antisymmetry (between the RNA and DNA) in cohesion of organic and homotypic correlations evolutionarily which cannot exist in chemical (inorganic) systems. Nutrition does this in biology from without. This happens because the proteins (amino acids) may be quantum-critical, insulators or conductors (Kaufmann with others 2015) and the seriality of electron motion across nuclei ordinates into the code over generations that quantum collapse forces. Maxwell was too quick to restrict Faraday’s electrotonic state theoretically within conductors. Atoms are outside of this but molecules may not be. There are supramolecular consequences of this for cytoplasmic structure.

Ok, enough of me for now. Let’s take a look at a slice through the history of quantum mechanics in biology and something quite shocking that I recovered from the literature as I attempted to make sense of my own bubbling expressions of writing something new. The letter featured at the start of this essay may have been the last look at a possible new theory in biophysics that WWII may have stopped and then socially buried but the interface of Linus Pauling’s interest in the subject might better explain why quantum mechanics in biology did not proceed along this path.

Jordan suggested that quantum mechanics might be involved in biology. I am not going to discuss Bohr’s response to this as this is hinted at in the quote that opens this essay.

But look, Linus Pauling really wanted to show that Jordan’s idea was incorrect and you can see by some research how after his attempt to show it mistaken in “Science” (details below) that the idea was never tested. Instead Wigner who had no objection and thought it might be tested later came out saying that quantum mechanics was not involved in life because there could be no synchronization between living states and nutrient states.

“Delbrück told Pauling about the Jordan papers one day when they ran into each other on campus. This was during the period when Pauling was finishing his antibody paper, and had been thinking hard about how proteins could bind to one another. Jordan’s idea of identical molecules sticking together was, of course, much different from Pauling’s antibody-based idea of complementary structures. He and Delbrück strolled to the Caltech library where Pauling found Jordan’s papers and started reading. Within a few minutes, Pauling decided that the ideas presented were, as he put it later, “baloney.” Their paper, “The Nature of the Intermolecular Forces Operative in Biological Processes,” published in Science in the summer of 1940, effectively demolished Jordan’s ideas about identical molecules, clearly stated Pauling’s views on the importance of complementary, die-and-coin relationships between biological molecules (the same sort he had seen sticking together antibodies) — and went almost unnoticed.”

What was good in what Pauling and Delbrück proposed was an empirical study of the actual molecules so as to decide on the properties of natural variational physical chemistry as to what was complementary and what was identical and that is all that I am suggesting too, only I am doing so by talking about the cases where Pauling would have classified them as the same and show that they are actually different and thus not ‘identical”.

The striking thing for me is not so much that the hypothesis was never tested — the argument appeared on a first read strong quantitatively. Pauling was an expert in quantum mechanics and chemical bonds. What Pauling missed was a logical implication — one that if more than theoretical may efface much of chemistry since.

Jordan had been arguing for a catalytic attraction of molecules through quantum mechanics. The computation that Pauling applied to show that it’s quantity was too small applied only to these supposed attractions. And from this Pauling argued that the structural consequences were nonexistent for any of the biological chemistry in which this was supposed to exist — any of Jordan’s ideas. If however the effects of a repulsion and an attraction were taken into consideration, then functional effects on biochemistry would however be something entirely different than Pauling wrote.

The interesting thing about logical implication is that one does not need to even do calculations, to double check the expert, to see that something is a-miss, I mean a mass — Look at Feynman in 1964 — He spent a good chunk of his lecture time at Cornell presenting with any and all manner of gesticulation that there is nothing mysterious about life being chemically chiral.

In the process, Feynman abstracted the idea of an organism as coming from the template view of inheritance that came from DNA sequencing — a Crick day to day thing, but in doing so he had moved away from what Haldane had suggested back when the question of Jordan’s ideas were still in circulation.

Haldane had then shewn that there was both a biological reproduction and a chemical copy and that these were not the same empirical things.

If chemical copies and biological reproductions are different things then an attraction and repulsion that may structure within and between this difference becomes a different biophysics than we have today since these different concepts are considered to be materially the same. Quantum biology is starting to appear interesting and I trace it’s rise to the failure to materialize the difference in these two concepts. There is a whole field of quantum genetics waiting to be born.

There is no doubt that Haldane was onto something by suggesting that offspring may not be able to know who their parent is but all of this was lost on Feynman who decided that since physics itself was chiral it did not matter how biology historically arrived at the same. To understand this we can use Kant’s project to transition then from biology into chemistry through physics.

I will demonstrate this in a deeper analysis of Pauling’s paper for it turns out Feynman was mistaken that identical molecules rather than complementary ones are evolutionarily more ‘fit’ — for in genetics it is the identical that is chemically copied — and this give rise to the homozygotes and it is the physics of recessive and dominance through the identities that a heteroygtoe evolved that was , that is the biological, in the copy. Pauling bet on Bohr when he should have on Jordan instead. Dirac knew better.

The structural chemist in Pauling eventually limited biochemistry to those biophysical circumstances when the identity was also complementary.

He concluded, “”The case might occur in which the two complementary structures happened to be identical; however, in this case also the stability of the complex of two molecules would be due to their complementariness rather than their identity. When speculating about possible mechanisms of auto-catalysis it would therefore seem to be most rational from the point of view of the structural chemist to analyze the conditions under which complementariness and identity might coincide.”

I say that organic correlations as discussed by Pearson with respect to copyable genetic traits however can disrupt this chemically enforced union and if the organic correlations are causal with a high enough selection pressure then biological reproductions may be able to separate what chemically copied eductions functionally keep identifiabely the same since with complentarity comes functional, disfunctional and afunctional chirality, what Feynman did not think about since he only thought chemical chirality was contingent.

I think then that auto catalysis is thus not to be evaluated from the perspective of the structural chemist which sees the rationality from where complementariness and identity MIGHT coincide because to do so restricts the theory in two ways — One from saying that the interactions of auto-catalysis only happens within the space of the two currently interacting molecules and also in that organic imposition, whatever it is, is restricted to the symmetrical cases.

The theory I work from as I displayed at the start is not so restricted on the relation of the chemistry and biology and this is needed as we attempt to describe and develop the symmetrical relations that quantum mechanics might have in evolutionary biology.

Pauling wrote of Jordan’s idea of interaction:

“which is of great importance for biological processes; in particular, he has suggested that this interaction might be able to influence the process of biological molecular synthesis in such a way that replicas of molecules present in the cell are formed.”

These replicas may be caused by biological reproductions or chemical copies (eductions (Kant)). Science does not have a molecular biology of biological molecular synthesis capable of differentiating biological copies from chemical copies the cells form. We just have the beginning of a study of what chemicals remain in the cell from which they originated and which ones are moved into new cells as they- the cells divide. If this process has in any way a bearing through chirality on the relative amounts of complementarity and identity in the replica then Pauling’s whole argument is wrong.

These replicas are not like artifacts but Paluing’s structural chemist bent and idea that the interaction of the two molecules is only what is between these two particular molecules makes it hard to make sure one is not considering these molecules to be artifacts or chemist made copies. The interaction of two identical molecules and two complementary molecules may be different depending not on those biological cases where the two properties coincide as Pauling proposed,and indicated in thoughts as being the most rational, but is rather I say on the total network of possible pairing identical and complementary molecules.

One needs the entire network of chemical production and destruction to decide the relative effects of the complementarity and identity when these are not coincident. Pauling argued against Jordan for whatever reason he did but he did so because he was not going to suggest how to recover this large formation and disformation of biochemicals that is the object of evolutionary biophysiological genetics. He could not because structural chemisty only works with what is in the the test tube in front of them. And thus to do so he forced an abstraction on nature.

This shows that the classifications of forces are depauperate for biochemisty. For me, I suggest how we might build that classification taxonomically up. And very interestingly it appears that the debate of Bateson and Pearson ( Mendelism vs Biometry) resolves within this classified classification when the homotype is applied to gene duplications mutatable from identical copies constrained by formal operations of molecular reversals, complements and reverse complements, how biochemistry since Pauling’s idea can receive a new overhaul.

Why was Pauling silent”” on the Frank Kamensky resonance proposal? Was this because again his idea of finding a structural chemical solution could never get him to the other side of the genetic code where forces from without affect the classifications within. His idea of the classifications of the forces was so restricted he would never have thought of this even if he was really reading well past Mayr on Kant. Of course he probably did not read a lot of what Mayr wrote about philosophy but …We generally fail to get to this other side of the interface because we use the template rather than the interpretation view of DNA inheritance (no matter how you read Schrodinger).

Any way this has gone the way of arguing that living things are complex systems and that perhaps Schrodinger was mistaken to speak of the a periodic crystal. but that is enough for now.

I have shown how Pauling’s insistence on structural chemistry rather than evolutionary chemistry made him unable to understand how to establish Jordan’s need , on Pauling’s own view, that the molecules be non-degenerate in their excited states. No- degeneracy can happen evolutionarily when a resonance repulsion connects with a resonance attraction that is part of a self-copying process — This is what error correcting proteins do for the genetic code. How to make bio theory of their organic possibilities remains. The inconsistency was wholly with Pauling.

“Summing up, then, we find that under the conditions of excitation and perturbation prevailing in aqueous solutions the resonance interaction could not cause a specific attraction between molecules and therefore could not be effective in bringing about auto-catalytic reactions.

Hence I have disproved , even without calculation, that Pauling’s sum-up is even true. It is false..logically.

AS in Computer Science and BS in Biology from Cornell University. Interested in evolution and blockchains