WHAT IS A GENE?


 

A QUANTUM STATE READY TO COMPUTE WITH THE ENVIRONMENT…

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Abstract: A few biological observations suggest that describing "genes" with just acid coding for proteins (be it DNA or RNA) comes short.  It would rather seem that a full description of heredity (of the so called "phenotype") shows it arising partly as an inheritance of geometrical elements. The full power of Quantum Physics then allows to entangle its informational content with that of the environment by Quantum computations.

More precisely, the deep nature of the gene is found to be any inheritable geometric structure (organelles are an example). The ability of Quantum computation to create greater complexity in a non local manner allows genes to bring initial conditions that are complexified by the information contained in the global nature of the environment. This turns the biggest mystery of Quantum physics into an explanation of how so much morphogenesis comes from so little local data. 

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The initial definition of the concept of "gene" dates from the nineteenth century, shortly after Mendel’s work. The idea was that a gene is defined as any smallest element of hereditability in a living organism.

This is much better than overspecialized definitions having to do with DNA. First of all, some viruses contain no DNA. But if one catches one of these viruses, they will feel very much alive: the SARS virus is an example. So one would have to replace "DNA" by "nucleic acid sequence having a functional effect".

But there are several drawbacks with this. First there is such a small number of "genes" using that nucleic acid definition, that it stretches the imagination towards incredulity that all the inheritable information is contained therein. It’s hubris to decide we know all, when obviously something seems so amiss.

Secondly, division of nuclear DNA is only part of what divides during cell division. Mitochondria (with their own DNA) also divides. So do many organelles, which acquire specific positions during division. For example the Golgi apparatus. The localization of other organelles also seems to indicate specific functions during cell division. In addition, organelle positioning mediated by the actin cytoskeleton is implicated in the inheritance of organelles by the daughter cells. In other words, there is a lot of geometry dividing when cells divide, beyond nuclear acid dividing.

Third, prions have been discovered. Prions are infectious agents that are composed of protein. Such agents have been discovered to propagate by transmitting a misfolded protein state. Of course, some people will declare that the propagation of a "geometrical state" is not the propagation of a "gene". According to the acid definition of "gene", certainly not. But, according to the original, and most general definition, why not?

Fundamentally, life is a form of nanotechnology, itself a form of Quantum Physics. Life is a form of organized Quantum. The Quantum is all about states. Quantum states, OK. But Quantum states are truly geometrical states. Just like the prion.

Conclusion: genes are inheritable geometrical states (in particular, some of them are pieces of nucleic acid states).

One could say: how did we progress here, besides having a more mathematical, more general definition of "gene"?

Well, Quantum states do not just lay in state. Quantum states are geometrical states obtained by mixing particular initial conditions with the geometry of the environment. And as they do so, they do more. That is the core of the dispute between Bohr and Einstein. Bohr believed that one could not detach the apparatus from the experience being conducted. So he introduced an element of non locality that infuriated Einstein. On that particular point, Einstein was wrong, as more and more experiments have definitively demonstrated.

Non locality shows up as a computation. For example, as a deep space, transgalactic photon meets a galaxy, the geometry of the photon state interacts with the geometry of the galaxy, producing gravitational lensing. Thus, from two geometries as initial condition, one gets, through a Quantum computation, a more complex one. Complexity has been Quantum generated. I propose that the complexity of life is generated (in part) through that exact Quantum mechanism.

Gravitational lensing is an observed fact. And, although a Quantum theory of gravity does not exist yet, the facts, as described here, are beyond dispute, at this level of generality (see the note for those who know advanced physics and would object to the gravitation-Quantum conflation just boldly evoked, in a conceptual leap).

Most probably, something of the same sort probably happens during biological morphogenesis. indeed, otherwise, one would have to invent some new facts to dispel reality as it is known to happen, both on the smallest (Quantum) and largest (Transgalactic) scale.

Hence combining geometrical genes with the geometry of the environment through a quantum computation generates the observed complexity of life.

Erwin Schrodinger, the Quantum physicist with the eponymous equation, wrote a short book, "What is life?" in which he carefully considered that a reproducing "aperiodic crystal" ought to be at the core of the genetic storage of life It was a good guess. It was credited by F. Crick, and several other most famous biologists, has having inspired them.

But that was a while ago (1944). Thus, it may have been time to make further informed guesses…

***

Patrice Ayme

http://patriceayme.com/

http://tyranosopher.blogspot.com/

 

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Note 1: I breathed through some physics so advanced above that it may well be false. But, if it false, known physics would have to be modified.

In particular, I gave gravitational lensing as an example of Quantum computation. On the face of it, this is completely silly, since gravitational lensing is purely "classical". But, philosophically, it is fully cogent. Let me explain.

In "general relativity", Einstein’s theory of gravitation, the matter-energy tensor determines the geodesics of space-time. Basically the heftier the mass-energy in a neighborhood, the more space-time is (positively) curved in this neighborhood: geodesics can converge. Photons describe geodesics, so they can converge to a point beyond a galaxy, and, sitting at that point, looking towards it, the galaxy has acted as a giant lens. This is how Einstein’s theory was confirmed by an Eddington expedition to Africa in 1919, as a solar eclipse allowed to observe that sun grazing light indeed deviated in the exact amount (twice that predicted by simple Newtonian gravity).

This is "classical", id est, non Quantum physics. In Quantum physics, though, the trajectory of the photon as it curves graciously around the galaxy, cannot be determined. Saying that the photon follows a geodesics, the mainstay of Einstein’s theory, has no meaning. Instead a mysterious happening a la Bohr is going on. But here the laboratory is the entire neighborhood around a galaxy, something hundreds of thousands of light years across. The Schrodinger cat is not just dead and alive, it has swallowed a galaxy, too. Whatever is going on is hidden, and not described by either Quantum theory or Einstein’s gravity.

The only thing we can say, for sure, is that some form of Quantum computation is going on. And that is what I said. In light of this, viewing biological morphogenesis as a Quantum computation is no more outrageous.

Note 2: I did not mention "non coding" DNA (so called junk DNA). Although it constitutes 95% of the genome, and, although it probably does much, it only adds more acid to the mix. Instead the process above, obtaining the apparition of massive complexity through the Quantum interaction of inherited geometry with the environment, is a completely new explanatory scheme.

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6 Responses to “WHAT IS A GENE?”

  1. FreeDem Says:

    My undergraduate embryology course pointed to things like fingers where at the time nerves, etc go to fingers the distance is short and direct. There must also be a great many other situational or fractal issues that would eliminate the need for special coding, including many you note at cell division.

    As you also note the dividing difference between a parasite, a commensal, and mitochondria, resides in the observer and not chemistry or evolution.

    However while much is happening at quantum levels I think that the butterfly effect might be a more relevant description. That very small critical differences, particularly with iteration could have a much larger effect than could be achieved by Quantum Physics

    Like

    • Patrice Ayme Says:

      FreeDem: Please do not underestimate the Quantum: it’s everywhere. I really do not believe we live in a classical world. That is why I gave gravitational lensing as a deliberately provocative example: it belongs to straight classical physics, General Relativity. But as I stated, this is an obvious mistake. Galactic lensing has got to be a Quantum effect … I have my own theory about the Quantum, but i will not push it too much, lest the cries of the Beotians, as Gauss used to say… I think the Quantum gives the arrow of time (it does so naturally in my theory).

      People always mention the butterfly effect, but I have my doubts: there are evolution theorems due to Poincare’ that imply a lot of classical mechanics is quasi periodic, thus insensitive in a sense to perturbations, in the fullness of time (sorry for putting a math researcher hat on for a secon or two here).

      As you say “situational”, or, as I say, geometrical (or even topological) effect can allow to eliminate a lot of coding. I just added Quantum computing in the mix.

      PA

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  2. MC Says:

    Patrice,

    I’ve often fantasized about morphogenesis and the effect of genes……It’s interesting on how robust morphogenesis can be with changes in the genes, in fact whole or partial chromosome additions or deficits e.g trisomy 21 an extra 21st chromosome results in Down’s syndrome. When you consider the amount of information involved Down’s syndrome…it results in a complete (but less robust) organism with all the basic parts in place. There are genes and groups of genes that are so vital that problems with them probably result in early demise of the embryo.

    From the evolutionary perspective, the gene activities seem to act like interacting “formulas” that result in multidimensional protein, lipid, intracellular, extracellular and inter-organ orchestration for development. Sometimes I think the most likely prospect is that the real mystery is the growth and development phase to birth. That’s where the real magic happens. Growth and development to sexual maturity is just increase in size, scope or organ systems and then hormonal activation for reproduction.

    In any case, my imagination tends toward seeing genes as formulas that interact in probablistic ballets that lead to reproductive vigor and durability in the environment. This is strictly from the point of view of an individual….There are likely evolutionary issues with species durability and co-evolution of species e.g. flowers and i nsects. Another layer of mathematical complexity for the formulas that makes to whole seem even more wonderful.

    Who needs religion? We are lucky enough to know now how beautiful and elegantly the universe behaves in the living world (even if we only have the outline). We’re very lucky to have this much insight.

    Merrill

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    • Patrice Ayme Says:

      Merrill: Agreed….

      My solution to the complexity of morphogenesis problem is not a classical twist (as “Catastrophe Theory” tried to do!)

      My solution is to view genes as sorts of initial conditions, in the mathematical sense, and then harness the environment to compute, because that is what Quantum mechanics does. As I explained, the intrinsic nature of the Quantum computation allows to create an immense complexities out of a simpler inputs. In a typical Quantum experiment, there is a particle, and it interacts with the labs’ geometry (what Dirac calls interacting with itself… which is demonstrably not always true, BTW). A galaxy is simple; it is sort of rounded, a potential well, very symmetric. the incoming photon is as simple as it gets too. Still the lensing effect produced is complex.

      This way the environment brings in enormous amounts of information that is flushed into the relatively paltry inherited geometry… hence the infuriating mystery of the measuring device becoming part of the result is turned to great advantage… for life, because out of rather simple inputs, the “genes”, one gets much more complex geometries. I view this as a deep insight, philosophically speaking: Quantum physics makes life, and even heredity, possible by presenting us with a massively generating externality… (It also makes the arrow of time possible as I brazenly showed on my secret site).

      Like

  3. MC Says:

    It seems like my biological intuition and your Math/Physics intuition concur to a degree. I like the concept of “initial conditions” introduced in to a geometrical environment….leading to complex yet consistently expressed results. The complexity of our life systems is vast, yet so “predictable” from the organisms point of view.

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    • Patrice Ayme Says:

      Merrill:
      Another way to say what I said in the essay is that the Quantum mechanics, per its intrinsically non local nature, allows to harness the environment during biological morphogenesis. Per its intrinsic complexity, Quantum mechanics allows to significantly complexify the initial geometrical input, so it makes morphogenesis complex (partly an inside joke, since QM uses complex analysis).

      PA

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