Posts Tagged ‘Organelles’

NON-DNA Genes

May 22, 2015

 

What Are Genes? Well, not what they thought… Yesterday.

NON-DNA INHERITANCE IS NOT JUST CULTURAL, BUT BIOLOGICAL:

A gene in a life form ought to be a mechanism or device which (partly) generates the life form.

Forget about restricting “genes” to DNA inside the nucleus, I am using a philosophical definition. It gives immediately rise to a mathematical definition of “genes”. A “gene” is any reproducible form.

Example: Prions. They reproduce a molecular form. They have nothing to do with DNA.
Do we know genes fully? Certainly not. That would mean we know fully the way a human being (say) is reproduced.

Much Of What's Inside A Cell Is NON-DNA Reproduced

Much Of What’s Inside A Cell Is NON-DNA Reproduced

In the case of humans, it is said by those that everything we are comes from 35,000 genes they distinguish deep down inside. It seems unlikely that one can get so much from so little.
So is there more than those 35,000? Yes. First there are extranucleic genes, part of extrachromosomal DNA. There are also contributions from viruses, which can insert their own genes inside ours. Permanently. All these are part of Non-Mendelian Inheritance.

Moreover, let’s consider cellular division. “VEGETATIVE SEGREGATION” results from self-replication and then partitioning of cytoplasmic organelles. If one just look at the mass of what’s replicated, when a large organism is reproduced most of the mass is generated by this geometric copying. That’s also true for the smallest cell with organelles.

Now it turns out that centrioles are also an example of NON-DNA reproduction. They are transmitted by sperm, whereas mitochondria are transmitted by eggs.

The study just published, from Lausanne’s EPFL University, shows that centrioles can carry information over the generations.

Genetically modified versions of the worm C. Elegans, the one with Free Will, had three different centriole proteins tagged with a fluorescent signal. Tagged male worms were mated to untagged females. Scientists could specifically track centriole components that were contributed from the father during the course of embryogenesis.

Gönczy’s team imaged the fluorescent signals at different cell divisions of the developing embryos, and discovered that paternally contributed centriole proteins persist up to ten cell generations. Centrioles are persistent in the embryos. They are Non-DNA/RNA genetic information carriers.
“Centrioles have always been seen as something that just jumpstarts the development of the embryo,” says Pierre Gönczy. “Here we show that centrioles could be the means of a unidirectional inheritance of information, with considerable impact in early development.”
Several disease are known to originate in centrioles.

The evidence is strong for what I expected all along: organelles themselves are information carriers, and inheritance is not all about DNA. It’s the entire geometry of eukaryotic cell which reproduces, DIRECTLY, geometrically, not just DNA.
That’s called a paradigm shift.

So much for the selfish gene, and similar philosophical reductions to the absurd, fed by provisional science. This shows how dangerous it is to devise hasty philosophy from poorly digested knowledge. We are not just our DNA.

Life reproduces, but life does not just reproduces digitally (that is, through DNA). Instead geometric, topological, and analogous reproduction is also at work.
Patrice Ayme’

WHAT IS A GENE?

September 2, 2009

 

A QUANTUM STATE READY TO COMPUTE WITH THE ENVIRONMENT…

***

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. 

***

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/

 

***

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.

***