Posts Tagged ‘DNA’

How Neanderthals, Dinosaurs Disappeared?

June 23, 2015

IS THE SAME FUNDAMENTAL MECHANISM AT PLAY?

Dinosaurs are still around: they are called birds. Birds are those dinosaurs which enjoyed high metabolism. In difficult circumstances, those who acted quick could stay warm, and make the slow, or their eggs, into lunch. Mammals, too, and probably even more, exerted deadly pressure on dinosaur reproduction.

Dinosaurs were big (the smallest, like Velociraptors, were feather covered, and turkey sized). To create the same number of average individuals dinosaurs may have required a thousand times more energy as for the average bird: obvioulsy after a disaster, their population would not rebound as fast.

The Past Is Printed With DNA, & We Can Read It.

The Past Is Printed With DNA, & We Can Read It.

[As we can read DNA like a printed book, Paleontology is becoming history, complete with written documents! Represented above: the 40,000 years old Homo Sapiens jaw which was sequenced, and found to be a Sapiens Sapiens- Sapiens Neanderthal hybrid.]

Much spectacular progress is made in paleontology, every month. In the latest, some dinosaur protein would have been isolated. Sequencing and making a Jurassic Park, someday, is not science fiction anymore. Such was the truth, in June 2015. (In the preceding month, that would have sounded like science-fiction.)

Now we have a new fact supporting the theory I hold that Neanderthal’s traits were outbred. Here is yesterday’s recap from Nature:

http://www.nature.com/news/europe-s-first-humans-what-scientists-do-and-don-t-know-1.17815

Neanderthals are also still around. Or more exactly Neanderthal genome: 1% to 3% (although some claim up to 9% of combined Neanderthal and Denisovan ancestry!). And more so in East Asia and among Native Americans. Some find strange that Neanderthal genome disappeared more in Europe, where Neanderthal reigned so long.

But it just means that genetic competition between Sapiens Neanderthal and Sapiens Sapiens traits was more in favor of the later there… Perhaps simply because winters are milder in Europe.

Neanderthals had evolved from Archaic Homo Sapiens, and ruled Europe for 300,000 years. Most of the time, the continent was in the grip of glaciation. Neanderthals evolved genetic adaptations to these Arctic conditions, such as a larger body mass, and a more compact, more muscular, powerful body.

However technological advances such as clothing, burning coal (!), the propeller (to launch javelins further), and the bow made those Neanderthal genetic modifications obsolete, moot, duplicative. A prime defect was higher mass. Reproducing the same number of Neanderthals required more energy than the same number of more gracile forms of Homo Sapiens.

When in competition, the reproductive advantage of the more gracile traits grow exponentially in time:
https://patriceayme.wordpress.com/2013/03/14/why-did-neanderthals-disappear/

It is not about Homo Sapiens Sapiens enjoying superior traits relative to Neanderthals.

The disappearance of Neanderthals is about most Sapiens Neanderthal traits having become excess evolutionary baggage. So the traits got out-selected. One should expect that the heavy, Arctic genetic traits were weeded out, and only superior traits (the 3%) were kept. As observed. And more so in Europe, as winters are milder there than in the rest of the Eurasian land mass (South Asia excluded). As observed. In other words, after an Arctic excursion, Neanderthals transmutated back into what they came from, keeping some useful mutations (many having to do with skin).

The tree of evolution is rather a network (with a non-trivial topology).

A case in point is Homo itself. The first prototypes (so to speak) may have separated from chimpanzee like ancestors, ten million years ago. But the official theory has it, at this point, that there was some interbreeding with chimpanzees, around six million years ago again.

BTW, it is not true that no Neanderthal DNA is found in sub-Saharan Africa. That’s so yesteryear, 2014. Neanderthal DNA has been found all the way down to South Africa’s tip (2015 discovery), and the migration route traced.

Patrice Ayme’

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’

Rosalind Franklin: Be A Blossom Of Wisdom

June 29, 2014

Rosalind Franklin, born in Notting Hill, London, was from a wealthy Jewish British family. Armed with a PhD, she spent nearly 5 years studying X ray technique in Paris. Back in Cambridge, she made a succession of discoveries, including the double helix structure of DNA.

Franklin died at the age of 38, a victim from ovarian cancer. I would venture to say that it is likely she got the disease from her work with radiation (as Nobels Marie and Irene Curie clearly did).

Rosalind, 4 Years After Elucidating the Double Helix

Rosalind, 4 Years After Elucidating the Double Helix

Is the human condition a vacation from nothingness? We live, and, in the long run, we die. So what do we live for? Fundamentally, because life is what animals are, that’s what they do. Yet, humans know they will evaporate. So, in their case, there is more: an esthetical choice.

They know their lives, in a way, are gratuitous acts. All proportion kept, they are like those insects who fly around just one day. Humans are erased as they die. The God illusion was invented to deny this. Yet, increasingly, most people do not believe in it, and never did.

So what to live for?

For eons, people learned all they could, and the best were called Shamans. They tried to transmit the knowledge and stories to their (spiritual) descendants. For at least 50,000 years, that process, a continual re-invention of the human condition, ruled. It was no doubt achingly painful for shamans to transmit the wisdom, before they died, and see it all slip back.

Visible progress accelerated only with the invention of civilization, herding and agriculture (in which order is not too clear; wolves certainly came first, at least 50,000 years ago, at least that’s my Neanderthal wolf theory).

Nowadays have writing. Writing was painfully evolved over the eons, and started with painting and other pictorial representations (as Robinson imagines in his book linked to above). We cannot just examine our existence, nowadays, but also the past.

“The results suggest a helical structure (which must be very closely packed) containing probably 2, 3 or 4 coaxial nucleic acid chains per helical unit and having the phosphate groups near the outside.” — Rosalind Franklin, official report, February 1952.

Franklin’s two manuscripts on the double helix DNA reached Acta Crystallographica in Copenhagen on 6 March 1953, one day before Watson & Crick completed their model saying what she wrote months prior.

The details on how Franklin made the discovery of the double helical structure of DNA are complex. The guy who stole her work, to give it to Watson and Crick, Wilkins, had suggested an helix. He probably wanted to exact vengeance on Franklin, who he viewed, erroneously, as having stolen the show, and a PhD student of his. Franklin was actually acting under orders from the head of the lab, who did not bother to warn Wilkins. Wilkins stole Franklin’s famous Photograph 51, and gave it secretly to Watson & Crick.

People who had stolen Rosalind Franklin’s work, were published first in the magazine Nature, although her earlier discoveries were fundamental (to the thieves). The thieves got the Nobel after her death, and insulted her, post mortem, just to make sure that their forfeiture would reign unchallenged (by the same way, in recent years, Watson was widely condemned for racist theories: nastiness is a way of life).

Grotesquely, but tellingly, the Nobels don’t mention prior discoverers. So Franklin was ignored. That makes this Nobel prize a tool of manipulative conspiracies, from the usual suspects. Just as Copernic and Newton are attributed discoveries that were made centuries EARLIER, not mentioning deceased discoverers allow to mangle the history of systems of thought, in arcane, but efficient ways.

That despicable tradition was (slightly) changed for the egregious case of the so called Higgs particle; a prior Belgian discoverer, by then deceased, was mentioned. But the particle is still called a Higgs, because Anglo-American white males are supposed to be dominant in most ways intellectual… Thus in all other ways.

Raping women is an old tradition, most fruitful.

A French professor called, Lejeune, a Catholic fanatic close to John Paul II was the guy who stole credit for discovering trisomy 21. Sleazy behavior like that qualifies automatically for sainthood in the Catholic church. It’s an old tradition started by the killing of Hypatia, an Egyptian female Einstein of 16 centuries ago, by Saint Cyril and his rape murdering sadistic goons.

So Lejeune was fast-tracked for sainthood. Unfortunately for the sleaze ball, his victim, differently from Franklin is still alive (although 88 years old, and having, as she says, better things to do than fighting for recognition, but viewing as a duty to set the record straight ).

The real discoverer of the chromosomal anomaly was a woman, Marthe Gautier, who had done all the cell work that led to the identification of the supplementary chromosome. She had learned in Harvard some ways of manipulating cells, and brought her knowledge back to Paris. She got a bit of space, some rudimentary equipment, and cultured cells using serum derived from her own blood. The same story happened as with Franklin: her pictures were stolen, and Lejeune presented them as his own.

That controversy was well known, so the Nobel committee did not attribute a Nobel for that major discovery, the first explicit roll-out of a genetic abnormality, and its exact mechanism.

It helped that all the discoverers, real or imaginary, were French: one of the missions of the Nobels is to prove the superiority of Anglo-American thinking, and thus of Vulture Funds over Argentina. Hence all the caviar in Manhattan.

Hey, corrupt Nobel clowns! Marthe Gautier is still alive! What about rewarding her, finally? It would be encouraging to all the women out there, who work hard in matters intellectual. Or, at least, it would make you look less corrupt with power and influence.

Here is a letter of Rosalind Franklin to Ellis Franklin, her father. It has no date, possibly summer 1940 whilst Rosalind was an undergraduate at Cambridge University.

“You look at science (or at least talk of it) as some sort of demoralising invention of man, something apart from real life, and which must be cautiously guarded and kept separate from everyday existence. But science and everyday life cannot and should not be separated. Science, for me, gives a partial explanation for life. In so far as it goes, it is based on fact, experience and experiment.”

Rosalind lived like a thinking rose. It’s the best choice we all have. The best metaphysics worth having. We are all roses, and may as well make beauty, the beauty of minds well blossomed, the pinnacle of creation.

Patrice Aymé

WHAT IS A GENE?

September 2, 2009

 

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…

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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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