Evidence requiring transcriptase quantum processing is identified and elementary quantum methods are used to qualitatively describe origins and consequences of time-dependent coherent proton states populating informational DNA base pair sites in T4 phage, designated by G-C--G'-C', G-C--*G-*C and AT--*A-*T. Coherent states at these 'point' DNA lesions are introduced as consequences of hydrogen bond arrangement, keto-amino--enol-imine, where product protons are shared between two sets of indistinguishable electron lone-pairs, and thus, participate in coupled quantum oscillations at frequencies of approximately 10(13) s(-1). This quantum mixing of proton energy states introduces stability enhancements of approximately 0.25-7 kcal/mole. Transcriptase genetic specificity is determined by hydrogen bond components contributing to the formation of complementary interstrand hydrogen bonds which, in these cases, is variable due to coupled quantum oscillations of coherent enol-imine protons. The transcriptase deciphers and executes genetic specificity instructions by implementing measurements on superposition proton states at G'-C', *G-*C and *A-*T sites in an interval Deltat10(-13) s. After initiation of transcriptase measurement, model calculations indicate proton decoherence time, tau(D), satisfies the relation Deltattau(D)10(-13)s. Decohered states participate in Topal-Fresco replication to introduce substitutions G'--T, G'--C, *C--T and *G--A. Measurements of 37 degrees C lifetimes of the keto-amino DNA hydrogen bond indicate a range of approximately 3200-68,000 yrs. Arguments are presented that quantum uncertainty limits on amino protons may drive the keto-amino--enol-imine arrangement. Data imply that natural selection at the quantum level has generated effective schemes (a) for introducing superposition proton states--at rates appropriate for DNA evolution--in decoherence-free subspaces and (b) for creating entanglement states that augment (i) transcriptase quantum processing and (ii) efficient decoherence for accurate Topal-Fresco replication.

Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can be considered as hardware and software of living systems that are co-optimized during evolution. We try to model DNA replication in this sense as a multi-body entanglement swapping with a reliable qubit representation of the nucleotides. In our model molecular recognition of a nucleotide triggers an intrabase entanglement corresponding to a superposition state of different tautomer forms. Then, base pairing occurs by swapping intrabase entanglements with interbase entanglements. We examine possible realizations of quantum circuits to be used to obtain intrabase entanglement and swapping protocols to be employed to obtain interbase entanglement. Finally, we discuss possible ways for computational and experimental verification of the model.

We present strong evidence for quantum entanglement in noisy non-equilibrium systems at high temperatures by determining the timescales and temperatures for which entanglement is observable in a protein structure that is central to photosynthesis in certain bacteria

Replication of DNA and synthesis of proteins are studied from the view-point of quantum database search. Identification of a base-pairing with a quantum query gives a natural ... explanation of why living organisms have 4 nucleotide bases and 20 amino acids. ... these numbers arise as solutions to an optimisation problem. Components of the DNA structure which implement Grover's algorithm are identified, and a physical scenario is presented for the execution of the quantum algorithm. ... This genetic information processing takes place at the molecular level, where quantum physics is indeed the dominant dynamics (classical physics effects appear as decoherence and are subdominant). It is reasonable to expect that if there was something to be gained from quantum computation, life would have taken advantage of that at this physical scale. For DNA replication, the quantum search algorithm provides a factor of two speed-up over classical search ... Quantum algorithms can provide a bigger advantage for more complicated processes involving many steps. ... During DNA replication, the intact strand of DNA acts as a template on which the growing strand is assembled. At each step, the base on the intact strand decides which one of the four possible bases can pair with it. This is exactly the yes/no query (also called the oracle) used in the database search algorithm. ... What matters is only the relative phase between pairing and non-pairing bases. During the pairing process, the bases come together in an initial scattering state, discover that there is a lower energy binding state available, and decay to that state releasing the extra energy as a quantum. ... the base-pairing takes place not with a single Hydrogen bond but with multiple Hydrogen bonds (two for A-T and A-U, and three for C-G) ... Multiple Hydrogen bonds are necessary for the mechanical stability of the helix. But they are also of different length, making it likelythat they form asynchronously. With a two-step deexcitation process during base-pairing, the geometric phase change ... [is] ... what is needed ... DNA replication is observed to occur at the rate of 1000 base-pairings/sec. ... DNA is accurately assembled, with an error rate of 10^(-7) per base pair, after the proof-reading exonuclease action. Proteins are assembled less accurately, with an error rate of 10^(-4) per amino acid ...

Let a DNA sequence be an element of {A,C,G,T}*, and suppose we’re allowed the following primitive operations: (1) insert a base pair anywhere we want, (2) delete any substring, (3) reverse any substring, and (4) copy any substring into any other part of the string. Then given a DNA sequence S, how hard is it to estimate the minimum number of operations needed to produce S starting from the empty string?

Closely related is the following problem: by starting from the empty string and applying o(n) operations, can we produce a “pseudorandom DNA sequence” of length n — that is, a sequence that can’t be distinguished in polynomial time from a uniform random one?

(Note 1: For both problems, we might also want to stipulate that every intermediate sequence should have size at most polynomial in n. Or better yet, maybe one can prove that such an assumption is without loss of generality.)

(Note 2: I’m also very interested in what happens if we disallow the powerful operation of reversal.)

For all I know, these problems might have trivial (or at any rate, known) answers; I just came up with them and haven’t thought them through.

What the problems are really getting at is this: is the “effective number of bits” in your genome (that is, the number of bits from a polynomial-time algorithm’s perspective) limited by how many ancestors you’ve had since life on Earth began? Or can it be vastly greater?

Update (11/4): Rereading the last few paragraphs of Eliezer’s post, I see that he actually argues for his central claim — that the human genome can’t contain more than 25MB of “meaningful DNA” — on different (and much stronger) grounds than I thought! My apologies for not reading more carefully.

In particular, the argument has nothing to do with the number of generations since the dawn of time, and instead deals with the maximum number of DNA bases that can be simultaneously protected, in steady state, against copying errors. According to Eliezer, copying a DNA sequence involves a ~10-8 probability of error per base pair, which — because only O(1) errors per generation can be corrected by natural selection — yields an upper bound of ~108 on the number of “meaningful” base pairs in any given genome.

However, while this argument is much better than my straw-man based on the number of generations, there’s still an interesting loophole. Even with a 10-8 chance of copying errors, one could imagine a genome reliably encoding far more than 108 bits (in fact, arbitrarily many bits) by using an error-correcting code. I’m not talking about the “local” error-correction mechanisms that we know DNA has, but about something more global — by which, say, copying errors in any small set of genes could be completely compensated by other genes. The interesting question is whether natural selection could read the syndrome of such a code, and then correct it, using O(1) randomly-chosen insertions, deletions, transpositions, and reversals. I admit that this seems unlikely, and that even if it’s possible in principle, it’s probably irrelevant to real biology. For apparently there are examples where changing even a single base pair leads to horrible mutations. And on top of that, we can’t have the error-correcting code be too good, since otherwise we’ll suppress beneficial mutations!

Incidentally, Eliezer’s argument makes the falsifiable prediction that we shouldn’t find any organism, anywhere in nature, with more than 25MB of functional DNA. Does anyone know of a candidate counterexample? (I know there are organisms with far more than humans’ 3 billion base pairs, but I have no idea how many of the base pairs are functional.)

Lastly, in spite of everything above, I’d still like a solution to my “pseudorandom DNA sequence” problem. For if the answer were negative — if given any DNA sequence, one could efficiently reconstruct a nearly-optimal sequence of insertions, transpositions, etc. producing it — then even my original straw-man misconstrual of Eliezer’s argument could put up a decent fight!

The so-called nucleosomes represent long parts of DNA, tuned around the histone octamer. This octamer consists from 4 pairs of histones (H2A; H2B; H3 and H4). The diameter of such nucleosomes (stable nuclear-protein complexes) is about 110 . The histones are able to modulate the DNA structure and functions. In accordance to our Hierarchic theory of condensed matter {}, the high density and stability of nucleosomes and native chromosomes provides condition for mesoscopic Bose condensation (mBC) at ambient temperature in their volume. The [mBC] may exist in form of so-called primary translational and librational effectons, representing 3D standing de Broglie waves of atoms/molecules of condensed matter (chromosomes in private case).

The existence of [mBC] and their coherent [C--W] pulsation, allows the quantum entanglement between chromosomes of distant cells and even between different organisms with similar properties of their molecular Virtual Replica (VR), as between and [R].

It leads from our model, that the synchronization of the interacting chromosomes dynamics by coherent photons of certain frequency and polarization, should enhance the effect of quantum entanglement and interaction of their (VRS and VRR), because of induced combinational resonance.

Вася Пи... еще немного и ты будешь стойким защитником теории и на конец то перейдешь и к опытам подтверждающими оную ..
ps

Петр, Инквизиция хоть и на праздниках но не может не отметить, что уровень дискурса Ваших оппонентов значительно культурнее

Пока у меня один оппонент - па улита. Она достойна именно такого стиля

И замечу, стиль обходится без привлечения не нормативной лексики. Все в рамках дозволенного.

На нас ссылается Вики. Помните об этом

Во первых, не очень то и в рамках...
А во-вторых это создает негативное впечатление о Ваших аргументах . На нас ссылается Вики. Помните об этом

Петрович ! На Ваше учение (в лице квантофорума) смотрит весь мир (в лице википедии)

Вики? Можно ссылку?

Впрочем, учту - добавлю сарказма. Это, надеюсь, не возбраняется?

Закладка Обсуждение - Обсуждение на форумах

Владимирович, а в самом то деле - там кажись убрали ссылку

Все на месте. Ссылки правда только на первые 5 томов

ru.wikipedia.org/wiki/%D0%9E%D0%B1%D1%81...BE%D0%B2%D0%B8%D1%87


Вот здесь, похоже, выступает Гаряев сотоварищи с одной стороны, молекулярные биологи и физики с другой: Часть 1, Часть 2, Часть 3, Часть 4, Часть 5. Пока от обвинений в занятии лженаукой ему отделаться не удалось --Q Valda 06:31, 9 марта 2010 (UTC)

чукч с Кольцовки, а попросту чайник555

Ооо ! чайник появилси. А я думал он сюда уже не заглядывает.

Вы ознакомились с Новогодним посланием Петровича к россеянам

Вот и мою 3-ю монографию взялись перевести

чукч с Кольцовки, а попросту чайник555,
1. Ходить все время гостем это моветон, да и лишние сложности
2. Клоуны и пр. также не поощряются
3. Мне дадут отдохнуть или нет?

limarodessa написал(а):Вы ознакомились с Новогодним посланием Петровича к россеянам

Уважаемый-Limarodessa!  Если можно по секрету всему -свету кто такой Петрович?

Если можно по секрету всему -свету кто такой Петрович?

Ежели узнаете, то лучше не станет... и спокойнее тоже...