That claim about DNA, mutations and quantum effects - well it makes the paper less credible. DNA and its replication and mutations are largely non-quantum and it is also not true at all that in DNA every matters; minor alterations of the do not produce invalid code.
DNA encodes the amino acid sequence. Quantum mechanics defines the folding. These two things combined determine the colour of your eyes, etc., etc. Encoding per se is meaningless without the folding.
Also, the way how RNA polymerase work (i.e., transcription) is of quite a quantum nature too.
Yes, the DNA encoded information is classic (please do not consider my comments as any kind of an endorsment of the OP article). But, as I said, this is only a half of the information you need to get any sensible predictions of the results. The rest is defined by folding, and it is very much quantum (heuristics aside).
> Proof?
I never heard of any polymerase simulation which did not involve computational quantum chemistry methods. Cannot even think of any possible classic approximation (again, heuristics aside - they're just masking the quantum nature of the underlying physics).
EDIT: as for transcription, do not forget about the operons. Theirs molecular mechanics is also very quantum.
The underlying quantum chemistry (which doesn't need to specifically invoke coherence or tunneling) is required to get truly accurate results. Classical approximations aren't sufficient to measure really subtle energy differences between folded forms.
I am not talking about RNA. I am talking strictly about. The way DNA stores information has nothing to do with the way it is folded. Proteins and some types of RNA require proper folding to function, DNA does not.
This is incorrect: DNA in the folded form of chromatin stores information. In particular, chromatin state is epigenetic and is used to deactivate many genes during the development process.
Further, even a duplex is a "fold" (coiled coils are a structural motif).
You're fixating on the A T G C base form of encoding; DNA contains a lot more information than just that, encoded in its quatenary structure.
The pull quote from the article is indeed misleading.
McFadden's work is an attempt to provide a foundation for adaptive mutation.
Adaptive mutation is where only well adapted mutations occur at odds with a random explantion.
From (the OP's author) McFadden's and Khalili's 1999 paper:
A quantum mechanical model of adaptive mutation
"The principle that mutations occur randomly with respect to the direction of evolutionary change has been challenged by the phenomenon of adaptive mutations. There is currently no entirely satisfactory theory to account for how a cell can selectively mutate certain genes in response to environmental signals. However, spontaneous mutations are initiated by quantum events such as the shift of a single proton (hydrogen atom) from one site to an adjacent one. We consider here the wave function describing the quantum state of the genome as being in a coherent linear superposition of states describing both the shifted and unshifted protons. Quantum coherence will be destroyed by the process of decoherence in which the quantum state of the genome becomes correlated (entangled) with its surroundings."
The author is a molecular biologist with several published books and over 100 peer-reviewed articles, so he definitely has a grasp on basic biology. I think that what you are missing is the assertion that each atom plays an individual role in the process. That is, there are low-level processes that take place on a small enough scale to depend on quantum effects that make direct contributions to DNA. The point is that quantum physics contributes a lot more than we usually think to macroscopic processes like biology.
The author's 1999 paper proposes a quantum mechanic to explain adaptive mutation.
They assert that E. Coli mutates to develop lactase in a lactose enviroment, it does this quickly and seemingly without adverse mutations - randomness fails to explain this.
McFadden and Khalili propose that adaptive DNA mutation is a quantum computation.
The many possible mutations are explored simultaneously and the quantum state collapses to one highly correlated to the enviroment.
Their 1999 paper A quantum mechanical explanation for adaptive mutation goes in depth.
"The principle that mutations occur randomly with respect to the direction of evolutionary change has been challenged by the phenomenon of adaptive mutations. There is currently no entirely satisfactory theory to account for how a cell can selectively mutate certain genes in response to environmental signals. However, spontaneous mutations are initiated by quantum events such as the shift of a single proton (hydrogen atom) from one site to an adjacent one. We consider here the wave function describing the quantum state of the genome as being in a coherent linear superposition of states describing both the shifted and unshifted protons. Quantum coherence will be destroyed by the process of decoherence in which the quantum state of the genome becomes correlated (entangled) with its surroundings. Using a very simple model we estimate the decoherence times for protons within DNA and demonstrate that quantum coherence may be maintained for biological time-scales. Interaction of the coherent genome wave function with environments containing utilisable substrate will induce rapid decoherence and thereby destroy the superposition of mutant and non-mutant states. We show that this accelerated rate of decoherence may significantly increase the rate of production of the mutated state."
I'm no physicist but this smacks of total BS. We know that DNA codes for proteins chemically and no sort of "entangled wave function" is going to spontaneously change an A to a G, split or recombine a DNA molecule along a particular gene boundary, or cause a duplication.
The fact that some cells might generate more mutations in response to environment changes doesn't demand quantum weirdness. Did the authors ever think _maybe_ there is a good old enzyme inside cells that intentionally alters the DNA at particular locations, thereby generating mutations?
Note that Jackie Barton has already shown that conjugated pi bonds formed along DNA chains can be used to transmit information; the theory of molecular orbitals is a quantum one.
Also, spontaneous mutations occur, and they're caused by interactions between bases and photons; again, these can only be explained by using quantum molecular orbital theory.
I'm not going to the argue the author of your quoted statement is likely to be correct.
The abstract maybe a tad general, but the paper specifically refers to the movement of a single proton :
" As initially proposed by Delbruck et al. (1935)
and Schrodinger (1944) and Watson and Crick
(1953), spontaneous mutations are initiated by
quantum jump events such as tautomeric shifts in
single protons of DNA bases."
You reference catalysts and there are some indications this is a quantum tunneling phenomena :
Here is a talk by Professor Nigel Scrutton of the University of Manchester who has many papers on this,
Quantum effects in biological catalysis
You say it makes you 'cringe', yet you offer no substantial argument to why you are fearful of their hypothesis. Saying things like "BS" and "WTF" is a weak attempt at hacking biases, and usually attributed to dissonance. I don't accept biased arguments as truths. Quite the contrary, I see them as indicators of an unresolved argument.
I'm not afraid of their hypothesis and I welcome the truth, however weird it may be.
I didn't read that as fear of their hypothesis. I read it as irritation with the enormous amount of quantum waffle offered by loons, quacks, and frauds. Evolutionary biology has also had to deal with pseudoscientific intrusion from the get-go.
This paper may be totally legit, and quantum magic may really be how biology works. But I can totally see why someone would whip out Occam's Razor and start slashing after reading that paragraph.
There are countless examples of mutations that are single letter transcription errors, insertions, duplications, recombinations. Quantum effects and superpositions aren't necessary to explain those. I wonder what extra explanatory power this theory adds over more conventional chemical models of DNA and what evidence exists that quantum effects are anything more than negligible.
If we're simulated, this would be a spectacularly good way to get a bit of us out of this reality and into another one. It would also allow only a singleton instantiation of you, which is important if you care about those things. Over 70 percent of us believe we have a soul. That number is dropping.
It seems like a science writer's scheme to tie theoretical physics to what "the informed reader" may have familiarity or interest in, ie. DNA, putting Schrodinger and Crick in the same orbit.
Technically speaking, molecular interactions must rely on quantum effects, therefor the encoding does exist at the quantum level, as opposed to the applesauce level.
But this article is not really about genetics or applesauce.
To me the "quantum level" distinction is the issue. This is like saying you need to use Newtonian calculations for one set of speeds and Einstein's for another as if reality "switched gears" like a race car. The quantum level is the only level, all distinctions are purely in the mind.
It is Schroedinger who said that, who, considering his time in history, had a very broad view of what quantum mechanics and DNA are.
Given his high level viewpoint he was correct, considering that he was making a reference to interactions at the level of the universe. Although it is actually your DNA which codes the colour of your eyes, it is also true that quantum mechanics plays a part in the DNA encoding itself, which is what makes his statement true. And the fact that furthermore an exact process was discovered actually makes his statement a remarkably good prediction, as shown here:
"And, just as Schrödinger predicted, ‘every group of atoms’ does indeed play ‘an individual role’, with the position of even individual protons – a quantum property – determining each genetic letter".
I'm a biophysicist. Almost most of my work uses entirely classical approximations to quantum (which themselves are parameterized using quantum chemistry and physics), I can assure you, that by definition, all biology is inherently quantum. The physics of hydrogen bonds practically guarantee it (to the extent we can make positive factual statements).
The biophysics of DNA mutation repair -- DNA mutations are a major contribution to genetic changes that lead to observable phenotypes -- are ultimately and firmly quantum. It's unclear at this point whether the quantum phenomena such as coherence or tunneling play any role, but the definition of "quantum" is much larger than just those phenomena. My intuition is that quantum tunnelling of electrons probably plays a role in the kinetics of DNA mutation repair, although this is purely speculative.
Further, some very interesting and mostly ignored experiments by Jackie Barton have demonstrated that the DNA backbone can be used to transmit information; the conjugated pi orbitals of the bases form a long-range, possibly coherent electron path(!) but it's not clear that these phenomena are relevant to evolution.
But isn't the reason that the classical approximations work so well that quantum effects are drowned out by the thermal noise floor at room temperature? And reliable processes like DNA replication have to depend on 'classical' chemical bond energies that are at least a couple of orders of magnitude above the noise floor, right?
No. I think part of the reason people are having so much trouble on this thread is they are confusing the field of quantum physics with quantum chemistry.
The processes of DNA replication actually involve hydrogen bonds, and comparing the relative energies of different forms of hydrogen bond groups, at or near the thermal limit (1-2 kcal/mol).
Each of the main points of the article has the feel that the conclusions are speculative wrt quantum mechanics -- any experts able to comment on them? Feels like an article over-selling inconclusive results.
Well, being surprised that "quantum physics is everywhere" is like being surprised every computer program runs on machine code. Surely you didn't think transistors run JavaScript natively? Quantum physics isn't a weird part of reality, it's the reality (or, to be precise, a low-level model of it).
Exactly. It's not quantum physics that is weird, it's our intuitions that are wrong (since we never had to explicitly deal with nanoscale before XX century).
Our intuition is so poor that it even gets many classical mechanics problems wrong. Most hilariously the various resonance-related things (my favourite practical example is a pendulum swinging upwards, which looks like pure magic).
Intuition is also very poor in dealing with nonlinear things (think soliton waves and all that stuff). So, trusting an intuition is always wrong and intuition got no place in science anyway, not just in nanoscale.
Yes, that's a good example. The recipe I used for such demos was based on an old Soviet electric shaver and a standard bicycle wheel spoke, it's a known combination to get an inverted pendulum (even at funny angles, not necessarily entirely upward).
Even better example, "Heavy things fall faster". Or "The sun revolves around the earth".
As a greater cultural trend there is often a bit of quantum-whitewashing that everything in physics is obvious and straightforward except quantum mechanics because I suffered thru the annoying math and need to show off superiority at being one of the few humans (on a percentage of entire population) who understand a good chunk of QM. Relativity gets the same treatment.
However its important to note that none of physics is very intuitive. Heavy things don't fall faster. The sun doesn't orbit the earth. The general public has some peculiar ideas about the laws of thermodynamics. Orbits in space are not perfect circles. Atomic structure is not a fractally small solar system. QM is typical and normal for physics in having non-intuitive dark corners, that's the norm for all of physics not a peculiarity of QM.
There is shibboleth value in that you define a physicist or a dude who knows physics as a guy who walks around saying QM is the only non-intuitive component of physics. Not because its true, but because that's one of the official physicist mating calls or whatever you want to call it, shibboleth I guess.
There is also the deus ex machina aspect that in all forms of non-technical drama (aka all of it) people who like to write magical fantasy have decided to fool us into thinking its new by copy-and-replace word processing "quantum" in for "Tolkienish magic", see also the multiverse people.
> Even better example, "Heavy things fall faster". Or "The sun revolves around the earth".
Except that those two particular examples are very easy to explain to (nearly) everybody:
1- you think that heavy things fall faster because this is true when there is air resistance.
2-Q:if you have one 'fixed' object and one rotating object, what do you see from the rotating object?
A: the same thing as from the 'fixed' object.
So is it the Sun which is revolving or the Earth?
You don't feel like the Earth is moving but observation of remotes stars have shown us that this is the case.
Which is NOT the case for QM!
A good example: QM 'spooky action at distance', QM predicts that there are non-local instantaneous (FTL) effects, but they cannot be used to send data FTL and this has been measured to be true (mostly).
> those two particular examples are very easy to explain
Explanations do not affect intuition at all, it's too primal to listen to any reason. Even despite the fact that everybody heard this explanation from the elementary school, watching this in action is still mind-blowing. Check it out yourself [1], and answer honestly - was your intuition puzzled by what you've seen?
It's always a shame when the Copenhagen interpretation of quantum mechanics is presented as how reality works. Most of the perceived weirdness of QM comes from the leaps of faith required to make the Copenhagen interpretation work.
There's a lot of truth in that, and the orthodox interpretation is indeed riddled with incoherence. But what fascinates me is that after so much effort, the quantum community seems to be further away than ever from coming to a consensus on interpreting the theory. Every proposed interpretation does away with some foundational issue, yet introduces another in the process.
If you mean "what has led you to think they're further away from consensus": mostly just gut feeling, as a (younger) member of that community. I've not seen any rigorous and comprehensive studies of which interpretations garner the most support, but it does seem like popularity is currently divided between the orthodox and several other interpretations that have evolved from "niche" to "significant minority" in recent years.
If instead you mean "by what process are they further away from consensus": I would suggest that the recent surge of research in quantum information theory has stimulated a greater interest in foundational issues, which in turn has led to an invigoration of the interpretations debate.
I meant "rigorous and comprehensive" to include "representative of the entire quantum community". That poll was conducted at a single conference and had 33 participants. The bias inherent in this approach can be seen when the same poll was conducted at two other conferences:
In both cases, de-Broglie Bohm interpretations ruled the day. As the abstract of the latter paper states:
> ...the results do strongly suggest several interesting cultural facts -- for example, that there exist, within the broad field of "quantum foundations", sub-communities with quite different views, and that (relatedly) there is probably even significantly more controversy about several fundamental issues than the already-significant amount revealed in the earlier poll.
My opinion is that the Copenhagen interpretation does not contradict DeBroglie in terms of nuclear chemistry, but solely thermodynamics.
The Copenhagen interpretation makes a leap of faith with the Born Rule as it is based on Maxwell-Boltzmann statistics. The work of t'Hooft is a more modern alternative for ensembles where the outcome is stochastic, rather than probabilistic. Photosynthesis has that property, as do many other enzymatic systems.
Not sure what you mean by "contradict". Certainly you won't easily find experiments for which the two offer different predictions. They are very different in terms of their ontology though: DeBroglie states that particles have definite positions and momenta at all times whereas Copenhagen does not.
Most of the contradictions arise as epistemological forks in the context of molecular spectroscopy with nuclear decay events. Thusly, it is a question of whose theories to use, and the Born rule is moot when the distribution of particles is not gaussian.
DeBroglie himself states that matter waves propagate according to a defined distribution; whereas Copehagen interprets that they are probabilistically distributed. In the former case there is a stochastic process, whereas it is only a random process in the latter case.
What do you mean by "moot"? The Born rule is simply that the probability of measuring a particle to be in a certain location is given by the squared amplitude of the wavefunction. This squared amplitude will generate the same predictions whether you are using deBroglie-Bohm or "Copenhagen" to imagine your underlying ontology.
The difference in ontology being that deBroglie-Bohm is deterministic, i.e. particles have definite positions of which we are merely ignorant, whereas "Copenhagen" is (usually) non-realist, i.e. it is not meaningful to talk about the positions of particles until the moment we measure it.
In this context, the word moot is a synonym for false.
You are omitting the word "normalized wave function" from your description of the Born Rule; it is a key part of the mathematical justification. The squared amplitude does not generate the same predictions under every theory, because the probability function is different.
That is also the difference between the theories of DeBroglie and Bohm, the former is stochastic while the latter is deterministic. Copenhagen theories describe the positions of particles probabilitistically; and the word 'measure' is not being used in the precise mathematical way that it should be. A better translation from Danish would be 'convolute'.
The thing to remember is that when one writes about physics which are centuries old, one must be historiographically consistent. If there is a hyphen between two names for a theory, such that one name is being attributed posthumously; then the student should infer the most recent name is making some error in translation.
When you separate DeBroglie and Bohm, on the basis of their lack of real cooperation, then it is clear to see who was ahead of their time. Bohm is abusing statistical terms in his translations from French, and the meaning of those words is an extremely important detail in the context of Quantum Information Theory. John Von Neumann was contemporaneously working in that context, but it was classified until recent times.
> The Copenhagen interpretation makes a leap of faith with the Born Rule as it is based on Maxwell-Boltzmann statistics.
The Born rule was introduced in Born's paper on description of a scattering experiment with help of the \psi function that is a solution of Schroedinger's equation. Maxwell-Boltzmann statistics had nothing to do with it.
Because thermodynamics at the time espoused normally distributed error as dictated by Maxwell-Boltzmann statistics; Born used a normalized wave function to solve Schroedinger's equation.
Thermodynamics and Linear Algebra have gotten more advanced, since then.
Pilot wave theory: the "weird effects" that QM displays are really just the result of space time being a thing that vibrates in a wave-like pattern influenced by mass.
And the reason this is cool is because when you put everyday objects in situations like that stated above, they exhibit quantum interference and everything else.
So this is essentially what is meant by the "deBroglie-Bohm" interpretation. There is an underlying definite configuration of all matter, but it is "guided" deterministically by the wavefunction psi. This avoids issues associated with wave function collapse, but by no means does it rid us of all the "weird effects". In particular, the pilot wave is explicitly non-local, in that for a Bell-type experiment the choice of measurement in one location will (instantaneously) affect the physical state of affairs in the other location.
Quantum mechanics is simply a set of equations that describe the universe. Whether or not those equations make sense or are interpretable is irrelevant, as our capability to understand intuitively is only based on the types of interactions we observe every day.
To ask somebody what interpretation they prefer is akin to asking a mathematician how they interpret the reality of ZFC they prefer. It's interesting, but ultimately pointless, because it has more to do with our ability to interpret than with the real meaning of the statements. To that end, Copenhagen makes the important point - "Shut up and calculate".
> To that end, Copenhagen makes the important point - "Shut up and calculate".
No, it doesn't. It adds a few assumptions on top of that. That's the point of the whole debate. To be fair, the many-worlds interpretation also does that.
That's how people used to view "imaginary" numbers...and the field of complex analysis laid dormant for 200 years. When a valid geometric interpretation was found that backed up the algebraic existence of these numbers, the field blossomed.
We're humans, we can't understand equations without knowing what they "mean."
The Copenhagen interpretation? Not so much. It's an interpretation. The actual physics is in the equations. I can believe the equations without believing the Copenhagen interpretation, or any interpretation.
Right. The various interpretations are not so much science as philosophy. At best, they're scientific hypotheses, and that's only if they turn out to be falsifiable.
Exactly. Many people seem to fall into trap of regarding established theories of theoretical physics as some ultimate truths about the world, instead of as currently used useful models which are necessarily imperfect simplifications of things. It is depressing to see science, which has contributed to exposition of fallacy of church teachings during the past centuries and help enlighten people, to be on its best way to becoming a church full of dogma and blind followers itself.
If the brain-splitting weirdness of human life has a basis in physics, all we can do is give up and succumb to the utter illogic of it all. Somehow that perspective makes me uncomfortable.
Not quite. They believe there are two separate universes, one in which the cat is alive and one in which the cat is dead. This is very different from thinking the cat is alive and dead simultaneously in the same universe.
It's not so much a matter of disagreeing. It's that the quantum mind is off-topic. Bringing it up here looks like an attempt to publicize the idea by riding on the coat-tails of a completely unrelated article. That's worthy of downvotes, whatever one thinks of the idea itself.
to me, the strongest argument for quantum weirdness (which isn't actually that weird once you appreicate that quantum laws don't actually allow you to break causality) in biology is photosynthesis. There is some pretty strong evidence- not completely agreed upon but still pretty strong- that coherence plays a role.
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[ 2.7 ms ] story [ 144 ms ] threadAlso, the way how RNA polymerase work (i.e., transcription) is of quite a quantum nature too.
> Also, the way how RNA polymerase work (i.e., transcription) is of quite a quantum nature too.
Proof?
> Proof?
I never heard of any polymerase simulation which did not involve computational quantum chemistry methods. Cannot even think of any possible classic approximation (again, heuristics aside - they're just masking the quantum nature of the underlying physics).
EDIT: as for transcription, do not forget about the operons. Theirs molecular mechanics is also very quantum.
This is an approximation:
http://mfold.rna.albany.edu/?q=mfold/dna-folding-form
The underlying quantum chemistry (which doesn't need to specifically invoke coherence or tunneling) is required to get truly accurate results. Classical approximations aren't sufficient to measure really subtle energy differences between folded forms.
Further, even a duplex is a "fold" (coiled coils are a structural motif).
You're fixating on the A T G C base form of encoding; DNA contains a lot more information than just that, encoded in its quatenary structure.
McFadden's work is an attempt to provide a foundation for adaptive mutation.
Adaptive mutation is where only well adapted mutations occur at odds with a random explantion.
From (the OP's author) McFadden's and Khalili's 1999 paper: A quantum mechanical model of adaptive mutation
"The principle that mutations occur randomly with respect to the direction of evolutionary change has been challenged by the phenomenon of adaptive mutations. There is currently no entirely satisfactory theory to account for how a cell can selectively mutate certain genes in response to environmental signals. However, spontaneous mutations are initiated by quantum events such as the shift of a single proton (hydrogen atom) from one site to an adjacent one. We consider here the wave function describing the quantum state of the genome as being in a coherent linear superposition of states describing both the shifted and unshifted protons. Quantum coherence will be destroyed by the process of decoherence in which the quantum state of the genome becomes correlated (entangled) with its surroundings."
http://www.researchgate.net/profile/Johnjoe_Mcfadden/publica...
Uh, nope.
They assert that E. Coli mutates to develop lactase in a lactose enviroment, it does this quickly and seemingly without adverse mutations - randomness fails to explain this.
McFadden and Khalili propose that adaptive DNA mutation is a quantum computation.
The many possible mutations are explored simultaneously and the quantum state collapses to one highly correlated to the enviroment.
Their 1999 paper A quantum mechanical explanation for adaptive mutation goes in depth.
http://www.researchgate.net/profile/Johnjoe_Mcfadden/publica...
This has led to a new scientific discipline Quantum Biology http://www.ias.surrey.ac.uk/workshops/quantumbiology/
"The principle that mutations occur randomly with respect to the direction of evolutionary change has been challenged by the phenomenon of adaptive mutations. There is currently no entirely satisfactory theory to account for how a cell can selectively mutate certain genes in response to environmental signals. However, spontaneous mutations are initiated by quantum events such as the shift of a single proton (hydrogen atom) from one site to an adjacent one. We consider here the wave function describing the quantum state of the genome as being in a coherent linear superposition of states describing both the shifted and unshifted protons. Quantum coherence will be destroyed by the process of decoherence in which the quantum state of the genome becomes correlated (entangled) with its surroundings. Using a very simple model we estimate the decoherence times for protons within DNA and demonstrate that quantum coherence may be maintained for biological time-scales. Interaction of the coherent genome wave function with environments containing utilisable substrate will induce rapid decoherence and thereby destroy the superposition of mutant and non-mutant states. We show that this accelerated rate of decoherence may significantly increase the rate of production of the mutated state."
I'm no physicist but this smacks of total BS. We know that DNA codes for proteins chemically and no sort of "entangled wave function" is going to spontaneously change an A to a G, split or recombine a DNA molecule along a particular gene boundary, or cause a duplication.
The fact that some cells might generate more mutations in response to environment changes doesn't demand quantum weirdness. Did the authors ever think _maybe_ there is a good old enzyme inside cells that intentionally alters the DNA at particular locations, thereby generating mutations?
WTF...
Also, spontaneous mutations occur, and they're caused by interactions between bases and photons; again, these can only be explained by using quantum molecular orbital theory.
I'm not going to the argue the author of your quoted statement is likely to be correct.
" As initially proposed by Delbruck et al. (1935) and Schrodinger (1944) and Watson and Crick (1953), spontaneous mutations are initiated by quantum jump events such as tautomeric shifts in single protons of DNA bases."
You reference catalysts and there are some indications this is a quantum tunneling phenomena :
Here is a talk by Professor Nigel Scrutton of the University of Manchester who has many papers on this, Quantum effects in biological catalysis
https://www.youtube.com/watch?v=SnxmHlbtJDI
----
Here is Donald's paper criticising McFadden and al-Khalili's ideas http://people.bss.phy.cam.ac.uk/~mjd1014/qevrev.pdf
and their rebuttal : http://arxiv.org/abs/quant-ph/0110083v1
---
The 2012 Quantum Biology Conference at the IAS has some excellent papers - which are (too briefly) summarised into the OP article. http://www.ias.surrey.ac.uk/workshops/quantumbiology/
I'm not afraid of their hypothesis and I welcome the truth, however weird it may be.
This paper may be totally legit, and quantum magic may really be how biology works. But I can totally see why someone would whip out Occam's Razor and start slashing after reading that paragraph.
Technically speaking, molecular interactions must rely on quantum effects, therefor the encoding does exist at the quantum level, as opposed to the applesauce level.
But this article is not really about genetics or applesauce.
http://lesswrong.com/lw/pc/quantum_explanations/
Is that true / nuanced in some particular way I don't know about?
The biophysics of DNA mutation repair -- DNA mutations are a major contribution to genetic changes that lead to observable phenotypes -- are ultimately and firmly quantum. It's unclear at this point whether the quantum phenomena such as coherence or tunneling play any role, but the definition of "quantum" is much larger than just those phenomena. My intuition is that quantum tunnelling of electrons probably plays a role in the kinetics of DNA mutation repair, although this is purely speculative.
Further, some very interesting and mostly ignored experiments by Jackie Barton have demonstrated that the DNA backbone can be used to transmit information; the conjugated pi orbitals of the bases form a long-range, possibly coherent electron path(!) but it's not clear that these phenomena are relevant to evolution.
The processes of DNA replication actually involve hydrogen bonds, and comparing the relative energies of different forms of hydrogen bond groups, at or near the thermal limit (1-2 kcal/mol).
All chemistry is quantum already.
Intuition is also very poor in dealing with nonlinear things (think soliton waves and all that stuff). So, trusting an intuition is always wrong and intuition got no place in science anyway, not just in nanoscale.
[1] https://www.youtube.com/watch?v=5oGYCxkgnHQ
Even better example, "Heavy things fall faster". Or "The sun revolves around the earth".
As a greater cultural trend there is often a bit of quantum-whitewashing that everything in physics is obvious and straightforward except quantum mechanics because I suffered thru the annoying math and need to show off superiority at being one of the few humans (on a percentage of entire population) who understand a good chunk of QM. Relativity gets the same treatment.
However its important to note that none of physics is very intuitive. Heavy things don't fall faster. The sun doesn't orbit the earth. The general public has some peculiar ideas about the laws of thermodynamics. Orbits in space are not perfect circles. Atomic structure is not a fractally small solar system. QM is typical and normal for physics in having non-intuitive dark corners, that's the norm for all of physics not a peculiarity of QM.
There is shibboleth value in that you define a physicist or a dude who knows physics as a guy who walks around saying QM is the only non-intuitive component of physics. Not because its true, but because that's one of the official physicist mating calls or whatever you want to call it, shibboleth I guess.
There is also the deus ex machina aspect that in all forms of non-technical drama (aka all of it) people who like to write magical fantasy have decided to fool us into thinking its new by copy-and-replace word processing "quantum" in for "Tolkienish magic", see also the multiverse people.
Except that those two particular examples are very easy to explain to (nearly) everybody: 1- you think that heavy things fall faster because this is true when there is air resistance.
2-Q:if you have one 'fixed' object and one rotating object, what do you see from the rotating object? A: the same thing as from the 'fixed' object. So is it the Sun which is revolving or the Earth? You don't feel like the Earth is moving but observation of remotes stars have shown us that this is the case.
Which is NOT the case for QM! A good example: QM 'spooky action at distance', QM predicts that there are non-local instantaneous (FTL) effects, but they cannot be used to send data FTL and this has been measured to be true (mostly).
Explanations do not affect intuition at all, it's too primal to listen to any reason. Even despite the fact that everybody heard this explanation from the elementary school, watching this in action is still mind-blowing. Check it out yourself [1], and answer honestly - was your intuition puzzled by what you've seen?
[1] http://www.iflscience.com/physics/dropping-bowling-ball-and-...
If instead you mean "by what process are they further away from consensus": I would suggest that the recent surge of research in quantum information theory has stimulated a greater interest in foundational issues, which in turn has led to an invigoration of the interpretations debate.
In short Copenhagen still (sadly) rules the day, followed by many worlds and QIT.
http://arxiv.org/abs/1303.2719
http://arxiv.org/abs/1306.4646
In both cases, de-Broglie Bohm interpretations ruled the day. As the abstract of the latter paper states:
> ...the results do strongly suggest several interesting cultural facts -- for example, that there exist, within the broad field of "quantum foundations", sub-communities with quite different views, and that (relatedly) there is probably even significantly more controversy about several fundamental issues than the already-significant amount revealed in the earlier poll.
The Copenhagen interpretation makes a leap of faith with the Born Rule as it is based on Maxwell-Boltzmann statistics. The work of t'Hooft is a more modern alternative for ensembles where the outcome is stochastic, rather than probabilistic. Photosynthesis has that property, as do many other enzymatic systems.
DeBroglie himself states that matter waves propagate according to a defined distribution; whereas Copehagen interprets that they are probabilistically distributed. In the former case there is a stochastic process, whereas it is only a random process in the latter case.
The difference in ontology being that deBroglie-Bohm is deterministic, i.e. particles have definite positions of which we are merely ignorant, whereas "Copenhagen" is (usually) non-realist, i.e. it is not meaningful to talk about the positions of particles until the moment we measure it.
That is also the difference between the theories of DeBroglie and Bohm, the former is stochastic while the latter is deterministic. Copenhagen theories describe the positions of particles probabilitistically; and the word 'measure' is not being used in the precise mathematical way that it should be. A better translation from Danish would be 'convolute'.
The thing to remember is that when one writes about physics which are centuries old, one must be historiographically consistent. If there is a hyphen between two names for a theory, such that one name is being attributed posthumously; then the student should infer the most recent name is making some error in translation.
When you separate DeBroglie and Bohm, on the basis of their lack of real cooperation, then it is clear to see who was ahead of their time. Bohm is abusing statistical terms in his translations from French, and the meaning of those words is an extremely important detail in the context of Quantum Information Theory. John Von Neumann was contemporaneously working in that context, but it was classified until recent times.
The Born rule was introduced in Born's paper on description of a scattering experiment with help of the \psi function that is a solution of Schroedinger's equation. Maxwell-Boltzmann statistics had nothing to do with it.
Thermodynamics and Linear Algebra have gotten more advanced, since then.
And the reason this is cool is because when you put everyday objects in situations like that stated above, they exhibit quantum interference and everything else.
To ask somebody what interpretation they prefer is akin to asking a mathematician how they interpret the reality of ZFC they prefer. It's interesting, but ultimately pointless, because it has more to do with our ability to interpret than with the real meaning of the statements. To that end, Copenhagen makes the important point - "Shut up and calculate".
No, it doesn't. It adds a few assumptions on top of that. That's the point of the whole debate. To be fair, the many-worlds interpretation also does that.
We're humans, we can't understand equations without knowing what they "mean."
Rather than what it is: our best model.
The Copenhagen interpretation? Not so much. It's an interpretation. The actual physics is in the equations. I can believe the equations without believing the Copenhagen interpretation, or any interpretation.
If the brain-splitting weirdness of human life has a basis in physics, all we can do is give up and succumb to the utter illogic of it all. Somehow that perspective makes me uncomfortable.
https://en.wikipedia.org/wiki/Alternative_theories_of_quantu...
Here is McFaddens and Khalili's 1999 paper A quantum mechanical model of adaptive behaviour http://www.researchgate.net/profile/Johnjoe_Mcfadden/publica...
It is an interesting new field and much more scholarly than the OP article allows.
They have a book which goes in depth and Jim has an excellent BBC tv show presenting the key ideas.
Here are Khalili's Royal Institution lecture, the book and tv show, which cover the same material in depth:
https://www.youtube.com/watch?v=wwgQVZju1ZM
http://www.amazon.co.uk/Life-Edge-Coming-Quantum-Biology/dp/...
http://www.bbc.co.uk/programmes/b04v85cj
The IAS 2012 workshop on Quantum Biology has a number of presentations:
http://www.ias.surrey.ac.uk/workshops/quantumbiology/report....
Here is Jim's 2012 presentation on the role of Quantum tunneling in Adaptive Genetic mutation. https://www.youtube.com/watch?v=iujZr42Aho4 https://www.youtube.com/watch?v=iujZr42Aho4
Except, of course, all those physicists that do. http://www.hedweb.com/everett/everett.htm#believes
Crystals: Check
Using established scientific terminology mashed together in a way that sounds rigorous on the surface but is really gibberish: Check!
http://www.chem.utoronto.ca/staff/SCHOLES/scholes_home.html
It's one of the most exquisite bits of biophysics I've ever seen.