Quantum jitters behind DNA mutations

It was just a matter of time before quantum mechanics were to be identified as the driving force behind DNA mutations…

“In the past, we knew DNA polymerases make mistakes during DNA replication but did not know how they do it,” said Zucai Suo, Ph.D., Ohio State professor of chemistry and biochemistry. “Now, our study provides a mechanistic sense for how the mistakes arise.”

The results provide “convincing validation for the chemical origins of mutations proposed by Watson and Crick in 1953,” said Myron Goodman, Ph.D., a professor of molecular biology and chemistry at the University of Southern California, who was not involved in the study. “It is significant scientifically, and even though it took about 65 years to prove, it also demonstrates the folly of ever betting against Watson and Crick.”

One of the surprising discoveries made by the team was that the frequency at which bases shifted their shapes varied with DNA sequence. In one of their experiments, Ohio State biochemists Zucai Suo and Walter Zahurancik essentially counted the number of times that polymerases incorporated the wrong base into the DNA. They found that mistakes were indeed not uniform: they appeared more frequently in some sequences than others. For example, a region with more Gs and Cs might form more quantum jitters, and subsequently more mutations, than an area that was rich in As and Ts.

But, it doesn’t end there…

The quantum jitters may be responsible not only for errors in replication, but also in other molecular processes such as transcription, translation, and DNA repair. Therefore, the researchers plan to continue to investigate how these alternative states might disrupt the seamless flow of information contained within our DNA..

https://www.sciencedaily.com/releases/2018/01/180131133343.htm

My personal favorite prediction is that quantum mechanics + is behind the self-assembly of biological systems, such self-assembling bacterial flagellum…

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49 thoughts on “Quantum jitters behind DNA mutations

  1. Those who are familiar with my fascination with quantum mechanics are probably not surprised by the OP. There will be more, God willing.

    Quantum biology, despite the resistance from evolutionary biologists, can’t be bullied out of the classroom by the courts. So, this relatively new voice in science presents a great opportunity for ID and the like, to enlighten the world out of the dark ages of Darwinism and materialism…

    This is in line with what Steven Weinberg once said:
    “After you learn quantum mechanics you are never really the same again…”

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  2. J-Mac,

    Struggling to find any substance in your repeated use of ‘quantum’ as an incantation. A mechanistic confirmation of Watson/Crick’s supposition that mutation has a chemical basis. Well, OK, but what does that show us? Biases?

    The mutations that get through appear to be contextual – they depend on DNA sequence (as an aside, I don’t know how that gets to be included in the ‘quantum’, given the huge distances involved relative to Planck length) There is also a known bias for transition (one purine or pyrimidine substituting for another) rather than transversion (purine/pyrimidine swap). There is error correction, which increases copying fidelity 10 fold. And there is selection/drift, which has no regard for the means by which mutation occurs.

    Any net influence of the quantum on mutation would tend to be swamped by the various biases, in my view. If some ‘force’ is driving evolution through quantum effects, in order to get a mutation ‘out there’ it has to deal with sequence context, error correction, transition/transversion bias, segregation (a kind of drift) and population effects before it can manifest itself as a widespread change.

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  3. Can anyone demonstrate why directed mutations would be more useful, in the long run, than stochastic mutations. With sufficient population size, every possible mutation will occur.

    It seems odd that drift occurs. If the current configuration was intentional, why the continuous change?

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  4. petrushka,

    There is some legitimacy. Adaptive mutations are (contended to be) a thing, and one proposed explanation is that decoherence of quantum waves could take the order of seconds, with the environment forming some analogue of a ‘measurement’ collapsing the wave. What I don’t understand is how, if true, this would tend more often to settle on the adaptive – as if the ‘observer’, the environment, casts a value judgement on the metaphorical cat being alive (or dead).

    Also takes more than a few seconds to get from mutation to effect – the DNA must be translated, taking time, and the resultant superposition includes two different chemical systems, as these proteins simultaneously assert their differences, and invoke further (quantum) downstream consequences, in the entangled state. And ‘a few seconds’ is hardly enough for organisms with generation times of the order of years.

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  5. Allan Miller: Struggling to find any substance in your repeated use of ‘quantum’ as an incantation. A mechanistic confirmation of Watson/Crick’s supposition that mutation has a chemical basis. Well, OK, but what does that show us? Biases?

    Yep. Biases. That’s just one aspect. The article does mention it but the actual mechanism of mutations is quantum tunneling.

    Allan Miller: The mutations that get through appear to be contextual – they depend on DNA sequence (as an aside, I don’t know how that gets to be included in the ‘quantum’, given the huge distances involved relative to Planck length) There is also a known bias for transition (one purine or pyrimidine substituting for another) rather than transversion (purine/pyrimidine swap). There is error correction, which increases copying fidelity 10 fold. And there is selection/drift, which has no regard for the means by which mutation occurs.

    Actually, there is more to it, which the article doesn’t mention.

    We find that the strength of the single base von Neumann entropy depends on the neighbouring sites, thus questioning the notion of treating single bases as logically independent units. We derive an analytical expression for the binding energy of the coupled chain in terms of entanglement and show the connection between entanglement and correlation energy, a quantity commonly used in quantum chemistry.

    http://theskepticalzone.com/wp/no-cloning-theorem-the-double-edge-sword/comment-page-1/#comment-265223

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  6. Allan Miller: There is some legitimacy. Adaptive mutations are (contended to be) a thing, and one proposed explanation is that decoherence of quantum waves could take the order of seconds, with the environment forming some analogue of a ‘measurement’ collapsing the wave. What I don’t understand is how, if true, this would tend more often to settle on the adaptive – as if the ‘observer’, the environment, casts a value judgement on the metaphorical cat being alive (or dead).

    Good for you…the measurement/observer problem….😊

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  7. Allan Miller: Also takes more than a few seconds to get from mutation to effect – the DNA must be translated, taking time, and the resultant superposition includes two different chemical systems, as these proteins simultaneously assert their differences, and invoke further (quantum) downstream consequences, in the entangled state. And ‘a few seconds’ is hardly enough for organisms with generation times of the order of years.

    Quantum effects are super fast, don’t forget…

    For example, the metamorphosis of a tadpole would take forever, if the process of the dissolving the cartilage tail didn’t involve enzymes using quantum tunneling…

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  8. J-Mac,

    Now you’re just saying ‘there’s this thing we call chemistry’. As expected, your own coherence (heh heh) does not persist.

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  9. petrushka: Can anyone demonstrate why directed mutations would be more useful, in the long run, than stochastic mutations

    In case of quantum tunneling mutations certain biases, or restrictions on what mutatations can happen, are involved rather than some kind of force directed mutations…
    To me, it’s all about quantum states in DNA and quantum information behind it…

    petrushka: It seems odd that drift occurs.

    Good point! The question remains what can it accomplish?

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  10. Allan Miller:
    J-Mac,

    Now you’re just saying ‘there’s this thing we call chemistry’. As expected, your own coherence (heh heh) does not persist.

    And how do you think chemistry operates, such as chemical bonds?
    No coherence here? 😉
    Here is quantum chemistry for dummies video:

    https://youtu.be/YjcmLiRSbFQ

    Come back, 1 year

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  11. J-Mac,

    and how do you think chemistry works …

    I know how chemistry works. Electron orbitals, Pauli exclusion principle, all that malarkey. What I don’t see is why saying ‘quantum’ has some kind of revelatory quality over and above all that, and I don’t anticipate this question being answered, given your appallingly bad communication skills.

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  12. petrushka: If the current configuration was intentional, why the continuous change?

    I’m not sure if this is what you mean but change is also a consequence of errors during DNA damage repair due to aging…

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  13. Neil Rickert: “Quantum” is just J-Mac’s alternative spelling for “magic poofing”.

    What’s more scientific? The poofing by the magical, super-natural selection?
    How do you prove that? Faith is not enough.

    Quantum processes can be experimentally determined by zapping lifesystem with laser light.
    It’s been proven in photosynthesis for example

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  14. J-Mac,

    Quantum processes can be experimentally determined by zapping lifesystem with laser light.
    It’s been proven in photosynthesis for example

    Not in dispute. Photosynthesis, respiration, vision, protein folding – quantum analysis has assisted understanding in these areas. And obviously, as discussed, chemistry and the physics of the atom are fundamentally shaped by their quantum nature.

    But the case you are failing to make is that quantum physics has some relevance beyond these – that, for example, the uncertainties that may be involved in DNA replication fidelity indicate some significant evolutionary role. Just saying “this is quantum mechanical” fails to establish any causal chain – that things are as they are at the organismal level directly as a consequence of QM, beyond the trivial.

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  15. J-Mac: What’s more scientific? The poofing by the magical, super-natural selection?
    How do you prove that? Faith is not enough.

    J-Mac won’t miss an opportunity to shoot himself in the foot. Hahaha

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  16. Neil Rickert: “Quantum” is just J-Mac’s alternative spelling for “magic poofing”.

    Well, materialists have zero explanation for all the magic poofing , so at least it’s something.

    Well, OK the materialists do have.. ‘just is..’.

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  17. phoodoo:
    Well, materialists have zero explanation for all the magic poofing , so at least it’s something.

    The magic poofing of what? Where do I go to observe this supposed magic poofing?

    phoodoo: Well, OK the materialists do have.. ‘just is..’.

    Are you telling me you do have an explanation for magic poofing? Let me guess, it’s “magic poofer does it”?

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  18. phoodoo: Which magic poofing?

    Yeah that was my question. Please tell me where this magic poofing you and j-mac spoke about takes place.

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  19. phoodoo: Which magic poofing?

    The poofing by super-natural selection.
    But first, the magical hydrothermal vents had done their magic poofing by creating life.
    But before that, the magical laws of nature did their magic by poofing the hydrothermal vents.
    But before that, the magical mother nature did her poofing and creating the laws of nature…and so on…
    In the end, it all boils down to which magic poofing is more reasonable.
    Materialist hate the idea of magical poofing that implies ID/God, so they worship the magical nature instead and cloak it in science to make them feel good…

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  20. Rumraket:

    : Which magic poofing?

    Yeah that was my question. Please tell me where this magic poofing you and j-mac spoke about takes place.

    The Etheric eliminates the need for magic poofing.

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  21. J-Mac: The poofing by super-natural selection.
    But first, the magical hydrothermal vents had done their magic poofing by creating life.
    But before that, the magical laws of nature did their magic by poofing the hydrothermal vents.
    But before that, the magical mother nature did her poofing and creating the laws of nature…and so on…
    In the end, it all boils down to which magic poofing is more reasonable.
    Materialist hate the idea of magical poofing that implies ID/God, so they worship the magical nature instead and cloak it in science to make them feel good…

    Ahh so no magic poofing at all, just a list of things you are personally ignorant about.

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  22. phoodoo: Well, materialists have zero explanation for all the magic poofing , so at least it’s something.

    Why is there something rather then nothing phoodoo?

    Astound us all with your “explanation”.

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  23. phoodoo: Rummy is going to try to use the, its in a book, in a mysterious vault somewhere, defense.

    But that’s your defense. Magic poofer did it, says so in a book.

    This is the great irony. You accuse evolutionists and materialists of saying things are just magically poofed into existence, then laugh at it “haha why would anyone believe that?”, and then you go and say no no, the real explanation is… actually magic poofing. By the magic poofer, who “just is“.

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  24. OMagain: Why is there something rather then nothing phoodoo?

    Astound us all with your “explanation”.

    It was magically poofed, because the magic poofer who “just is” wanted to do it.

    Says so in a book.

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  25. As a metaphysical naturalist, it doesn’t cost me anything to say, if asked “why are the laws of physics as they are?”, simply to respond with “I have no idea.”

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  26. My point is it makes no difference what causes mutations, or whether they are directed. Mutation does not direct the direction populations take.

    To the extent a mutation makes a difference, selection drives.

    To the extent a mutation is neutral, chance drives.

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  27. Rumraket,

    At least we can name the book, and where it says this.

    Your book is hidden in some unknown library in an undisclosed location by an unknown author, without a title.

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  28. phoodoo: At least we can name the book, and where it says this.

    So are you conceding to your stunning hypocricy? That yes, you yourself are in fact guilty of answering all the things you just wasted your time scolding “materialists” for?
    It’s magic poofing you believe in? Check!
    The magic poofer “just is”? Check!
    It says so in a book? Check!

    phoodoo: Your book is hidden in some unknown library in an undisclosed location by an unknown author, without a title.

    I don’t claim to have any such book. I’m with KN here, wrt to fundamental questions about how the world works, (depending on what specific question) I am not claiming to know. And book-referencing isn’t a rationally defensible answer.

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  29. Kantian Naturalist:
    As a metaphysical naturalist, it doesn’t cost me anything to say, if asked “why are the laws of physics as they are?”, simply to respond with “I have no idea.”

    The question remains: Is such a response, or worldview, intellectually fulfilling?
    Don’t you feel intellectually compelled to investigate WHY the laws of physics are the way they are?
    Someone like you shouldn’t be displaying such ignorance, I think…

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  30. phoodoo: Rummy is going to try to use the, its in a book, in a mysterious vault somewhere, defense

    Even the “simplest” form of life, a cell, requires poofing to explain it’s origins.
    The many components of a cell are irreducibly complex-interdependent, so they couldn’t have arisen by gradual poofing. The functioning cell requires hundreds, if not thousands, of proteins. So, it is not credible to assume a functioning cell could have arisen by gradual poofing.

    All components of the functioning cell degrade outside of a cell membrane, so an instantaneous poofing of the components along with the cell membrane surrounding them and preventing from degrading is a more plausible explanation…

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  31. petrushka:
    My point is it makes no difference what causes mutations, or whether they are directed. Mutation does not direct the direction populations take.

    To the extent a mutation makes a difference, selection drives.

    To the extent a mutation is neutral, chance drives.

    If you assume that mutations eventually lead to an increase of information…

    But, do they?

    If each basepair contains information about the neighbouring basepair,
    as “‘the strength of the single base von Neumann entropy depends on the neighbouring sites, thus questioning the notion of treating single bases as logically independent units.

    https://arxiv.org/abs/1006.4053

    In other words, each mutation usually leads to the loss of information and a degradation of organism, as proven by Behe in Darwin Devolves… Sometimes the loss of information will lead to change of the organism and might help it survive but this is not really the evolution from simpler organism to more complex…

    It’s the other way around.

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  32. J-Mac: The question remains: Is such a response, or worldview, intellectually fulfilling?
    Don’t you feel intellectually compelled to investigate WHY the laws of physics are the way they are?
    Someone like you shouldn’t be displaying such ignorance, I think…

    I consider it rather a gesture of humility to accept that some questions cannot be answered by a finite mind. I think that accepting one’s limitations is an important part of intellectual maturity.

    So no, I don’t find that my intellectual fulfillment depends upon understanding the origins of the universe or why the laws of physics have turned out to be as they are.

    There is a lot in Kant that I reject and I’m much less committed to Kant’s project than I was when I chose this username, but one thing about Kant I still admire is his acceptance of human finitude and that ignorance is, in the long run, ineliminable. The mind is finite, the universe is infinite, and there is much that cannot be comprehended.

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  33. Kantian Naturalist: I consider it rather a gesture of humility to accept that some questions cannot be answered by a finite mind. I think that accepting one’s limitations is an important part of intellectual maturity.

    I agree.

    Kantian Naturalist: So no, I don’t find that my intellectual fulfillment depends upon understanding the origins of the universe or why the laws of physics have turned out to be as they are.

    I find this response lacking.
    I personally feel that the search for meaning in the universe is, or it should be, our primary focus in life. This is what separates us from animals…

    Kantian Naturalist: There is a lot in Kant that I reject and I’m much less committed to Kant’s project than I was when I chose this username, but one thing about Kant I still admire is his acceptance of human finitude and that ignorance is, in the long run, ineliminable. The mind is finite, the universe is infinite, and there is much that cannot be comprehended.

    I’m not familiar with this work. Sorry.

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  34. J-Mac: I find this response lacking.
    I personally feel that the search for meaning in the universe is, or it should be, our primary focus in life. This is what separates us from animals…

    I think there’s a rather crucial distinction between searching for a meaningful or purposeful life — that is, committing oneself to an ethical, aesthetic, or intellectual project — and having answers to ultimate metaphysical questions. I don’t see why being a passionate human rights lawyer, or a brilliant scientist, or dedicated musician depends upon having any explanation for why the laws of physics allow for locally anti-entropic processes such as life and mind.*

    To be sure, I do find it utterly fascinating that the universe does allow for locally anti-entropic processes — and I would like to understand why it does! — but I don’t know if I would feel intellectually unfulfilled if I never understood why.

    * I’ve recently developed a keen interest in the cybernetics movement, from the 1940s to 1970s, and especially Norbert Wiener. The idea that life and mind should be conceptualized as locally anti-entropic processes is one that I got from Wiener’s The Human Use of Human Beings.

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  35. Kantian Naturalist: I think there’s a rather crucial distinction between searching for a meaningful or purposeful life — that is, committing oneself to an ethical, aesthetic, or intellectual project — and having answers to ultimate metaphysical questions. I don’t see why being a passionate human rights lawyer, or a brilliant scientist, or dedicated musician depends upon having any explanation for why the laws of physics allow for locally anti-entropic processes such as life and mind.*

    One can be passionate about his work. His work can lead to breakthroughs that can help millions of people. There is a some kind of a personal, or scientific sense of satisfaction, or accomplishment, that comes with that. Nothing wrong with that.

    To me personally, in the end, it all leads to the same big question…

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  36. Kantian Naturalist: To be sure, I do find it utterly fascinating that the universe does allow for locally anti-entropic processes — and I would like to understand why it does!

    What I personally find fascinating is this: Why do the laws of nature refer to people making the measurement? If there were no humans, there would be no nature?

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  37. J-Mac: If there were no humans, there would be no nature?

    How did the craters on the moon get there?

    How does the milk you leave in your fridge know to spoil if it stops existing when you’re not looking at it? How does it know how long it was since last time you looked, if it stopped existing in the mean time?

    The most simple and obvious explanation that accounts for an incomprehensible number of similar such phenomena is that the world really just continues to exist regardless of whether you, or anyone, is conscious of it or not.

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  38. J-Mac:
    What I personally find fascinating is this: Why do the laws of nature refer to people making the measurement?

    You’ve got it backwards J-Mac, it’s us people who refer to natural phenomena when we make measurements and put them into the formulas that we call “laws.”

    J-Mac:
    If there were no humans, there would be no nature?

    Again backwards. There’s been nature for a lot longer than humans. We depend on it thoroughly. Without nature there would be no humans.

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  39. Rumraket,

    Pretty sure he’s referring to QM’s measurement problem. He still believes that a conscious mind is required to make sense of it. The guy is hopeless. (Not like we didn’t know that already)

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  40. dazz: Pretty sure he’s referring to QM’s measurement problem.

    Yeah I know. It’s the quantum-version of the “how do you know anything exists when you’re not looking?”. For some reason the question is always posed rhetorically, as if we could not have good reasons for thinking the world is really there even when we’re not looking at (aka “interacting” our consciousness with it).

    Unsurprisingly there’s been a simple and obvious answer to that question ever since it was first dreamt up.

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  41. J-Mac:
    Nobel Prize winner Steven Weinberg’s comment on the measurement problem:

    https://youtu.be/mBninatwq6k?t=40m00s

    Weinberg is channeling Bell in that comment. Both were being ironic. That is, they are making fun of the idea that consciousness is needed to “collapse the wavefunction” .

    The idea of “collapse” is also a bad way of thinking about it. It’s better to understand decoherence. Interestingly enough, this is an area where physics borrows themes from evolutionary biology, namely via quantum Darwinism.

    https://www.quantamagazine.org/quantum-darwinism-an-idea-to-explain-objective-reality-passes-first-tests-20190722/

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  42. BruceS: Weinberg is channeling Bell in that comment. Both were being ironic. That is, they are making fun of the idea that consciousness is needed to “collapse the wavefunction” .

    Of course, because he doesn’t like the implications of the collapse of the wavefunction requiring consciousness.

    He hasn’t proposed an alternative that would explain it better.
    Ether could be implemented but then, it would have to have consciousness like properties…

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  43. J-Mac: Of course, because he doesn’t like the implications of the collapse of the wavefunction requiring consciousness.

    How do you know what someone else is thinking? What are those implications? Unless you spell them out it’s all just guessing what’s going on in other peoples minds.

    J-Mac: He hasn’t proposed an alternative that would explain it better.

    Whereas you have? Citation please.

    J-Mac: Ether could be implemented but then, it would have to have consciousness like properties…

    Which are what properties precisely? What makes us conscious? Provide a list.

    Could a AI collapse the wave-function? etc etc.

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  44. Also, J-Mac, have you ever considered the possibility that people reject your ideas not based on the implications for their worldview but simply because they know better and therefore know you are wrong?

    Your pretense of understanding “the quantum” for example.

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