Genetic code is a programming language

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Specifically, it looks like the genetic code is a LISP dialect.

Operon structure of genetic code:
– https://s3-us-west-2.amazonaws.com/courses-images/wp-content/uploads/sites/1094/2016/11/03164740/OSC_Microbio_11_07_Operon.jpg

LISP function structure:
– http://support.ircam.fr/docs/om/om6-manual/res/listprefix.png

Nested genes:
– https://player.slideplayer.com/31/9782148/data/images/img11.jpg

Nested LISP cons cells:
– https://www.tutorialspoint.com/lisp/images/treestructure.jpg

151 thoughts on “Genetic code is a programming language”

  2. J-Mac,

    The funny thing about Darwinism is that all the evolutionary intermediates are suspiciously missing just like the intermediates of the code through a “doublet” phase

    We’re still in the ‘doublet’ phase, or rather GenCode release 2.5. Most codons are 3rd- or 1st- position-blind. Those where a 3rd base is involved tend to be base-blind within the purines or pyrimidines. You imagine a doublet code implies a 2 base reading frame. It doesn’t.

    As to why there aren’t any strictly doublet exemplars alive today – evolution. Natural Selection tidies up after itself. It does not predict that everything will survive. Quite the contrary. If a richer code gives an edge, what do you think will happen to those outcompeted or predated?

  3. Gordon Davisson: Do you understand QM at even a basic level

    I admire the hard work behind your QM test post for J-Mac, but just to manage expectations: You’re dealing with someone who at one point claimed his kids had disproved GR via some experiments on their pool table,

    I agree with your assessment of Eric’s OP and his responses in the thread. I think it provides more confirmation for Joe’s April post at Panda’s Thumb describing Joe’s view of Eric’s approach to debate: That is, walking away without dealing with the substance of the arguments.
    I am looking forward to Joe’s response to Eric’s post on CSI in the other thread to see if Joe has changed his mind on that after he has a chance to review Eric’s CSI response in detail.

  4. Corneel: It’s called developmental genetics. If you are genuinely interested, I suggest you look it up.

    Doesn’t it bother you that (developmental) genetics has no clue where the spatial information is coming from In embryo development and protein folds?

  5. Gordon Davisson: Yes, I do know what a quantum state is. I took a year of graduate-level QM while I was in college. I don’t claim to be an expert (and I’m certainly rusty), but I’m familiar with the basics and relatively used to thinking in quantum terms.

    No, you don’t. If you had, you wouldn’t write this:
    “Gordon Davisson: Nope. Quantum information cannot be copied (thanks to the no-cloning theorem), but the entire point of DNA is that the information in it can be copied.”

    What DNA information CAN be copied?

  6. J-Mac: What DNA information CAN be copied?

    So you can’t answer his questions? You are just going to ignore them?

    Here they are again:

    Gordon Davisson: Yes, I do know what a quantum state is. I took a year of graduate-level QM while I was in college. I don’t claim to be an expert (and I’m certainly rusty), but I’m familiar with the basics and relatively used to thinking in quantum terms.

    Do you understand QM at even a basic level? Can you actually say anything more specific than “it’s quantum information!” like some sort of magic incantation, and quote other people on the subject? Do you know how to think in quantum terms?

    Here’s a quick quiz about QM, quantum information, and the relevance of the no cloning theorem (in a simple case). It doesn’t require any particularly deep understanding, just a basic knowledge of the notation, jargon, and some algebra. If you actually understand QM as well as you seem to think, this should be easy for you.

    (Ok, there’s a kind of annoying amount of algebra, to the point where I can’t guarantee I didn’t lose track of the sign of any terms when I worked through it. My goal isn’t to make you do the algebra, but to make you prove you know what algebra to do, and needing to work through it is just part of proving that. ‘Course, if you’re a real expert, you’ll probably just set up the relevant transformation matrix and let Mathematica do everything for you…)

    Suppose we have a a qbit, with the usual basis states |0⟩ and |1⟩. Suppose we have a qbit “copier” that, given a gbit in the state |0⟩ produces a pair of qbits in the state |0⟩|0⟩, and given one in the state |1⟩, produces a pair in the state |1⟩|1⟩. Straightforward so far, right?

    (I did think about doing this with a 4-state system with {|A⟩, |C⟩, |G⟩, |T⟩} as its basis, but it just made the algebra sloggier.)

    Now, let’s define two other states for our qbits, |+⟩ = (|0⟩ + |1⟩)/sqrt(2) and |-⟩ = (|0⟩ – |1⟩)/sqrt(2). These are orthogonal and unitary, so they form another basis for our qbit’s state space.

    Question 1: Suppose we fed a qbit in the state |+⟩ into the “copier”. What state would the pair of qbits it produces be in?

    Question 2: Suppose, given two qbits in the state from question 1, we measured each of them in the {|+⟩, |-⟩} basis. What’re the possible combinations of results we might get and their probabilities?

    Question 3: Suppose we lost the copy (i.e. the second qbit). Is there any test we can perform on the first qbit that’ll distinguish it from being in a random state? If so, what is it?

    So there’s your challenge. Either answer the questions, or admit that you don’t understand QM well enough to.

    I’ll make sure that I post them every day, don’t worry.

  8. OMagain: Coward.

    It does have an easy answer though: the sequential base information in a DNA strand can be copied. Why a world expert on DNA should even ask such a question is a bit of a puzzle.

    But yes, I’d be interested to see J-mac answer Gordon’s questions. Or flail.

  9. Allan Miller: the sequential base information in a DNA strand can be copied.

    That it can replicate is kind of the most basic thing you might want to know about DNA. That J-Mac does not seem to realize this demonstrates unguessed at levels of further barrel bottoms.

  10. J-Mac: Doesn’t it bother you that (developmental) genetics has no clue where the spatial information is coming from In embryo development and protein folds?

    Oh, good heavens! The only person that “has no clue ” is you, J-Mac. There’s tons of information from decades of research on the nature of positional information in embryo development, a significant portion of it just a few mouse clicks away. You are online on a daily basis, so just look it up!

  11. Corneel: Oh, good heavens! The only person that “has no clue ” is you, J-Mac. There’s tons of information from decades of research on the nature of positional information in embryo development, a significant portion of it just a few mouse clicks away. You are online on a daily basis, so just look it up!

    Really?
    I don’t believe you…Do you know why? If it existed, I would be able to find it and you would link it at least once…All I see from you and other blind Darwinist are excuses and hand-waving…
    I’m all ears and eyes… lol
    Let’s see…;-)

  13. The genetic code experiment proposal:

    Since the genetic code apparently evolved from a simpler code…obviously…let’s test it and see it that was really the case…
    But how do we do it?
    Let’s use an organism with a simpler genetic code and put in under selective pressure, or something, to make it evolve a more complex code…

    What organism uses a simpler genetic code, like a doublet predecessor of a triplet code?

    Please don’t overwhelm me with too many, just a few organism will do…;-)
    I’m sure this time there will be no excuses just links to the real scientific research… 😉

  14. J-Mac: I don’t believe you

    I don’t believe you know the first thing about “quantum” either. Why are you not even acknowledging the chance to prove your knowledge on the subject?

  15. J-Mac: Let’s use an organism with a simpler genetic code and put in under selective pressure, or something, to make it evolve a more complex code…

    How would you know if it became more complex? How would you measure that change?

  16. J-Mac,
    Your thoughts about the quantum show you have some knowledge. But if you can’t answer these questions:

    Do you understand QM at even a basic level? Can you actually say anything more specific than “it’s quantum information!” like some sort of magic incantation, and quote other people on the subject? Do you know how to think in quantum terms?

    Here’s a quick quiz about QM, quantum information, and the relevance of the no cloning theorem (in a simple case). It doesn’t require any particularly deep understanding, just a basic knowledge of the notation, jargon, and some algebra. If you actually understand QM as well as you seem to think, this should be easy for you.

    (Ok, there’s a kind of annoying amount of algebra, to the point where I can’t guarantee I didn’t lose track of the sign of any terms when I worked through it. My goal isn’t to make you do the algebra, but to make you prove you know what algebra to do, and needing to work through it is just part of proving that. ‘Course, if you’re a real expert, you’ll probably just set up the relevant transformation matrix and let Mathematica do everything for you…)

    Suppose we have a a qbit, with the usual basis states |0⟩ and |1⟩. Suppose we have a qbit “copier” that, given a gbit in the state |0⟩ produces a pair of qbits in the state |0⟩|0⟩, and given one in the state |1⟩, produces a pair in the state |1⟩|1⟩. Straightforward so far, right?

    (I did think about doing this with a 4-state system with {|A⟩, |C⟩, |G⟩, |T⟩} as its basis, but it just made the algebra sloggier.)

    Now, let’s define two other states for our qbits, |+⟩ = (|0⟩ + |1⟩)/sqrt(2) and |-⟩ = (|0⟩ – |1⟩)/sqrt(2). These are orthogonal and unitary, so they form another basis for our qbit’s state space.

    Question 1: Suppose we fed a qbit in the state |+⟩ into the “copier”. What state would the pair of qbits it produces be in?

    Question 2: Suppose, given two qbits in the state from question 1, we measured each of them in the {|+⟩, |-⟩} basis. What’re the possible combinations of results we might get and their probabilities?

    Question 3: Suppose we lost the copy (i.e. the second qbit). Is there any test we can perform on the first qbit that’ll distinguish it from being in a random state? If so, what is it?

    So there’s your challenge. Either answer the questions, or admit that you don’t understand QM well enough to.

    Who are you to question others understanding who can answer those questions?

  17. J-Mac: But how do we do it?

    We don’t. You do. Why don’t you give it a try? Or are you still busy disproving things in your basement with your kids?

  18. J-Mac,

    Oh Christ, this again, old Johnny One-Note. Such an experiment would tell us nothing about the historicity of the actual code, nor would its failure give any greater credence to alternative theories.

    But this has provided a useful opportunity for J-Mac to avoid Gordon’s questions, so let’s all now swivel our chairs round and look at J-Mac not answering them.

  19. Allan Miller: so let’s all now swivel our chairs round and look at J-Mac not answering them.

    What questions?

    Suppose we have a a qbit, with the usual basis states |0⟩ and |1⟩. Suppose we have a qbit “copier” that, given a gbit in the state |0⟩ produces a pair of qbits in the state |0⟩|0⟩, and given one in the state |1⟩, produces a pair in the state |1⟩|1⟩. Straightforward so far, right?

    (I did think about doing this with a 4-state system with {|A⟩, |C⟩, |G⟩, |T⟩} as its basis, but it just made the algebra sloggier.)

    Now, let’s define two other states for our qbits, |+⟩ = (|0⟩ + |1⟩)/sqrt(2) and |-⟩ = (|0⟩ – |1⟩)/sqrt(2). These are orthogonal and unitary, so they form another basis for our qbit’s state space.

    Question 1: Suppose we fed a qbit in the state |+⟩ into the “copier”. What state would the pair of qbits it produces be in?

    Question 2: Suppose, given two qbits in the state from question 1, we measured each of them in the {|+⟩, |-⟩} basis. What’re the possible combinations of results we might get and their probabilities?

    Question 3: Suppose we lost the copy (i.e. the second qbit). Is there any test we can perform on the first qbit that’ll distinguish it from being in a random state? If so, what is it?

    So there’s your challenge. Either answer the questions, or admit that you don’t understand QM well enough to.

    Do you mean those questions or some other questions J-Mac is ignoring like who had most of their brain removed and continued to function normally?

  20. It was none other than mathematician Douglas Hofstadter who described biological cells as Quines in the ultimate Geek cult classsic:

  22. Gordon Davisson: Quantum information cannot be copied (thanks to the no-cloning theorem)

    Thanks for that. I didn’t know about the no-cloning theorem till you mentioned it.

    In physics, the no-cloning theorem states that it is impossible to create an identical copy of an arbitrary unknown quantum state. This no-go theorem of quantum mechanics was articulated by James Park in proving the impossibility of a simple perfect non-disturbing measurement scheme,[1] in 1970 and rediscovered by Wootters and Zurek[2] and by Dieks[3] in 1982. It has profound implications in quantum computing and related fields. The state of one system can be entangled with the state of another system. For instance, one can use the controlled NOT gate and the Walsh–Hadamard gate to entangle two qubits. This is not cloning. No well-defined state can be attributed to a subsystem of an entangled state. Cloning is a process, the result of which is a separable state with identical factors.

    The no-cloning theorem is normally stated and proven for pure states; the no-broadcast theorem generalizes this result to mixed states.

    The no-cloning theorem has a time-reversed dual, the no-deleting theorem. Together, these underpin the interpretation of quantum mechanics in terms of category theory, and, in particular, as a dagger compact category.[4][5] This formulation, known as categorical quantum mechanics, allows, in turn, a connection to be made from quantum mechanics to linear logic as the logic of quantum information theory (in the same sense that classical logic arises from Cartesian closed categories).

    Great stuff. Thanks Gordon.

  23. Gordon,

    Regarding the no-cloning theorem, does that mean if we have a some known atom with electrons in an UNKNOWN orbital (unknown principle quantum number), that this quantum number can’t be arbitrarily cloned? Am I understanding the no-cloning theorem correctly with respect to this tiny example?

    It would suggest then that the reason a laser is able to work is that we “known” the frequency we are trying to create with the laser. We are hence able to clone the photon energies becasue we “know”.

  24. J Theor Biol. 2005 Apr 21;233(4):527-32. Epub 2004 Dec 29.
    The triplet genetic code had a doublet predecessor.
    Patel A1.
    Author information

    https://www.ncbi.nlm.nih.gov/pubmed/15748913

    Abstract
    Information theoretic analysis of genetic languages indicates that the naturally occurring 20 amino acids and the triplet genetic code arose by duplication of 10 amino acids of class-II and a doublet genetic code having codons NNY and anticodons GNN. Evidence for this scenario is presented based on the properties of aminoacyl-tRNA synthetases, amino acids and nucleotide bases.
    “There exists a broad consensus in biology that evolution, acting through natural selection on variations produced by genetic mutations, has brought living
    organisms to their present state, and would continue to take it still further.
    Evolution attempts to explain the highly complex mechanisms of life, observed
    in present day organisms, as arising from accumulation of small changes on
    simpler predecessors and over a long time scale. Among the many possible
    changes in a working system, most are harmful and a beneficial change occurs only rarely. But natural selection wipes out the undesirable changes,
    and amplifies the rare beneficial mutation. This view of evolution is very well
    supported by systematic analysis of fossil records and genome sequences. In
    this view, it is quite logical to believe that evolutionary changes can only be
    incremental, because a large change in a vital part of life would be highly
    deleterious (Crick, 1968)”

    The consensus brings us to the evolution of genetic code:

    “All this can only be the first step towards unraveling the mystique surrounding
    the origin of life. There are further questions one may ask:
    (i) “Why did the translation machinery for the doublet code move in steps of
    three bases, even when only two bases carried information, leaving the third
    base as a punctuation mark?” The answer is likely to be found in the stereochemistry between amino acids and tRNA acceptor stem nucleotide bases.
    (ii) “How did the genetic machinery involving 10 class-II amino acids come
    about?” The optimality criteria point towards a still earlier predecessor involving 4 amino acids, perhaps encoded by one pair of complementary nucleotide
    bases.
    (iii) “Is there a relation between the doublet code and the RNA world?” The
    doublet code is intimately tied to the properties of amino acids, and hence has
    to appear after replacement of ribozymes by polypeptides. May be it would
    be easier to construct a mapping between properties of ribozymes and the
    smaller set of class-II amino acids.
    Although conjectures can be made, clear answers to such questions would
    9 require more clues and careful modeling”

    Everything is possible and makes sense in the science fiction stories as it has to…Otherwise…:-)

  25. stcordova:
    Gordon,

    Regarding the no-cloning theorem, does that mean if we have a some known atom with electrons in an UNKNOWN orbital (unknown principle quantum number), that this quantum number can’t be arbitrarily cloned?Am I understanding the no-cloning theorem correctly with respect to this tiny example?

    It would suggest then that the reason a laser is able to work is that we “known” the frequency we are trying to create with the laser.We are hence able to clone the photon energies becasue we “know”.

    Sal,
    Darwinist here think that when DNA is copied, a classical information is copied, such as ACTG…etc.
    The ACTG letters stand for a compounds adenine, cytosine, guanine, thymine which are four constituent bases of nucleic acids. They vibrate constantly…
    These compounds have their quantum states/ quantum correlations with each other and its neighboring base pairs…
    There are nice courses on line and books for all of them 😉

  27. J-Mac: Sal,
    Darwinist here think that when DNA is copied, a classical information is copied, such as ACTG…etc.

    There is some classical information copied, that’s why we have genetic engineering that is based on classical information. There are aspects of the DNA that likely have quantum strangeness, just like proteins such as the one I described with Spin Chemistry in Bird Magnetic sensing and which YOU found had some pretty cool Quantum stuff.

    Physics and chemistry are framed as a mix of classical and quantum. The classical framework is an approximation that makes analysis easier.

  28. Here you go J-Mac:

    http://adsabs.harvard.edu/abs/2017bhns.work…61H

    Recent studies of DNA show that the hydrogen bonds between given base pairs can be treated as diabatic systems with spin-orbit coupling. For solid state systems strong diabaticity and spin-orbit coupling the possibility of forming Majorana fermions has been discussed. We analyze the hydrogen bonds in the base pairs in DNA from this perspective. Our analysis is based on a quasiparticle supersymmetric transformation which couples electronic and vibrational motion and includes normal coordinates and the corresponding momenta. We define qubits formed by Majorana fermions in the hydrogen bonds and also discuss the entangled states in base pairs. Quantum information and quantum entropy are introduced. In addition to the well-known classical information connected with the DNA base pairs, we also consider quantum information and show that the classical and quantum information are closely connected.

    GAG! It’s been a while since I studied “Majorana fermions.” Man, I’ve forgotten soooo much in so little time.

  30. J-Mac,

    Yeah yeah, whatevs, quantums make atoms go wibble. Now, those questions you have been avoiding …

  31. stcordova: There is some classical information copied, that’s why we have genetic engineering that is based on classical information.

    Genetic engineering is the manipulation of an organism’s genes/ DNA.
    So while you may use classical information to do it (Venter digitized biology)
    the quantum correlations may remain. That’s why it is so hard to create DNA from scratch….

  32. Allan Miller:
    J-Mac,

    Yeah yeah, whatevs, quantums make atoms go wibble. Now, those questions you have been avoiding …

    Stop embarrassing yourself! Again…;-)

  33. The Majorana Fermions mentioned above are apparently these creatures:

    https://en.wikipedia.org/wiki/Bogoliubov_quasiparticle

    In condensed matter physics, a Bogoliubov quasiparticle or Bogoliubon is a quasiparticle that occurs in superconductors.[1] Whereas superconductivity is characterized by the condensation of Cooper pairs into the same ground quantum state, Bogoliubov quasiparticles are elementary excitations above the ground state, which are superpositions (linear combinations) of the excitations of negatively charged electrons and positively charged electron holes, and are therefore neutral fermions (spin-1/2 particles).

    One way a quasiparticle is defined is:

    a quantum of energy in a crystal lattice or other system of bodies which has momentum and position and can in some respects be regarded as a particle.

    If DNA can create and use these kinds of quasi-particles, that would be cool.

    From Basic Biochemistry, I know that Plants use quasi particles called excitons.

  34. J-Mac: Stop embarrassing yourself! Again…;-)

    So you can’t answer the questions? Well, I’m shocked, shocked I say. It’s almost like you were bluffing.

  35. stcordova:
    If DNA can create and use these kinds of quasi-particles, that would be cool.

    From Basic Biochemistry, I know that Plants use quasi particles called excitons.

    From Basic Biochemistry, you should know that there is a world of difference between the light-harvesting centres of chloroplasts and the largely inert molecule DNA. Indeed, its very inertness makes it persistent.

    It’s amazing watching Creationists stroke their collective chins when one of them says ‘quantum’.

  36. J-Mac: What DNA information CAN be copied?

    If you’d answered my quiz, you’d have a much better idea.

    Hint: in the setup, I assume a “copier” that can copy the |0⟩ and |1⟩ states with no problem. You could also have a system with orthogonal |A⟩, |C⟩, |G⟩, and |T⟩ states, and copy those with no problem. But those aren’t arbitrary quantum states, are they?

    If you can work out the answers to the quiz, you’ll learn something about why copying arbitrary quantum states doesn’t work. If you can admit that you don’t know how to answer the quiz, I’ll tell you the answers and you’ll learn something about why copying arbitrary quantum states doesn’t work. But if you’re not able to either answer the quiz, or admit that you can’t answer the quiz, then there’s no point in trying to educate you.

  37. stcordova:
    Gordon,

    Regarding the no-cloning theorem, does that mean if we have a some known atom with electrons in an UNKNOWN orbital (unknown principle quantum number), that this quantum number can’t be arbitrarily cloned?Am I understanding the no-cloning theorem correctly with respect to this tiny example?

    Hi, Sal. As I said, I’m not a proper expert on this, but I think I’ve got a reasonable handle on the basics, so I’ll have a go at it. Short answer: it depends on exactly what you mean by “an UNKNOWN orbital”. If you’re willing to pick out an orthogonal set of states (orbitals) that the “input” electron might be in, then you can (at least in principle) copy that state to another electron. But if the input electron isn’t in one of those specific states — if it’s in a superposition of them (i.e. a hybrid orbital) — then the result will be weird. If the input electron is entangled with something else, that can also complicate matters.

    Consider the three (orthogonal) 2p orbitals. They all have the same two-lobe shape, the only difference is which directions the lobes stick out: along the x-axis, the y-axis, or the z-axis. You could also have hybrid 2p orbitals that’re superpositions of those, and therefore have their lobes sticking out in other directions. But which directions we pick as our axes is arbitrary (other than being at right angles to each other), so the choice of which orbitals are basis states and which are hybrid is arbitrary! This means you could have a copier that worked with electrons in a 2p orbital with its lobes along any of three (arbitrarily chosen) axes, but it would have trouble with an electron in a 2p orbital with lobes in any other direction.

    This is why classical information stored in a quantum system can be copied. When you store classical information, you’re just going to be using a set of orthogonal states (or clusters of states that’re orthogonal to each other), and cloning those isn’t a problem. (And I’ve just given away part of the answer to J-Mac’s question. Oh, well.)

    It would suggest then that the reason a laser is able to work is that we “known” the frequency we are trying to create with the laser.We are hence able to clone the photon energies becasue we “know”.

    Sort of. I’m leery of using the word “know” here (largely from experience over at UD), because it doesn’t have anything to do with whether a human knows anything about it. I’d say the no-cloning theorem isn’t relevant because it’s not cloning a particle (photon) in an arbitrary state, but one specific state determined by the emission line of the lasing medium and the geometry of the resonant cavity. A set of just one state is trivially pairwise-orthogonal, so cloning works.

  38. Allan Miller: So you can’t answer the questions? Well, I’m shocked, shocked I say. It’s almost like you were bluffing.

    Have I missed the part of the discussion where someone explains how the possible existence of these quantum mechanisms has any bearing on the evidence and arguments for biological evolution? For example, if the quantum information embedded in a quantum entangled DNA cannot be copied, why does that matter to biological evolution?

    In any event, speaking of highly improbable events like J-Mac providing a coherent (or even decoherent) response to the quantum questionnaire, you may be pleased to learn that in Sean C’s latest Mindscape Patreon AMA, he says he has backed away from the views on Boltzmann Brains in his books, and instead now believes that the most likely cosmological scenarios make them rare or impossible.

    Quote from Sean C: “Therefore in the far future of our universe, I don’t expect to see Boltzmann Brains. I expect to see the universe settled down into a particular static quantum wave function”.

    His reasons are cosmological, not thermodynamic, but could one interpret your two positions as an example of convergent evolution? Or would that be too close to the cultural version?

  39. BruceS: Have I missed the part of the discussion where someone explains how the possible existence of these quantum mechanisms has any bearing on the evidence and arguments for biological evolution?For example, ifthe quantum information embedded in a quantum entangled DNA cannot be copied, why does that matter to biological evolution?

    Hi Bruce! I have certainly missed the part where someone presents an actual argument based on quantum phenomena. People seem to feel it sufficient to just mention them in passing. Weirder still are the frequent occasions when their fellow evolution-skeptics join in, as if they had said something profound, or at least comprehensible!

    In any event, speaking ofhighly improbable events like J-Mac providing a coherent (or even decoherent) response to the quantum questionnaire, you may be pleased to learn that in Sean C’s latest Mindscape Patreon AMA, he says he has backed away from the views on Boltzmann Brains in his books, and instead now believes that the most likely cosmological scenarios make them rare or impossible.
    […]
    His reasons are cosmological, not thermodynamic, but could one interpret your twopositions as an example of convergent evolution?

    Haha! As long as he has converged to me, and I don’t have to go anywhere, that’s cool! 😃 I have actually had an OP on entropy and BBs in draft for some time, but until I retire (soon) have left it on ice. It was actually written to commemorate the passing of Frank Lambert last December, but I have since had some interesting exchanges with keiths, who is not a fan, so I want to be in a position to defend it adequately.

  41. Allan:

    It was actually written to commemorate the passing of Frank Lambert last December.

    Tragedy! He’s done so much to further understanding of chemical physics.

    I hope someone maintains his website for all time!

  42. BruseS

    Have I missed the part of the discussion where someone explains how the possible existence of these quantum mechanisms has any bearing on the evidence and arguments for biological evolution?

    I don’t think QM directly explains evolution nor creation. QM indirectly suggests the existence of God depending on how one interprets QM, as I describe here:

    The Quantum Enigma of Consciousness and the Identity of the Designer

    and that consciousness may be fundamental to reality:

    https://www.thriftbooks.com/w/quantum-enigma-physics-encounters-consciousness_fred-kuttner_rosenblum/345766/?mkwid=sX2e1aPQO%7cdc&pcrid=70112897472&pkw=&pmt=&plc=&pgrid=21329102112&ptaid=pla-366084668232&gclid=Cj0KCQjwjYHpBRC4ARIsAI-3GkFCygf825GcxTHi16gkpEF6FsPh_ItezEcUMgGtS99Z_yWVLOpLL-EaAvI1EALw_wcB#isbn=019534250X&idiq=5660883

    Quantum Enigma Oxford University Press
    Quantum mechanics reveals a mystery at the boundary of physics: that observation strangely influences what is observed. Quantum Enigma focuses on this increasingly discussed skeleton in physics’ closet, its encounter with consciousness.

    Quantum Enigma‘s treatment is understandable without prior physics background. An American Journal of Physics review says: “…Rosenblum and Kuttner manage to convey much of the exquisite subtlety of quantum mechanics without ever resorting to an equation. Their treatment of two-slit interference ranks right up there with (but differs interestingly from) Feynman’s famous “comes in lumps” approach, and their nontechnical description of Bell’s theorem is one of the best I’ve seen, and by far the least mathematical.”

    Comments on Quantum Enigma:
    Click here to read full quotes

    A remarkable and readable presentation…

    Charles Townes: Winner of the Nobel Prize in Physics

    This book is unique. …clearest expositions I have ever seen.

    George Greenstein: Professor of Astronomy, Amherst College,
    Co-author of The Quantum Challenge: Modern Research on the Foundations of Quantum Mechanics

    The ultimate consciousness would thus be GOD!

    So if there is a God, and evolution is not the natural course of events, then a miracle happened, and the most likely Miracle Maker is the God that is predicted by Quantum Mechanics (notwithstanding other interpretations of QM).

    A few Christians identify the God of predicted by certain interpretations of Quantum Mechanics with the Christian God who they believe is also the Intelligent Designer.

  43. stcordova: I don’t think QM directly explains evolution nor creation. QM indirectly suggests the existence of God depending on how one interprets QM, as I describe here:

    I read Quantum Enigma some time ago. As I recall, its popularized explanation of the QM and Bell’s results were fine, but its reliance on consciousness to address the measurement problem remains far from the mainstream of philosophers and physicists working in the field of QM interpretations.

    Today the big three realist interpretations are Many-Worlds, Bohm, amd GRW, with QBism being the main anti-realist approach. AFAIK, almost no one working in this field takes seriously the Copenhagen interpretations (plural intended).
    And almost all think that Einstein was right, Bohr misunderstood him, and Bohr’s replies to Einstein’s EPR paper do not withstand serious scrutiny.

    My favorite books on QM interpretations, in increasing order of math and philosophical sophistication:

    I don’t really understand your linked post on QM and the existence of God. Are you saying that the Copenhagen/Consciousness interpretation needs an ultimate Observer, who is God? If so, it sounds something like Berkeley’s argument for God given Berkeley’s idealism (as nicely captured in the God in the Quad limericks).

    https://myopicpoets.blogspot.com/2009/07/god-in-quad-knox-limerick.html

  44. Allan Miller: have actually had an OP on entropy and BBs in draft for some time, but until I retire (soon) have left it on ice. It was actually written to commemorate the passing of Frank Lambert last December,

    Sean’s new BB position is captured in latter parts of section 4 this paper, I believe, which I did not come across until very late in our exchange on BBs. The Mindscape AMA makes Sean’s position very clear; the cosmology in the paper is above my pay grade. I found the paper cited in the Wiki article on BBs Isee someone added Sean’s podcast there

    https://arxiv.org/pdf/1702.00850v1.pdf

    As for entropy and disorder, Sean’s AMA also addresses that!

    He explains Acguirre position that, at least for systems that are not in TD equilibrium (I think), we can take both info and disorder views: a disorder view based on Boltzmann’s approach to macrostates, and an information view based on the Gibbs/Shannon approach applied to microstates. I’ll post an extended excerpt from the AMA if there is interest.

    Acquirre’s popularization explaining the idea is here

    (I’m part way through — an enjoyable read but I could do without the koans

    The technical description is linked here; again the math is something I’d have to seriously work on to gain even a partial understanding of.

    https://arxiv.org/pdf/1905.03841.pdf

    See also the 41:41 section of the transcript of Sean’s conversation with Acguirre (which is not as clear, however, as the AMA):

    Episode 51: Anthony Aguirre on Cosmology, Zen, Entropy, and Information

  45. BruceS:

    AFAIK, almost no one working in this field takes seriously the Copenhagen interpretations

    It depends whom you ask.

    From the textbook I studied at JHU by Griffiths, Introduction to Quantum Mechanics, page 4:

    The Orthodox position:
    …
    This view (the so-called Copenhagen interpretation), is associated with Bohr and his followers. Among physicists it has always been the most widely accepted position.

    Not that I aim to prove one view over another, as it suffices for many to simply argue for plausibility of an Ultimate MIND that can be a miracle maker. Personally, I think the ideas are formally undecidable, we can only make our best guess.

    To that end, I’ve said to the extent evolutionary theory or abiogenesis is inconsistent with the normal operation of physics and chemistry, then that suggests a miracle happened.

    Regarding the “realist” many worlds interpretation, how is this significantly more or less outrageous than a God-hypothesis?

    In addition to many-worlds interpretation of Quantum Mechanics, there are the Multiverse hypotheses associated with the Big Bang. When a respected evolutionary biologist, National Academy member, like Eugene Koonin invokes Multiverses to solve abiogenesis, to my mind, how is this any more or less outrageous than invoking an Inteligent Designing God? To me, this suggests the God interpretation of QM might be correct.

  46. This was the cover of Griffiths book with Schrodinger’s cat in the live state. On the back cover, the cat is in the dead state!

  47. BruceS,

    we can take both info and disorder views

    Lambert’s view – arguing for the best way to teach, not necessarily to analyse – was to emphasise the delocalisation of energy associated with entropy change. There is a geometric component, not well captured in the maths of counting permutations. Energy becomes unavailable for work because it’s not ‘there’ anymore! It’s mechanistic, which I like. In that wider space, of course, there are more ways to be ‘not-there’, all giving the same macrostate reading.

  48. Allan Miller:
    BruceS,

    Lambert’s view – arguing for the best way to teach, not necessarily to analyse – was to emphasise the delocalisation of energy associated with entropy change.

    Yes, you are right.

    I realized after posting that I was not clear in on why Lambert suggested energy spreading instead of disorder and how Acquirre was using concept of disorder differently.

    I agree Lambert was mainly concerned with teaching TD entropy to novices. . Acquire’s stuff is really not relevant to that since he using ‘disorder’ differently from Lambert. Acquire is trying to popularize some post-statistical mechanics and post-quantum theory work he did with others.

    But on spreading: I did come across this paper which tries to generalize the spreading idea to other degrees of freedom of the state space beside volume, eg it includes a section trying to account for Gibbs paradox on mixing of same/different gases via a spreading generalization.

    https://www.researchgate.net/publication/227218780_Entropy_Its_Language_and_Interpretation

    From abstract “The language of entropy is examined for consistency with its mathematics and physics, and for its efficacy as a guide to what entropy means. Do common descriptors such as disorder, missing information, and multiplicity help or hinder understanding? Can the language of entropy be helpful in cases where entropy is not well defined? We argue in favor of the descriptor spreading, which entails space, time, and energy in a fundamental way”

  49. stcordova: It depends whom you ask.

    From the textbook I studied at JHU by Griffiths, Introduction to Quantum Mechanics, page 4:

    I agree Copenhagen is used in introductory textbooks for physics undergrads. The reason is it provides an easy intuitive path to the real objectives of these books, which is teaching mathematics and techniques for physics calculations needed for problem solving with systems whose behavior can only be studied through QM…

    Textbooks for teaching QM to undergrads are not relevant.to understanding the measurement problem and why Copenhagen ignores it instead of addressing it.

    Instead, you need to look to books written by physics-trained philosophers or by physicists and who are working in the field of QM interpretation. Second best are popularizations of their work, like Becker’s book..

    I agree Many Worlds goes counter to everyday intuition. So do many scientific theories. The standard for judging such ideas is whether they survive scientific scrutiny and then philosophical scrutiny for cases unresolved by science alone.
    Everyday intuition is irrelevant..

    Sean C has a new book populatization on the Many Worlds interpretation coming out in September which you may interest you.

  50. Bruce,

    Re “spreading” interpretations of entropy, there’s really only one kind of “spreading” that invariably accompanies increases of entropy, and that’s the spreading of probability over more microstates, not the spreading of energy over more volume.

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