Dear Jack

Two points here:

First, I have recently been persuaded that I should really use the term "top down realisation" rather than "top down causation". Causation happens at each level of the hierarchy of structure and causation rather than up or down, whereas realisation is the downward relation and emergence is the upward relation.

That being said, causation does indeed happen at each level at the same time: in the brain for instance, 1. electrons flow in axons according to Maxwell's equations, 2. genes are turned on and off according to the state of gene regulatory networks, 3. information flows down axons to synapses where signals are summed and used to decide if new spike trains should be sent on, 4. pattern recognition takes place via the neural network structures formed by the neurons, and 5. logical thought takes place at the psychological level, for example deciding if Maxwell's equations are a good description of electromagnetism. The lower levels enable the higher levels to function, but it is the logical highest level that decides what the final result is (Maxwell's equations get written down as a good description of reality)

Second, "causation itself a singular event/operation that necessarily requires a singular explanation". No, there are multiple causal relations in action at the same time, as indicated above, and as point out by Aristotle in the Wikipedia article on Four Causes. I elaborate further in my book on top down causation, taking the example of why an aircraft flies. It flies 1. because of air particles impinging on the wing, 2. because the pilot is flying it, 3. because it was designed to fly, and 4. because someone is making a profit out of its flying. These four causes operate simultaneously; and without any one of them, it would not fly. Physics is concerned only with level 1. The other three levels are also essential.

Dear Professor Ellis,

I read your essay with great pleasure. I want to mention a few things that I hope will be useful in your research of

adaptation and plasticity Life depends on adaptation to its environment.

We found that in the nanotubes with a diameter of 14.5 nm and a length of a few microns, including carbon ones, there is a giant diamagnetic effect, which is like the Meissner effect in superconductors. This effect is observed from helium temperatures (-270°C) to temperatures of +93.5 °C. This effect we call "hot" superconductivity. For example, our discovery of the "hot" superconductivity clearly explains the effect of diamagnetic levitation samarium cobalt magnets in the man's hand and a live frog at room temperature. US Patent No 6,570,224

We have found that this effect is determined by the diamagnetic properties of the tubulin microtubes that make up the cytoskeleton of cells, rather than the diamagnetic properties of the water of the human body. The inner diameter of the microtubes is about 14.5 nm. As a result, the resonance conditions for motion of electrons inside the microtubules are created. This leads to a giant diamagnetic effect at normal temperatures.

Best regards

    Professor Ellis, thank you for your reply.

    From your answer, it seems to me (just as a participant in this essay contest) that there may be a specific hypothesis to test this idea about a system of systems-- that a hierarchy with many levels of structure built upon each other has a different description and vocabulary suitable for each level of the hierarchy that is related to the effective entities which occur at that level.

    And, that a selection from possibilities at a higher level can, by changing context, change the possibilities for a lower level-- perhaps making some possibilities at the lower level impossible; perhaps changing the probability for a possibility to be selected at that lower level.

    As an example, you have talked about "cell" as one such description. I would use hypersets to say: "cell = (cell)." It is using a computer science concept called "coalgebra" or "stream." Specifically when you use this language, say, to talk about information produced by the cell: "cell = (signal, cell)."

    Today, there is some talk by physicists about "consciousness." Classically this may be self-awareness, or "consciousness of self." It does seem to me that to be conscious, one must be conscious of something. So before consciousness, there must first be "self," which again I would phrase in terms of hypersets as: "self = (self)."

    Then there can be language, for example, about thinking, and the beliefs which are based on thinking: "self = (thinking, self)".

    Using such language for the "higher level module" of interest, how would it emerge from lower level systems?

    Again to use concepts from computer science, I think of a single transition in a Petri net, with a single output arrow to a single "place" in the Petri net, and another arrow from that single place-- an input arrow back to the same transition. The label for this Petri net place is "self."

    So in terms of this picture, the question of how "self=(self)" emerges from lower level systems or lower level modules is then "How does the feedback loop in the above Petri net get going?"

    The feedback loop would then comprise those "lower level modules" of which you speak-- in this case ion channels.

    An experiment:

    Radioactively label the ions. Study a pregnant laboratory animal. One hypothesis is that the feedback on which "self = (self)" emerges is the breath, involving specifically the proprioceptors involved in breathing and their ion channels. On the birth of the laboratory animal, when it first breathes, what can be seen with neuro-imaging?

    In opposition to this hypothesis, test for the same kind of images, but for the ion channels for the interocepetors required for the heart to beat.

    According to this language of Petri nets, a feedback loop is required for "self=(self)" and it may involve either the interoceptors or the proprioceptors. And-- the respective ion channels.

    (It seems to me-- again just as a contestant-- that the KAVLI Institute might be interested in funding such an experiment. If you were a principal.)

    Best Regards,

    Lee Bloomquist

    Thank you for the kind words. "I would like to add that I see us responsible for more reasonably steering the evolution of mankind." I can only agree.

    Dear Alexander Ilyanok,

    That is very interesting. The question this raises for me is whether the diamagnetic properties of the tubulin microtubes can be used to construct logic gates. If so that would be most interesting, and maybe even important (it might relate to Roger Penrose's conjections about the brain)

    Dear Lee Blomquist,

    you say

    "From your answer, it seems to me that there may be a specific hypothesis to test this idea about a system of systems-- that a hierarchy with many levels of structure built upon each other has a different description and vocabulary suitable for each level of the hierarchy that is related to the effective entities which occur at that level.

    And, that a selection from possibilities at a higher level can, by changing context, change the possibilities for a lower level-- perhaps making some possibilities at the lower level impossible; perhaps changing the probability for a possibility to be selected at that lower level."

    Exactly so, that is a nice summary.

    The experimental suggestions sound interesting - I'd have to think about them more, specifically the difference between interoceptors and proprioceptors.

    What is a good reference to the computer science concepts you mention?

    George Ellis

      Hello Mr Ellis,

      I loved your general works about our neurons process.The informations always and this evolution of adaptation.

      I rank all since many years more than 20 years.It is in ranking that I found this theory of spherisation....H.....CNO....H2C2 HCN CH4 NH3 H2O....ine ase...unicells and this and that givent complexification and increasing mass on this line time.I studied the works of Darwin and Lamarck.Lamarck also was relevant considering the adaptation with environments and mutations.We encode at each instant.Lamarck had found an intersting link with the will.In resume if a giraf has a long neck, it is because an encoding has been made to eat the leaves higher.Darwin, Lamarck and now the modern theories of evolution consider many paramters.The informations and encodings become very complex.The classifications become so universal keys.I am persuaded that we must consider two main systems.One electromagnetic, the other gravitational.The standard model is one thing.The gravitation an other.That said our biology seems correlated only with the earth and the standard model.

      Congratulations for your essay and good luck, you are going to be well ranked ,you merit a prize :)

      Best Regards

        Your essay was cogent and well argued. It relies upon the issue of top-down causation or correlation, which as you argue is a sort of emergent biological structure, not a physical law or principle. You make a rather interesting statement:

        there is a resulting space of possible proteins of vast dimensions: a kind of Platonic space of possible structures [18].

        These structures are then selected for, such as with the model you have for a projector operator. As an aside I will say that many physicists and even a lot of mathematicians chafe at the suggestion of Platonic realm. However, we can think of this as a sort of state space of possible structures. Given conditions at the time the particular E(X) exists. Maybe for all we know other E(X)'s that do not exist on Earth and never have existed do so on other planets or elsewhere in the universe.

        This state space is the subject of my essay, though I am a bit conservative in saying this is a Platonic realm. I have this conjecture the world at the very low IR energy limit, such as what we ordinarily observe, has a duality say a modular or T-duality with the UV limit. The UV limit is near the Planck scale. This is observed as quantum hair on black holes; it is observed as highly red shifted quantum fields on the stretched horizon. It is here that the set of all possible structures can exist.

        For a potassium channel gate, such as the one I attach here, these structures have a lot of symmetry in them. In particular the alpha helix chains rotate upon phosphorylation, which occurs with a voltage or action potential, so the negative charged amino acid residues present themselves to permit the ion to pass through. Similar structures are found and one of the most amazing is ATP synthase. These have physical or chemical physical properties on a small scale that match requirements of the large scale system, such as in a top down correlation. Of course maybe there is in face top-down and bottom-up properties in an interplay. These structures do seem to have some intrinsic properties in the universe.

        I argue these have their existence in UV hair on black holes or cosmologies in an open entanglement system http://fqxi.org/community/forum/topic/2737 . This is the thesis of my essay. I don't make mention of this, but it may the the ultimate set of structure are with the monster group and monstrous moonshine. There are 8.1x10^{53} roots, which means this is enough to cover a 10^{15} solar mass black hole. This is larger than black holes today, though in the distant future if a good percentage of galaxy clusters get eaten up in black holes they might reach these proportion in around 10^{20} years.

        To extend this to consciousness the fitness paradigm is similar to Daniel Dennett's hetero-phenomenology. It is similar to his idea of competing neural narratives from which emerges the optimal representation of the world.

        LC

          Professor Ellis,

          Here's a paper by Samson Abramsky.

          In this paper he asks about using Channel Theory to model the three-valued Chu space he obtains as a full representation based on Wigner's theorem.

          I've answered, with more references (and references to references) here.

          Dear Lee Blomquist

          this is very interesting, thanks. It will take time to understand it fully, but it seems to me that it takes seriously the measurement problem by means of the evaluation function eH, which presumably implies collapse of the wave function; and that is a projection operation of the form (8) given in my essay. I developed an approach that is a bit similar (but much simpler in mathematical terms) in a paper on quantum theory here: arXiv 1108.5261.

          I will cogitate on this further, and also comment over at your essay.

          George Ellis

          Dear Lawrence Crowell

          thanks for that. I talked with Andrew Wiles last year about the Platonic nature of Mathematics, and he strongly believes that good working mathematicians all agree they are exploring mathematical structures rather than inventing them. Andreas Wagner in the book I mentioned writes very convincingly about the nature of Platonic spaces of possible biological microstructures: Gene Regulatory Networks, Signal Transduction Networks, Metabolic Networks, and Proteins. I strongly recommend that book. These possibilities all follow from the underlying physics, which is what you are commenting on. Maybe the biological properties follow from the symmetries you mention. Fascinating linkages.

          George Ellis

          I do think there is some objective nature to mathematics. I tend to be dissatisfied with the idea mathematics is just a set of rules as in a game and proving theorems is just playing different outcomes in the game. Plato had his idea on this as a realm of pure forms. Aristotle had the concept of potentia, in particular with the relationship between physical world and mathematics.

          It is not that often though one reads a paper discussing scientific matter that platonic ideas come up/

          Cheers LC

          Hi,

          the key argument some philosophers have had against Platonic mathematics is that there is then no way the human mind could interact with it. However Paul Churchland has clarified how this is possible in his great book Plato's Camera, based on the neural network nature of the mind (which of course is a result of evolutionary adaptation). My favourite example is the fact that the square root of 2 is irrational - a timeless eternal truth. Such facts can be claimed to constitute the deep nature of cosmology. I will be writing a book about this later in the year.

          Cheers GE

          Hello George, and thanks for this impressive essay.

          You have dealt with how goal-oriented systems arise out from goal-free underlying physics, but you seem not to have addressed aims and intentions, which are different from goal-orientation in that an aim or intention is chosen by a mind, and can be altered.

          I think there is a nice complementarity between your essay and my "Reality Re-Envisaged" which focuses on this higher level. Do you agree?

          Best regards,

          ...george...

          Dear George

          Thank you for your comments.

          You say, "You have dealt with how goal-oriented systems arise out from goal-free underlying physics, but you seem not to have addressed aims and intentions, which are different from goal-orientation in that an aim or intention is chosen by a mind, and can be altered." ... Well I had to stick with the length allowed! So I only had space to develop the bottom level; the higher level possibilities develop from this.

          "Today's physics is framed on the assumption that the only things that truly exist are material in nature. Yet it is undeniable that ideas and concepts (including aims and intentions) are an aspect of reality. Although they cannot be seen or weighed or have particles bounced off them, they govern our lives. Laws, language, manners, mathematics, maps, literature; we live in a rich tapestry of abstractions. Thus, if we

          are to address the Problem, we will need to find a more general frame, one that admits the existence of an immaterial "field" of ideas and concepts" - I agree, they exist and are indeed causally effective. My book How Can Physics Underlie the Mind? makes this point quite clearly. So we agree on this issue, and there is indeed a nice complementarity between our essays.

          Best regards, George

          George,

          Your essay is my favorite that I've read so far (including the one that my colleagues and I submitted). :)

          The first time I read through it, I kept thinking about a computer program to model the logical choices that you describe, similar to the BOIDS program for bird movement that was developed back in the 80s that describes the chaotic movement of bird flocks into simple computer logic that simulates their path. Then, I saw your technical notes and notice that you already mention computer programs. Have you done any work computer modeling any biological examples (you mention a few such as bee dances)?

          I imagine that this would be very complex to go from the logic of the electromagnetic force that holds atoms and molecules together (which is where you started with your paper), and then building upon the logical choices as molecules build DNA, which builds sensors such as eyes, etc, to then use this information to make logical choices in the brain. But if each has logical step, it would be fascinating to see if a computer could run these steps over time and if basic electrons and protons would run its course to create complex systems with the ability to make decisions.

          Your paper is very thought provoking. Thank you for submitting it.

            Dear Jeff,

            thanks for those kind words.

            I have not done computer modelling of biological examples, but I have done such modelling of decision processes. The key always is the control branching structure in whatever language you are using (implemented for example by IF .. THEN .. instructions, or WHILE ... DO ... loops, or FOR I = 1 To N loops, etc).

            Yes what you suggest would be a great project. You mention "the logical choices as molecules build DNA" but the really important choices are the logical choices made as molecules build proteins. DNA is just a step on the way (even though it has had a much better press than proteins!) The process is controlled by the complex logic of Gene Regulatory Networks, and that is where good modelling comes in.

            Best wishes

            George

            George Ellis,

            Sorry to be so blunt, but many parts of this essay are just illogical. In particular, the essay section "5.2 Their coming into being, evolutionary aspects" is illogical: DNA does not really exist outside the cell, and for multi-cellular organisms the cell does not really exist outside the organism. Selection pressures are exerted on the whole organism: the whole organism must first exist for selection pressures to be exerted on the organism and the DNA. I.e. selection pressure does not explain the existence of organisms or the existence of their DNA. Yet this essay muddies the waters on that issue, somehow claiming that "Darwinian adaptive selection" is responsible for their "coming into being", and that their "existence has to be explained on the basis of natural selection". It's the existence of mutation outcomes that need to be explained, not the subsequent selection outcomes. Based on more recent, modern evidence, Masatoshi Nei (one of the founding fathers and pioneers of what is now called the field of molecular evolution) and many other evolutionary geneticists claim that mutation, not natural selection, drives evolution.

            But this essay also muddies the waters on the quantum randomness that seemingly leads to much mutation. Quantum randomness is non-deterministic. The existence of instantaneous non-deterministic outcomes at all levels of reality is not explained. As you will appreciate, this issue is quite separate to the fact that long-term outcomes of deterministic complex systems can't be determined/known because of the complexity of the system.

            I also find very muddy and questionable your assertions and arguments that "the key difference between physics and biology is function or purpose" and that "Organisms exist to reproduce".

              Dear Mr.

              Your essay is excellent.

              I Agree:

              "Adaptive selection is not the same as energy minimisation, although that will play

              an important part in determining what can happen, nor is it entropy maximisation. It

              cannot be deduced by statistical physics methods, nor by a consideration of force laws

              such as (2-4) or from the standard model of particle physics. It is not implied by physics,

              which has no concept of survival of a living being (or for that matter, of a living being),

              but is enabled by it...

              But if we just want to find the cause derived from physics, it's the attractions and repulsion. This physical process is common and essential to all levels of structures and phenomena. For adaptive selection too.

              Regards,

              Branko

                Dear Lorraine Ford

                thanks for your comments.

                My essay had to fit in the limits set by the essay criteria, so I have had to use shorthand for longer descriptions I would have used had more space been available. If it is misleading, I will clear that up in revisions. In essence I agree with all most of your points except the last, but I think you are a bit unfair in how you refer to what I have written.

                1. "DNA does not really exist outside the cell, and for multi-cellular organisms the cell does not really exist outside the organism." - agreed, that is a point I make strongly in my book on Top Down Causation. I do not I think imply otherwise here.

                2. "Selection pressures are exerted on the whole organism: the whole organism must first exist for selection pressures to be exerted on the organism and the DNA." I essentially make that point clearly in my discussion of the coming into being of sight. Please read it again. It is also made clearly in my book on Top Down Causation.

                3. "It's the existence of mutation outcomes that need to be explained, not the subsequent selection outcome" - wrong, they both need to explained. They have to come into being, and they then have to be selected for, both steps are necessary. I refer in my essay to Andreas Wagner's book "Arrival of the Fittest" where the first step is explained in depth, and to the book by "Cycles of Contingency: Developmental Systems and Evolution" by Oyama, Griffiths, and Gray where the second step is explained in depth. Of course mutation is necessary. That won't get you a entity that fulfills a specific purpose unless it is then selected for.

                4. "But this essay also muddies the waters on the quantum randomness that seemingly leads to much mutation. Quantum randomness is non-deterministic. The existence of instantaneous non-deterministic outcomes at all levels of reality is not explained." - I have often made the point that quantum theory is non-derministic, e.g. arXiv 1108.5261 (the case has to be made because there are a number of physicists who don't believe it). I have also written and talked about this effect on evolution elsewhere, for example the last chapter of my book on top-down causation referred to above. In this essay I put in one sentence to refer to this whole deep discussion, which I make a central feature in various articles on the philosophy of cosmology. But in any case, quantum randomnesss is only one of the effects that lead to mutation. There is also for example gene variation due both to sexual combination and horizontal gene transfer.

                5. "As you will appreciate, this issue is quite separate to the fact that long-term outcomes of deterministic complex systems can't be determined/known because of the complexity of the system." Of course I appreciate that.

                6. "I also find very muddy and questionable your assertions and arguments that "the key difference between physics and biology is function or purpose" and that "Organisms exist to reproduce"." - That is not my assertion, it is an assertion by Hartwell et al, as is clear in my essay. He happens to be a Nobel prizewinner for the discovery of protein molecules that control the division (duplication) of cells. And if that is not the essential difference, please tell me what is? Are you saying that non living systems have function of purpose? If so, please explain. For example, what is the purpose of the Moon or an electron? Or are you saying that physiological systems do not have function or purpose? That the eye is not there to enable vision, for example? Please read that paper carefully to see the full range of issues that paragraph is intended to summarise. Given what else I needed to say, I could not summarise their paper at greater length in my essay. As to ""Organisms exist to reproduce", that is a brief summary of Darwinian logic and an explanation of existence of crucial physiological systems and of a great deal of animal behaviour. If they are not there for that purpose, why do they exist?