Dear Natesh

> 1) The key difference between the logic of physics and biology in your essay seems to be the presence of a context in biology that is seemingly missing in physics (Am I still missing something else here?).

No, it is that biology can entertain *arbitrary* logical functions, whereas physics is governed by a set of *fixed* physical laws

> I would argue that for a system S, C is like any other physical system that influences it's state, and the 'context' or lack thereof is derived from the interactions (governed by physical law) between S and C.

- Well it is the word "governed" that is at issue here. The fact that sight is advantageous to animals is partly governed by physical law, but is essentially based in the fact that sight is good for survival. That's not a physical law (survival of an animal is not a physics concept).

> For example: in the case of the microbe (S) and poison (C), it is the specific interaction between S and C and the action that S performs or doesnt perform due to that interaction, that imbues C with it's context with reference to S.

- Yes

> The context of the physical system C to S is not something determined apriori. Of course if the system is capable of memory and learning, then it can use that to remember the poison and it's actions for a future situation. I would further argue that "If...then...else" like logical statements can be achieved in hardware in computers, that can be purely described using physics based statements.

- yes indeed. If someone has already programmed it in.

> What type of system S can recognize the context that is has imbued C with because of its interactions? I think that is an important question that needs to be worked out.

- Can't quite get that. Maybe a typo.

> 2) The agency I am talking of (takes the definition from philosophy and it) is simply the capacity to act. To act involuntarily, unconsciously or consciously with a purpose will all fall under it. The moon with the ability to act on earths waters makes it an agent, but doesn't have to fall under the category of making it a purposeful one for the moon or even that the moon is capable to generating its own purpose like we do.

- OK. Its an unusual use of these words ....

> It is very possible to think of physical systems that have no agency-can change their state based on the influence of external systems but do not have the ability to 'act' and affect its environment.

- Newton's law: action and reaction are equal and opposite??

> It is thus possible to have systems that have 'agency' as I define, but not have a purpose or intent for that agency. I would point out that it is not just hierarchical systems that have a sense of agency, but minimally dissipative systems (from my essay) whose dynamics can be achieved in an hierarchical predictive coding model that will be capable of a sense of agency. The sun, earth, etc will not satisfy the condition of being minimally dissipative.

- I would not use the words sense of agency in that context

> 3) The complexity constraint is using a statistical complexity measure like the mutual information between the system and all the inputs in the past that has influenced it's state. The finite complexity constraint is necessary for I am dealing with finite state automata models with an emphasis on finite and this constraint would ensure I dont end with trivial solutions like 'have an infinite number of distinguishable states and remember everything'. Furthermore the problem is mathematically formulated so that the tradeoff parameter in the optimization problem beta can be moved like a knob to play around with the complexity and see how that affects external input-system correlations. While it is possible to have both extremely complex structures or minimally dissipative systems that do not learn, we can see that the type of learning dynamics we see in certain biological systems is a tradeoff between the dissipation and complexity, parametrized by beta.

- OK. I'd need more time to look at this.

> 4) "If it is adaptation, there is some selection principle in action which cannot be captured simply by the idea of dissipation." England's idea is that those selection mechanisms themselves are instantiations of larger thermodynamic dissipation principles. There are of course some caveats there in his hypothesis and there is much work to be done to make it a more developed proposal.

- and my point is that there must be some selection principle acting which is at a higher level than thermodynamic dissipation principles. I cannot see how those alone can possibly lead to wings or eyes or brains.

Regards

George

Dear George,

Thank you for your answer on my essay "The Purpose of Life" and the reference to von Helmholz.

I agree with you that NOW is never eternal in our emerging reality, we experience a FLOW of time.

This 'flow" is the result of the capacity of our memory. The continuation of this flow is created by the addition of a new NOW moment. This new NOW moment is originating from Total Simultaneity where it is a timeless entity (so eternal) and I called it the ENM. The ENM is NOT existing in our emergent phenomenon called REALITY.

Our experience (like you are saying is continually changing) of NOW is entangled with its "ENM" in TS but NOT existing in our experience of reality. The timeless ENM becomes an addition to a timeless experience in our memory.

I hope to have explained my interpretation.

best regards

Wilhelmus

    Dear Wilhelminus

    thanks for that.

    > I agree with you that NOW is never eternal in our emerging reality, we experience a FLOW of time.

    yes.

    > This 'flow" is the result of the capacity of our memory.

    I'd see it the other way round: Memory is a record of that flow, but not the cause of that flow.

    > The continuation of this flow is created by the addition of a new NOW moment.

    Yes. That is what makes it a growing block universe.

    > This new NOW moment is originating from Total Simultaneity where it is a timeless entity (so eternal) and I called it the ENM. The ENM is NOT existing in our emergent phenomenon called REALITY.

    This is the part I can't grasp. I don't know what Total Simultaneity means or where it lives. The field equations of general relativity show how a new 3-geometry emerges at time t+dt from the one at time t. How this happens is dicussed here.

    > Our experience (like you are saying is continually changing) of NOW is entangled with its "ENM" in TS but NOT existing in our experience of reality. The timeless ENM becomes an addition to a timeless experience in our memory.

    Well memory is a rather fallible thing and is not timeless (if you are talking about real human memory). But yes what happens at each transient present moment gets added to our memory.

    Ragrds

    George

    Dear George

    * I perceive our emergent memory also as an excitation of the Eternal NOW Moment in Total Simultaneity. The ENM "contains" the whole memory, so we become aware of the flow via the ENM.

    *Total Simultaneity is a "dimension" without space and time that can be reached by trespassing the Planck Wall in our emergent reality. As this is impossible ( we can reach out only hyperbolical) Total Simultaneity is source of all emergent realities because I argue that it is a Hilbert space , of ALL ENM's (also from so called paralel universes and every universe predicted by MWI.

    * As each emerging NOW moment is an excitation (maybe of a Planck time) that directly becomes past (inluding ALL memory) it is through our emerging experience that time (for us) seems to enter, in fact in my proposition the whole of our life is just ONE excitation. The origin of this awareness (illusion) lies in the timeless (eternal) ENM. Of its own character it could be compared to a singularity. Now imagine a sphere around this singularity which is very difficult in a spaceless entity, the surface of this sphere contains like a hologram your whole life. Your emergent NOW moment is entangled with its ENM....Space and Time are created as emergent phenomenea...

    In my essay I am explaining how this perception can explain some quantum unrealities like "spooky action at a distance".

    In my article : Total Consciousness in Total Simultaneity, published in the "Journal of Consciousness Exploration & Research (vol 8 nr 1 2017) I also treat the subject of time travel.

    best regards

    Wilhelmus

    Dear George,

    In your approach, you are trying to see the scientific ground for subjectivity. I fully agree that this line of thinking is important; however, I suppose the essence of subjectivity is still going to be missed in this way. At best, an objective door for all subjectivity could be found, like QM uncertainty showed a possibility for the free will. I appreciate your efforts and think your approach is complementary to ours. Your comments to our paper are more than welcome.

    Yours, Alexey Burov.

      Dear Alexay,

      your essay deals with important aspects of the higher (philosophical/ mental) level. I am dealing with the lower levels that provide the basis on which those higher levels can emerge, having their own logic and causal powers. Thus our essays are indeed complementary. Both are needed.

      Best regards

      George

      Professor Ellis

      "No, it is that biology can entertain *arbitrary* logical functions, whereas physics is governed by a set of *fixed* physical laws."

      --> I am a little confused by what you mean by 'arbitrary' here. If you mean that the "else" and "then" part depend upon the "if" part in a "if...then...else" statement, I think those are not unique to biology. These are (Markov chains) finite state automata/machines, in which the next state depends upon the current state and external input, and they can be described with physics alone.

      "yes indeed. If someone has already programmed it in."

      --> Yes, I agree that historically computers have been programmed but that tide is changing. I just got back from a conference where we were talking about having hardware that is just allowed to run in response to external inputs, without any algorithms or programs and constrained by larger thermodynamic constraints (aptly called thermodynamic computing). These can be described as "if...then...else" statements without being programmed. Here is a small blog post about it from another attendee. The talk by Todd Hylton is what I am talking about.

      http://knowm.org/review-of-2017-energy-consequences-of-information-conference/

      "K. Its an unusual use of these words ...."

      --> I really need to work on making my definitions clearer, elucidating differences with other popularly used definitions. Think it also applies how I think about and use the word "action" in this essay.

      "The fact that sight is advantageous to animals is partly governed by physical law, but is essentially based in the fact that sight is good for survival. That's not a physical law (survival of an animal is not a physics concept)."

      "- and my point is that there must be some selection principle acting which is at a higher level than thermodynamic dissipation principles. I cannot see how those alone can possibly lead to wings or eyes or brains."

      --> I am attaching the link to England's paper on the idea how thermodynamic principles can end up manifesting itself as selection mechanisms. It is a lower level argument and does not provide the richness of detailed selection mechanisms but that doesnt diminish the idea itself. Birds have wings because those structures have a rich history of better work absorption and dissipation. We see structures for eyes and wings, if they have a very particular history described purely in terms of heat dissipation and not of selection mechanisms.

      "Dissipative adaptation in driven self-assembly"- http://www.nature.com/nnano/journal/v10/n11/abs/nnano.2015.250.html

      Cheers

      Natesh

      Dear Natesh

      >> G: No, it is that biology can entertain *arbitrary* logical functions, whereas physics is governed by a set of *fixed* physical laws."

      --> N: I am a little confused by what you mean by 'arbitrary' here. If you mean that the "else" and "then" part depend upon the "if" part in a "if...then...else" statement, I think those are not unique to biology. These are (Markov chains) finite state automata/machines, in which the next state depends upon the current state and external input, and they can be described with physics alone.

      - Physicists see physical laws as described by Hamiltonian dynamics. According to Wikipedia, "A finite-state machine (FSM) or finite-state automaton is a mathematical model of computation. It is an abstract machine that can be in exactly one of a finite number of states at any given time". IN other words it is a computer, which I mention in my Appendix, which can perform arbitrary logical functions. Yes you can design them and make them out of physical elements; it is that designed structure that gives them the ability to carry out arbitrary logical and mathematical functions, because the design makes it so (and allows logical branching). This is quite different than Hamiltonian dynamics.

      >> G: "yes indeed. If someone has already programmed it in."

      --> N: Yes, I agree that historically computers have been programmed but that tide is changing. I just got back from a conference where we were talking about having hardware that is just allowed to run in response to external inputs, without any algorithms or programs and constrained by larger thermodynamic constraints (aptly called thermodynamic computing). These can be described as "if...then...else" statements without being programmed.

      - well that is a very interesting development. But the starting point is human design: that is what enables it to get off the ground.

      >> G: "The fact that sight is advantageous to animals is partly governed by physical law, but is essentially based in the fact that sight is good for survival. That's not a physical law (survival of an animal is not a physics concept).".... "and my point is that there must be some selection principle acting which is at a higher level than thermodynamic dissipation principles. I cannot see how those alone can possibly lead to wings or eyes or brains."

      --> N: I am attaching the link to England's paper on the idea how thermodynamic principles can end up manifesting itself as selection mechanisms. It is a lower level argument and does not provide the richness of detailed selection mechanisms but that doesn't diminish the idea itself. Birds have wings because those structures have a rich history of better work absorption and dissipation. We see structures for eyes and wings, if they have a very particular history described purely in terms of heat dissipation and not of selection mechanisms.

      - England's paper is very interesting. It may be that Birds have one particular wing structure that enables flight rather than another wing structure which also does so, because of thermodynamic reasons. But birds have wings because this enables them to fly; there is no way that thermodynamics can determine that it is biologically advantageous to have wings. At a lower scale, thermodynamics by itself cannot lead to existence of proteins such as hemoglobin or kinesin in the timescales available since the start of the universe. Please see the book by Andreas Wagner I refer to for detailed discussion.

      - Where thermodynamics comes in is in the metabolic networks that have to be evolved for life to come into being. The key feature in Wagner's work is existence of huge functional equivalence classes of genotypes that lead to the same phenotype, in all the cases he examines. It is this fundamental role of functional equivalence classes that is missing in England's thermodynamic analysis; and that is why it cannot in the end be the full picture. It is missing key elements of what is going on.

      Cheers

      George

      Dear Dr. Ellis:

      Your paper is presents an elegant biological framework built upon the fundamental theme of the purposelessness of physics as you state in your paper- "The key difference between physics and biology is function or purpose. There is no purpose in the existence of the Moon or an electron or in a collision of two gas particles. By contrast, there is purpose and function in all life [7]."

      However, I present an alternative approach in my paper -FROM LAWS TO AIMS & INTENTIONS - A UNIVERSAL MODEL INTEGRATING MATTER, MIND, CONSCIOUSNESS, AND PURPOSE by Avtar Singh, wherein the universe is regarded alive wherein the eternal and omnipresent universal laws are identified as the universal awareness or consciousness. It demonstrates the power of a wholesome consciousness-integrated science to reveal the physical basis for purpose, aims, and intentions in the universe and life in it. The approach of the scientific research is three-fold. First is to complete the picture of reality via integrating consciousness into a physical model and explain the observed universe behavior resolving the current paradoxes, singularities, and inconsistencies of the mainstream scientific theories. Second is to develop a framework for an integrated model of matter, mind, and consciousness founded on the wholesome reality. And lastly, demonstrate how the so-called mindless physical laws lead to the ultimate purpose, aims, and intentions. A successful agreement between the predictions and empirical observations of the universe demonstrates the validity and credibility of the proposed approach. The predictions are further testable and falsifiable via future observations. The goal-oriented behavior is shown to be an orderly physical/cosmic trend governed by the laws and not an accident or an imperative.

      With your broad and in-depth expertise, I would deeply appreciate your comments on my paper from cosmological and physics perspectives.

      Best Regards

      Avtar Singh

        Dear Avtar

        I have commented over there. It is an interesting try, but in the end I stick with the statement "The key difference between physics and biology is function or purpose. There is no purpose in the existence of the Moon or an electron or in a collision of two gas particles. By contrast, there is purpose and function in all life". Quantum randomness is not equivalent to purpose, as your essay seems to suggest. And I do not believe that dark matter has anything to do with mind or consciousness.

        I do think an integration is a great idea. But I think it must separate physics from biology, and show how the latter can arise from the former.

        regards

        George

        Thank you for your very well written essay. We fully agree with your emphasis on the role of emergence as key for the understanding of the origin of adaptive selection in physical terms.

          George

          Excellent job again.

          I don't have the reservations expressed above as we seem to agree on all fundamentals including key roles for Maxwell, QM, Darwin, Branching logic, gates, hierarchical structures, remorseless repetition, importance top down AND bottom up influence, inadequacy of thermodynamics, undecidability of an origin, etc. My essay is thus similar in ways but deals more with the top and a 'lower' bottom. By comparison yours fleshes out the important centre from proteins upwards quite brilliantly. But some questions;

          1. Do you really think 'Life' always; "collects and analyses information in order to use it to plan and execute future purposeful actions"? Do you not agree most sensory input is 'collected' ad-hoc for no such specific purpose?

          2. You 'wave towards' QM frequently. I agree that's valid because logic fails when stepping closer. So do you subscribe to the belief that logic will always fail at that scale? or that our understanding may one day improve?

          Perhaps answer that last one both before and after reading mine because I venture to identify a shocking revalation anticipated by John Bell and allowing classical derivation (down to reducing fractal recursion) of the full predictions! (you may recall precursors in my last 2 essays).

          I'd greatly value your opinion.

          Very Best

          Peter

          Dear Peter

          I am glad about our agreements!

          >> 1. Do you really think 'Life' always; "collects and analyses information in order to use it to plan and execute future purposeful actions"? Do you not agree most sensory input is 'collected' ad-hoc for no such specific purpose?

          Well life collects whatever information is available, sifts it for meaning, and compares it with our predictions of what ought to be happening. If it is what was expected, it is ignored; if it is unexpected, it becomes the focus of attention. So a great deal is collected just in case! Most is discarded - but that which is used is crucial.

          >> 2. You 'wave towards' QM frequently. I agree that's valid because logic fails when stepping closer. So do you subscribe to the belief that logic will always fail at that scale? or that our understanding may one day improve?

          Well its not so much logic that fails at that scale as predictability; also the nature of existence is somewhat different. What we don't understand is the quantum to classical transition. That may well be understood one day.

          >> Perhaps answer that last one both before and after reading mine because I venture to identify a shocking revalation anticipated by John Bell and allowing classical derivation (down to reducing fractal recursion) of the full predictions! (you may recall precursors in my last 2 essays).

          I'll take a look.

          Best wishes

          George

            George,

            Your argument is clear and cogent. I can understand your distinction between living systems and the inanimate, but the distinction is less crisp when you think of microorganisms and some new theories like Jeremy England's. Does a virus, bacteria, fungi or protozoa have a goal or purpose and does it grow, reproduce or metabolize?

            Jeremy England's new theory regarding the second law of thermodynamics says the difference between the animate and the inanimate is that living things are much better at capturing energy from their environment and dissipating that energy as heat.

            "You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant," England said.

            Well done link of physics to logic, but is there also a cosmic or long-term link between physics and logic. What is the mixed-bag process of clouds of supernova elements forming into rocks vs microorganisms and are the latter alive or potentially alive but not the former?

            Obviously we have limited space to present our views. In the allotted space you have done a tremendous job of clearly presenting your views.

            Sincerely,

            Jim Hoover

              Thank you so much for your essay, it was a pleasure to read. In the title, you focus in macromolecules. In the essay, however, you also make of evolution a key character. I tend to believe that the latter is more fundamental that the former. So this is my question. Could the emergence of goal-directed behavior also be possible in a substrate that is not based on the chemistry of carbon? Your question at the beginning seems to be how to connect the logic of physics with the logic of life. The logic of life, however, is not limited to be implemented by biochemistry, at least not from a logical point of view. So do you think there is an essential feature that these macromolecules have, that allow them to do the job? Could that feature be found in some other structure? Or do you think macromolecules are the only possible solution?

                After just the few three sentences, already...a problem.

                To state that lifeless beings have no purpose must be a self-evident metaphysical axiom...since there's no evidence offered to support it. So there's one problem - it's not self-evident.

                If the lifeless are purposeless, then why do they exist? If life forms have a goal, what is it?

                Granted that life has a purpose - is it Darwinian materialism.... survival and reproduction? If so, then every life is a failure at surviving and sometimes at reproducing! As all life forms die, can we say that the purpose of life is death? If the purpose of life is survival then it fails...every time...unless there's an immaterial life beyond the material!

                Physical laws determine evolution of a physical system in a purposeless inevitable way.

                Then - how can life forms exist without the support of inanimate beings, George? Doesn't the use of the inanimate by life forms give them a purpose? If life forms require energy and motion to survive, and energy and motion are the subject matter of physics, doesn't life depend on the subject matter of physics?

                Purpose and function seem used here univocally....implying the world of physics has no function in biology?

                But realism separates function vs. purpose as distinct: efficient cause vs. final cause! That purpose can only be perceived by the (immaterial) intellect leads once again to an immaterial source.

                Without human perception purpose would be present but unrecognized.

                When inert food is consumed by life forms, does the food then have a purpose when metabolized?

                Does a life form lose its purpose when it dies?

                Without inert material, life could not exist. So it does have a purpose ...to support life.

                This is all part of the general view that unfolds later on as the philosophy of materialism, naturalism and scientism tries to explain what only the (immaterial ) mind can apprehend - purpose.

                Materialism can be dismissed by simply asking what vital material substance leaves a living body upon death? It must be material, since only matter exists. Does DNA leave? The ion channels?

                Since there is a clear difference between life and death, a material cause cannot explain the difference...but an immaterial cause is possible.

                Scientists who accept mathematics are tacitly rejecting materialism, since math is an immaterial abstraction of quantity from the physical world. Math exists in an immaterial way, in an immaterial order of reality. Materialistic claims are self-contradicting so the foundations.

                All essays should start with common ground agreements, on using the scientific method and a historically proven philosophical view like realism to correctly design and interpret experiments. Realism - the heritage of Western culture - predates and surpasses the modern philosophies of choice; it uses self-evident axioms over 24 centuries old: an objective world exists, independent of observation; axioms of non-contradiction, finite and sufficient causality, etc.

                Science alone lacks the scope of knowledge domains like philosophy and theology to address the full range of human issues .

                The path to understanding the purpose of all reality as higher level immaterial causes has been described by such as Blaise Pascal who considered two "orders" of reality, matter and mind. "there is, first of all, the order of quantities - and that is enormous and infinite, the inexhaustible object of natural science. Besides that, the order of the mind, the second great realm of reality, appears, on the basis of quantity, as simply nothing, since quantitatively it takes up no space whatever. And nonetheless, a single mind is greater than the entire order of the quantitative cosmos; because mind, which has neither weight nor length nor breadth, is able to measure the entire cosmos."

                To Wolfgang Smith objects of measurement are 'physical objects' of quantity; the math order only captures a physically measurable dimension of reality. He then terms substances of quality having an immaterial order (of the mind) 'corporeal objects'.

                To this Joseph (Cardinal) Ratzinger added, "Yet above that stands the order of abstraction of qualities like truth , justice and love. Love signifies the presence of personhood, personality, the ego. That order too is, at first blush, simply 'nothing' in the order of 'mind,' of scientific intelligence, since it cannot be the object of scientific demonstration, And nonetheless, a single motion of love is infinitely greater than the entire order of 'mind,' because only love represents what is truly creative, life-giving and saving power."

                This is the level of the person, where mind introspects to become self-conscious, the level of choice, of volition, and of goal processing: setting, planning , execution and attainment of...a purpose or end ......the level of a living soul.

                In a video presentation George has stated that:

                Bottom -up causation can give emergence to the level of sand-piles of fusion reactions; there's a ceiling to the complexity possible before top-down causation. We still don't understand how the transition to Darwinian evolution occurred ...once it started we still don't know how we jumped over until top-down causation became effective in generating information.

                The Mystery of the Origin of Life's Genetic Information

                The transition to evolution - biogenesis - is only rationally comprehended via an immaterial source...which is outside the scope of science. Even then George admits ignorance of the link to top-down causation.

                But top-down causation from a final physical cause has not been covered in the essay. Describing a host of material, efficient and formal causes will not make the connection to a final goal-oriented cause a reality - unless that cause is immaterial.

                Tying up loose ends:

                ... outside religious belief, rocks and stars have no purpose.

                One star, the Sun , has a clear purpose - to support all biota. In general, recognizing the true source of immaterial goals is impossible with a materialistic philosophy, but conceivable in realism...and without divine intervention.

                Selection for function has produced the living cell, with a unique set of properties that distinguish it from inanimate systems of interacting molecules.

                Purely a description of the living cell differing from the physical components in a dead cell..... but no logical solution offered as to why the difference.

                Cells exist far from thermal equilibrium by harvesting energy from their environment.

                Then physics is needed...and so serves a purpose! Can life forms disobey the basic laws of energy transfer and motion?

                [Cells] are composed of thousands of different types of molecule. They contain information for their survival and reproduction, in the form of their DNA".

                How does purpose or function emerge from physics? .... At the micro level, through epigenetic effects in cell development [5] via gene regulatory networks [5] and through adaptive effects in signal transduction networks [9] and synapses [10]. And these are all based at the lower levels in specific molecules: proteins [14] and nucleic acids [19

                These are all physical changes. If true, the effect (life) would have greater state of being than the cause(non-life), violating the axiom of realism on sufficient causality. To wit: An effect cannot have an ability/function greater than potentially exists in the cause. In the vulgar form: Something can't give what it ain't got.

                The classic question - can one get blood from a stone?

                .... this paper will focus on voltage gated ion channels.

                If VGIC give purpose or function to life, then the VGIC must be common to all life and all VGIC be dysfunctional at death, when life ends. No evidence is presented in the body or references to support this statement.

                ... Quantum mechanical interactions based on these forces underlies the existence of the structures of neurons and their component parts.

                QM is then just another layer between the physical world and the cause of directed activity - the vital purpose.

                In the end, daily life is governed by Newton's laws of motion and Galileo's equations for a falling body, together with Maxwell's equations: and nothing can change those interactions.

                The laws have to be changed to agree with experiments. The laws of mechanics and EM have to be modified to include aethereal interactions, which make Maxwell's laws Galilean covariant ...in the form of the Hertz EM laws.

                Life collects and analyses information in order to use it to plan and execute future purposeful actions in the light of memory.

                Information content is immaterial; the form of coding is physical. More evidence of the immaterial necessity for an immaterial final cause for life.

                The key point is that the functions T(X), F1(Y) and F2(Z) are not determined by the underlying physical laws;

                These functions could just be undiscovered physical laws. Or is the contention that all the laws of physics are now known...TOE or GUT? That's a whole new achievement to challenge...

                .......they can be shaped by evolutionary or in highly complex ways..

                Evolution by random selection or complex ways is not a logically complete explanation for the means by which material objects can achieve immaterial operations...without sufficient causality in their nature.

                Unlike the case of physical laws, where the relevant interactions cannot be changed or chosen because they are given by Nature and are invariable, these interactions can fulfil widely varying biological or social or mental purposes.

                Assumes that all laws of physics are known...and that those known are all correct and complete.

                Demonstrably false.

                ... a digital computer can carry out arbitrary computations,

                Arbitrary means random - without reason or logic. The computer carries out the input instructions according to its programmed logic.

                Is this somehow an oblique reference to a Turing machine?

                Epigenetics: gene expression at lower levels is controlled at lower levels by gene regulatory networks to meet higher level needs

                The subject of epigenetics was once called introns or junk DNA...as there was no purpose seen in their presence. (Another proof that purpose is recognized only in the immaterial intellect, not in the material world. In the case of humans this recognition is obviously fallible.)

                The point is: does George believe that the book is now closed on genetic control mechanisms?

                If so, how is the role of histones and methyl groups discarded?

                Physical realisation The hierarchy of structure that underlies existence of life

                Can a structure plan itself? Did we humans plan our own genetic structure?

                The link of physics to logic: the molecular basis The logic of what happens is enabled by voltage gated ion channels in axon and dendrite membranes ......The implication is that, at least in the brain, ..... Biomolecules perform logical operations.

                VGIC and biomolecules are effects, not causes of logical operations... sufficient causality again... what is the real and credible source of the logic?

                Energy is of course used in carrying out these logical processes,

                So physics does have a function to perform.... enabling vital processes. Should the opening sentences be revised?

                ..... the necessary energy usage for cellular function is controlled by complex metabolic regulatory networks that determine what energy transactions will take place on the basis of logical operations;

                This is nominalism ..... a name of itself doesn't provide the causal power to organize and convert non-living objects into life forms. Did Aristotle's taxonomic hierarchy explain why the life forms were alive?

                The possible existence of biomolecules, and particularly the proteins that govern biological activity, results from quantum interactions mediated by the electromagnetic force.

                The same is true of inorganic molecules, George. And how do the possibilities become instantiated as actual biomolecules by physical agents?

                .....how have the specific proteins that exist and control biological function come into being? .....The relevant proteins exist because of the reading of the genetic information written into our DNA through developmental processes

                Where's the adequate causation of the genetic info written in our DNA? As usual, the premise of existing life is necessary- with no material theory to support the first occurrence of life.

                These extraordinary complex molecules with specific biological functions (for example, hemoglobin exists in order to transport oxygen in our blood stream) cannot possibly have arisen by chance.

                And so the very roots of Darwinism are discarded! Amen to irreducible complexity.

                Bottom-up self-assembly will not do the job. They have to have been selected for through the process of Darwinian adaptive selection [2] which creates new information (embodied in the sequences of base pairs in DNA [19]) that was not there before.

                But this process is teleological as described, not Darwin's theory of RANDOM SELECTION. The end(final cause) must be known to "adapt" to the desired effect. Adapting to a final end by knowledge of that end is in fact strictly forbidden by random natural selection.

                Then reading out that information by cellular processes creates the string of amino acids that forms proteins such as hemoglobin. It then has to fold to give its biologically active form. In principle that step is an energy minimisation operation;

                Energy minimization is a mathematical and hence an immaterial process governed by the Lagrange variational principle.

                .... a random input ensemble of entities is filtered to produce an ordered output ensemble, adapted to the environment via specific selection criteria.

                In this one sentence the contradictions are apparent... random entities produce an adaptation based on criteria from unspecified logical sources ... How can random chaos produce an ordered and desired change based on logic not possessed in the physical world?

                Again and again....a physical and material cause is functionally impotent to order reality to conform to a final cause.

                .....It is the remorseless continual repetition of the process of randonisation and subsequent selection that gives evolution its extraordinary creative power, underlying the emergence of complex life forms

                Does continual addition of 1 ever reach the end of the number system? Neither can any finite number of physical processes explain the life process.

                The repetition can only occur over the 5000 years of scientific history, the testability limit of the scientific method...

                Insufficient causality, in a nutshell.

                In the human case, that reshaping is achieved by technological means derived from the creative activity of the human mind.

                Yes...finally...the source of the vital logic supporting life is seen as analogous to the human mind's capability to form new immaterial forms that FOLLOW THE MIND'S FINAL PURPOSE.. But where is Nature's immaterial mind, George?

                Development of vision is a multi-level process, with higher level needs driving lower level selection of structure and function: 7 • The top level need is for a visual system that will enhance survival; • The next level need is for eyes, an optic tract, thalamus (a relay station for signals on the way to the cortex), and neocortex to analyse incoming data; • The next level is a need for photo receptor cells within the retina, and neurons and synapses to constitute neural networks to analyse the data; • One then needs specific kinds of proteins to make this all work , for example rhodopsins in Light Harvesting Complexes and voltage gated ion channel proteins in the cortex;

                Two problems - at least:

                this vision solution via evolution must occur all at once; intermediate steps would be discarded by natural DESELECTION as ineffectual.

                Development of vision implies a goal defined by a material nature incapable of future planning.

                Thus natural selection is a top down process adapting animals to their environment in suitable ways, thereby altering the details base-pair sequence in DNA.

                Why haven't the gene labs copied this ersatz top-down process and altered the DNA base pairs to produce designer life forms, as nature does?

                When the human genome was first decoded promises were made of great advances in knowledge of the genomic code. But a transparent blueprint it was not. No more than converting an unknown human language into another unknown human language would increase comprehension of the content. Most advances in the 16 years since the translation have been in treatment of diseases ...by trial and error(the old way), not by using 'top-down adaptation'

                "Evolution is essentially a process in which natural selection acts as a mechanism for transferring information from the environment to the collective genome of the species".

                Information is immaterial in content, so evolution must be , too!

                [natural selection] is doubly a top down process, through the environment creating niches (opportunities for life) on the one hand, and through the selection criteria on the other.

                Darwinism's natural selection is random unguided undirected physical mutation of the genome and random selection by survival of the fittest. This is bottom-up , not top-down.

                ...noise provides the basis for selection of outcomes on the basis of higher level selection criteria, thus creating order out of disorder....

                And violating the 2nd law of thermodynamics . The scientific universe is closed in space and time.

                Statistical randomness between levels provides the material on which selection processes can operate.

                Selection processes chosen by what? Or Whom? Selection/adaptation is a conscious choice; random is not...But inanimate objects are unconscious.

                ...there are many other biomolecules that are used in interaction networks to carry out logical operations.

                What is the physical source of the logical operations?

                In particular transcription factors binding to specific DNA sequences enable logical operations

                The mechanism(efficient cause) is not the reason/purpose . Another link in an incomplete chain of causality.

                Adaptation and plasticity Life depends on adaptation to its environment.

                By immaterial processes infused into their nature...

                The brain plasticity at macrolevels that underlies our adaptive behaviour is enabled at micro levels by biomolecules acting as logical devices choosing alternative outcomes......

                The mind chooses alternate outcomes, not the physical brain...

                Adaptive selection could not take place without physics, but unlike physics is a purposeful process in that it has the logic of increasing fitness.

                It's difficult to see how adaptive selection due to increasing fitness benefits the random survivors of extinction catastrophes...which account for more than 90% of all extinctions.

                It is irreversible, because species die out in order that others succeed;

                The dodo, passenger pigeon and wooly mammoth have recently become extinct. What extant species are documented as owing their survival to their failure to survive?

                We know the environment today and the species dependencies on the environment.... So which ones will die out; which will succeed?

                In mass extinctions survivors seem to succeed by blind luck, not because others were extinguished.....don't you think?

                the development of the language capacity ....distinguishes us from the great ape.

                Testing by scientific methodology goes back at most 5 millennia; this history shows development of different languages, but not language per se. The formation of humans with intrinsic language capability, both physical and mental, is another scientific option.

                The key thing that enabled this all to happen was the origin of life, when adaptive evolutionary processes came into being. We still do not know how that happened.

                Nor does mainstream science know what drives life to exist amid non-life....the life principle

                AMDG,

                Robert Bennett

                James,

                thanks for your thoughtful comments.

                >> I can understand your distinction between living systems and the inanimate, but the distinction is less crisp when you think of microorganisms and some new theories like Jeremy England's. Does a virus, bacteria, fungi or protozoa have a goal or purpose and does it grow, reproduce or metabolize?

                I am not an expert on all these simple organisms/entities. A virus does not count as it is not self-sufficient. The others do all those things, I think. I must clarify that the statement by Hartwell et al I quoted in my essay about purpose is not I think meant to be a metaphysical statement about the meaning of life: it is a statement about all the physiological and developmental systems that underlie life, each of which does indeed have a purpose. Thus a bacteria has flagella because they enable it to move; a bird has wings because they enable it to fly.

                >> Jeremy England's new theory regarding the second law of thermodynamics says the difference between the animate and the inanimate is that living things are much better at capturing energy from their environment and dissipating that energy as heat.

                His thesis is very interesting but I think it is only part of the story. You can't capture the full nature of life by statistical mechanics methods alone, although they will be playing a significant role at the micro level. In particular what is missing is the element of genotype selection for phenotype advantage, with the key feature that a vast number of genotypes give the same phenotype outcome. This multiple realisability of higher level function is the key element discussed by Andreas Wagner in the book I mention, and cannot I think be encapsulated by statistical physics methods, because they do not refer to function.

                >> "You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant," England said.

                I don't think he can have seriously read the literature on the origin of life. No one knows how that happened. In particular we don't know if metabolism or information came first. Nor is it likely that life originated from plants. Indeed it did not, because the early atmosphere of the Earth had no oxygen.

                >> Well done link of physics to logic, but is there also a cosmic or long-term link between physics and logic.

                We don't understand that one. Roger Penrose writes nicely about it.

                > What is the mixed-bag process of clouds of supernova elements forming into rocks vs microorganisms and are the latter alive or potentially alive but not the former?

                Yes indeed.

                Regards

                George

                Dear Inez

                Evolution is of course the key, but it has to have something to work on. I believe the only possible substrate is carbon, because it alone allows existence of molecules such as DNA, RNA, and proteins. It is the latter that are truly extraordinary: a wonderful book about this is Protein Stucture and Function (Primers in Biology). Yes I believe macromolecules are the only possible solution.

                George