Wandering Towards a Goal: The Key Role of Biomolecules by George F. R. Ellis

Dear Mulugeta

you have no authority to tell me what I should and should not do.

Furthermore, you completely misunderstand the relation between science and religion: they are not in conflict with each other, despite what people like Richard Dawkins may say. There is a substantial literature on how they can be regarded as in harmony with each other, of which you seem unaware.

Your postings are frankly verging on the offensive. You do not seem able to treat others with respect if they disagree with you. I will not respond to any further postings you may choose to make.

George Ellis

Repeating this obscure statement several times on this thread is spamming.

Please desist.

George Ellis

Please stop repeating this on my thread.

Responding to the second last:

> I hope you don't mind, but I don't agree with Platonism for the following 3 reasons: 1) Platonism seems to imply that the power to bestow rules exists outside the universe, with the Platonic realm being like a puppeteer, and the universe being like a poor puppet.

- Well in a sense that may be the case. It is unclear if the possibility spaces of physics and biology precede the existence of the universe, or come into being with it. Some people believe the former: that the laws of physics brought the universe into being. In any case they certainly dictate what is and what is not possible, once the universe is in existence; and they are timeless eternal relationships, hence of a Platonic nature.

> 2) Platonism seems to hypothesise (i) that all rules must abstractly exist, rather than (ii) hypothesising that what exists is the raw material to make rules (where the raw material is an inherent ability to create rules/categories; rules being equivalent to categories because a category is like an equation re-arranged so that the category is on one side of the equal sign).

- (i) is true of Mathematical Platonism, which I subscribe to. (ii) may be true of physical and biological platonism (for the latter, see Wagner's book I refer to).

> 3) Platonism is seemingly uneconomical about numbers as well: it seems to hypothesise that all numbers must abstractly exist, rather than hypothesising that what exists is the raw material to make numbers. Surely numbers, even numbers like pi, must ultimately derive from the fact that with some rules/relationships, you can cancel the numerator and denominator categories, and end up with a number: a thing without a category. I'm contending that numbers are essentially due to relationships, rather than being like little rocks. (I also contend that the set theory view of numbers is too unlike the equation-like structure of law-of-nature rules, for numbers-as-sets to exist at the level of fundamental-level reality.)

- I am open to discussion about numbers; you may be right. What I have in mind is facts such as the square root of 2 is irrational. That is a timeless unchanging mathematical fact, hence has a Platonic nature.

> In any case, I think the hypothesis that what exists is the raw materials with which to make new rules/categories and numbers, is no more fantastical than the hypothesis that what exists is an (uneconomical!) Platonic realm of every possible rule and number.

- yes but where do the rules of logic come from? They are a set of unchanging possibilities that we discover and explore with our minds. They have a Platonic nature.

> I hope you don't mind if I say that Platonic realms seem to be all about deterministic mechanisms and a universe that has no control over the functions bestowed upon it by the realm;

- yes

> complex systems are all about deterministic mechanisms and the illusion that new function could evolve purely from the mechanism;

- well I don't think its an illusion, because that view rests on the assumption there is only bottom up causation, which I dispute;

> but actual reality is both mechanism and continually creative of the truly new:

- yes here we agree.

> Also on the radio this morning: Bees are smarter than we give them credit for - "They may have tiny brains, but it turns out that bumblebees can not only learn to use tools by observing others, they can improvise and make the task even easier", http://www.abc.net.au/news/2017-02-24/smart-bees-learn-how-t

o-use-tools-by-watching-others/8297576 .

Ah bees are very intelligent. They can understand abstract symbols. That is an emergent power that physics enables but does not dictate.

regards

george

Responding to the last:

> I think that the argument in your essay hinges on black-boxing: i.e. the question of how new function appears in reality is left unanswered. The overall essay, while excellent in itself, gives a sense that something has been explained, but to me, it actually hasn't been explained because the important details have been black-boxed.

Well I only had 9 pages.

> It cannot be shown that new function emerges from e.g. an x,y graph of a function, no matter how complex the function represented, and by analogy no purely deterministic system can ever "evolve" new function. The "emergence" of new function has been black-boxed in your essay.

It is discussed in detail in the paper by Tononi et al I referred to, and is the topic of all the literature on how gene regulatory networks, signal transduction networks, and metabolic networks emerge from networks of interactions between more elementary networks, as well as all the literature on neural networks. This is not usually equivalent to how new mathematical functions emerges from simpler ones. It is how new logical functions emerge from simpler ones. To see one example of how this works, see Uri Alon's writing on Network motifs: simple building blocks of complex networks.

George

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 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 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

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 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