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

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.

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 George,

Thanks for your detailed reply. From what you say and from your "Philosophy of cosmology" paper, we seem to agree that the mutation issue is important, but we don't agree about how multiple theoretically possible outcomes could turn into actual outcomes. I maintain that physical structure is built on what amounts to rules/laws; and so reality resolves multiple theoretically possible physical outcomes by in effect creating new, one-off local rules; and that models of systems show that rules can't emerge from complexity. I too am very interested in the issue of what a model can tell you about reality, but I have a different take on it: I maintain that, unlike models, the actual universe is an isolated system that must therefore generate/create its own rules; and that the particles ("little parts" of the universe) are the generators and carriers of fundamental-level rules.

Re "Of course mutation is necessary. That won't get you a entity that fulfils a specific purpose unless it is then selected for": I think that an entity doesn't need to fulfil a purpose in order to exist - an entity only needs to fit into a niche, or create a niche. The subjective experience of all sorts of information (consciousness) via interaction with the rest of reality (not necessarily people or animals) is what is fulfilling about life: purpose is not necessary.

Re "Organisms exist to reproduce": I know that that is a quote, and not your assertion, but one might wonder about the many people who do not or cannot reproduce, or people who are past reproduction age: why do they still bother to exist?

My opinion about aim or purpose is that, like everything, it develops from existing proto-aspects of reality, but only single- or multi-celled organisms have the molecules, structure and molecular interactions to have significant capital "P" Purposes. So, an electron could have proto-purpose (proto-consciousness), but the moon or a computer does not have the structure, the molecules or the interactions to have purpose. We exist for our own purposes, but through love or other reasons, we can dedicate ourselves to what we consider to be a higher purpose than ourselves. The higher purpose might be the good of the whole of which we are an individual subjective part. Not just human beings, but animals like hens with baby chicks can have higher purposes.

Dear Professor Ellis,

More information is available at conference paper A.Ilyanok, I.Timoshchenko "Nanoclusters as superatoms and supermolecules". For the first time the opportunity of transfer functions of the human cerebral cortex in silicon neurochip of 10 cm3 with 3D nanojet printer is shows. This is due to the fact that in the last 10 years a new direction in nanotechnology has appeared - the creation of organic and inorganic nanoclusters of certain size, called superatoms, that exhibit the unique properties of elementary atoms and can formally establish a new "periodic table". The development of an entirely new field of science opens the possibility to use cheaper isoelectronic analogues instead of expensive items. From the standpoint of superatoms we can consider the physical and chemical properties of proteins like supermolecules formed from superatoms. For example, the protein tubulin which forms nerve fibers and nuclear scaffolds and cells shows unique physical properties. It forms nanotubes with a diameter of 14.5 nm. The developed technology of jet nanolithography allows us to grow inorganic artificial neurons, while watching their growth using the methods of nanophotonics. From these superatoms and supermolecules we can create artificial neural logic elements whose dimensions are 2-3 orders of magnitude smaller than the size of brain cells.

https://www.academia.edu/12908500/Nanoclusters_as_superatoms_and_supermolecules

https://www.researchgate.net/profile/Alexander_Ilyanok/publication/278018684______/links/55787d3808ae7521587037d4.pdf

https://www.researchgate.net/publication/278018597_Nanoclusters_as_superatoms_and_supermolecules

Best wishes

But of course it is not easy of course to forget the electromagnetic chains of this special relativity.It is after our only basis in sciences,the photons.But they are not the primordial codes.They are not the only one piece of puzzle.That has no sense to consider only our standard model.Like if in less of 200 years of science we have understood this universe in its whole with these phtons.It is so reductor like principle whjen we analyse what is this gravitational universal sphere in spherisation of matter energy.The photons are just a fuel and a system of photonic encodings correlated with our gravitational earth.The soul is more than this simple analyse.The evolution of matters, bodies,minds, souls are more complex than we can imagine.

The evolution is universal and general everywhere inside this universal sphere 3D for me.The biology evolves everywhere like the geology, the minerals....,the complexification and optimisation improvement are foundamentals for all matter, bodies, souls,minds, consciousness.If a soul for example must nourrish its consciousness with universalism and altruism,so we can consider than we die electromagnetically but not gravitationally.So if the souls are ramdomly resynchronised in a being of a planet, so the consciousness and brains are correlated .The relevance and God has well made the things is that we are never on the same place.Interesting like evolution.You see that evolution and gravitation are more than we can imagine.Fascinatin,g isn't it ?

Dear George,

I have read your beautiful essay and concur with top down causation or realization process that you have laid out to explain how biological life drives evolution, what if we can extend this theory to levels of consciousness and see that a higher level of consciousness being responsible for manifestation of different lower levels of it self. A gene is a part of organism and there is no organism with out the gene, it's a singular system. So is consciousness a singularity and we are all a part of it. I request you to kindly read There are no goals as such it's all play

Love,

i.

I have been down with influenza so have been slow and still am. Thanks for the link to Churchland's book. This get into philosophy, which was a minor I did in college, which is fun and helps to frame thinking. Roger Penrose goes on a track of sorts with physics, mathematics and the mental world all connected as joints in a paradoxical triangle.

I tend to focus a bit more locally in my thinking in that if there is a duality between IR and UV physics, then maybe quantum hair on black hole horizons, such as what Strominger argues with BMS symmetry, has structure that appears in the more ordinary world. Black hole quantum or BPS hair is in the UV domain that appears by red shift in the IR range, think of a highly time dilated Planck mass oscillator. I think somehow this equivalency between UV and IR gives what might be called euphemistically a yin and yang relationship between bottom up and top down causal or correlations.

Cheers LC

Professor Ellis,

A wonderfully written essay! Learnt a lot from it. I particularly enjoyed the sections on the differences between the logic of physics vs biology. I had the following question that I was hoping you would help me with:

If we took the example of a bacteria detecting poison and moving away from it, the poison would correspond to context C; let us call the bacteria system S, and we can form the corresponding context dependent statement "If C,THEN S will move away, ELSE S will move toward." Would you agree that if I decided to redraw the 'boxes' differently and looked at the joint system (C,S) together, then the earlier context dependent statement can be restated as a statement one would expect under the logic of physics? If the global (C,S) joint system has to follow physical law and can be analyzed from it, we should then be able to understand the 'purpose' in the local relationship between C and S. Would you agree on that?

Thanks.

Natesh

PS: I explore this C-S relationship in my submission 'Intention is Physical' which I have turned in, and should be up sometime next week. I would be happy if you could take a look at it, and any and all feedback is welcome.

Dear Prof. Ellis,

you've provided a cogent and well-argued essay. One point that---perhaps only to me---has some special significance is where you present Maxwell's equations: I remember very well the moment when I first understood them, which I guess a more religiously minded person might call 'revelatory'. As you note, those few, simple equations, together with gravity, govern essentially all that we encounter in everyday life---I don't think anybody who isn't awestruck by that has truly appreciated this lesson.

I think it's that moment, more than anything, that makes me look at purported explanations of the mind appealing to supernatural or extra-physical powers somewhat askance: it would be profoundly dissatisfying if the simplicity of fundamental physics would have to be muddled by the addition of the essentially mysterious in order to give an account of mind.

Consequently, I think I share your general approach to the matter: let's not throw in the towel and appeal to the ghost in the machine, but let's try and do some more science. Your essay is a welcome contribution to that.

However, I'm not quite sure your essay really cuts to the heart of the matter---or perhaps, I just don't quite see how. You appeal to the 'logic' of ion channels; but I feel one must be a bit more careful not to conflate semantic, meaningful information with the essentially syntactic operations occurring at the physical ground level. One risks introducing what was meant to be derived into the basic assumptions, at least courting circularity.

As an example, I would not say that an overflowing basin implements the logic 'if water level w > h, emit water' (where h is the depth). So even though the basic process can be brought into a 'if...then...else'-structure, I don't think that this automatically licenses us to attribute any genuine information-processing to a system.

One always runs a great risk to import interpretations into one's models, only to then rediscover them---after all, to the human mind, almost everything appears meaningful. As an example, consider the lamp lit at Old North Church by Paul Revere: you might suppose it means 'the English will attack by land', but it does so only to a human mind, who knows how to 'decode' the information, i.e. who knows 'one if by land, two if by sea'. The lamp itself does not carry meaningful information---without the background knowledge, it's just a source of illumination. But this background knowledge itself depends on the semantic capacities of any onlooker.

So I'm not sure I see how your example actually generates meaning and purpose. To me, it seems that these biomolecules are far more like the overflowing water basin than they are like an intentional organism choosing between alternatives, based on relevant information.

It's possible that you intend to circumvent this difficulty by appeal to biological function, as introduced via evolution, in a similar manner to the 'biosemantics' of Ruth Millikan and others, perhaps utilizing the (effective) downward causation to get the 'evolved meaning' to the ground level of ion channels and the like. If so, then I think this line of argument may have merit, and would like to see it fleshed out some more.

Anyway, thanks again for an intriguing contribution to the debate!