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

Alexey/Lev Burov

Dear George,

Thank you for the answer.

Alexey Burov.

James Hoover

George,

The contest is drawing to an end, and I am reviewing those I've read and am not sure that I rated. Yours I did on 3/1. Short memory.

Hope you enjoyed the interchange of ideas as much as I did and still do.

Jim Hoover

George Ellis

Thanks Jim.

Indeed.

George

Michael Popov

George,

When physicists assume an existence of the first quasi - particle into becoming Universe, they also must assume an existence of mathematical rules for such particle as well as transcendental constants. Thus, physics without mathematics or particle without some mathematical rules cannot exist at all. This is well - forgotten Kantianism. Kant used notion "Synthetic a priori judgments" in order to understand an existence of such sort of a priorism of the becoming processes.

Similarly for biological processes - there is no such things as simply physical stone, biological cell, CRISPR cas9 immunity rules, etc. without mathematical rules and goals. Thus, purely scientific materialism is very limited. Probably Kurt Godel was right when he suggested that Einstein's Relativity contains embedded Kantian idealism ( some details of such forbidden approach could be found in my obviously - must - be- rejected essay entitled " Kantian answers " ).

with the best wishes

Michael.

George Ellis

Dear Michael

>> When physicists assume an existence of the first quasi - particle into becoming Universe, they also must assume an existence of mathematical rules for such particle as well as transcendental constants. Thus, physics without mathematics or particle without some mathematical rules cannot exist at all.

Well that is one approach. Yes many physicists adopt it. It assumes mathematics rules physics rather than just describing it.

>>> This is well - forgotten Kantianism. Kant used notion "Synthetic a priori judgments" in order to understand an existence of such sort of a priorism of the becoming processes.

I will have to study that more. It is an interesting debate.

>> Similarly for biological processes - there is no such things as simply physical stone, biological cell, CRISPR cas9 immunity rules, etc. without mathematical rules and goals.

Rules and goals, yes. Mathematical - well that is how we describe them. I'm not sure it is intrinsic to them. There are rigid Platonic possibility spaces for biology at each level, as described for example by Andreas Wagner in his book Arrival of the Fittest. They can be described by genotype to phenotype maps that have a Platonic nature, hence these are abstract relations.

>> Thus, purely scientific materialism is very limited.

Are, true.

>> Probably Kurt Godel was right when he suggested that Einstein's Relativity contains embedded Kantian idealism

I tend to go towards Platonism.

Best wishes

George

Jonathan Dickau

Greetings Professor Ellis,

I greatly enjoyed this essay, although it required considerable effort to read and digest, despite my knowing a bit about neurology as well as Physics. It appears your main intent was to elucidate how bio molecules evolved - through a combination of bottom-up and top-down processes - to be information carriers. Is this correct? I have long been a student of how the two creative modes operate interactively, and how both are necessary to some goals or aims, but I see a lot of this more abstractly than you do. There are several ways the top-down bottom-up scenario plays out actually, and it appears nature uses all of them.

The notion of additive vs. formant synthesis comes to mind where a sculptor can add or shave away bits of clay, or a sound designer can add more primary tones or start with a harmonic-rich waveform and use filters to subtract, and arrive at the same end result. During your discussion about coding for the action of letting the cat out and in; I thought about what happens when the cat is no longer there. A living being would know to pare away that subroutine, while a machine likely would not. It could not adapt; if you had the bad judgement to leave your cat with Dr. Schrödinger for the weekend.

But the metaphor of involution, as a complement to evolution (of a system rather than an organism), is useful to explain the feedback mechanism in the bottom-left feedback loop of Fig. 1 - 'protein machinery selects...' Since involution implies turning inward; protein folding is an especially elegant example of that principle. As I see it; the folding action encodes information both topologically and via geometrical alignments, to squeeze in more information than would otherwise fit in a 3-d arrangement. I have written and lectured on how fractals accomplish that information squeezing act, but this is obviously similar.

In your Fig. 1 bottom-left example; how things fold determines which traits are expressed, and therefore accomplishes a top-down feedback loop due to conscious selection. This supports your hypothesis that the information carrying capacity of these structures allows them to enhance survival. In the example of evolving vision; I view things more abstractly again. To facilitate the organism's survival; the top-level need is to see! This of course requires that visual apparatus of some sort be developed or evolved, and the rest of the steps proceed and their precursors are arranged exactly as you state. But this is a minor quibble.

I find no points of disagreement. It agrees in large measure with the views I present in my essay, where I use a metaphor from Arthur Young's "The Reflexive Universe" in support of the idea that evolutive properties arise from dynamism in non-associative Maths - specifically the Octonions in my example. Young argues that the fundamental forces are motivic and undergo binding and combination, until we arrive at a level of fixity in the mineral phase. Then Organic Chemistry is the first step toward greater motivity, proceeding in stages, resulting in the evolution of life and consciousness. I think this exactly agrees with what you present.

All the Best,

Jonathan

George Ellis

Dear Jonathan

thanks for that.

>>> It appears your main intent was to elucidate how bio molecules evolved - through a combination of bottom-up and top-down processes - to be information carriers. Is this correct?

Yes indeed.

>> I have long been a student of how the two creative modes operate interactively, and how both are necessary to some goals or aims, but I see a lot of this more abstractly than you do. There are several ways the top-down bottom-up scenario plays out actually, and it appears nature uses all of them.

Agreed.

>>> The notion of additive vs. formant synthesis comes to mind where a sculptor can add or shave away bits of clay, or a sound designer can add more primary tones or start with a harmonic-rich waveform and use filters to subtract, and arrive at the same end result.

Nice point. Nature does both.

>> During your discussion about coding for the action of letting the cat out and in; I thought about what happens when the cat is no longer there. A living being would know to pare away that subroutine, while a machine likely would not. It could not adapt.

Indeed. One needs a meta-analysis, which in terms of my classification is TD5: adaptive selection of adaptive selection criteria.

>>> But the metaphor of involution, as a complement to evolution (of a system rather than an organism), is useful to explain the feedback mechanism in the bottom-left feedback loop of Fig. 1 - 'protein machinery selects...' Since involution implies turning inward; protein folding is an especially elegant example of that principle. As I see it; the folding action encodes information both topologically and via geometrical alignments, to squeeze in more information than would otherwise fit in a 3-d arrangement.

Well protein folding is aided my molecular chaperones, which are themselves proteins that need to be folded ...

>> In your Fig. 1 bottom-left example; how things fold determines which traits are expressed, and therefore accomplishes a top-down feedback loop due to conscious selection. This supports your hypothesis that the information carrying capacity of these structures allows them to enhance survival. In the example of evolving vision; I view things more abstractly again. To facilitate the organism's survival; the top-level need is to see! This of course requires that visual apparatus of some sort be developed or evolved, and the rest of the steps proceed and their precursors are arranged exactly as you state. But this is a minor quibble.

I think we are agreeing ... maybe I have not stated it clearly enough

>> I use a metaphor from Arthur Young's "The Reflexive Universe" in support of the idea that evolutive properties arise from dynamism in non-associative Maths - specifically the Octonions in my example. Young argues that the fundamental forces are motivic and undergo binding and combination, until we arrive at a level of fixity in the mineral phase. Then Organic Chemistry is the first step toward greater motivity, proceeding in stages, resulting in the evolution of life and consciousness. I think this exactly agrees with what you present.

I am unaware of his work. Something more to read.

Regards

George

Jonathan Dickau

Thanks George for your thoughtful reply..

I think you'd greatly enjoy Young's book "The Reflexive Universe" for a very different look at how the top-down / bottom-up paradigm plays across all categories of form in the universe. It explores how things move from the abstract toward the definite, and then in a reflexive arc swing back the other way - where life is seen to incorporate layers of variability and abstraction on top of fixed forms. In this way; it is the progression from abstract to definite, and from definite back toward the abstract, that creates what we see as an evolutionary trend.

Organic molecules that can move or change form to serve as conduits or receptacles of information are the first step toward greater abstraction, from the mineral state where molecules have their greatest fixity - so they indeed start the process arc moving back toward motivity. You prove that point quite eloquently. Which is why I agree with the consensus that your essay is one of the best.

Warm regards,

Jonathan

All the Best,

Jonathan

George Ellis

Hi Jonathan

thanks for that.

... "Organic molecules that can move or change form to serve as conduits or receptacles of information are the first step toward greater abstraction, from the mineral state where molecules have their greatest fixity - so they indeed start the process arc moving back toward motivity. "

Please see my post of Apr. 6, 2017 @ 19:06 GMT for an interesting further note on this.

Regards

George

Jonathan Dickau

Will do..

Thanks, JJD

George Bizadellis

Mr. Ellis:

Your essay is excellent. It is well reasoned and well presented. I liked the framing statement "Life collects and analyses information in order to use it to plan and execute future purposeful actions in the light of memory (stored information)." This sets the stage for integrating the entire essay and for addressing some of the approached suggested in the contest's description.

I enjoyed your step by step build up from non-living systems to man in your narrative, from the logic of physics to the logic of life. It mirrors the steps in reality that might have occurred, which is a wonderful symmetry.

Also excellent is the caption under figure 1. "Epigenetic control of lower level processes by higher level contexts, which control which logic will operate at lower levels by switching genes on and oï¬€." The path from epigenetic control influenced by environmental factors, chance included, closes the loop quite nicely!

Roger Penrose, in his book 'Shadows of the Mind', has an interesting theory of the specific brain structures that give rise to man's consciousness. He believes that in man the "appropriate physical action of the brain evokes awareness, but this physical action cannot even be properly simulated computationally." He makes a sharp distinction between the computational nature of a Turing machine with the noncomputational nature of human consciousness, which he assigns to possible quantum dynamics occurring in the dimers of micro tubes in the brain. This could account for the flexibility you discuss in section 3.1 in your essay. And it also might provide a physical substrate for the ion channels you discuss in section 5 of your essay.

Thank you for a great, thought provoking essay. I have rated it very highly. Good luck in the contest.

Highest regards,

George Bizadellis

(Author of the essay Wu)

George Ellis

Dear George Bizadellis

Thanks for those kind comments.

>> Roger Penrose, in his book 'Shadows of the Mind', has an interesting theory of the specific brain structures that give rise to man's consciousness. He believes that in man the "appropriate physical action of the brain evokes awareness, but this physical action cannot even be properly simulated computationally."

That seems plausible to me.

>> He makes a sharp distinction between the computational nature of a Turing machine with the noncomputational nature of human consciousness, which he assigns to possible quantum dynamics occurring in the dimers of micro tubes in the brain. This could account for the flexibility you discuss in section 3.1 in your essay. And it also might provide a physical substrate for the ion channels you discuss in section 5 of your essay.

This is controversial but worth exploring. Where I disagree with him is the idea that gravity is involved in this process (if that were the case, astronaut's brains might not function when they were in free fall). I think the quantum wave function collapse process might relate to consciousness, as you say allowing some freedom for local top down processes to select what happens.

Best regards

George Ellis

David Cosgrove

Hi George

Yes, I have to acknowledge that there have been considerable amounts of interesting new material and approaches in the field of quantum foundations over recent times - and avidly await the results of such experimentalists (progressively refining their investigative precision around probes of macroscopic superposition/entanglements)!

I even think it possible that, down the track, larger and more fully functioning Quantum Computers might actually turn out to be suitable test beds for QM interpretations - i.e. by not working entirely like adherents of standard unitary-evolution QM expect them to!

David C.

George Ellis

General note: a great article by Noa Liscovitch-Brauer et al just appeared here , with this abstract:

"RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function. "

Thus squids can alter the proteins I'm talking about in my essay, by top-down action ("cephalopods diversify their proteomes extensively by RNA editing") that changes gene regulation and hence nervous system function: "Voltage-dependent potassium channels of the Kv2 subfamily, also known as ''delayed rectifiers,'' are expressed across the metazoa. In the mammalian central nervous system, they regulate excitability, action potential duration, and repetitive firing. As with most voltage-dependent potassium channels, they are predominantly closed at negative membrane potentials and open at positive ones. When switched between negative and positive potentials, they open or close with characteristic rates. At positive potentials, channels will also spontaneously close after opening, a process known as ''inactivation.'' The kinetics of these three processes play a vital role in determining how the channels regulate electrical signaling."

Lorraine Ford

Dear George,

I commented on your essay in late February, but I had to get my own (third attempt at an) essay in.

If you don't mind me saying so, your essay has not demonstrated a deterministic (i.e. logical) emergence of new function (i.e. new rules) as a consequence of the existing rules/laws-of-nature that control the universe-system. Models show that a system is essentially stagnant without the addition of new rules, but rules can never deterministically/logically emerge - there are no models that can show the emergence of new rules in a system controlled by an existing set of rules.

True emergence requires that new rules must be added to the system, and even new initial-values for system variables as a result of quantum randomness counts as adding new (initial-value) rules to the system. The addition of new rules to a system could be due to an algorithm controlling the universe-system, but as you no doubt appreciate, there can be no such algorithm controlling the universe. The real issue is the rules that control the system, not the results of the rules, not what is called "emergence".

Nevertheless, this is an excellent essay, and I am giving your essay a very good rating.

Re "I am open to discussion about numbers... What I have in mind is facts such as the square root of 2 is irrational":

I have written a post entitled "Numbers in a universe without a Platonic realm" on my essay page. Essentially I am saying that: numbers always remain relationships - they are never finished products i.e. pebbles; numbers are similar types of things to law-of-nature relationships - if they were like pebbles or like sets, then this would be an anomaly which would have to be explained; numbers ultimately derive from relationships/rules where (if represented mathematically) you can cancel the numerator and denominator categories, and end up with a number i.e. a thing without a category. So, I'm saying that the square root of 2, if it is found in nature, represents a hidden relationship between categories, "hidden" because the categories are cancelled out. Categories being essential categories of information from the point of view of the universe, things like mass and charge, or their more primitive antecedents.

Regards,

Lorraine

George Ellis

Dear Lorraine

>>> ... your essay has not demonstrated a deterministic (i.e. logical) emergence of new function (i.e. new rules) as a consequence of the existing rules/laws-of-nature that control the universe-system.

Two things: I emphasized that the universe is not deterministic, because of quantum effects. And new functions/rules have indeed emerged if you look at the historical development of the universe. Example: processes of Darwinian selection did not exist 15 billion years ago, because there were no living things in existence then. They did exist later, say one billion years ago.

>>> Models show that a system is essentially stagnant without the addition of new rules,

What kind of models? How do you know they correctly represent the real universe in all its complexity?

>> but rules can never deterministically/ logically emerge - there are no models that can show the emergence of new rules in a system controlled by an existing set of rules.

Well then we need to develop such models in order to describe the real universe.

>>> True emergence requires that new rules must be added to the system, and even new initial-values for system variables as a result of quantum randomness counts as adding new (initial-value) rules to the system.

New rules are added to the system as higher levels of emergence come into being. That is the whole point of emergence.

>> The addition of new rules to a system could be due to an algorithm controlling the universe-system, but as you no doubt appreciate, there can be no such algorithm controlling the universe. The real issue is the rules that control the system, not the results of the rules, not what is called "emergence".

The real issue is that the rules that control the universe do indeed allow emergence to occur. That is proven by the historical record.

>> Re "I am open to discussion about numbers... What I have in mind is facts such as the square root of 2 is irrational": I have written a post entitled "Numbers in a universe without a Platonic realm" on my essay page. Essentially I am saying that: numbers always remain relationships - they are never finished products i.e. pebbles;

Numbers are not themselves relationships, in my view. Rather they are abstract representations of physical relationships. I don't know of anyone who talks of them as being like pebbles.

>> numbers are similar types of things to law-of-nature relationships -

Well no, they are independent of the properties of matter, although our understanding of them probably derives from our appreciation of conservation of matter and specifically conservation of physical entities such as cups and spoons

>> if they were like pebbles or like sets, then this would be an anomaly which would have to be explained; numbers ultimately derive from relationships/rules where (if represented mathematically) you can cancel the numerator and denominator categories, and end up with a number i.e. a thing without a category.

Not sure what you mean by `category' here. Are you talking Category Theory?

>> So, I'm saying that the square root of 2, if it is found in nature, represents a hidden relationship between categories, "hidden" because the categories are cancelled out. Categories being essential categories of information from the point of view of the universe, things like mass and charge, or their more primitive antecedents.

I don't understand that.

Regards

George

Lorraine Ford

Dear George,

The whole point of what I'm saying is that reality emerges from the rules that control the system. The rules define the full possible functionality of the system. No new functionality can emerge unless you add a new rule.

Controlling rules do not miraculously emerge from within a system that is controlled by an existing set of rules. As Tommaso Bolognesi says in his blog: "...nobody has ever been able to set up a simple program that exhibits more than one level of emergence", (September 28, 2016, https://tommasobolognesi.wordpress.com) , and what he calls "emergence" is not rules that actually control the system.

The fact that new rules seemingly "emerge" in reality requires a proper explanation. You can't just say that they emerge, and leave it at that, as though no explanation is necessary. "Emergence" is all about the emergence of rules, not about the emergence of structure: structure depends on the rules.

Regards,

Lorraine

George Ellis

Hi Lorraine

>>> The whole point of what I'm saying is that reality emerges from the rules that control the system. The rules define the full possible functionality of the system. No new functionality can emerge unless you add a new rule.

Ah, Ok, what you are talking about is what I call possibility spaces. These are timeless unchanging Platonic spaces that underlie what comes into existence physically. For example, Andreas Wagner describes the nature of possibility spaces underlying the existence of molecular biology beautifully in his book Arrival of the Fittest.

>> Controlling rules do not miraculously emerge from within a system that is controlled by an existing set of rules.

No the existing rules must be structured so as to allow this to happen.

>> As Tommaso Bolognesi says in his blog: "...nobody has ever been able to set up a simple program that exhibits more than one level of emergence", (September 28, 2016, https://tommasobolognesi.wordpress.com) , and what he calls "emergence" is not rules that actually control the system.

Well then the simple programs need to be made more complex, to allow emergence of multilevel modular hierarchical structures such as actually exist in biology. Grady Booch's book on Object Oriented Programming show in detail how to do this in the case of computer systems, see here for a summary, where multiple levels of emergence are represented by a tower of virtual machines each built on the one below, and related to each other by compilers or interpreters.

>> The fact that new rules seemingly "emerge" in reality requires a proper explanation. You can't just say that they emerge, and leave it at that, as though no explanation is necessary. "Emergence" is all about the emergence of rules, not about the emergence of structure: structure depends on the rules.

Yes. See above. The possibility spaces underlying what can happen, which can be represented by a set of rules, are structured so that true emergence is indeed possible. Why they are structured that way is a philosophical question.

Regards

George

George Ellis

General posting:

an example of the kind of higher level logic that emerges out of the interactions of lower level component. Dr Arthur Guyton's computer model of the cardiovascular system is an example of a non-linear physiological relationship at the system level, expressed in a signal-flow graph. At lower levels its is based in protein properties.

George Ellis

Here is the missing image (I hope)

$Guyton\'s physiological systems$

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