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

George Ellis

Yes they could in principle.

Our essays are indeed complementary.

George

Lorraine Ford

Dear George,

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. 2) Platonism seems to hypothesise that all rules must abstractly exist, rather than 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). 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.)

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.

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; complex systems are all about deterministic mechanisms and the illusion that new function could evolve purely from the mechanism; but actual reality is both mechanism and continually creative of the truly new:

Les Poules à Colin perform live on the radio this very morning: http://mpegmedia.abc.net.au/rn/podcast/2017/02/bst_20170224_0848.mp3 (song starts at 2:56 of 7:43), http://www.abc.net.au/radionational/programs/breakfast/les-poules-%C3%A0-colin-perform-live-in-the-studio/8299720 .

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

Mulugeta Wudu

Dear Mr. George F. R. Ellis:

You, like Mr. Stephen Hawking, are at the pinnacle of science. I am challenging you on the foundational questions of science because you are science's standard bearer. I understand prestige takes center stage in science quarters but it is not about you in person, it is about science - the whole enterprise. I am showing here that science is the tower of babel made of bricks of falsehood. You have to engage here in reason because you have made a public submission for open commentary. I am presenting facts here. The results of experiments carried out hundred years ago hold true today. "Life moved on" regarding evolution after Mr. Wilhelm Ludvig Johannsen's lie-shattering experiment only in the political sphere, not in the arena of truth. OK, let's get down to today. The long term evolution experiment on E-coli bacteria that has been going on at Michigan State University for the last twenty nine years speaks loudly against Mr. Darwin's idea. Science's evolution claims the wild ape became bipedal and then became the thinking European man in close to eighty thousand generations. Mr. Richard Lenski's e-coli bacteria are the same e-coli bacteria after sixty-seven thousand generations despite the mutation rate of the e-coli bacterium being much higher than the ape. The experiment proved beyond a shadow of doubt that there is no such thing as descent with modification from preexisting species; but the political circus to promote adaptation as evolution is rampant. The dishonesty of the science culture and language is appalling.

Regards,

Mulugeta

George Ellis

Dear Mulugeta

"I am showing here that science is the tower of babel made of bricks of falsehood." - well there goes scientifically tested drugs such as penicillin that have saved countless lives, cell phones and all else that follows from Maxwell's equations, nuclear power, solar power systems, GPS systems, aircraft that fly, etc etc ... all those outcomes that are based on scientific understanding. Do you really not understand that these are the outcomes of scientific thought? Or are you claiming that none of them work?

You know perfectly well that evolutionary theory is not my area of expertise. But I do know that we have a lot more detailed knowledge about evolution than we did over a century ago - when we had no idea of the existence and structure of DNA. We have far more evidence than then. Do you really not understand that we now know a lot more about genetics than when Johannsen wrote his paper? And as to Lenski's work, please see the the Wikipedia page on the E. coli long-term evolution experiment (LTEE) ("an ongoing study in experimental evolution led by Richard Lenski'). It says there, "Over the course of the experiment, Lenski and his colleagues have reported a wide array of phenotypic and genotypic changes in the evolving populations". Which is the opposite of what you claim.

Please try to check your claims more carefully before indulging in these kinds of immoderate attack.

Mulugeta Wudu

Dear Mr. George F. R. Ellis:

Long before the modern science of the west, people built structures, made medicine, rode horses, did agriculture etc. - all with moderation. The point is, the faculty that man has to do stuff is bestowed on man by God, not by science. The Wright brothers, Orville and Wilbur, who built and flew the airplane knew no science at all. All science does is manipulate this endowed faculty to man and use it to deadly end. Some of the things you mentioned were not of science but I will give you all. In order to cure diseases, to provide cell phones, cars, airplanes, to build atomic bombs, particle accelerators, space crafts etc, science messed up the earth's ecosystem, erased its megafauna, poisoned its waters, tainted its air, squeezed out its vital and life sustaining juice dry lemon. And the chaos in the ecosystem that science caused triggered exponential explosion in the human population that science wants to get rid of now by some evil means. So, when you listed the penicillin and the cell phone and the GPS, you forgot to also list that science murdered the earth in its totality. Would you say it is a great thing a stranger bought you a car but killed you the next day? I don't want to stray from your essays subject matter and it is unfair to you for me to discuss it here, but we can discuss this particular area under my essay: " an appeal to stop doing science."

I want to focus on your essay. You claimed that physical laws determine the evolution of a physical system. You said physical laws are purposeless. Then you said physical laws determined the flow of ions through ion channels, which you related to all sorts of biological functions. And for the biological functions which you used as stepping point, you adopted the idea of evolution as given. If the idea of evolution is false, your whole story is false. What I gathered from your essay is what science says. The whole point of your story is to replace God with "natural law" and to make this "natural law" as dumb as possible in order to ensure complete removal of God from thought. I want to prove to you that there is only God's law in nature and I will demonstrate to you that God lives and that your discussion of a purposeless dummy law in nature that governs the whole world is wrong. Laws in nature have purpose. The things that living things do have purpose and this purpose is God's. The proof is reproduction. Asexual reproduction is not made by the desire of the organism because the organism doesn't think. Sexual organisms have motivational elements to drive them to sexual union and their motivation is sexual union, not reproduction, but their union leads to reproduction. From this two facts it can be established that the purpose of the sexual motivational elements is reproduction. Since the organisms do not copulate for reproduction but rather to relieve the motivational urge, it is clear the purpose of reproduction is not theirs, but of that higher than them. It is God's. The part in which you said organisms live to reproduce doesn't make sense. Mules don't live to reproduce. Organisms reproduce to live by progeny and they don't have the capacity to plan life by progeny. So, clearly the purpose of reproduction is devised by preeminent power higher than the organisms. And he is God. From this fact it becomes immediately evident that natural laws (regularities in nature) are set by the same preeminence.

Regards,

Mulugeta

P.S.

Certainly, Mr. Lenski's bacteria experiment proved fatal to the idea of evolution. close to sixty seven thousand generations for bacteria is enough space to see everything. In the absence of change of bacteria form, there was effort by all Darwin enthusiasts to claim almost anything - movement, action, reproduction, adaptation and the sort, as constituting modification of form. At one point it was claimed that one group of the bacteria started feeding on the citrate accessing more food and gaining 'survival advantage' over the other group that fed on glucose alone, and this "fit group of bacteria drove the unfit to extinction." It was heralded around the world as a spectacular display of natural selection in action no sooner than a simple replay test using the frozen bacteria as control proved the claim to be without foundation. Again, in the absence of transition of form in this experiment Mr. Darwin's folks did at one time play with a curious attribute called fitness to these bacteria and there was claim that the fitness of the bacteria improved over time and the claim cites any changes in time, mostly spikes, as some kind of Darwin event. To science, bacteria fitness is supposedly a measure of how reproductive the bacteria are and is measured as the natural logarithm of the ratio of the final and initial cell density of two measurements in the culture. It is like inferring change of form (speciation) directionality in the European man by comparing the fertility rates of the Swiss and the French or by noting fertility fluctuations over time within the French. The Lenski experiment is a shameful spectacle to evolution society.

George Ellis

Dear Mulugeta

I am ignoring your first paragraph of your comment as it does not relate to my essay.

As regards the second paragraph, "I want to prove to you that there is only God's law in nature and I will demonstrate to you that God lives and that your discussion of a purposeless dummy law in nature that governs the whole world is wrong. Laws in nature have purpose. The things that living things do have purpose and this purpose is God's."

This is proof by assertion, with no evidence of any kind to support it. In other words, it is just your opinion.

"The proof is reproduction. Asexual reproduction is not made by the desire of the organism because the organism doesn't think. Sexual organisms have motivational elements to drive them to sexual union and their motivation is sexual union, not reproduction, but their union leads to reproduction. From this two facts it can be established that the purpose of the sexual motivational elements is reproduction."

Actually I agree with the core of what you are saying here. The motivational elements you are talking about are Panksepp's primary affective systems, and they include one that drives sexual reproduction. However that does not prove anything about God. Rather it shows the evolution has channeled our biological systems in such a way as to create the primary affective systems, as this increases our reproductive effectiveness. There is no need to introduce God into this argument, as Laplace said.

As to your comments on evolution, I recommend you read the wikipedia article on the topic here. It is more reliable than whatever reference you have been using. Notice that I am not supporting the Dawkins toy model of evolution, but the current much more sophisticated evo-devo view.

George Ellis

Mulugeta Wudu

Dear Mr. George F. R. Ellis,

You said you agree with the core of what I am saying about reproduction but you commented that "there is no need to introduce God into this argument." I am not asking you to introduce God in science. Science is a doctrine of falsehood which is not compatible with the majestic, loving and life-giving ways of God. What you should have done is quit science as soon as you found, like in the case of reproduction, there is no true knowledge outside God. The whole logical insight reproduction furnishes is God, yet you insist running away from it. That is not wise. In the fact of reproduction we see that the purpose of it is survival of the organism by progeny, but we also see that the organism, including the thinking man, is incapable of planning long term survival by progeny. So, what crystallizes out of this is that the purpose of reproduction is not of the organism itself but of that higher in planning and vision than the organism. There is no escape out of this truth. A dummy code written by a dummy law that comes from nowhere that you and your science are suggesting (the assumption itself is ridiculous) cannot plan and envision more remotely and broadly than does the thinking man, can it? If it can, then it is not dummy. I am convinced that your denial of God is deliberate and the whole project of science is a deliberate plot against God.

Regards,

Mulugeta

P.S.

I am writing this as post script because you said "evolution is not your area of expertise." The Lenski experimental data is public. I read the experimental observations directly from the experiment's public website. Any reasonable person who analyzes the Lenski experimental data will conclude that the entire idea of evolution is false. Clearly there is political passion particularly among the western elite for the idea of evolution emanating mainly from the urge to defeat the Christian faith in order to carry out wicked projects of depopulation particularly against Africans. The idea of evolution is natural resource driven. The science men see the Christian faith as hostile to such intentions and the political circus falsely hyping up the idea of evolution as "fact for which exists overwhelming evidence" is dramatic. An experimental result such as the e-coli long term one, which clearly demonstrated that the idea of evolution is false, is deliberately being twisted and the twisting is being decorated by spurious nomenclature just to hide the truth and to advance falsehood. It is a sad story. The e-coli long term evolution experiment's result rejecting the idea of evolution is not alone. Also, the global ocean sampling expedition carried out by the Craig Venter Institute (an evolution project itself) also confirmed in 2011 that the tree of life (the phylogenetic tree) is an artifact of an earlier study which is not holding up experimentally. Mr. Craig Venter underlined that there is no tree of life in a conference at Arizona State University. He further stated that from his institute's deep sequencing of organisms in the ocean, out of about sixty million different gene sets, he reported that they found no common ancestry except twelve that looked like a very deep branching, perhaps fourth domain of life. Here is the conference link

Mulugeta Wudu

Here is the link, it didn't appear in the previous post: https://www.youtube.com/watch?v=xIHMnD2FDeY

George 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

Domenico Oricchio

The essay is crystal clear, elegant and interesting.

Could all the dynamics in the biologic system a statistical dynamics of simple conditional expression? So that is there an overlap of many simple conditional expression like your basic selection process?

Another point, I think that the complexity of the Turing test is only the language, so that an Artificial Intelligence could be verified using a low-level language: a crow does not speak, but it has intelligent behavior; so that a game player (little number of rules and a conditional programming), or a conditional movement (low-level answers like movements) in a labyrinth or in a hostile environment could make human control indistinguishable from an artificial control, and the lack of a certain response could be an indication of an intelligent behavior (if the conditional expression have not guaranteed results, like some statistical results).

George Ellis

Dear Domenico

thank you for your comment.

> Could all the dynamics in the biologic system be a statistical dynamics of simple conditional expression? So that is there an overlap of many simple conditional expression like your basic selection process?

I think that is worth exploring, but I don't think a statistical dynamics will work in the end. It is the specific connections in a network that make it work as it does, building up higher level logic out of lower level logic; and that is captured by black-boxing rather than coarse graining, as I briefly mention in my technical notes.

George Ellis

Wilhelmus de Wilde

Dear George,

Your essay gives a very good understanding of two emergent phenomenae : life and physics. Each form of life is conscious. Physis is one of the ways we are trying to understand life and the perception of life of reality.

I almost am convinced to say that consciousness is the counter force of entropy in the reality awareness that we are experiencing. In my perception reality is just an excitation, we seem to have arrived throug "living" in our memory the NOW moment, that becomes directly past.

I hope that you can find some time to read just another different approach of the subject and read and maybe rate my essay "The Purpose of Life".

best regards

Wilhelmus de Wilde

George Ellis

Dear Wilhelmus

"I almost am convinced to say that consciousness is the counter force of entropy in the reality awareness that we are experiencing. In my perception reality is just an excitation, we seem to have arrived through "living" in our memory the NOW moment, that becomes directly past."

- you are expressing a view on the passing of time that agrees very much with my own view.

I will look at your essay.

Ragrds

George

Gary Simpson

George,

Your essay is the most informative to me that I have read thus far. I have read it several times to glean as much as possible from it. Previously, I was very skeptical of the notion of emergence. It seemed to me like magic rather than science. You have convinced me that emergence is true.

What stands out the most to me is the need for CONTEXT. This is linked to the ability of some things to have more than one function. Concepts that you do not mention but that might be significant are competition and scarcity. For example, if food availability cycles between abundance and scarcity, then the ability to store food as fat is a significant advantage. If the climate is cold, then this layer of fat has the added benefit of acting as thermal insulation. But if the food supply is unlimited, then morbid obesity results and fat storage becomes a liability unless organisms choose to limit food intake or compensate by some other means.

Allow me please to ask a somewhat ignorant question regarding equation 4. I am educated as an engineer. One of the standard problems we must solve is to compare the strength of electro-magnetism to that of gravity. We are also taught that the net force acting upon an object is the vector sum of all the individual forces. So, I understand exactly how you get equation 4. My question is "Has this relation ever been empirically confirmed?". The reason for my question is fairly simple. Suppose that both gravity and electro-magnetism are mediated by the vacuum. It might be possible that they are mutually exclusive. The vacuum might be able to mediate one or the other but not both simultaneously.

All in all, an outstanding effort.

Best Regards and Good Luck,

Gary Simpson

George Ellis

Dear Gary,

thank you for your kind comments.

> What stands out the most to me is the need for CONTEXT.

Right: this is key.

> This is linked to the ability of some things to have more than one function.

Indeed. This is true at many levels, from epigenetics to the way the brain works as a whole.

> Concepts that you do not mention but that might be significant are competition and scarcity. For example, if food availability cycles between abundance and scarcity, then the ability to store food as fat is a significant advantage. If the climate is cold, then this layer of fat has the added benefit of acting as thermal insulation. But if the food supply is unlimited, then morbid obesity results and fat storage becomes a liability unless organisms choose to limit food intake or compensate by some other means.

Good. Context changes selection criteria and so changes adaptive outcomes.

> Allow me please to ask a somewhat ignorant question regarding equation 4. I am educated as an engineer. One of the standard problems we must solve is to compare the strength of electro-magnetism to that of gravity. We are also taught that the net force acting upon an object is the vector sum of all the individual forces. So, I understand exactly how you get equation 4.

Good

> My question is "Has this relation ever been empirically confirmed?". The reason for my question is fairly simple. Suppose that both gravity and electro-magnetism are mediated by the vacuum. It might be possible that they are mutually exclusive. The vacuum might be able to mediate one or the other but not both simultaneously.

Good question. You need to look at the motion of charged particles on the surface of the Earth (as that equation uses a constant gravitational acceleration). It never occurred to me that it needed testing. It surely can be done. Indeed maybe it has been tested in cloud chambers.

Best regards

George

Lorraine Ford

Dear George,

Thanks very much for this discussion.

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.

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.

Some might not notice this, or not consider this detail to be important, but actually, this detail is crucially important to the way we view everything about reality/the universe.

George Ellis

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

Please desist.

George Ellis

Please stop repeating this on my thread.

George Ellis

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

George Ellis

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

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