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

Professor Ellis,

I have addressed some of the questions raised on my submission page over there. I will address the rest here. Think there are some fundamental differences on some key ideas/definitions that I would like to differentiate so that we can clearly draw our intellectual battle lines so to speak :)

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?). 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. 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. 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.

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.

2) (This is a repeat of what I wrote on the other thread) 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 tht the moon is capable to generating its own purpose like we do. 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. 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) whoses 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.

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.

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.

Think I have addressed most of the important issues you raised here to the best I can over a post. Appreciate your questions. I have learnt that I need to be a lot clearer with some of my definitions.

Natesh

Dear Mr. George F. R. Ellis,

Your essay looks an epitome of science itself. It may win the prize because it has all the elements that the community of science are looking for. I am going to comment here and my comment has nothing to do with prizes or such things as ornamental matters. The earth is in great danger and I am making a last minute pleading in a bid to avert the danger. I see before me how falsehood prospered by trampling the truth to the ground. This same falsehood that I see before me is what is driving the earth and its inhabitants to unprecedented catastrophe. The purpose of my discussion is, therefore, to revive the truth and to avert the calamity.

The story you told in your essay can be summarized. You did not include the part of science that says: 'first there was nothing [vacuum] and in that nothing was physical law and that physical law created matter'. You started from matter. So in summary (my summary of your story) you said: 'there was matter and in it were physical laws. These physical laws were and are, and they are purposeless and these purposeless physical laws drove matter aimlessly towards a goal. At some point the physical law wrote a logical operation code, which is not a law but a rule, and this rule gave rise to life. The rule also later wrote new logical operation codes and this codes created the diversity of life that we see on earth'. The imagination is more amazing than magical illusions.

So then, you may not know it has a purpose, but how do you know the stone does not have a purpose? How do you know the moon does not have a purpose? You assumed authority in saying so. Also, how do you know organisms exist to reproduce? I know you quoted it, nonetheless agreeing with it, but are you sure it is not the other way around? If you think it is the other way around, which is that there is reproduction in order to make organisms live, whose purpose is reproduction then? Can you answer clearly whose purpose reproduction is?

You claimed the existence of "physical laws." You further claimed these "physical laws" determine the evolution of a physical system, saying that physical processes obey these laws. So the purpose of the "physical laws" is to dictate the process of physical systems, yet you stated the laws drive the physical processes in a purposeless inevitable way. Clearing all the semantics and going to the substance of it, 'law' does not imply inevitability but it does imply purpose. It is a contradiction you are espousing here. Laws are there for a purpose. The very concept of law is purpose. Since you inferred purposelessness in physical laws, you have to explain with clarity how physical laws are purposeless.

In your information section you presented purpose as different from physical laws and that purpose and functions emerged later by way of evolution. The earth is an ecosystem and the system includes non-living things. An ecosystem like the earth is a purposeful organization and how does it differ in purpose from your voltage gated ion channels? Any number of natural phenomena can be expressed in logical operations but to use this ability of expressing them as a basis for a hypothetical claim of emergence of life is, the way I see it, much of a stretch.

Many claims you made are based on speculations. The references themselves don't lead to facts but to other speculations. You depended heavily on the notion of Mr. Darwin's idea which was later named "evolution." You quoted some tutorial instruction saying: "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." That claim was experimentally disproved more than a century ago, but you are advancing it as if it is true. Mr. Wilhelm Ludvig Johannsen's experimental report of 1903 demonstrated clearly that an organisms genetic line is unalterable by the environments encountered by its members. In fact, as documented in 'Johannsen W. Experimentelle Grundlagen der Deszendenzlehre; Variabilität, Vererbung, Kreuzung', Mr. Johannsen stated: "Mr. Darwin's theoretical presuppositions with respect to inheritance were in principle incorrect and thus the Darwinian theory of selection finds absolutely no support in genetics." That is the founder of genetics who did the first hand experiment who rejected Mr. Darwin's idea. How do you expect to get it right when you base your idea on faulty foundation? You also provided a reference to a book titled "the arrival of the fittest." The book is speculative and doesn't have factual basis. However, the book underlines one important point: it admits that evolution by way of mutations is not plausible. The author states that there is not sufficient time for random mutations to create life. After rejecting evolution or the emergence of new functions or life by mutations alone, the author attempted to provide a substitute for it by providing the alternative of "robustness" by adaptation. In trying to introduce adaptation as a means of "accelerated evolution," he fell back to Mr. Darwin's refuted idea of environmental stress on the reproductive system and he calls the environment the 'hidden architecture of life'. The author forgot or was totally oblivious of the fact that the environmental notion that he is alluding to was long experimentally refuted.

Whether or not you wrote an equation for it, your 'selection process' presumption is not factual. What is factual is the results of Abbot Gregor Mendel's experiments which gave rise to the 'punnett square' which is now being used by men of science to determine the probability of an offspring having a particular 'genotype'. The punnett square rejects the notion of Mr. Darwin's evolution. It is easy to convert the punnett square into a mathematical statement, and since it is experimentally proven, this mathematical statement would be valid.

Regards,

Mulugeta

Dear George,

Please see the attached diagram for levels of consciousness i envisioned.

By singularity i mean the feeling of oneness we experience as spiritual beings, that we are one with the universe. Please see the video divide by zero and pay attention to 0/0 segment in it and compare it with the diagram of SOUL that i am attaching here, you will see what i mean by singularity of consciousness, with out that point of origin none of this duality or relative existence is possible.

Love,

i.Attachment #1: 3_Consciousness.jpgAttachment #2: 3_SOUL.jpg

Dear Professor Ellis,

I am sorry that you find the truth about the real visible Universe unacceptable.

Joe Fisher, Realist

Dear Professor Ellis,

I am sorry that you find the truth about the real visible Universe unacceptable.

Joe Fisher, Realist

Dear Professor Ellis,

I am sorry that you find the truth about the real visible Universe unacceptable.

Joe Fisher, Realist

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 .

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.

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).

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,

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