Pre-Darwinian evolution proceeds according to hierarchical thermodynamics, as does biological evolution.

Yes, it does appear to be plausible. The formation of the biological compounds, first genetic system and then to protocells most likely defies strict Darwinian selection. It possibly could have been absolutely random and the products came out by pure chance, without any particular fitness. To every process that worked, an alternative pathway could have made the same. This might be the reason why abiogenesis is difficult to understand. So many possiblities before life arose, i.e. Darwinian evolution.

Dear Aleš,

Thank you for your answer.

In a recent unpublished 2019 paper you say that two important articles have been brought to your attention, ie Kolchinsky and Wolpert’s 2018 and Scherer et al.’s 2017 papers (Kralj 2019).

Scherer S et al.’s paper is based on experiments of the Miller-Urey type. Miller’s experiments hypothesized that abiotic production of organics by photochemistry could have occurred by Strecker synthesis in an very early, reducing (NH3, CH4, and H2O), pre Moon-forming impact (∼ 4.5 Ga) atmosphere (Miller 1953). However, more recent studies indicate that the early, outgassed atmosphere was not so reducing, consisting instead of H2O, CO2, and N2, with only small amounts of CO and H2 (Holland 1984, cited by Westall and Brack 2018).

I read Kolchinsky and Wolpert’s paper with interest.

However I have a major problem with their definition of “information”, in particular with what they call “semantic information”.

They say, “We propose a formal, intrinsic definition of semantic information, applicable to any physical system coupled to an external environment, whether a rock, a hurricane, a bacterium, or a sample from an alien planet”.

I disagree that the notion of “information” is applicable to “any physical system coupled to an external environment”, in particular to a rock, a hurricane, or a sample from an alien planet. Actually, I agree with Howard Pattee that “a molecule doesn’t become a message because of any particular shape or structure or behavior. A molecule becomes a message (ie information) only in the context of a larger system” (Pattee 1969). A bacterium is of course such a system. A given protein is only a message if it has a function in an organism such as a virus, a bacterium, a eukaryote, or also in any proto-organism capable of Darwinian evolution. Thus, I refute Kolchinsky and Wolpert’s definition of “information”.

If I do not wholly disagree with Kolchinsky and Wolpert that “semantic information is then defined as information which helps the system to achieve its goal” I disagree with the use of the term “goal” as is teleonomic. As most biologists, I am overly cautious about goal-oriented language. Certainly, the process of Darwinian evolution itself is necessarily non-teleonomic. There is no purpose per se. Only a posteriori is possible to note that a given population was capable or incapable to survive in a given environment at a given time (eg the extinction of dinosaurs after a dramatic change of the environment in too short a time was unpredictable a priori). Likewise, only a posteriori is possible to note that structures subsist or disappear in a given population. The explanation of say a given disappearance of a structure or a function can be proposed only a posteriori.

I have not yet finished reading Mayfield’s book. Thus I cannot comment it too much for the moment. However, I read a few interesting excerpts such as about the general features shared by all evolutionary processes according to him. When the author says, “with evolutionary systems and more generally with any system that learns, we know any information acquired must capture some aspect of whatever is being fit to (evolutionary system) or learned about. This observation does allow meaning to be loosely quantified under the assumption that the information wouldn’t be there if it didn’t mean something” he omits to specify that the observation is made a posteriori and that in addition the information can only mean something for a given population of organisms. For example, a given molecule may mean something for a specific population of eukaryotes but not at all for a specific population of bacteria. Thus the notion of information wholly depends on the involved population of organisms. This is a crucial statement. As, I already said it, a given molecule is a message (ie information) only for specific populations of organisms.

The author says, “Bénard cells form because coordinated movements of molecules happen to most efficiently transport energy from hot to cold; there is no advance plan”. I agree, but likewise, in no way an advance plan is at stake when natural selection operates. Again, only a posteriori is possible to try to explain why a given trait was selected.

References:

Holland HD (1984) The Chemical Evolution of the Atmosphere and Oceans. Princeton University Press, Princeton p. 582

Kralj A (2019). Evolutionary computations in Chemical Evolution, Chemical evolution functions and exploitation search revisited – II (unpublished)

Kolchinsky A, Wolpert DH (2018). Semantic information, autonomous agency and non-equilibrium statistical physics. Interface focus 8: 20180041.

Mayfield JE (2013) The Engine of Complexity: evolution as computation. Columbia University Press, New York

Miller SL (1953) A production of amino acids under possible primitive earth conditions. Science 117:528–529

Pattee HH (1969). How Does a Molecule Become a Message? Developmental Biology Supplement 3:1-16

Scherer S et al. (2017). Chemical Analysis of a “Miller-Type” Complex Prebiotic Broth. Origins of Life and Evolution of Biospheres 47:381-403

Westall F, Brack A (2018). The Importance of Water for Life. Space Sci Rev 214:50

According to you, Is what you call "biological evolution" the same as "Darwinian evolution"?

I don't distinguish "biological evolution" from "Darwinian evolution".

In my opinion, only Darwinian evolution enables any evolution in complexity over time.

The following conditions are needed for Darwinian evolution to emerge (Tessera 2017):

1. Local conditions allowing the emergence of open non-equilibrium systems organized on a macroscopic level, generated by a continuously supplied flow of matter and energy. These open far-from-equilibrium systems can maintain themselves far-from-equilibrium because they are able to use the matter and energy supplied by the local environment;

2. The systems should be able to reproduce;

3. They should be capable of inheritance.

I don’t think possible to define what is named "biological evolution". This is because the concept of “life” is questionable as terms like “biological”, “biotic”, “pre-biotic” etc. given that they are linked to the concept of life.

You say, “Biological evolution is already fairly advanced in terms of achieved complexity”. Actually, if I refer to the conditions needed for Darwinian evolution to emerge on early Earth, the probability that these were in place was not too low (Tessera 2017).

References:

Tessera M (2017) Research program for a search of the origin of Darwinian evolution. Orig Life Evol Biosph 47:57–68.

Tessera M (2018) Is pre-Darwinian evolution plausible? Biology Direct 13:18

It impossible to look separately

Thank you for the reference of the paper by Donoso et al. I read with great interest.

You say, “the brain does evolutionary exploratory and exploitation searches". I would not use the term "evolutionary". I would rather say, as specified by the authors, "among the prefrontal regions, the frontopolar cortex (FPC) is likely specific to humans, which suggests that the ability to jointly infer multiple possible causes of observed contingencies and, consequently, to test new causal hypotheses emerging from long-term memory is unique to humans". Clearly such a complex unified prefrontal “inferential system subserving reasoning in the service of adaptive behavior prefrontal system” is the product of Darwinian evolution: “a phylogenetically recent reorganization of frontal cortical circuitry may have been critical to the emergence of human-specific executive and social-emotional functions” (Teffer and Semendeferi 2012, cited by Donoso et al.).

When you use the term “evolutionary" what do you mean exactly?

Regarding “evolutionary computation", "evolutionary algorithms" and so on I'm not comfortable, of course, commenting the field. Well, if I correctly understand the matter, an evolutionary algorithm is a subset of evolutionary computation, a generic population-based metaheuristic optimization algorithm. It uses mechanisms inspired by biological evolution, such as reproduction, mutation, recombination, and selection. Candidate solutions to the optimization problem play the role of individuals in a population, and the fitness function determines the quality of the solutions.

When comparing evolutionary computation with Darwinian evolution I see two major issues

· How to choose a plausible fitness function, ie determining the quality of the solutions, traducing the real conditions in which Darwinian evolution, in particular natural selection, operates? In the natural conditions there is, a priori, no such a fitness function (ie which would determine the quality of the solutions) and even a posteriori.

· How can evolutionary algorithms show any inheritance property?

Reference:

Teffer K, Semendeferi K (2012) Human prefrontal cortex: Evolution, development, and pathology. Prog Brain Res 195:191-218

Evolutionary Computation (EC) is fully abstract and disembodied: no energy and no matter are taken into account. EC answers are not answering any of the eight questions that are critical to the search of the origin of Darwinian evolution (Tessera 2018):

1. What was the initial chemical substrate?

2. Are there experimental data supporting the main hypothesis?

3. What were the sources of the needed energy and matter?

4. Is the chiral question solved?

5. What is the ability of multiplication of the systems?

6. Is there any heredity?

7. Were there plausible site(s) where the initial chemical substrates might arise?

8. Is the evolutionary path plausible?

EC is based on a specific definition of “information” I fully disagree with (see my previous comment on it). To me, a given microscopic configuration (eg a molecule) is meaningful only for specific populations of organisms (ie in term of function, eg enzyme, structure, eg collagen, genetic storage, eg nucleic acids etc.). In other words a given molecule becomes a message (ie information) only in the context of a larger system. You seem to agree with such a statement, “functional information is relative to those to whom it is readable” (Kralj 2017). Thus, I don’t agree that the notions of entropy and information are of the same nature. Besides, you agree with that when you say, “the thermodynamic-entropy-like mathematical tool called Shannon entropy (Shannon 1948) should not be confused with thermodynamic entropy, which reflects the chemical or physical configuration” (Kralj 2017). In statistical mechanics, entropy is an extensive property of a thermodynamic system. It is closely related to the number of microscopic configurations (known as microstates) that are consistent with the macroscopic quantities that characterize the system (such as its volume, pressure and temperature). Entropy has existed in the universe since the beginning (if such a beginning has ever occurred) while the notion of information (ie the meaning of specific microscopic configurations) has emerged only when organisms have emerged.

In the end, I don’t see any valid argument supporting the hypothesis that EC may significantly contribute to the search of the origin of Darwinian evolution.

References:

Kralj A (2017) Inventive processes in nature: from information origin in chemical evolution to technological exhaustion. Earth Perspectives 4:5

Tessera M (2018) Is pre-Darwinian evolution plausible? Biology Direct 13:18

PS: you say, “the brain does the inheritance in a less explicit way”. Indeed there is no relation between brain and inheritance, except if you believe in the inheritance of acquired characteristics.

Classical information and “functional information”:

According to Shannon’s approach, “information theory” studies the quantification, storage, and communication of information. It was originally proposed by Claude E. Shannon in 1948 to find fundamental limits on signal processing and communication operations such as data compression, in a landmark paper entitled "A Mathematical Theory of Communication”.

This Shannon’s notion of “communication of information” refers clearly to communications between humans. Thus, such information means something only for humans.

Jack W. Szostak published a relevant paper in Nature on “functional information” (Szostak 2003):

Here are some of the excerpts that relevant for our discussion, relevant:

“The information content of biopolymers is usually thought of in terms of the amount of information required to specify a unique sequence or structure. This viewpoint derives from classical information theory, which does not consider the meaning of a message, defining the information content of a string of symbols as simply that required to specify, store or transmit the string”.

“A new measure of information — functional information — is required to account for all possible sequences that could potentially carry out an equivalent biochemical function, independent of the structure or mechanism used”.

“By analogy with classical information, functional information is simply -log2 of the probability that a random sequence will encode a molecule with greater than any given degree of function”.

“The functional information required to specify that activity is log2 of the fraction of sequences above the plane. Expressing this fraction in terms of information provides a straightforward, quantitative measure of the difficulty of a task. More information is required to specify molecules that carry out difficult tasks, such as high-affinity binding or the rapid catalysis of chemical reactions with high energy barriers, than is needed to specify weak binders or slow catalysts.”

According to Jack W. Szostak, “functional information” relates to functions carried by biopolymers in organisms, such as affinity binding or catalysis of chemical reactions.

If you agree that “information” or “functional information” relates to the meaning of “messages” (eg molecular messages) you would agree that the former notions only apply to organisms.

Has the notion of “a message” to a rock, a planet, a star etc. any meaning?

Questions relative to the search of the origin of Darwinian evolution:

You admit that EC does not answer 1-7.

You claim nevertheless, “However, in my opinion, EC makes questions 1-7 redundant and superfluous. It most decidedly answers nr. 8. For no. 8 it does not matter what structures undergo evolutionary complexity upgrade. It only matters that they do. EC also makes assumptions of the early earth chemical composition a redundant issue”

I wonder how the evolutionary path could be plausible in any model that doesn’t answer the other questions.

Could you clarify your point?

According to you, some authors would claim that their purely formal and disembodied Turing-like models are able to answer the question of the origin of Darwinian evolution. You have to argue your statement. Besides, Alan Turing has never claimed that his approach could answer the question.

You say, “it merely matters that the "soup" was capable of forming metastable (i.e., selectable) structures under the power sources available”.

“For 80 years it has been accepted that early life began in a "primordial soup" of organic molecules before evolving out of the oceans millions of years later. Today the "soup" theory has been overturned in a pioneering article which claims it was the Earth's chemical energy, from hydrothermal vents on the ocean floor, which kick-started early life” (Wiley-Blackwell 2010).

References:

Szostak JW (2003) Molecular messages. Nature 423:689

Wiley-Blackwell (2010). New research rejects 80-year theory of 'primordial soup' as the origin of life. ScienceDaily

Following answers

Signatures of the very beginning of Darwinian evolution:

“I'm afraid, A to C can only be determined if its fossil recost would be found”.

It depends what you mean by fossils. The discovery of the earliest signatures of the very beginning of Darwinian evolution is plausible. For example, if my model of the origin of Darwinian evolution is correct it predicts specific signatures such as chiral carbon-based molecules in the oldest Earth sedimentary rocks.

With regards to your assertion that there are authors who claim that purely formal and disembodied Turing-like models are able to answer the question of the origin of Darwinian evolution (named “the origin of life” by most experts in the field) I would be grateful if you could provide me a few references.

Prediction of a model:

One of the main criteria that distinguish a scientific from a pseudo-scientific model is its predictive power. If the prediction is confirmed then the model gains credibility. With regards to my model the synthesis of chiral carbon-based molecules (not necessarily amino-acids) is a straightforward consequence. However, I agree with you that, even if the model is correct, the discovery of such a signature is problematic because of the low probability for chiral carbon-based molecules to subsist chiral after near four billions years.

References supporting your thesis:

I apologize for the misunderstanding.

At least, could you provide a few references in favor of your thesis?

Models:

In addition to the model predictive power I forgot to mention experimental data.

If scientists were capable to reproduce populations of systems showing Darwinian evolution (DE) with specific consequences (eg synthesis of chiral carbon-based molecules) the model would be validated.

References supporting your thesis:

With regards to Antoine Berut et al. here is a citation I find particularly relevant: “The entropy cost required to reset the demon’s memory to a blank state is always larger than the initial entropy reduction, thus safeguarding the second law. Landauer’s principle hence seems to be a central result that not only exorcizes Maxwell’s demon, but also represents the fundamental physical limit of irreversible computation”. The experimental verification of Landauer’s principle by the authors means that the second law is safeguarded even in the Maxwell’s ‘demon "thought-experiment". According to this "thought-experiment", the demon would be able to decrease the entropy of the system without performing any work himself, in apparent violation of the second law of thermodynamics. Finally, the paradox of the apparent violation of the second law can be resolved by noting that during a full thermodynamic cycle, the memory of the demon, which is used to record the coordinates of each molecule, has to be reset to its initial state (ie the Landauer’s principle).

The notion of information in that kind of publications is related to computation. Computation is only related to human information.

Thus, I don’t see how such a kind of publication could support your thesis that EC may significantly contribute to the search of the origin of Darwinian evolution.

With regards to John E. Mayfield's book I must recall you that you wrote to me, “I find John E. Mayfield's book indicative about evolutionary computing at best. The book contains no teaching how to apply evolutionary computing on chemical evolution”.

At last, what is the relation, according to you, between R. Dawkins’ viewpoint on Darwinian evolution and EC?

Reference:

Berut A et al. (2012) Experimental verification of Landauer’s principle linking information and thermodynamics. Nature 483:187-190

I agree with this statement: The "only" remaining part to fully prove chemical evolution is to show that it can do the "heritable search" - the exploitation search. Chemical evolution is guided by hierarchical thermodynamics, which uses the principle of substance stability.

Dear Georgi and Aleš,

I'm not sure I understand clearly Georgi’s comment when he cites Aleš’ statement.

However I am interested in his expression “hierarchical thermodynamics, which uses the principle of substance stability”. I have just read the abstract of Georgi’s paper “Biological Sciences – The time has come to revive and develop the classics: hierarchical thermodynamics and life”. Unfortunately, the full text is not in English. I find, however, his expression in accordance with what we describe, Guy Hoelzer and I, in our 2013 paper “On the thermodynamics of multilevel evolution” (Tessera and Hoelzer 2013).

Have you read the paper? If not, you could take a look at it or at least at the following abstract.

We noted “biodiversity is hierarchically structured both phylogenetically and functionally. Phylogenetic hierarchy is understood as a product of branching organic evolution as described by Darwin. Ecosystem biologists understand some aspects of functional hierarchy, such as food web architecture, as a product of evolutionary ecology; but functional hierarchy extends to much lower scales of organization than those studied by ecologists. We argue that the more general use of the term “evolution” employed by physicists and applied to non-living systems connects directly to the narrow biological meaning. Physical evolution is best understood as a thermodynamic phenomenon, and this perspective comfortably includes all of biological evolution. We suggest four dynamical factors that build on each other in a hierarchical fashion and set the stage for the Darwinian evolution of biological systems: (1) the entropic erosion of structure; (2) the construction of dissipative systems; (3) the reproduction of growing systems and (4) the historical memory accrued to populations of reproductive agents by the acquisition of hereditary mechanisms. A particular level of evolution can underpin the emergence of higher levels, but evolutionary processes persist at each level in the hierarchy. We also argue that particular evolutionary processes can occur at any level of the hierarchy where they are not obstructed by material constraints. This theoretical framework provides an extensive basis for understanding natural selection as a multilevel process. The extensive literature on thermodynamics in turn provides an important advantage to this perspective on the evolution of higher levels of organization, such as the evolution of altruism that can accompany the emergence of social organization”.

I would appreciate your comments on the ideas developed in the abstract.

Of course, if you wish, I will be happy to send you the full text.

Reference:

Tessera M Hoelzer GA (2013) On the thermodynamics of multilevel evolution.

Biosystems 113:140–3.

Dear Mark,

Thanks. Of course, please send your work. However, I will note in advance that it contains some misunderstandings related to the use of the concept of entropy. I have been developing hierarchical thermodynamics, as a section of classical thermodynamics (equilibrium thermodynamics and thermodynamics of systems close to equilibrium) since 1977. I have a lot of work in English. For example, look:

Gladyshev G.P., Natural Selection and Thermodynamics of Biological Evolution, Natural Science, 2015, 7, pp. 117-126. http://dx.doi.org/10.4236/ns.2015.73013

Gladyshev G. P., Hierarchical Thermodynamics: Foundation of Extended Darwinism. Imperial Journal of Interdisciplinary Research (IJIR), 2017, Vol-3, Issue-2, ISSN: 2454-1362.

https://www.researchgate.net/publication/314082150_Hierarchical_Thermodynamics_Foundation_of_Extended_Darwinism http://imperialjournals.com/index.php/IJIR/article/view/4265/4085

Works in Russian are now easy to translate into English with the help of a Google translator, which is an acceptable translation.

Best,

Georgi

Dear Georgi,

I read your 2015 paper “Natural Selection and Thermodynamics of Biological Evolution” published in Natural Science.

The style is strange as the expression “the author” (ie “you”) is mentioned so often (25 times !). Isn’t self-consideration?

You claim, “It is alleged that living dynamic structures are the quasi-closed and quasi-equilibrium supra-molecular systems”. This is of course fully wrong. Every qualified scientist knows that the thermodynamic state of organisms, usually called “living” entities, is far-from-equilibrium. And naturally I agree with you when you say, “This approach highlights the difference between hierarchical thermodynamics and Prigogine's thermodynamics of systems far from equilibrium”.

Another wrong assertion: “the idea of living dissipative structures cannot be considered thermodynamic” (!).

You admit, “the author published many studies in peer-reviewed Russian scientific journals, which are not internationally known” but nevertheless you dare claim, “Thermodynamic theory of biological evolution represented by the author, was published in leading journals”. The term “leading journals” is indeed misleading. For example your 2015 paper was published in “Natural Science” that is a modest journal with a quite low Google Scholar metrics (h5-index=17; h5-median=22, see the link https://scholar.google.com/citations?hl=en&view_op=search_venues&vq=life&btnG=).

By comparison:

• Nature: h5-index=362; h5-median=542;
• Biology Direct: h5-index=26; h5-median=38.

The “Norwegian Journal of development of the International Science” (your 2019 paper “Biological Sciences – The time has come to revive and develop the classics: hierarchical thermodynamics and life”) is not even mentioned in Google Scholar metrics.

Likewise, The “Imperial Journal of Interdisciplinary Research” (your 2017 paper “Hierarchical Thermodynamics: Foundation of Extended Darwinism”). In addition, the journal is published in India by Finlogy, a publisher listed on the well-regarded “Beall’s List of Potential predatory scholarly” and it is suspected to be a fake journal (!).

Clearly, there no need to comment further …

Dear Mark,

Thank you for reading my article and making a detailed comment.

At first, I didn’t want to respond to your thoughts. But then I realized that I should write a response due to the fact that you, in my opinion, do not fully know the exact sciences, especially thermodynamics. I am sure that you have no idea what science is.

You refer to my text and write:

“It is alleged that living dynamic structures are the quasi-closed and quasi-equilibrium supra-molecular systems”. This is of course fully wrong. Every qualified scientist knows that the thermodynamic state of organisms, usually called “living” entities, is far-from-equilibrium…».

You do not even understand what equilibrium I am writing about! Your statement suggests that you do not even have an idea about the thermodynamics of the phenomenon of life and in general about thermodynamics. What kind of qualified scientists are you writing about? About "scientists" which are like you? My work deals with supramolecular equilibrium (and other equilibriums within hierarchical structures) that exist in living systems! You write about the absence of chemical equilibrium between the "chemical composition of the body" and the environment. Of course, I know about this fact. My thermodynamic theory explains this fact! Your thoughts are mockery or complete scientific illiteracy!

Then you write: «Another (your) wrong assertion: “the idea of living dissipative structures cannot be considered thermodynamic” (!) ». Here we are talking about the "thermodynamics" of Ilya Prigogine systems far from equilibrium, which uses entropy, which does not have the full differential. Without state functions that do not have full differentials, there is no thermodynamics! Please study the works of R. Clausius, J.W. Gibbs and other classics, as well as textbooks.

Regarding your comments on the style of the article and the ratings of the journals in which I published my recent work, I will not express my opinion. The fact is that your considerations are irrelevant from the point of view of a scientific problem with which you are not familiar. If you do not, sooner or later someone will do it for you.

I believe that you follow fashion in science and scientific corruption. It would be nice if you published a review of my works in any scientific journal with a high rating (for example, in Nature, Science or the Journal of Theoretical Biology). In this case, I could give an answer to your confused and irresponsible scientific statements.

Best,

Georgi