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Charles Darwin 12 Feb 1809 – 19 Apr 1882 |
Today, Darwin's 213th birthday, I will publish a blog about how the
theory of evolution has changed since Darwin.
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Fig. 1. Two empires: the virus (left) and the cellular (right)
empire (source) coronaviruses (single-stranded
positive sense RNA viruses) (added, modified) |
I am amazed how Darwin could construct a general theory of biological evolution that essentially still holds today considering the biological knowledge of the time. That knowledge of his time is rather primitive compared with our knowledge today. A cursory look at the illustration above is enough to realize that most of our current knowledge of the biological world was simply absent at the time Darwin wrote On The Origin of Species (1859).
Darwin did not know Bacteria. Darwin did not know viruses. Darwin did not know Eukaryota (at least the concept). Darwin did not know Archae. In fact everything that is present in the above illustration!
The concept of the eukaryote has been attributed to the French
biologist Edouard Chatton (1883–1947). It was reintroduced into biology
in 1962. Definitely long after Darwin. Darwin, of course, knew animals
and plants, but he didn't know that they are eukaryotes. So, strictly
speaking he knew nothing of every item in fig. 1. And that is basic
biology today.
Bacteria: at the time of Darwin's 1835
Galapagos Island expedition, the germ theory of disease had yet to be
described. Then, in 1977, Carl Woese proposed that Archaea are
different from bacteria and constitute the third domain of life. The
three domains together constitute the cellular empire (see figure
1). Cellular life is contrasted with viruses which are a-cellular.
The left side of the illustration shows viruses.
Viruses are not cells. These days seven different groups of viruses are recognised. One group
is Corona viruses. One of the
Coronaviruses, SARS-CoV-2, started a pandemic in December
2019. Viruses were unknown in Darwin's time. In 1898 the Dutch
microbiologist Martinus Beijerinck introduced the word 'virus'. Darwin
died in 1882.
But Beijerinck did not know RNA and DNA. He called viruses
contagious living fluid.
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| Fig. 2. The three-domain tree of life (source) |
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| Fig. 3. A network representation of the evolutionary process (source) |
The theory of evolution was substantially upgraded with the rediscovery of Mendel's laws of heredity in 1900 and with the discovery of the structure of DNA in 1953. In 2000 the complete human genome was sequenced. Thanks to DNA sequencing and comparative analysis of genomes it was discovered that Horizontal Gene Transfer between Archaea and Bacteria was extensive. The Tree of Life (fig. 2) became a Network of Life (fig. 3). A fundamental change. The green lines in Fig. 1. show extensive gene transfer between the three domains of life and the viruses.
Adaptation of SARS-CoV-2
In a previous blog The evolution of a pandemic virus: SARS-CoV-2 I showed an illustration of SARS-CoV-2's growing number of mutations during the past 2 pandemic years. Darwin had no idea of a 'mutation'. He could not know, because a mutation is a change in DNA and he didn't know DNA. However, he did know the concept of heritable variation. He did know some variation is advantageous, and some is disadvantageous. That was enough for him the construct his theory of evolution.
SARS-CoV-2 does not only produce mutations and heritable variation. Some of the variation is advantageous for the virus and increases its fitness. New variants outcompete existing variants. For example the Omicron has outcompeted the Alpha and Delta variant. The SARS-CoV-2 virus is surprisingly well adapted to its human host. Virologists discovered how sophisticated the adaptation of virus to its human host is. For a start, the virus speaks the same genetic language as humans. It has the same genetic code. Its RNA is like a messenger RNA (mRNA). It is the same type as humans use for the transfer of the genetic information from DNA to proteins. That's why human cells start immediately to translate those viral RNAs into proteins. The virus also knows how to enter human cells. It has adapted to the human ACE2 receptor. The virus also knows how to reproduce and self-assemble in human cells. The virus knows how to get out of the cell. The virus has adapted to the human respiratory system. That's its environment. The virus also knows how to evade attacks of the human immune system. The virus knows how to spread from human to human by droplets and aerosols.
These are all adaptations. In other words: SARS-CoV-2 is a prime example of evolution by adaptation and natural selection.
Darwin would have loved it!
Happy birthday!
Sources
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Eugene V. Koonin and Yuri I. Wolf (2012): Evolution of microbes and viruses: a paradigm shift in evolutionary
biology?
In fig.1. I added 'Coronaviruses'
(red), but note that at the time of the publication SARS-CoV-2 did not yet exist! In Fig.2 and 3 I added the 3 domain names.
- Omicron’s Surprising Anatomy Explains Why It Is Wildly Contagious, Scientific American 11 Feb 2022. This article explains the molecular basis of four adaptations of Omicron to the human host. Impressive how Omicron has discovered new ways to adapt to the human host to increase its own fitness without damaging its host too much!
Postscript 19 Feb 2022
I discovered that I already on 8 June 2020 paid attention to the fact that Corona virus obeys Darwinian evolution: Waarom zijn corona virussen zo groot? KNAW lezing van Eric Snijder 19 mei 2020. (Dutch)
Further Reading
- Thermodynamic Dissipation Theory of the Origin and Evolution of Life by Karo Michaelian. A review by Gert Korthof. 2018
- Review of Karo Michaelian's Thermodynamic Dissipation Theory, Part 2. Darwin and Natural Selection. 2018
- The difference between physics and biology, 14 August 2020
The article by Koonin that you use as the starting point for your blog post is very interesting. I didn’t know viruses (according to Koonin?) belong to another empire. Is this classification also recognized by other scientist?
ReplyDeleteIt is every time again wonderful to see that what Darwin wrote does not have to be adapted to what we now know. The foundation is solid. I recently got interested in phototropism and noticed that Darwin, together with his son, discussed and wrote a lot about it in The power of movement in plants. Beautiful!
One day too late, Happy Darwin Day Gert!
Hi Marleen. Thanks for your comment. Koonin uses "empire" in quotes, I think it is his concept. However, it is an interesting concept. Koonin points out that:
ReplyDelete"while cellular life forms all use a uniform replication-expression strategy based on double-stranded (ds)DNA replication, transcription of genes into mRNA or non-coding RNA, and translation of mRNA into protein, viral genome can be represented by all known forms of nucleic acids, and alternative replication processes such as RNA replication and reverse transcription are widely used."
Good point! indeed the genetic system of viruses is very diverse (as you know), here are the seven different kinds of viruses in the illustration:
+R, positive-strand RNA viruses;
−R, negative-strand RNA viruses;
dsR, double-stranded RNA viruses;
dsD, double-stranded DNA viruses;
ssD, single-stranded DNA viruses;
RT, retro-transcribing elements/viruses;
VR, viroids.
these are in fact 7 different types of genetic system.
That could be a fundamental difference between viruses and cellular life forms. I didn't realize it before!
Phototropism: Darwin could observe it in his time, just as we can today. Today, we can explain it on molecular level, that does not change Darwin's observations.
Marleen, Happy Darwin Day+1 !
(I am afraid I have forgotten his birthday several times... :-()
Hi, First time commenter. Very interesting blog. And very interesting post.
ReplyDelete1.Answering Marleen, IMO it is still unclear (for everybody) if viruses are primordial forms of life (i.e. they were already present in abiotic phase of life, and we could construct a phylogenetic tree of them),as some propose, or if they are only degenerate forms of life (i.e they all derive from cellular life and therefore we can not construct a phylogenetic tree). I would say Koonin proposes the first hypothesis/theory (primordial) but this is not mainstream.
2.Re the matter of the post, IMO what is new now since Darwin, are, first, the thermodynamics (non-equilibrium) view of life, second, the chemichal-molecular view of life (which is subcellular, I here include systems chemistry and molecular biology), and third the abstract formal models of life (Rosen, Varela and Maturana, Eigen, Kauffman etc...and many other formal / mathematical approaches to biology). Re thermodynamics, Koonin (with co-author Vanchurin and others) is precisely one of the authors which is following this long term trend (started with Boltzmann at a narrative level, renewed by Schroedinger, at the same narrative level and since then with more and more detailled quantitive approaches: England, Smith-Morowitz, Lane, Michaelian etc...). IMO an eventual next biological synthesis (who knows when this will take place) would involve the integration in a coherent theory of these thermodynamic views, these chemical views and these formal model views, with the evolutionary biology views. The usual Extended Synthesis (evo-devo, epigenesis, niche construction, natural genetic engineering etc...) claims can be acomodated in the evolutionay frame without problems, but this is unclear regarding these three novelties. And this synthesis should integrate two strands of research which has followed independent paths until now: origin of life and evolution of life. You have talked about many of these approaches in your blog I think...
Best
Anonymous, welcome to this blog. Thanks for your interesting comments.
ReplyDelete1. "if viruses are primordial forms of life (i.e. they were already present in abiotic phase of life,": would that be equal to the RNA-world? replicating RNA molecules.
What I want to add to the blog: one does not require a definition of viruses to delimitate viruses from cellular life. I learned from Koonin that one can simply describe unique non-overlapping properties of both empires. And you're done.
2. Indeed, this this blog is not an exhaustive summary of everything that is new since Darwin. You mention Karo Michaelian. Unfortunately, it is hard to discuss fruitfully with Karo (I added 3 blog links about his work under caption Further Reading, see above). He does not accept the core principles of evolution (and maybe of biology), and even refuses to think about it...
You refer to the study of Vanchurin, Wolf, Koonin 'Thermodynamics of evolution and the origin of life', PNAS February 8, 2022 ? If so, this is a highly theoretical, mathematical study, and I have difficulty to see practical implications. The authors conclude:
"The phenomenological theory of evolution outlined here is highly abstract and requires extensive further elaboration, specification, and, most importantly, validation with empirical data; we indicate several specific predictions for which such validation appears to be straightforward." ... "There are no data underlying this work".
I hope that this theory can be tested empirically, if successful, that would certainly be a great achievement. I know Koonin is a very data minded researcher, he is able to integrate and interpret huge quantities of data, so if anybody can do it, he is the right person.
Thanks.
Hi Gert, Thank you for your answer.
ReplyDelete1. Re viruses, does what you say solve the mistery of their evolution ? I mean does this clarify if they can be rooted to a common phylogenetic tree as some think ?.
2.Re thermodynamics in biology, before answering to you, let me comment a personal experience. Of course anecdotic. I overlooked this approach in the past. I even could not finish Schroedinger book: I had the feeling he was not talking about biology. That every time I tried. But, for some reason I have studied some works in the last weeks with this approach, and I have to say that they have been highly enlighting for me. After these readings, I would say that studying biology without thermodynamics is as studying astronomy without gravity. That has been done for milleniums, but as soon as gravity (newtonian view) appeared, the whole logic, that was absent before, was completely apparent. For me, from chaos to cosmos.
In this path, I learned about Michaelian work, I have read (not in deep some of its works (papers and some chapters of his book), and it is one of the sources that made me realise about the novelty and relevance of the approach. What I like of Michaelian proposal is that it is detailled and complete. On the other hand it might not be correct. But in a way as Lamarck was not correct: he (and others, but I would say that mainly him) created a new (dynamic) view in biology and others, as Darwinn, followed his path with the (partially, due to pangenesis) correct mechanism. I read weeks ago your three posts about Michaelian his work and the later discussion in comments. It is a pitty you both finally part sides as the discussion was interesting.
What to say about thermodynamics biological theory and evolution theory ? That´s complex matter and time will tell. In my view what is correct in evolution theory should remain correct under the thermodynamics umbrella. This is how scientific theories integration work. But maybe some evolutionary issues will lose relevance under the thermodynamic view, and some others we will see them differently. This is usual as well when a theory of a higher level (biology) integrates into a wider theory of lower level (thermodynamics). In this sense, I am not sure that Michaelian is completelly against evolution. What I felt (and I think this is what you are saying) is that he focus on the origin phase but does not knows too much about evolution. His references are old. As far as I remember he does not mention Modern Synthesis authors nor results...So I agree he needs to do an effort, learn about it and integrate it in his theory.
TO BE CONTINUED
Other authors with thermodynamic approach (but not the approach as Michaelian), I think you know them all, are Eric Smith and Morowitz (of the SFI school). Besides their book (which I have not read) there is a very good summary of their approach: The Origin of Life. BY JAMES TREFIL, HAROLD J. MOROWITZ, ERIC SMITH. A case is made for the descent of electrons. You can see the value added by Trefil, which is a very good science writer. Relevant: I remind I have read a paper from Smith on which he compared the thermodynamic and evolutionary views (at a high level), but I can not recover it. Jeremy England´s papers are quite technical and I have to read them in detail (I am now refreshing / studying thermodynamics more deeply to get there). I have not read his book. Differently to Michaelian, whose work is based in classic irreversible thermodynamics (i.e Prigogine), England´s uses some of the last advances in non-equilibrium thermodynamics (Jarzinsky, Crooks), but I think he is more interested in earliest abiotic phases. Re Nick Lane he ollows a more traditional evolutionary approach but his focus on energetic issues makes that his approach has a thermodynamic flavour.
ReplyDeleteRe Koonin, Vanchurin and coauthors, I refer to two 2021 papers you can find in arxiv: Towards a Theory of Evolution as Multilevel Learning and Thermodynamics of Evolution and the Origin of Life. Also interesting is Koonin book, although I think thermodynamics is not much presente there (2019). It is in these two new papers that they introduce their thermodynamic view. What is different in their approach, comparing with the others approaches mentioned above, is that they introduce learning theory. They see origin of life and evolution as a learning process. This not new as Valiant (a theoretical computer scientist, expert un computational complexity) already had this approach, but without thermodynamics. Other author that combines thermodynamics and learning is Bartett.
As you know, thermodynamics in biology is not new. There was a wave in the 80´s and 90´s that ended in nothing, I think. The difference is that at this time it was lead by biologists that wanted to introduce non equilibrium thermodynamics in biology. Now it is physicists that want to apply this theory to biology (except maybe Koonin). I feel that at each iteration, thermodynmics is approaching more and more the correct view of biology. This is what made me think about a Next Synthesis, as I said in my previous comment....Of course as you say what is needed is that they test experimentally their theories (and I think all of them are trying). This is not easy but nNow we have more data than ever. And Koonin, one of the fathers of genomics, is one of researchers that can achieve this.
Best
I'll reply tomorrow.
ReplyDeleteYou wrote: I read weeks ago your three posts about Michaelian his "work and the later discussion in comments. It is a pitty you both finally part sides as the discussion was interesting. "
ReplyDeleteNice to hear you've read the posts! I am curious on which points do you agree/disagree with Michaelian?
The issue thermodynamics in biology: living creatures have to obey physical laws because they live in a physical universe. But how can biologists apply those laws in a precise, useful and meaningful way? Physical laws are designed to explain physical phenomena (= dead objects), so cannot be applied directly to living bodies. The question is: how exactly do you apply those physical laws to living creatures? reformulate physical laws?
Do you think thermodynamics is mainly useful for the Origin of Life question, or is it also useful explaining day to day business, metabolism, adaptation?
So far, the emphasis in biology is on DNA, genes, genomics, evolution. Does thermodynamics throw light on for example the famous question what makes humans different from chimps? or is this kind of question a genetic issue? This is only an example to get the whole thermodynamics approach delimitated and focussed.
I have discussed with a physicist who was convinced that Turing processes (algorithms) for pattern formation in development is extremely important. And indeed, sometimes they help our understanding when integrated with the genetic-biochemical approach. But I think there are clear limits; without genes no pattern can be formed at all. Turing processes are a general physical background on the basis of which genes can do their work of constructing the organism.
So what do you think about these matters?
Hi Gert, Thanks for your answer.
ReplyDelete1. I have not read completelly Michaelian book. So I can not judge it. In stead of giving a detailled account I will give a general answer. In some other proposals that applies the thermodynamics approach to biology, I only see generalities. But this is not what we need. As generality we already have what Boltzmann said. What we need (from any theory, thermodynamical or not) are concrete and correct explanations of biological phenomenology. So what I like of Michalian proposal is, first, that it is concrete (no generalities) and second that it is quite complete, regarding the origin of life phase. In this sense Michaelian proposal is exactly what I would expect for a thermodynamic proposal, even if at the end his proposal is not correct. And what I don´t like is that, in the evolution phase of life, his proposal is neither concrete nor complete (in fact it is almost absetn). What he does is preciselly to ignore biological phenomenology and answer these matters with generalities. For instance, he does not talk about metabolism or chemiosmosis in his book (I checked that); he focus on information molecules or polymers. Compare this with Nick Lane proposal (which I find also quite detailled and complete), on which you find the contrary: metabolism and chemiosmosis, but not information molecules.
In all it was reading some of Michaelian and Lane writings that my eyes were opened. But Lane alone would have not opened them, because he is a biologist, his view is that of a biologist. So it can be said that if I would had not read Michaelian´s, I would have not been writing these lines...
TO BE CONTINUED.
2. I will answer to your interesting and key questions the best I can.
ReplyDeleteIn the last weeks, with the readings I have commented in previous comments, I have thought a lot about some of these issues so I have some ideas, even some models. I will just try to answer to some of your questions using these ideas / models. Please note that it is not that I am interested in using your platform to publicize my ideas (I have already published them, they are available on the web, but not in english). But I think that explaining them, you can have an ida of what value can thermodynamic view could add to biology.
I am not going to comment about Turing processes, chimp / man etc.... First, because I think that the best level to appretiate the power of thermodynamics in biology is the molecular level. This is the closest level to physics. The next level to molecules are physical principles, so in some sense the step to thermodynamics is the natural next step once you have reached the molecular level. Second, I am somewaht weismanian (an underrated biologist i think), so for me key in life is germinal line. I am not saying that development is not important nor that thermodynamics has nothing to say about this. But since this comes later logically and historically (multicellular organisms came later), I have not devoted time to it and I have not ideas.
So, so far, in these matters I think in terms of molecules and, at maximum at prokaryote level (not even in terms of unicellular eukaryotes, so not to speak of multicellulars and its development...).
TO BE CONTINUED.
3. Now, answering to your questions:
ReplyDeletea) First, in my view thermodynamics should be relevant for both origin and evolution. If you see, in all the last proposals all the researchers (Smith-Morowitz, England, Michaelian, Lane etc...) address (or try to address) both, origins and evolution. This has a logic: if you have a correct thermodynamic theory of life, you can not draw a frontier between origin and evolution. The same physical principles that explains origins should be at work for other biological matters, such as those you mention (metabolism, adaptation, evolution in general). I think that this happened to all: they started with origin of life and realised that you can not draw a frontier. You can not stop once evolution arises. In fact, in my view the whole evolutionary biology could be translated to thermodynamic / physical / chemistry language. The bridge is as follows: evolution focus on differential reproduction or replication; thermodynamics on optimal dissipation. I think that in the future it will be shown that the optimal replicator is just an optimal dissipator. I think England is working on this lin of thinking. Linking dissipation to replication is one of the steps the next synthesis must accomplish. There are many others.
b) Also you say: "Physical laws are designed to explain physical phenomena (= dead objects), so cannot be applied directly to living bodies. The question is: how exactly do you apply those physical laws to living creatures? reformulate physical laws?". In my view these questions goes exactly to a very relevant point. Apparently, there is a contradiction in the view that life is only physical with the fact the one of the more apparent properties of life, autonomy. To solve this contradiction some thinks that to exlain autonomy we need new laws.
If you see all the abstract models of life I talked about in an earliest comment above (Ganti´s chemoton, Rose´s, Varela-Maturana´s autopoiesis, Kauffman´s autonomous agents,etc...) focus preciselly on this autonomy issue. And I think that to say that life shows autonomy just because this property evolved (which is the usual evolutionary generality which is given as answer) is not satisfactory. Not for me. This is why I consider that these abstract models adds value to biology, besides (complementary to) the ecolutionary view.
TO BE CONTINUED
From my side I have a model that might answer these questions (how it could have happened). Your questions can be rephrased as follows: how is it possible that a physical entity is autonomous ?. How did the autonomy property emerged in a world of physical laws ? These are very deep questions. And for answering them you have to think thermodinamically. My model is as follows (I will explain it in a series of propositions; hope you do not find it a generality !!):
ReplyDelete--The motor of life are gradients (this is a key concept; think about the photonic gradient of Michaelian or many other before him, or about the CO2-H2 gradiente Trefil, Smith and Morowitz talk about). This idea is already a topic. Of course it is not mine. The first time I heard of it was in a book of Margulys and Dorion Sagan. Also Sagan and Schneidr have wroten a book about it.
--When there is a gradient, there is a disipator of this gradient which arises. A disipator is not alive. It is something completely physical. It arises naturally with the gradient and disappear when the gradient disappear. He has not the autonomy property. So far we have not moved from physics. Again, this is not new. I would say this is a topic since Prigogine and now mainstream.
--To each gradient, its own disipator. For me this proposition (which is hypotethical) was new and was key as an eye opener. I have not seeing it expressed this way in any other place. But maybe it is in some previous paper. I reached this conclusion reading Michaelian proposal which is based in photonic gradient, and Lane, Smith-Morowitz which are based on CO2-H2 gradient. Both try to get different kinds of dissipations from an unique gradient, which I (hypothetically) think is not possible. For instance in photonic gradient, you will get polymers of any kind (of adn, of arn, of aminoacids etc...), since these are the best disipators for this gradient. This gradient provides or produces naturally monomers (materials of the polymers) and the energy for bonds of monomers (phosfodiester or peptidic). With that polymers come naturally. On the other hand , in CO2-H2 gradient you will not get polymers but other kind of dissipators, metabolic dissipators (non-catalized autocatalytic metabolic cycles). What this proposition says implicitly is that you are not going to get a polymer in CO2-H2 gradient and that you are not going to get a metabolic disipator under the photonic gradient. For me to try to get this (as many researchers are doing) is alchemy. And again, these concrete disipators that correspond to concrete gradients, which might even reproduce or replicate in some primitive way, are just physical entities. They are physycal entities, not alive yet. Not alive because if the gradient disappear, the disipator will disapear with it.
TO BE CONTINUED.
--Now, for some astronomical or geological reason, two different gradients can come into contact. And when two different gradients come into contact, their own disipators will come into contact as well. And it is during this contact that autonomous living entities can emerge. The only life we know, earth life (which is composed of polymers that do the information tasks and metabolism that do the materials and energy task) could have arised this way. The two gradients (photonic and CO2-H2) come into contact, their dissipators mixed (maybe during milleniums) and the result is an entity on which a metabolic dissipator provides the materials (monomers) and energy, and the polymers provides the code for the enzymes of the metabolic dissipator. Before that "symbiosis", materials and energy was provided to polymers physically by his photonic gradient. And, in the same way, metabolism arised naturaly (non catalysed, with no cinetic control) in its own gradient. But after the contact, each component of the "symbiosis" provides what the other element needs. So when two gradients mix, the two disipators "help" each other to become independent of its own gradient. When this happens, even if the gradient disappear, this entity composed of the two disipators can endure, can survive. Now you´ve got an autonomous entity, an alive entity (according to all the abstract models of life mentioned above).
ReplyDeleteThis thermodynamical model based on gradients and dissipators and on the fact that each gradient generates its own kind of generator, explains (very roughly of course) how autonomous alive entities could have arised physically, under purelly physical laws. Of course, next (and I think that was your main question) is to explain how these autonomous entities can live a thermodynamic life, after having become autonomous, independent of their gradients. I think this fact can be explained as well, but I still don´t have a concrete narrative just a general idea. The main idea is that autonomous live is gradient independent, but not dissipation independent. What they do after independence from a gradient is to dissipate, but not a concrete gradient, they can potentialy (thanks to evolution) dissipate any gradient. This way they are still linked to physycal laws (they have to dissipate gradients), while at the same time carrying an independent life that to the not thermodynamically aware observer will appear as completely independent of physics.
ReplyDeleteBut in fact, in my route (which I really started unintentionaly, just after seeing how fertile high level thermodynamics approach was for biological matters, how ideas flowed so naturally) before going in deep about this "what happened after dissipator symbiosis" matter, I am focusing on, thinking about logically previous issues: what was the dissipators situation before their gradients contacted. Concretelly about how in the photonic gradient, a complete molecular information system could have arised physically (i.e dependent on the photonic gradient), before the contact with the other gradient (CO2-H2). It is in this context that I already have a very concrete model that could explain thermodynamically a lot or at least some of the phenomenology of genomics. Still speculative but according to this model several properties that genomes should have are obtained (that is a prediction about genomes). It remains to be seen experimentally if real genomes has these predicted properties or not. Some (the easy ones) has been already confirmed. And thinking about this issue has led me to study the origin and evolution of ribosomes. I think this is a hot matter right now in biology, as we have not a definite correct theory, just several proposals. I am convinced that thermodynamical models has a lot to say about this matter. But now, just reading in deep aboout this; I really have not a thermodynamical high level model about ribosomes origin and evolution, just a very general thermodynamical idea of what explains thermodynamically their emergence.
Once you have clear what was the situation of the dissipators before their gradients came into contact, next step is to explain how this disipator "symbiosis" could have hapened to get as a product an autonomous entity (this will not be easy to explain, and again I don´t have a full thermodynamical model, just some general ideas). And next how this autonomoys life could have lived a gradient-independent life, but still determined by thermodynamics.
It should be noted that while I arrived at such a model of the origin of life by my own reflections, later I learned that one researcher (Terrence Deacon) had a similar model (only regarding the fact that, in my words, life could have arised as a mix of different dissipators). I do not know it in detail, he wrote a book about it titled Incomplete Nature (maybe you know it), and later several papers. And I think we were led to think about all this issues by the same reason: how was the concept of information used in biology, what is biological information. This author considers that (in my words), gradients distributed in a whole solar system are needed for the origin of life (that is earth gradients are not enough to generate the life we know...).
4. Gert I would have a lot more to say about these matters. For instance I could have talked about how to compare the MEPP with DKS as alternative explanations in biology, the first being thermodynamic and the second based on chemistry. Comparing these two approaches says a lot about what the thermodynamic view means.
ReplyDeleteBut I think that with all the already commented matters (even at a so high level), you can have an idea of how a thermodynamics approach to biology can be implemented, and its reach. You have an idea of What biological phenomenology it can explain (for instance genomes). You have an answer (or attempt of answer) to your questions.
In fact, before adopting this approach, whenever I used to read about biology (evolution, physiology etc...) I always had the same impression: we can describe with complete detail life phenomenology, we can even use these descriptions to get some biological technologies (medicines), but we can not understand why life is the way it is. We lack the organizing principles. Astronomy without gravity. And evolutionary explanations are not, in general satisfactory for me. Not because they are wrong, but because they don´t explain too much about many facts. They don ´t really supply the organizing principles. I think that thermodynamics can fill this gap.
Best
P.s. Sorry Gert for so much comment, one after the other. But you have a limit for the size in comments. And maybe I wright too much !!.
Dear unknown, I need to read and reread your comments (they are for a great part outside my biological education). So, I need time to digest them and think about them. And probably I have some questions. Thanks a lot for your efforts to post your thoughts on this blog.
ReplyDeleteA request for clarification. You wrote "I would say that studying biology without thermodynamics is as studying astronomy without gravity. That has been done for milleniums, but as soon as gravity (newtonian view) appeared, the whole logic, that was absent before, was completely apparent."
ReplyDeleteNewton made it possible to calculate and predict the paths of the planets around the sun with mathematical precision. This was not possible before Newton. Now, what properties can be predicted or calculated about organisms (including bacteria) with the thermodynamic theory what can not be done without it?
This is a starter for me, to get a grip on the whole issue.
Hi Gert, I was unable to find your email, but this post was the most recent that mentioned Carl Woese. I was an undergraduate student of his and I wrote a tribute to him here: https://iotmote.substack.com/p/a-tribute-to-carl-woese Also, I'd agree that many evolutionary properties require an understanding of physics and math (Woese was a physicist by training), but that it is possible to have a partial understanding of evolution without the thermodynamic properties (the codon table, etc).
DeleteHi Giovanni,
ReplyDeletethank you very much for your comment. You are very lucky to have Woese as a teacher! And that you signed up for his course was a very wise decision. If Woese gave courses at Utrecht University, when I was a student, I certainly would have signed up. I have read your blog; it gives nice anecdotes about Woese and a lot more.
If you don't know about my website, I wrote a page about Carl Woese here:
https://wasdarwinwrong.com/korthof88.htm
I will add a link to your blog.
Have A Nice Day,
Gert
Hi Gert! Thank you for your reply! I just saw this upon response after helping a friend locate the when animals arose from Eukaryotes but apparently I did not receive (or forgot to sign up for an email notification) when you replied last week. I did read that wasdarwinwrong post on Woese before reaching this newer blog. Thanks again!
DeleteP.S. My friend was referring to this article: https://www.syfy.com/syfy-wire/mysterious-origins-of-cambrian-ediacaran-creatures
Darwin is one of the fascinating persons;)
ReplyDelete