Dear John,

this question should may be divided into two like:

reverse evolution due to physiological or ecological adaptations;

back changing of organs (against Dollo's law – irreversibility of evolution).

Cases you are explaining belong to the first group and second variant is normally possible only due to mechanisms of compensation but not re-growing of organs!

Robert H.Cruickshank and AdrianM.Paterson The great escape: do parasites break Dollo’s law? TRENDS in Parasitology Vol. 22 No.11 pp. 509-515.

But I agree that in cell level re-appearance of some lost functions is much more possible. It can help to understand e.g. the appearance of contractile vacuoles in cells of ciliates emigrating from the sea habitats into fresh water. Much more simple adoptive feature is size changing! In free-living ciliate Stentor coeruleus that can be not much less than 1 mm I found stable population in satellite flood-plain lakes near the Dnieper 200-300 mk in stretched state, that means in mass 30-40 times smaller!!! So, all physiology will be different and the most important – generation time will be seriously shorter…

But about adaptations Peter Calow says in his famous book “Evolutionary Principles” 1983:

3) adaptations are based on the modification of common themes and are often not as good as they could have been had they been constructed de novo, without the constraints imposed by pre-existing structures. Imperfect solutions, apparently useless characters and vestigial organs are, somewhat paradoxically, support for a process of evolution based upon natural selection of random variation within the constraints of pre-existing forms. They do not readily fit in with the concept of an Omnipotent Designer. (p. 9).

So, seals and whales can live in water but they have no gills. Pisciformes former parasites without intestine in adult didn’t form it…

Andrey

Dear Dr Torday,

I must directly react to your question because translated in my native language (French) it sounds odd.

"Evolution" always means going forward in time, so natural evolution cannot be reversible ! It might go forward towards kinds of diversification that look very similar to species (or adaptations to niches) having existed in the past, but it remains irreversible evolution.

It still involves adaptation to the environment and selective advantage for the fittest.

Also heterochrony recognizes that : see the abstrat of your joined pdf : "...evolution can now be understood as adaptive changes in the cellular-molecular signaling mechanisms underlying its ontogeny and phylogeny ...".

Moreover natural selection is not teleologic (see books of Stephen Gould) nor can it be spoken of retrogradation in the sense of reversibility from an improved situation.

I don't know the monograph of Jean Guex (maybe you could post some illustrative extracts of it ?)  but the use of the words "Retrograde evolution" in the title must be some kind of provocative (editorial ?) way to draw the attention of the potential reader. Of course, adapting to the extreme environmental stressors conveyed during major extinction crises may result in situations giving the feeling that things had gone backward. But evolution remained irreversible even in these periods. By the way, all 5 last major extinction crises have resulted in an increase of biodiversity (increase of number of families) on evolutionary scales.  

In summary, evolution is just "swarming" in all directions as usual, and remains irreversible even when some directions could look very similar to past situations.

Kind regards

Andrey, I am not sure why you unequivocally assumed that my question about the reversibility of evolution was "reverse evolution due to physiological or ecological adaptations", not "back changing of organs (against Dollo's law – irreversibility of evolution)". I am actually referring to both, because in my way of thinking about evolution, it is holistic, originating from the unicellular phenotype- actually, we never parted from the unicellular phenotype, given that we return to it during the life cycle. In this context, it is helpful to think about the debate as to whether evolution is gradual (Darwin) or episodic (Gould). Seen from the cellular perspective, it is actually both. The gradual changes can only be seen at the microscopic level as genetic changes in cell-cell communication; the episodic changes are those that are at the macroscopic level, but they derive from the microscopic changes, i.e. it's a matter of scale. Reverse evolution occurs beginning at the microscopic level in response to physiologic stress, either challenging the reaction norm for the trait, or reverting back to an earlier pre-adaptive pathway. Depending upon the external environment, the biologic properties involved will either remain at the preadative equipoise or change in adaptation to the environment. John

Dear Dr Torday,

I mostly agree with you. Thank you for the joined pdf's. I need a little bit time to read them.

Of course, time does not move forward. Time is a way used by humans to measure how things (e.g. the way biological entities adapt to their environment) move forward.

Concerning the primary level of selection, I can only note your claim that it is the unicellular state that is the primary level of selection as the origin of First Principles of Physiology and read your contributions and your staff's to the issue. I suspect to learn a lot doing it. I'm convinced that the "emerging science of epigenetic inheritance" has a high potential of development and that there is much to be learnt by experimenting on it.

Now, according to my understanding, this does not really invalidate the irreversibility of evolution. It just emphasizes that the unicellular condition is at its roots. Evolution would just proceed forward that particular way. As you put it interestingly "it is the unicellular condition that is being selected for, and it, in turn, determines the phenotypic changes that we think of as evolutionary change in adaptation to the environment". So even if the cornerstone of evolution is at unicellular level, evolution would proceed irreversibly.

Agai, I don't see any contradiction when you write that the First Principles of Physiology (that gave rise to the eukaryotic cell) must be followed for a species to survive. It might be that the fundamental mechanisms are at unicellular level and that the macroscopicv result is Darwinian evolution.

If what you mean is that you intend to prove that there is no time asymmetry at unicellular level even if there is time asymmetry at macroscopic (species) level in the same way as there is no time asymmetry in the physical laws at fundamental level even if time asymmetry is observed at macroscopic level (coffee cup doesn't restore itself, we cannot walk in the past, etc.), I'd surely support your view and your group's research.

But, I've first to read the papers ...!

Cheers     

Dear Colleagues,

some interesting questions had been discussed in RG forum 1 year ago before appearance of Dr. Guex book: URL

https://www.researchgate.net/post/What_are_the_origins_of_atavisms_and_retrograde_evolution_in_biology_and_recent_organisms

But I want to ask one question: NEOTENIA is progress or regress? If it is middle stage of individual development and is used for survival of a population – what it has with progressive development?

In all gymnophionan Amphibians species fertilization is internal. They can be oviparous, sometimes with direct-development, or viviparous, with a placenta-like structure in some species. But limbs are absent ! Look, please, Chapter 4 Vertebrate Evolution:  The Strange Case of Gymnophionan Amphibians by Jean-Marie Exbrayat and Michel Raquet In:

Pierre Pontarotti Editor “Evolutionary Biology: Concept, Modeling, and Application”!

So, it is progress or regress, may be cannot categorize evolution in this manner?

What about hybrids ?

As well numbers of examples in parasitology.

I’m not specialist in the field but trying to reply some questions from my students! Help me…

Best,

Andrey

John,

I just read your answer to Andrey (probably posted simultaneously with my former post). I can fully agree with this view that one has to clearly differentiate what happens at microscopic level from the macroscopic level. And that e.g. Darwin's and Gould's views can be reconciled that way.

Cheers   

Dear Dr. Crevecoeur, thank you for your thoughtful reply......I look forward to hearing back after you've read the articles I attached. My way of thinking about biology and evolution is unconventional, but then again, the conventional way of thinking in biology and medicine remains descriptive and non-predictive, so we need a paradigm shift. Given your expertise in the realm of Physics, it will be challenging to bridge disciplines, but I know it can be done......Best, John

Andrey, regarding your question about Neoteny, it is neither regressive nor progressive, because those terms infer direction for evolution. I don't think that there is direction in evolution.....that is an anthropocentric perspective. To my way of thinking (again), we misinterpret the life cycle as going from adult to adult, when in fact it goes from zygote to zygote. Samuel Butler is famous for saying that 'A hen is an egg's way of making another hen'. Those ideas come out of new knowledge of epigenetic inheritance, how the environment directly affects the organism through the acquisition of epigenetic marks during its life cycle. Those 'marks' (DNA adducts) change the read-out of DNA, and can become constitutive over time. So neoteny is the way that the organism responds to environmental stress, reverting to an earlier stage in its evolution, providing options for its develomental/phylogenetic trajectory. I have attached a paper on the topic fyi. John

John,

If we take the case of sea mammals, some of their terrestrial mammalian characteristic are still very much present : they use lungs, that has not been reversed.  They still have a mammalian brain which allows them to be cooperative and live in pods and fish or hunt cooperatively and with sonar based communication. They still have the same method of incubation of the youth and of breast feeding and mother and pod caring for the youngs and all the associated feeling.  Eye contact wit sea mammal is very much like other mammals and very unlike reptile, amphibian and fishes. The list is very long.  Where they reverse is the exterior surface of their body that has become hydrodynamic and the reversal in the use of the limbs.   A lot of them are musical and and not a single other non-mammal sea creature and their echo-location migh as well be the best.  All that because of their mammalian nervous system.  The reversion is very very partial.

An example of reverse evolution in humans is the decalcification of bone and loss of the homeostatic principle in the lung in Astronauts; this is why they wear pressure suits and exercise in Space, though the effects are not completely neutralized. The reversal of evolution occurs because in microgravity the evolved physiologic traits in adaptation to earth's gravity are reversed.

John,

It would be interesting to see if the children fathered by  astronauts after their space mission have some problems.  These effects are not really devolutionary effects but degenerative effects resulting from submitting their bodies to conditions so drastically different that it cannot adapt.  We are earth-bonded and not made to become astronauts. All these star trek movies were very good but exploring physically the galaxy is not our destiny.  

I do not think evolution is possible in reverse gear. Come to think of it, evolution presupposes adaption of organisms to livong conditions in their environment in a bid to survive. The best foot sort of is put foward. Evolution is a foward movement, I think. Even if earlier features reappear in the species, which is quite possible because I believe the universe is capable of anythinhg another word will have to coined to capture the new reality.

@Louis, Ales, RN, with all due respect, the loss of calcium from bone and homeostatic control of alveoli in the lung are evolved traits. They are regulated by Parathyroid Hormone-related Protein (PTHrP), a gene signaling mechanism that duplcated during the water-land transition in vertebrates. If you delete PTHrP in embryonic mice their bones will not calcify and their lungs do not form alveoli, Both traits are necessary for adaptation to land, i.e. they are evolutionary, not pathologic as you suggest.

Mechanotransduction determines the structure and function of lung and bone: a theoretical model for the pathophysiology of chronic disease. Torday JS, Rehan VK. Cell Biochem Biophys. 2003;37(3):235-46.

Parathyroid hormone-related protein is a gravisensor in lung and bone cell biology.

Torday JS. Adv Space Res. 2003;32(8):1569-76

@Ales, I respectfully disagree. The conventional way of thinking of injury-repair is as independent of the ontogeny and phylogeny of the organism = evolution. Thus, methods of treatment are not thought of as a recapitulation of the mechanisms by which structure and function evolved, but as ad hoc means of fixing the problem as it presents. Health and disease continue to be thought of as dichotomous, not as a continuum of evolution. By citing your Nr.2 you are contradicting yourself by saying that devolution does not occur, in my opinion. If it doesn't then how can healing follow along evolutionary lines? Please explain.

@Ales, thank you for your reply. However with all due respect, you have misconstrued what I have been saying about 'reverse evolution' based on evolution as a continuuous process. Injury-repair, evolution and 'reverse-evolution' are all a result of cell-cell communication based on homeostasis and the First Principles of Physiology. These processes are not chance events, they are founded on deterministic rules that have evolved in response to the physical environment. The Tyagi paper you provided is predicated on chance changes, not the underlying mechanisms that determine them, such as Quorum Sensing in bacteria. This is not Darwinism, which as you know is based on random mutations; this approach to an understanding of evolution is predicated on mutations within the constraints of the physical and cellular environments. I have attached two position papers expressing these ideas. Please let me know if you have further questions.

@Ales, I agree that 'evolution' can mean many things, so the terminology is ambiguous unless it's seen in context.......using the term evolutionary biology is more precise, but can get worn out when read, hence the liberal if imprecise use of the term evolution as a proxy. As for Tyagi's experiment it is interesting but non-mechanistic, like all of Biology.....we need to shift to mechanistic biology if we are to make progress. Like Chemistry as Alchemy or Astronomy as Astrology, biology must become predictive hard science or remain associations and correlations....Ernst Rutherford's 'All science is either Physics or stamp collecting'.

Ales, thank you for your thoughtful reply. I respectfully beg to differ with your assessment of the possibility of prediction in biology. We have all been imbued with DNA as the operating system for biology, but that is not correct. It is the result of an overly reductionist attempt to understand evolutionary biology. It has freely been admitted that cell biology is totally absent from the evolution literature (with the exception of my own publications, but I am not an evolutionist so apparently I don't count). Cell biology is the fundament of all biology and medicine, so no wonder there is a disconnect of evolution theory from both. Once it is acknowledged that the cell membrane is the demarcation of the internal and external milieus, and that all complex physiology evolved from the cell membrane (Torday and Rehan. Evolution, the Logic of Biology) the ontology and epistemology of  biology can be seen from its origins, moving forward, instead of reasoning after the fact. In my own work, by focusing on the water-land transition that occurred 500 million years ago, not only the skeletal changes, but the visceral changes can be understood both developmentally and phylogenetically. There were three gene duplications and a specific mutation that account for the adaptation of vertebrates to land (given that they had no other options). One of these duplications (=amplifications because they were all cell surface receptors) was the Parathyroid Hormone-related Protein (PTHrP) Receptor. If you knock that gene out in a developing mouse, it doesn't form alveoli, a skin barrier or a calcified skeleton, all of which were existential for adaptation to land......so the 'logic' of evolutionary biology is tractable and predictable. 

Essentially.

@Aleš,

>> … biology is a science about experiments conducted in nature.

No, not in permanence and not everywhere if by “experiments” it is meant “noisy search” and “exploration”.

>>… biology can to a limited extent predict behaviour of biological systems which behave within previous experiences being coded genetically

No, prediction in biology is wider than that.

Noisy search and exploration with creation of information is a good candidate for explaining the origin of life but with all respect it should not be applied to all natural phenomena, in particular any biological phenomenon. Biology is not only a science about experiments conducted in nature (with the idea “contrary to physics”). There is no permanent noisy search and exploration in biological systems as if biology would be restricted to "a science about experiments conducted in nature". In multi-cellular organisms for instance once an organized system is established (cell, organ, nervous system, …) it must stay. The important thing is that it is maintained. These are all the observed negative feedbacks including homeostasis, homeothermy, ….. Probably this corresponds to what you call “exploitation”. But there is no question of further (permanent) exploration in parallel to exploitation by say lever cells, fibroblasts, or ovules,...  Because any exploration would increase the risk of destruction of an organ, the skin, the reproductive system, … This opens a whole field of predictability even outside "previous experiences being coded genetically", i.e. even if there are changes in the genetic code. There are slight changes in the genetic code (random or induced mutations by UV radiation …., loss of telomeres, …) all the time, but the biological systems adapt to them saving their internal organization (you would probably say the part of the functional information necessary to maintain the internal organization).

Also bacterial system can be maintained for millions of years. Even if noisy search and exploration is at work in bacteria in parallel to this “maintenance” activity, it is within strong environmental constraints. This makes that even in those cases (the bacterial world is hugely bigger than the multi-cellular world) a lot of predictions are possible under given limits (statistical distributions, …). And noisy search and exploration is to be seen as an epiphenomenon not a central one.

This is general feature for established biological systems. For instance, it has been shown in laboratory that a mutation in gene daf-2 of the nematode worm Caenorhabditis Elegans more than doubles its adult lifespan on the condition that gene daf-16 is active. If there would be permanent experimenting conducted in nature (if exploration would be continuously at work) on established biological systems, this kind of creative changes should be observed as a general rule in nature : it is not.

Of course one cannot predict the unpredictable (something like mutatis mutandi the fall of the Berlin wall in 1989 or the election of Donald Trump in 2016) because of the many parameters at stake. But one can be assured that there is a lot of predictability potential in biology (under defined validity conditions) as there is in “harder” sciences like physics.

Dear Ales, I agree with Guibert that 'noise' is an epiphenomenon of the central principles involved in the establishment and sustaining of life. In its purest form, life began with the cell membrane distinguishing the internal and external environments (Claude Bernard's 'milieu interieur'). The internal membranes generated energy via Chemiosmosis (Peter Mitchell, 1961), allowing for negative entropy (Schrodinger, 1944) to elude the Second Law of Thermodynamics. That deceit caused an ambiguity between the internal and external environments of the cell, which is what I think you are calling 'noise'. Evolution has decreased that noise, or free energy over the course of biological history.

Dear Aleš,

Thank you for the enlightment on how stability of life was achieved (huge decrease of noisy search from RNA to sexual DNA). I know your view on noisy search and exploration as summarized in your last post. However my reaction was merely on predictability in biology. Probably it confirms that we have different views on the meaning of the word « prediction » in scientific practice. You seem to consider that prediction must be with 100% certainty. For me, there may be less than 100% certainty provided that the prediction is new and precise (allowing for further investigation and better knowledge of the limits of the theory).

Dear Aleš,

>>Noisy search has to be viewed as a cybernetic algorithm, and as such, it is not bound exclusively to molecular noise dealing with thermodynamic (configurational) information. All other functional information carriers are exposed to noise at their respective levels as well.

Now you make me doubt of my correct understanding of what noisy search actually is. I saw it as exploration of new possibilities. This makes sense in the frame of the appearance of life and of variety of new life forms during the process of evolution. But with a. m. sentence, you seem to see it rather as the result of exposure to noise. Then algorithmic evolution would just be an AI wording for adaptation to environmental constraints. This would be confirmed by the next sentence : “John has noticed that there is an intra-cell evolution as well (responding to the local environment)” Same for Tyagi’s experiment : problem in absence of environmental signal (!?).

@Guibert, I fully agree with your comment about the failure to systematically pursue an observation such as the extension of the C. elegans life span by manipulating daf-2. As I see it, the primary constraint on expanding such an observation is that Darwinian evolution would have us think that this is a random mutation, so how could one expect to find an underlying mechanism to explain principles of longevity in other organisms. On the contrary, as I have expressed it to you previously, my bias is that such events are not chance, they are based on internal selection principles that refer all the way back to the First Principles of Physiology- negentropy, chemiosmosis, homeostasis- in which case the effects of daf-2 on life span should be deterministic, not probabilistic. But once we agree on this hypothesis, the actual phenomenon is not length of life, it's the underlying role of epigenetics in determining the future state of the organism- the phenotype of the organism (including its life span) is an agent for the collection of epigenetic information from its environment (see attached). So longevity is interlinked with all of the other phenotypic attributes of the organism. I think that all of these characteristics funnel through the cytoskeleton, which can either be in a homeostatic, mitotic or meiotic state- that is what causes the life span trait. The Target of Rapamycin (TOR) gene is bound to the cytoskeleton and transduces all cellular traits. I base this idea on the way TOR controls the life spans of yeast, slime molds and mice alike experimentally.  I hope that was clear/made sense.

Even if someone can reduce biological processes to some elementary principles, I don't think it can be used for prediction in large scale. There are many other factors, e.g. complexity, which prevent basic principle from useful principles.

Dear Aleš,

Interestingly, you describe a « bathtub curve » with a first learning stage (with erase of failed experiments) followed by a steady stage (where exploration is progressively replaced by exploitation) followed by a third stage of exhaustion !  Assessing this quantitatively would then help making some rough predictions e.g. on the position of a given system in the timescale of the process as it develops (evolves) in it  :=)

@Y.Azizi, the beauty of a focus on cell-cell communication is that it is scale free based on the principle of homeostasis. If you are interested I can send you the paper.

@Aleš, yes such analogies are milestones helping to grasp in short time the essence of the thinking of others that developed it over years ! Researchers of previous centuries didn’t have present communication means but they enjoyed being a few and not overloaded by information ….

@Ales, perhaps you could put your thoughts about the 'physics of biology' into biological terms? As they stand now they are a description of properties, but they are not integral to anything I can recognize as a biologist. Other physicists like Prigogine and Polanyi were unable to find the common ground between physics and biology necessary for explanation of the latter by the former. I maintain that this is because biology is pseudophysics.

Aleš,

very interesting and instructive.

With kind regards,

Marko

Marko Vitas

Laze pri Borovnici 38,

Borovnica 1353,

Slovenia

Tel.: +386 41 362 111

[email protected]

http://www.anali-pazu.si/?q=sl/avtor/marko-vitas

http://rdcu.be/kojs

http://vitas-evolution.com/

http://www.dlib.si/details/URN:NBN:SI:DOC-UY4WVSCK/

https://plus.google.com/u/0/+MarkoVitasorigins/posts