Evolution Reflected in Development

Below is an image of the developmental path from human conception to adult in comparison with evolutionary path from prokaryote to human.

Unlike Haeckel’s biogenetic law with its focus on physical forms, the comparison above also concerns activity, lifestyle and behaviour. Comparative stages may be vastly different in detail, but the similarity of general lifestyles and consecutive stages are there to be observed.

Human life begins in an aquatic environment. Toddlers gradually learn to walk upright from a previous state of crawling and moving around on all fours. The brains of children develop through daily interactions and experiences. This brain development accompanies the child’s increasing ability to achieve complex manipulation skills using hands that have been released from the task of providing support and locomotion, and also the practice of producing sounds using the various muscles of the mouth. Well developed brains allow for rational thinking and the creative use of language.

Human minds have brought about technological advances which have allowed human activities to engulf the planet. Signs of intelligent human activity are evident a good distance beyond the earth spreading ever further out into space.

The various forms of extant animals and all other life forms have evolved as an integral component of the living earth and the whole forms a dynamic system.

The various animal forms should be studied in the context of the complete system in both time and space.  Conditions would have been very different prior to the terrestrial colonization of earthly life In all probability none of the present aquatic animals would bear any resemblance to the aquatic ancestors of humans and other higher vertebrates save that at some stage they all require an aquatic environment for their continued existence.

From a point of view which regards physical organisms as the individual expressions of overarching general forms, the evolution of cetaceans need not have involved moving to the land only to return to the water at a later time. They may have reached the mammalian stage of evolution but in a way that was suitable for an aquatic lifestyle. They adopted the archetypal mammalian form in a way that suited an animal living in an aquatic environment and there would be no need to posit a terrestrial stage in their evolution.

It’s my belief that higher consciousness is ever present. Evolution is the process whereby higher forms of consciousness descend from the group level to the individual level. The most fully developed individual consciousness which I am aware of on earth can be found in humans but it is still rudimentary compared to the higher level group consciousness.

Plasticity is a fundamental feature of living systems at all levels from human brain development to the radiation of multicellular life. Paths are formed by branching out and becoming fixed along certain lines. It would be impossible to forecast specific paths but, nonetheless, there is a general overall direction.

Now that biological life has reached the stage where social organisms have become individually creative and rational, the all encompassing Word is reflected in single beings. This could not have come about without preparation and the evolution of earthly life is the evidence of this preparation. We, as individuals, are only able to use language and engage in rational thinking because our individual development has prepared us to do so. Likewise humanity could not arrive at the present state of culture without the evolutionary preparation in its entirety.

Focussing in at the lower level gives a picture of ruthless competition, of nature “red in tooth and claw”. But from a higher vantage point life benefits from this apparent brutality. For instance if a sparrowhawk makes regular hunting visits to a suitable habitat in your neighbourhood it signifies that this environment supports a healthy songbird population. In the case of the continued evolution of physical forms, survival of the breeding population is more important than any individual’s survival. In the evolution of consciousness the individual is the important unit.

I think it is a mistake to see biological evolution as a blind random groping towards an unknown and unknowable future.

896 thoughts on “Evolution Reflected in Development

  1. CharlieM: Because the system operates for the benefit of the organism, not the cell.

    As said before, it is the cell itself that executes the apoptotic program. Did the cell decide to be unselfish and sacrifice its life? Perhaps unlike you it is truly free?
    Or perhaps the survival of the organism is in the interest of the cell and it is being selfish after all?

    OR … perhaps you are anthropomorphising cells and projecting your own desire to survive on them?

    What do you think?

    CharlieM: If organisms were not destined to have finite lifespans and to die then there could be no evolution.

    Not true. Do you know why?

    CharlieM: Apoptosis means that the cell can no longer pass on its genome.

    Somatic cells don’t do that anyway. So if apoptosis is deleterious for the cell, then what exactly is being sacrificed?

    CharlieM: The shared interest of cells is for the benefit of the organism and the shared interest of the individual organism is for the benefit of the group or the species?

    Then why do you not self-destruct upon infection by a virus to prevent it from spreading, like many somatic cells do?

  2. Alan Fox:
    CharlieM: And as your link makes clear cells live and die just as organisms live and die.

    Alan Fox: The connection is that anything to be alive must constantly maintain itself out of equilibrium with its environment. Death is equilibrium.

    And what about our gut flora and fauna? Their environment is within a living being.

    Living systems maintain a dynamic equilibrium by the balancing of what is taken in by what is excreted. Consistency of form is achieved by the turnover of material substances.

    Talking about the balance of nature, I remember many years ago I was in an aircraft hangar and the following happened.

    I heard a crash and looking for the cause I saw masses of maggots scattered around me and the remains of a pigeon very close to where I stood. The dead pigeon must have lain balanced on the rafters high above. As the maggots moved through it eating the flesh the c of g shifted causing it to fall. A couple of more steps and I could have been wearing it for a hat.

    And how’s this for the balance of nature? 🙂

  3. Corneel:
    CharlieM: I know my use of analogies pleases you so here is one for you.

    Corneel: Be still, my heart.

    Not to still I hope. 🙂 I nice steady rhythmic, dynamically balanced motion will do.

    CharlieM: The natural selection seen in the Luria-Delbrück experiment is like a simple aircraft autopilot. It does not determine the overall path but it does allow the current path to be maintained by compensating for any deviations from it.

    Natural selection is to living systems what automatic heading correction is to aircraft.

    Corneel: Minor quibble: There is no natural selection in the Luria-Delbrück experiment. That was sort of the point; the resistance mutations arose in the absence of a selective agent. Careful experiments like this contradict your claim that biologists merely assume mutations are undirected random events just because it fits their preferred narrative.

    Yes but the experiment was carried out to demonstrate that the variety that natural selection acted upon was caused by random mutations which had nothing to do with the virus. And this was no doubt true in this limited experiment done in artificial conditions.

    But the reality of the real world is not so limited. In the real world where there is less isolation, changes within genomes are not all as random as in this experiment.

    CharlieM: Is the system faulty because it has a built in tolerance of changes, regardless of the source of these changes? This integral flexibility prevents stagnation under changing external conditions. That is the wisdom of living systems which allows them to progress into the future.

    Corneel: Since the majority of non-neutral mutations are deleterious it is more easy to see “errors” then to see “wisdom”.

    Deleterious to what? It’s all relative. Mutations that “cause” melanism are deleterious, except when they’re not!

    Regarding top predators, some of them fail in the majority of instances of catching prey. Should we then regard hunting as deleterious to the predator?

  4. Corneel:
    CharlieM: The peppered moth might have had darkened forms in ancient times due to other DNA variables.

    Corneel: Sure, melanistic morphs are most likely produced all the time, just like the resistant bacteria in the Luria-Delbrück experiment. They just tend to remain at low frequency because they are conspicuous to predators. This is what temporarily changed in 19th century industrial Britain.

    And that is the wisdom of intra-species variety. It allow for changing conditions.

  5. Corneel:
    CharlieM: I’m not an educator. Although I do try to educate myself and to question everything.

    Corneel: Good. Start by questioning whether “mutation” is really a dirty word.

    It is a perfectly sensible word when used in a carefully considered manner. But it has acquired a lot of baggage.

    CharlieM: What we might think of as errors from one perspective might be seen as beneficial from a higher perspective. Talking of cells having favourites is to succumb to the all too human error of anthropomorphizing

    Corneel: Whereas glorifying the “wisdom of living systems” is perfectly neutral, I suppose. Very well, so let me rephrase: What type of mutations are preferentially generated and/or retained by the cell and why?

    None are preferentially generated if we restrict “mutations” to be random changes to the sequence. But many changes to genome sequences are carried out by purposeful processes. I would not call these mutations.

  6. Corneel:
    CharlieM: Say I go out hunting and shoot a deer. As I drive back home I hit a deer and kill it. In both cases I am responsible for the death of a deer. Is the level of responsibility the same in both cases?

    Corneel: Say I spent a few hours enjoying a beer in the sun. In one universe this increases the risk that I get DNA mutations that cause skin cancer. In another the mutations are a mere “factor in the development of the disease” and it is the “excessive exposure to the sun” that causes skin cancer. Is the level of control I have over my fate (and the level of responsibility for developing cancer) the same in both cases? If it is, then is it worth the bother of discussing semantics?

    “Excessive exposure to the sun” will not be a sole cause of skin cancer. Reality in living systems is never that simple.

  7. CharlieM: And what about our gut flora and fauna? Their environment is within a living being.

    Bacteria have a cell wall and maintain themselves out of equilibrium with their niche, the human gut, by aerobic and anaerobic chemical reactions that provide the energy.

    Living systems maintain a dynamic equilibrium by the balancing of what is taken in by what is excreted.

    No, let me repeat, all living organisms maintain themselves out of thermodynamic equilibrium with their niche environment. When they stop, they die.

  8. CharlieM: I heard a crash and looking for the cause I saw masses of maggots scattered around me and the remains of a pigeon very close to where I stood. The dead pigeon must have lain balanced on the rafters high above. As the maggots moved through it eating the flesh the c of g shifted causing it to fall. A couple of more steps and I could have been wearing it for a hat.

    Lucky escape. And a good example of how death is a return to equilibrium.

  9. CharlieM: But the reality of the real world is not so limited. In the real world where there is less isolation, changes within genomes are not all as random as in this experiment.

    In what way would the limitations of the experimental environment have caused mutations to behave differently from those outside of the experimental setting? I don’t see any reason to suppose they were.

    CharlieM: Deleterious to what? It’s all relative. Mutations that “cause” melanism are deleterious, except when they’re not!

    No, it’s not “all relative”. Mutations that cause Duchenne muscle dystrophy or cystic fibrosis are never beneficial. Neither are unconditional lethals. Why did you make such a nonsensical claim?

  10. CharlieM: None are preferentially generated if we restrict “mutations” to be random changes to the sequence. But many changes to genome sequences are carried out by purposeful processes. I would not call these mutations.

    You are REALLY trying my patience. What type of changes to the DNA sequence are preferentially generated and/or retained by the cell and why?

    It’s been said before and I’ll say it again: Your answers are often not actually wrong, but they are unresponsive and deliberately obscure. Most of the answers above fit the bill, I am sorry to say. Why do you seek to muddy the waters? What are we going to learn from “but the real world is different”, “It’s all relative” and “reality is never that simple”? Nothing!

  11. Corneel: In what way would the limitations of the experimental environment have caused mutations to behave differently from those outside of the experimental setting? I don’t see any reason to suppose they were.

    Ah yes. If the experiment doesn’t support the hypothesis, there’s something wrong with the experiment. In much the same way, if data falls just outside the prespecified criteria, you just tweak ’em post hoc. It’s all perfectly respectable…

  12. Corneel:
    CharlieM: Because the system operates for the benefit of the organism, not the cell.

    Corneel: As said before, it is the cell itself that executes the apoptotic program.

    And what triggers this response?

    Corneel: Did the cell decide to be unselfish and sacrifice its life? Perhaps unlike you it is truly free?

    I don’t believe cells have a sense of self.

    Corneel: Or perhaps the survival of the organism is in the interest of the cell and it is being selfish after all?

    How can self-annihilation be a selfish act? This makes no sense.

    Corneel: OR … perhaps you are anthropomorphising cells and projecting your own desire to survive on them?

    What do you think?

    Cells show no signs of being capable of having desires.

    CharlieM: If organisms were not destined to have finite lifespans and to die then there could be no evolution.

    Corneel: Not true. Do you know why?

    Why?

    CharlieM: Apoptosis means that the cell can no longer pass on its genome.

    Corneel: Somatic cells don’t do that anyway.

    Somatic cell division is the process whereby genomes are passed on within the organism.

    Corneel: So if apoptosis is deleterious for the cell, then what exactly is being sacrificed?

    The continued existence of that individual cell.

    CharlieM: The shared interest of cells is for the benefit of the organism and the shared interest of the individual organism is for the benefit of the group or the species?

    Then why do you not self-destruct upon infection by a virus to prevent it from spreading, like many somatic cells do?

    By continuing to exist while harbouring viruses, I like to think I’m doing my bit for the continued future of life. 🙂 As some have pointed out

    “If all viruses suddenly disappeared, the world would be a wonderful place for about a day and a half, and then we’d all die – that’s the bottom line,” says Tony Goldberg, an epidemiologist at the University of Wisconsin-Madison. “All the essential things they do in the world far outweigh the bad things.”…

    The vast majority of viruses are not pathogenic to humans, and many play integral roles in propping up ecosystems. Others maintain the health of individual organisms – everything from fungi and plants to insects and humans. “We live in a balance, in a perfect equilibrium”, and viruses are a part of that, says Susana Lopez Charretón, a virologist at the National Autonomous University of Mexico. “I think we’d be done without viruses.”

  13. CharlieM: And what triggers this response?

    Developmental cues, DNA damage, viral infection among other things.

    CharlieM: How can self-annihilation be a selfish act? This makes no sense.

    In evolutionary terms, it does.

    CharlieM: CharlieM: If organisms were not destined to have finite lifespans and to die then there could be no evolution.

    Me: Not true. Do you know why?

    Charlie: Why?

    Because new organisms can still change the genetic composition of a population.

    CharlieM: Somatic cell division is the process whereby genomes are passed on within the organism.

    Sure, and cul de sacs make for a nice long walk.

    CharlieM: Corneel: So if apoptosis is deleterious for the cell, then what exactly is being sacrificed?

    Charlie: The continued existence of that individual cell.

    What does continued existence mean to something that does not possess a sense of self?

    CharlieM: By continuing to exist while harbouring viruses, I like to think I’m doing my bit for the continued future of life.

    You believe you are doing us a favour by propagating pathogens? Mmmm, don’t bother.

  14. Alan Fox:
    CharlieM: And what about our gut flora and fauna? Their environment is within a living being.

    Alan Fox: Bacteria have a cell wall and maintain themselves out of equilibrium with their niche, the human gut, by aerobic and anaerobic chemical reactions that provide the energy.

    We have differing ideas of what it means to be in equilibrium. Considering the gut environment minus its flora and fauna, what sort of internal equilibrium is it in of itself? It is an ever changing dynamic system.

    CharlieM: Living systems maintain a dynamic equilibrium by the balancing of what is taken in by what is excreted.

    Alan Fox: No, let me repeat, all living organisms maintain themselves out of thermodynamic equilibrium with their niche environment. When they stop, they die.

    What systems or processes would you consider to be in thermodynamic equilibrium?

    Consider the earth’s atmosphere, would you say that it is or has ever been in thermodynamic equilibrium? Temperatures are not equal throughout the planet but the range has been consistent enough to have supported life for billions of years. If through our ignorance we cause a runaway temperature rise which is out of control, then the balance is lost and life on earth is doomed. Everything is relative.

    You are wrong to conclude that living systems cannot survive periods of being at the same temperature as their surroundings. (If that is what you mean by thermodynamic equilibrium.) Some systems can remain dormant but still alive for long periods of time.

  15. Alan Fox:
    CharlieM: I heard a crash and looking for the cause I saw masses of maggots scattered around me and the remains of a pigeon very close to where I stood. The dead pigeon must have lain balanced on the rafters high above. As the maggots moved through it eating the flesh the c of g shifted causing it to fall. A couple of more steps and I could have been wearing it for a hat.

    Alan Fox: Lucky escape. And a good example of how death is a return to equilibrium.

    Return of what to equilibrium? The material body of that pigeon has been dissipated and much of it is probably active within the bodies of various other organisms or is moving about as part of the atmosphere. Death is a loss of self-organization and a return to being wholly determined by external forces.

  16. Corneel:
    CharlieM: But the reality of the real world is not so limited. In the real world where there is less isolation, changes within genomes are not all as random as in this experiment.

    Corneel: In what way would the limitations of the experimental environment have caused mutations to behave differently from those outside of the experimental setting? I don’t see any reason to suppose they were.

    This all comes down to how mutations are defined. if they are defined as changes to the genome, then directed processes such as the changes made by the CRISPR-Cas system would be classed as mutations.

    The Luria–Delbrück experiment used e coli and I’m not sure if there is any evidence that e coli use Crispr-Cas as an immune response.

    CharlieM: Deleterious to what? It’s all relative. Mutations that “cause” melanism are deleterious, except when they’re not!

    Corneel: No, it’s not “all relative”. Mutations that cause Duchenne muscle dystrophy or cystic fibrosis are never beneficial. Neither are unconditional lethals. Why did you make such a nonsensical claim?

    We were talking about mutations in general and the majority of mutations being deleterious. What percentage of these deleterious mutations are lethal? You are making my point that it is relative to the specific mutation under discussion.

    We can all expect the act of living to be lethal at some point.

  17. Corneel:
    CharlieM: None are preferentially generated if we restrict “mutations” to be random changes to the sequence. But many changes to genome sequences are carried out by purposeful processes. I would not call these mutations.

    Corneel: You are REALLY trying my patience.

    Please don’t let your emotions get the better of you. If our exchanges upset you then you can always ignore my comments. Although I would prefer you to carry on with your criticisms.

    Corneel:What type of changes to the DNA sequence are preferentially generated and/or retained by the cell and why?

    It’s been said before and I’ll say it again: Your answers are often not actually wrong, but they are unresponsive and deliberately obscure. Most of the answers above fit the bill, I am sorry to say. Why do you seek to muddy the waters? What are we going to learn from “but the real world is different”, “It’s all relative” and “reality is never that simple”? Nothing!

    I am not trying to muddy the waters. Admitting that life is complex and there are very rarely any black and white answers should not stop us from exploring its intricate processes.

    My involvement here has recently taught me a lot about industrial melanism, cell motility and immune responses just to mention a few topics. One small example is that I have learned there is no single gene for melanism in peppered moths. It’s not that black and white 🙂

  18. CharlieM: The Luria–Delbrück experiment used e coli and I’m not sure if there is any evidence that e coli use Crispr-Cas as an immune response.

    So Escherichia coli is incapable of generating directed mutations DNA changes? Any other organisms we can add to this impromptu list? Fruitflies? Mice? How about humans?

    CharlieM: We were talking about mutations in general and the majority of mutations being deleterious. What percentage of these deleterious mutations are lethal? You are making my point that it is relative to the specific mutation under discussion.

    Not seeing how your “point” is relevant. Unless you are claiming that most mutations DNA changes are beneficial in any particular environment, my point still stands: the extreme rarity of beneficial mutations DNA changes strongly suggests that there is no “wisdom” behind their generation.

    CharlieM: We can all expect the act of living to be lethal at some point.

    You are mistaken; It’s the act of dying that is lethal.

    CharlieM: I am not trying to muddy the waters. Admitting that life is complex and there are very rarely any black and white answers should not stop us from exploring its intricate processes.

    Yet you have declined answering my question again:
    What type of changes to the DNA sequence are preferentially generated and/or retained by the cell and why?

    CharlieM: One small example is that I have learned there is no single gene for melanism in peppered moths. It’s not that black and white

    That’s a pretty dark sense of humour you’ve got there.

  19. Allan Miller:
    Corneel: In what way would the limitations of the experimental environment have caused mutations to behave differently from those outside of the experimental setting? I don’t see any reason to suppose they were.

    Allan Miller: Ah yes. If the experiment doesn’t support the hypothesis, there’s something wrong with the experiment

    Recognizing the limitation of experiments is not the same thing as claiming they are wrong. I do not argue against the fact that genomes experience mutations which cannot be predicted. But I also recognize that there are compounding factors affecting mutations. Stress-induced mutagenesis and population density-associated mutation-rate plasticity are among the factors which must be taken into account when we try to understand how mutation rates vary and how they affect an organism.

  20. CharlieM: Recognizing the limitation of experiments is not the same thing as claiming they are wrong.

    Sure, I was just having a bit of fun with your tendency to confirmation bias.

    I do not argue against the fact that genomes experience mutations which cannot be predicted.But I also recognize that there are compounding factors affecting mutations. Stress-induced mutagenesis and population density-associated mutation-rate plasticity are among the factors which must be taken into account when we try to understand how mutation rates vary and how they affect an organism.

    Is stress-induced mutagenesis a positive response to the stress or a stress-related reduction in fidelity? This is an important distinction if one wishes to claim a role for it.

    I have learned that there is no single gene for industrial melanism in moths.

    Very few variations are under the control of a single gene. But also, selection acts on phenotypes. Genotypes are viewed as through a glass, darkly. There is nothing stopping multiple alternative genotypes arising with the same phenotype. Against each other, they drift (assuming no selectable pleiotropic distinction); against wild-type, they are selected.

  21. Corneel:
    CharlieM: And what triggers this response?

    Corneel: Developmental cues, DNA damage, viral infection among other things.

    Yes, the response is triggered through systemic information, not a reaction to local perturbations. A cell is not going to spill the destructive contents of its lysosomes just because of a localized DNA double strand break.

    CharlieM: How can self-annihilation be a selfish act? This makes no sense.

    In evolutionary terms, it does.

    Now you are jumping from implying the cell is acting selfishly to saying a specific arrangement of nucleotides is the selfish agent. And note, it’s not the actual physical sequence but the pattern that is somehow being selfish.

    CharlieM: If organisms were not destined to have finite lifespans and to die then there could be no evolution.

    Me (Corneel): Not true. Do you know why?

    Charlie: Why?

    Corneel: Because new organisms can still change the genetic composition of a population.

    Do you understand what would happen if new organisms kept appearing but none died? The living world would become so overpopulated that it would collapse and annihilate itself.

    CharlieM: Somatic cell division is the process whereby genomes are passed on within the organism.

    Corneel: Sure, and cul de sacs make for a nice long walk.

    The point is that even if somatic cells do not outlive the organism to which they belong, they are still capable of passing on their genomes until that time. Dinosaurs such as Tyrannosaurus rex also passed on their genomes as they approached the end of their cul-de-sac. The whole reflected in the parts.

    Corneel: So if apoptosis is deleterious for the cell, then what exactly is being sacrificed?

    Charlie: The continued existence of that individual cell.

    Corneel: What does continued existence mean to something that does not possess a sense of self?

    It means nothing to it, but it does mean something to those of us who can observe it.

    St Paul’s cathedral continued to exist after the bombing of London during WW2. It this fact dependent on this building having a sense of self?

    CharlieM: By continuing to exist while harbouring viruses, I like to think I’m doing my bit for the continued future of life.

    Corneel: You believe you are doing us a favour by propagating pathogens? Mmmm, don’t bother.

    Try removing all these pathogens from your gut microbiota and see how healthy you remain. You think because a select few viruses are pathogenic to humans they must all be tarred with the same brush?

  22. CharlieM: Yes, the response is triggered through systemic information, not a reaction to local perturbations. A cell is not going to spill the destructive contents of its lysosomes just because of a localized DNA double strand break.

    Perhaps you missed the “DNA damage” part. Anyway, without the cooperation of the cell, no apoptosis occurs. Cancer cells often have mutations DNA sequence changes that enable them to resist initiation of apoptotic pathways.

    CharlieM: Now you are jumping from implying the cell is acting selfishly to saying a specific arrangement of nucleotides is the selfish agent. And note, it’s not the actual physical sequence but the pattern that is somehow being selfish.

    There is no such thing as naked DNA, or so I’ve been told. It is the whole of the cell that is expressing the selfish DNA bits, no?

    CharlieM: Do you understand what would happen if new organisms kept appearing but none died? The living world would become so overpopulated that it would collapse and annihilate itself.

    It appears you forgot that you specified a scenario where organisms couldn’t die.

    CharlieM: The point is that even if somatic cells do not outlive the organism to which they belong, they are still capable of passing on their genomes until that time.

    Could you tell me what the difference is between germline and soma and why this distinction is relevant to evolution?

    CharlieM: St Paul’s cathedral continued to exist after the bombing of London during WW2. It this fact dependent on this building having a sense of self?

    Your metaphors are becoming extremely hard to follow. Do British cathedrals self-destruct in order to save their cities?

    CharlieM: You think because a select few viruses are pathogenic to humans they must all be tarred with the same brush?

    Not me. I never meant anything other than human pathogens.

  23. Corneel:
    CharlieM: The Luria–Delbrück experiment used e coli and I’m not sure if there is any evidence that e coli use Crispr-Cas as an immune response.

    Corneel: So Escherichia coli is incapable of generating directed mutations DNA changes? Any other organisms we can add to this impromptu list? Fruitflies? Mice? How about humans?

    I don’t have enough knowledge to know what E coli is capable or incapable of. I did find this so it would seem there is evidence of its use in that way.

    Although two different CRISPR can be found in E. coli, only one of the analysed strains harbours both sets of associated CAS genes, suggesting that, in general, one active system suffices to meet the CRISPR-based immunity demands of the species.

    We have learned a great deal about bacteria but we’d be foolish to claim we know everything about the capabilities of E coli.

    CharlieM: We were talking about mutations in general and the majority of mutations being deleterious. What percentage of these deleterious mutations are lethal? You are making my point that it is relative to the specific mutation under discussion.

    Corneel: Not seeing how your “point” is relevant. Unless you are claiming that most mutations DNA changes are beneficial in any particular environment, my point still stands: the extreme rarity of beneficial mutations DNA changes strongly suggests that there is no “wisdom” behind their generation.

    If a virus can change the DNA of its host in order to ensure the continued existence of its kind, would that not be a wise move on the part of the virus? The fact that viruses mutate indicates that it is not the DNA sequence but the virus species or kind that is being preserved. Their DNA varies which enables them to survive as a group.

    CharlieM: We can all expect the act of living to be lethal at some point.

    Corneel: You are mistaken; It’s the act of dying that is lethal.

    Heraclitus: “Immortals are mortal, mortals immortals: living their death, dying their life.”

    CharlieM: I am not trying to muddy the waters. Admitting that life is complex and there are very rarely any black and white answers should not stop us from exploring its intricate processes.

    Corneel:Yet you have declined answering my question again:
    What type of changes to the DNA sequence are preferentially generated and/or retained by the cell and why?

    I have answered: None are preferentially generated if we restrict “mutations” to be random changes to the sequence.

    But changes such as crossing over in meiosis or sequence insertions in bacterial CRISPR-Cas systems are regulated processes which serve a purpose.

    CharlieM: One small example is that I have learned there is no single gene for melanism in peppered moths. It’s not that black and white

    Corneel: That’s a pretty dark sense of humour you’ve got there

    And here I was trying to lighten the mood. 🙂

  24. CharlieM: We have learned a great deal about bacteria but we’d be foolish to claim we know everything about the capabilities of E coli.

    What would really be foolish IMHO is to have learned so much and then act like we cannot explain something simple …

    The Luria-Delbrück experiment supports the notion that most mutations DNA sequence changes are random with regard to their fitness effects.

    CharlieM: If a virus can change the DNA of its host in order to ensure the continued existence of its kind, would that not be a wise move on the part of the virus? The fact that viruses mutate indicates that it is not the DNA sequence but the virus species or kind that is being preserved. Their DNA varies which enables them to survive as a group.

    The “virus kind”? Honestly, Charlie. You are the all-time world champion of “they all look the same to me”.

    But very well, let’s play another round of the naming game. So … are all viruses one kind or are there multiple kinds? If the latter, name some. Since you mentioned “change the DNA of its host”: Are retroviruses like HIV playing on the same team as, say, coronaviruses like SARS-CoV-2?

    CharlieM: Me:Yet you have declined answering my question again:
    What type of changes to the DNA sequence are preferentially generated and/or retained by the cell and why?

    Charlie: I have answered: None are preferentially generated if we restrict “mutations” to be random changes to the sequence.

    Which is tautologically true. But I have never restricted the definition of mutations to be random sequence changes.

    CharlieM: But changes such as crossing over in meiosis or sequence insertions in bacterial CRISPR-Cas systems are regulated processes which serve a purpose.

    Recombination is not mutation: it cannot generate new variation in an isogenic population. The purpose of CRISPR-Cas is performing an immune function. Can we agree that there are no known processes that have the purpose of bringing about self consciousness and individuality?

  25. Allan Miller:
    CharlieM: I do not argue against the fact that genomes experience mutations which cannot be predicted. But I also recognize that there are compounding factors affecting mutations. Stress-induced mutagenesis and population density-associated mutation-rate plasticity are among the factors which must be taken into account when we try to understand how mutation rates vary and how they affect an organism.

    Allan Miller: Is stress-induced mutagenesis a positive response to the stress or a stress-related reduction in fidelity? This is an important distinction if one wishes to claim a role for it.

    Why can’t a reduction in fidelity also be a positive response for a colony? Life depends on balance. Stress induces an imbalance. A loss of fidelity is also a gain in variability. This could be fatal for a high percentage of the individuals in a colony but it could also produce individuals which can tolerate the external disruption. Hence the colony can regrow and regain a balanced condition.

    Alan Fox brought up the subject of equilibrium. Conditions within living systems must maintain a certain independence from their environment. We have selective barriers at all levels from our skin down to the barrel-like structures of some chaperone proteins. At all these levels the systems must function in environments in which there are orderly, upbuilding forces and substances, also disruptive, destructive forces and substances. But just because some things are disruptive and destructive does not mean that cannot be beneficial.

    Some living systems can tolerate high levels of environmental changes while others only narrow limits. Most Antarctic fish spend their lives within a very narrow environmental temperature range and will die of hyperthermia at temperatures above about 4 degrees Celsius.

    CharlieM: I have learned that there is no single gene for industrial melanism in moths.

    Allan Miller: Very few variations are under the control of a single gene. But also, selection acts on phenotypes. Genotypes are viewed as through a glass, darkly. There is nothing stopping multiple alternative genotypes arising with the same phenotype. Against each other, they drift (assuming no selectable pleiotropic distinction); against wild-type, they are selected.

    In peppered moths the ability to produce dark scales is very ancient. The typical form would not be peppered if areas of scales were not darkened. Even in the modern moths alteration to the cortex gene is only associated with a percentage of melanic forms. The estimated percentage is high but it is not total.

  26. CharlieM: Why can’t a reduction in fidelity also be a positive response for a colony?

    It could. But if there is an active mechanism, I would expect it to be under some kind of specific control – some mechanistic relationship in which the stressor causes a consistent constitutional change which is not a byproduct, rather than the organism simply diverting resources and taking the mutagenic hit as collateral damage; an unavoidable secondary consequence. If a mutagenic chemical agent is introduced into a population, for example, is the population positively responding to it, or is its normal operation being interfered with? Now replace ‘mutagenic chemical agent’ with ‘stress’.

    Life depends on balance. Stress induces an imbalance. A loss of fidelity is also a gain in variability. This could be fatal for a high percentage of the individuals in a colony but it could also produce individuals which can tolerate the external disruption. Hence the colony can regrow and regain a balanced condition.

    Mutations can be beneficial, you say? Gosh.

    Alan Fox brought up the subject of equilibrium. Conditions within living systems must maintain a certain independence from their environment. We have selective barriers at all levels from our skin down to the barrel-like structures of some chaperone proteins.

    I hope you’re not equivocating on the term ‘selective’. It has a very specific meaning in evolution, and it’s not that.

    At all these levels the systems must function in environments in which there are orderly, upbuilding forces and substances, also disruptive, destructive forces and substances. But just because some things are disruptive and destructive does not mean that cannot be beneficial.

    You are describing something close to the ‘standard view’ of mutations.

    Some living systems can tolerate high levels of environmental changes while others only narrow limits. Most Antarctic fish spend their lives within a very narrow environmental temperature range and will die of hyperthermia at temperatures above about 4 degrees Celsius.

    You seem to be just waffling, here. It’s certainly true that organisms vary in the range of their environmental tolerances.

    In peppered moths the ability to produce dark scales is very ancient. The typical form would not be peppered if areas of scales were not darkened. Even in the modern moths alteration to the cortex gene is only associated with a percentage of melanic forms. The estimated percentage is high but it is not total.

    OK, and…?

  27. Allan Miller: I hope you’re not equivocating on the term ‘selective’. It has a very specific meaning in evolution, and it’s not that.

    I would love to hear this one. Let me take a guess what it means specifically ~ not dead?

  28. phoodoo: I would love to hear this one.Let me take a guess what it means specifically ~ not dead?

    No, phoodoo. That you have been involved in so many discussions on the concept of selection, but come up with something so dopey, does not reflect well on you – even though, in your head, you’re killing it. That just makes it worse.

  29. Allan Miller,

    Oh, the specific meaning is a secret? How does one join the skeptical bones club? Besides giving up on thought are there any fees?

  30. Corneel:
    Allan Miller,

    Happy Groundhog day!

    If there was a specific meaning surely it would be easy to type? But just before he can hit the keys the alarm clock rings again…

  31. Corneel:
    CharlieM: Yes, the response is triggered through systemic information, not a reaction to local perturbations. A cell is not going to spill the destructive contents of its lysosomes just because of a localized DNA double strand break.

    Corneel: Perhaps you missed the “DNA damage” part. Anyway, without the cooperation of the cell, no apoptosis occurs. Cancer cells often have mutations DNA sequence changes that enable them to resist initiation of apoptotic pathways.

    No I didn’t miss the “DNA damage” part. Cells have a measured response to DNA damage and apoptosis occurs if the damage becomes unrepairable. Apoptosis is a controlled demolition process and the destructive forces are contained so as not to cause more extensive damage.

    CharlieM: Now you are jumping from implying the cell is acting selfishly to saying a specific arrangement of nucleotides is the selfish agent. And note, it’s not the actual physical sequence but the pattern that is somehow being selfish.

    Corneel: There is no such thing as naked DNA, or so I’ve been told. It is the whole of the cell that is expressing the selfish DNA bits, no?

    I do not believe that selfishness applies to nucleotide patterns.

    CharlieM: Do you understand what would happen if new organisms kept appearing but none died? The living world would become so overpopulated that it would collapse and annihilate itself.

    Corneel: It appears you forgot that you specified a scenario where organisms couldn’t die.

    Only in order to demonstrate the absurdity of the consequences.

    CharlieM: The point is that even if somatic cells do not outlive the organism to which they belong, they are still capable of passing on their genomes until that time.

    Corneel: Could you tell me what the difference is between germline and soma and why this distinction is relevant to evolution?

    In the case of prokaryotes there is little distinction between germline and somatic cells. For multicellular creatures like us germline cells have the capability to be heritable and so instigating lines of descent of individual organisms (evolution). Somatic cells have the capacity to create lines of descent of cells within a developing individual organism (development).

    CharlieM: St Paul’s cathedral continued to exist after the bombing of London during WW2. It this fact dependent on this building having a sense of self?

    Corneel:Your metaphors are becoming extremely hard to follow. Do British cathedrals self-destruct in order to save their cities?

    That example was in response to your implication that continued existence and a sense of self were mutually dependent on each other. Why else would you ask. What does continued existence mean to something that does not possess a sense of self?

    CharlieM: You think because a select few viruses are pathogenic to humans they must all be tarred with the same brush?

    Cornell: Not me. I never meant anything other than human pathogens.

    Then why didn’t you say it’s only a select set of viruses that you don’t want me to bother harbouring?

  32. phoodoo:
    Allan Miller,

    Oh,the specific meaning is a secret?How does one join the skeptical bones club?Besides giving up on thought are there any fees?

    Of course it’s not a secret. It has been discussed – with you, inter alia – repeatedly in these pages, and is also available on one of those new-fangled search engines, or any textbook, for anyone who isn’t a lazy fucker. But no … you want me to dance.

  33. CharlieM: Me: There is no such thing as naked DNA, or so I’ve been told. It is the whole of the cell that is expressing the selfish DNA bits, no?

    Charlie: I do not believe that selfishness applies to nucleotide patterns.

    I didn’t say that selfishness applies to nucleotide patterns (though it does, metaphorically speaking). I said that if you were being consistent, you’d have accepted that it is the whole of the cell that is displaying selfish behaviour, not just the DNA.

    CharlieM: Me: It appears you forgot that you specified a scenario where organisms couldn’t die.

    Charlie: Only in order to demonstrate the absurdity of the consequences.

    No, you introduced this scenario to argue that the death of organisms was a requirement for evolution to occur, which is false. You also suggested that the death of organisms is in some way analogous to apoptosis, which is also false.

    CharlieM: For multicellular creatures like us germline cells have the capability to be heritable and so instigating lines of descent of individual organisms (evolution). Somatic cells have the capacity to create lines of descent of cells within a developing individual organism (development).

    Close enough. So consider this: If somatic cells lost their ability to execute apoptosis and if this change would be mitotically heritable, what would be the chance this change would end up in the offspring? And what would happen to the chances the poor organism these cells were part of would leave any offspring?

    CharlieM: That example was in response to your implication that continued existence and a sense of self were mutually dependent on each other. Why else would you ask. What does continued existence mean to something that does not possess a sense of self?

    And you replied that meaning came from the observer, not from buildings or cells. So when I asked: “So if apoptosis is deleterious for the cell, then what exactly is being sacrificed?”, the answer should have been: “Absolutely nothing is sacrificed from the perspective of the cell, but Charlie felt bad for it anyway.”

    Guess what? Corneel doesn’t pity this cell at all, ’cause apoptosis is not deleterious. The word “deleterious” has a specific meaning in genetics: it means lowering fitness or predisposing to disease. Apoptosis doesn’t do either of those things. Hence, apoptosis is not deleterious to a cell.

    CharlieM: Then why didn’t you say it’s only a select set of viruses that you don’t want me to bother harbouring?

    I am pretty sure I mentioned infection. The viruses that infect you are definitely not going to give you good times. It is you that views all viruses as a big happy family helping each other for the benefit of all viruskind.

  34. phoodoo: How does one join the skeptical bones club? Besides giving up on thought are there any fees?

    You also must have empathy for your fellow humans.

    phoodoo: All Uighurs aren’t in jail for crying out loud. The people who are jailed are suspected of conspiring to do terrorist harm. They don’t jail people because they are Uighurs or Muslims.

    The people who are jailed are suspected of conspiring to do terrorist harm. So no, you can’t join.

    Millions of people suspected of conspiring to do terrorist harm should have turned into millions of trials where that suspicion can be demonstrated to be based on fact, or not. Has that happened yet, phoodoo?

  35. Allan Miller,

    Do you learn your bluffing techniques from Alan?

    Oh how you hands must cramp at the thought of backing up your vacuous claims with the arduous act of typing.

  36. phoodoo:
    Allan Miller,

    Do you learn your bluffing techniques from Alan?

    Oh how you hands must cramp at the thought of backing up your vacuous claims with the arduous act of typing.

    Thing is, I know this has been discussed with you on a good half dozen occasions. And you know it too. Now, you act as if it’s the first time you’ve heard of it.

    We’ve even played this stupid game before where you try and get me to type it out and I decline, because I know you’re just trolling, and getting me to do something pointless: say what you already know, or could look up in a jiffy. As Corneel says, it’s Groundhog Day.

  37. Allan Miller,

    The specific meaning of the word selection, which is unique to evolution, and somehow different than how Charlie used the word, or anyone else uses the word?

    Bulllshit.

    It has a vague, entirely not-specific meaning when used by the athesist-skeptic crowd. There is nothing specific whatsoever about it.

  38. phoodoo:
    Allan Miller,

    The specific meaning of the word selection, which is unique to evolution, and somehow different than how Charlie used the word, or anyone else uses the word?

    Bulllshit.

    It has a vague, entirely not-specific meaning when used by the athesist-skeptic crowd.There is nothing specific whatsoever about it.

    Please yourself, phoodoo. Phoodoo no remember. Phoodoo had sleeps. Poor fella.

  39. Corneel:
    CharlieM: We have learned a great deal about bacteria but we’d be foolish to claim we know everything about the capabilities of E coli.

    Corneel: What would really be foolish IMHO is to have learned so much and then act like we cannot explain something simple …

    The Luria-Delbrück experiment supports the notion that most mutations DNA sequence changes are random with regard to their fitness effects.

    Most mutations may be random with respect to fitness. But living systems can still use these changes in a beneficial way. The fact that bacteria living in colonies are not exact clones of each other allows the colony to survive external threats because there is always a chance that some of the individuals will have a form that can deal with the threat.

    Bacteria are wise enough not to put all their eggs in one basket. The reason bacterial species are so successful is not because they all share a common genome, it is because they have a range of genomes with slight variation between them.

    CharlieM: If a virus can change the DNA of its host in order to ensure the continued existence of its kind, would that not be a wise move on the part of the virus? The fact that viruses mutate indicates that it is not the DNA sequence but the virus species or kind that is being preserved. Their DNA varies which enables them to survive as a group.

    Corneel: The “virus kind”? Honestly, Charlie. You are the all-time world champion of “they all look the same to me”.

    And just as I mentioned above, bacteria are not all clones, it is the same with viruses. We can see that there are different strains of coronavirus but they are all recognised as the same virus. Organisms can be individually different but of a common species or kind. Surely you can see this?

    But very well, let’s play another round of the naming game. So … are all viruses one kind or are there multiple kinds? If the latter, name some. Since you mentioned “change the DNA of its host”: Are retroviruses like HIV playing on the same team as, say, coronaviruses like SARS-CoV-2?

    I don’t need to name any because you have done it for me above.

    Me (Corneel):Yet you have declined answering my question again:
    What type of changes to the DNA sequence are preferentially generated and/or retained by the cell and why?

    Charlie: I have answered: None are preferentially generated if we restrict “mutations” to be random changes to the sequence.

    Which is tautologically true. But I have never restricted the definition of mutations to be random sequence changes.

    Then some changes are preferentially generated. For example bacteria and archaea may use CRISPR-Cas systems to make changes within their own genomes.

    CharlieM: But changes such as crossing over in meiosis or sequence insertions in bacterial CRISPR-Cas systems are regulated processes which serve a purpose.

    Corneel: Recombination is not mutation: it cannot generate new variation in an isogenic population. The purpose of CRISPR-Cas is performing an immune function. Can we agree that there are no known processes that have the purpose of bringing about self consciousness and individuality?

    We can leave out speculations about purpose, but we do know that the evolutionary process has brought about self consciousness and individuality.

  40. Allan Miller,

    Even if you believed you had actually said what the specific meaning was, somewhere, sometime, some mysterious post that exists in some ether, what the hell difference would that make if you are going to throw out some claim (that evolution has a VERY SPECIFIC meaning for “selection”, that shouldn’t be confused with Charlie’s use of the word and then refuse to say what that specfic meaning is, AS IF NO ONE ELSE ever would read your post, and wonder what you are getting at. You have supposedly told me before (you haven’t) so its not necessary for you to say what you mean to anyone else who reads here.

    If you thought it was important enough for you to correct Charlie, what kind of horseshit rationale is there that you can say its not necessary for you to say what the hell that specific thing is.

    “Hey Charlie, I just hope you are not using this word wrongly, when it is supposed to mean… (sssssshh, its a secret) something else that I can’t say because everyone already knows the secret word meaning. Except Charlie according to you. And Charlie also doesn’t belong to the bones scociety so you can’t say it to him either.

    What a joke.

  41. phoodoo,

    If Charlie has a problem with what I said to Charlie, Charlie can ask me to clarify. Who asked you to stick your fat schnozz in? Rules insist that I act as if you post in good faith. And yet you know this has been discussed extensively with you on many occasions. Anyone who’s observed this site sufficiently over the years knows it too. And you know you could just google ‘natural selection definition” and come up with a consistent set of expressions of the same broad concept, not a bunch of vague obscurities. Try it. But this is the patented Phoodoo Move: get someone to define selection, or fitness, for the umpteenth time, so phoodoo can then riff hilariously upon a deliberate misunderstanding of it. Such as ‘selection means being alive, right?’. Right.

    It has changed little since 1859. So as far as I can tell, you are either trolling, or you’re dumb.

  42. Allan Miller,

    Ok, now you are upping the bullshit Allan. Here is what Charlie wrote:

    We have selective barriers at all levels from our skin down to the barrel-like structures of some chaperone proteins.

    Your response to THAT was :

    I hope you’re not equivocating on the term ‘selective’. It has a very specific meaning in evolution, and it’s not that.

    Where did you read “natural selection” Allan? You are not dumb right? You are not trolling, right? Is this a new form of argumentation Allan? Where you just get to make up things they said, and then claim they are wrong for saying things they never said?

    You point with Charlie is SO off base (note I didn’t say military base, or basement, or baseball…) that its absurd in its wrongness. So being as how this is a forum, and not some kind of email link between you and Charlie, don’t mind if I stick my fat shnozze in and say, (because other people presumeably do read this web page and all) What the fuck are you talking about Allan?

    Furthermore, the next time you write a sentence like

    And what would happen to the chances the poor organism these cells were part of would leave any offspring?

    just for fun I am going to object with something super stupid, like-I hope you are not equivocating on the word “poor” or the word “chance”, or the word offspring, because Offspring is a rock band, and poorboy sandwiches have a very specific meaning, and chance has a very specific meaning when talking about biology, only no one knows what “chance” means in biology because the idea that there are specific meanings in biology that make sense in terms of evolution is the greatest lie ever told.

    Note Allan- This post is intended to be read by ANYONE ELSE WHO READS THIS FORUM AND WISHES TO SEE DISUSSIONS ABOUT SCIENCE DEBATES, or at least wishes to see an interesting counterpoint to the nitwit skeptical perspective of circular horseshit non-reasoning.

  43. phoodoo,

    Furthermore, the next time you write a sentence like

    “And what would happen to the chances the poor organism these cells were part of would leave any offspring?”

    I don’t recognise that sentence as anything I wrote. Could you point me to it?

  44. phoodoo,

    To repeat, the term ‘selective’ has a specific meaning in evolution, and it’s not the way Charlie used it. It may well have been an irrelevant aside. Still, if I feel like expressing myself in such a way, rather than the way some over-excited all-caps jockey tells me I should express myself … why, by golly, I will continue to pick my own words, and fuck ’em.

    Your concern for Charlie brings a tear to my eye. The position you wish to present to the world is that ‘selective’, having nothing to do with ‘natural selection’, has a definition which is a closely guarded secret available to no-one armed with a search engine or biology textbook, and I must, instead, type it out on your demand, should anyone dare to use it in conversation with a third party. To be honest, it’s more fun watching your self-righteous frothing. I guess that could be classed as ‘trolling’.

  45. In a parallel universe:

    Me: I hope you’re not equivocating on the term ‘selective’.
    Charlie: No, I’m not.
    Me: Ah, righto.

    😁

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