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: Producing variety of animal forms takes more than a bit of tinkering with DNA.

    See Alan’s response. To hammer this point down: most of the heritable variation in gene regulation is also encoded in the DNA. Admittedly, there are some interesting effects of chromatin remodeling and position effects, but to remove DNA from its central position in evolutionary biological thought, you need to find a source of heritable variation that is not based on the transmission of polynucleotide sequences.

    Your self imposed restriction to animal forms amused me BTW.

  2. Corneel:

    CharlieM: Functional sequences are of no use if they are not in a position where they can be acted upon to produce messenger RNA. Genes cannot be expressed if they cannot be accessed.

    Me: If genes are never expressed then they are not genes.

    Charlie: In that case the number of genes in various cell types varies and “silent genes” is a meaningless term.

    Corneel: Just because the expression of genes is regulated does not mean that regulation is ‘just as important’ as the DNA sequence. In fact, most of the heritable variation in gene regulation is encoded … wait for it … in the DNA.

    And how does DNA change from generation to generation? Lately the term “gene variants” has been used as a replacement for “gene mutations”. I think this is a better term.

    DNA variations can be both disruptive changes from external sources or orchestrated changes from within. Why is it assumed that evolution is driven by the former? Because it fits with the narrative that life is just a fortuitous accident and that evolution proceeds by more fortuitous accidents.

    It is not just strings of DNA that get passed down the generations, it is living systems. The zygotes from which we have developed were fully functional living systems just as any normal prokaryote is a fully functional living system.

  3. CharlieM: Lately the term “gene variants” has been used as a replacement for “gene mutations”. I think this is a better term.

    I prefer “alleles”.

    CharlieM: DNA variations can be both disruptive changes from external sources or orchestrated changes from within. Why is it assumed that evolution is driven by the former? Because it fits with the narrative that life is just a fortuitous accident and that evolution proceeds by more fortuitous accidents.

    That is just not true. We assume evolution is fueled by undirected random mutations because there is ample support that the vast majority of mutations arise in this way. You have spent enough time here at TSZ that you should be familiar with the Lederberg replica plating experiment and the Luria-Delbrück experiment. As has been conceded by several people here, mutations of the “orchestrated” type exist as well but they typically require dedicated systems (such as CRISPR-Cas) that clearly evolved themselves to support some specific task. That leads us to conclude that directed situation-appropiate mutations are the exception.

    BTW, you never answered my request to clarify yourself: Is it your claim that the cell is able to distinguish beneficial from deleterious mutations, even among those mutations that are not the result of a sophisticated system like CRISPR-Cas? What exactly is being “orchestrated”, as you put it?

    CharlieM: It is not just strings of DNA that get passed down the generations, it is living systems. The zygotes from which we have developed were fully functional living systems just as any normal prokaryote is a fully functional living system.

    This is of course true, but is not really relevant to the question how evolutionary change comes about. Evolution proceeds by change in the heritable characteristics of a population. This is why we focus on the compound we know to carry the heritable information i.e. DNA.

  4. Alan Fox:
    Here is a fairly recent paper on mouse embryology. The factors the researchers note as whose presence organises development are referred to as proteins. Proteins are encoded in…

    DNA.

    I enjoyed reading that paper.

    Looking at just one protein from the networks of multiple proteins involved in mouse development, we can get some idea of the coordination necessary for normal development.

    Nodal is a prominent player in development. Near the beginning they tell us:

    Around E5.0, a subset of visceral endoderm cells at the distal tip of the embryo responds to signaling by the TGFβ superfamily member Nodal by expressing a specific repertoire of genes [5.]. At the same time, genes later involved in primitive streak formation such as Nodal and Wnt3 are expressed in a ring of proximal epiblast cells abutting the extraembryonic ectoderm.

    Leaving aside how Nodal interacts with other complexes and focusing in on how the protein itself is produced, here we can see that it consists of over 6000 nucleotides (I presume) long and is the proteolytically processed product of 3 exons. A fair bit of manipulation is required to get from the DNA to the functional protein.

    We witness complex coordination at every level.

    It is interesting to note that in the very early embryo the primitive streak does not align with the anterior/posterior axis of the organism but only later becomes aligned Cell migration plus control of gene expression must work together to ensure normal development.

    Talking of cell motility, here is the first of two good videos on this subject and the remarkable methods that cells use to move around.

  5. It’s my belief that higher consciousness is ever present

    What do you think “higher consciousness” means? A more advanced watchmaker or a being that has discovered the present?

  6. Corneel:
    CharlieM: Let me give you an explicit example as you have requested. The CRISPR Cas system in prokaryotes that I have mentioned above is such an example.

    Using this system the cell inserts strings of DNA into its own genome and destroys DNA inserted into the bacterial genome by viruses. This system has been set up to prevent invasive changes to the cell’s genome.

    Yes, I am familiar with the CRISPR-Cas system and agree that it generates situation-appropriate mutations. Your example doesn’t really answer my questions though: What type of changes is the cell trying to preserve? What type of changes is it trying to correct? How does the cell tell the difference?

    The CRISPR-Cas system works by capturing pieces of phage DNA and inserting them into the CRISPR locus, a dedicated genomic locus for the storage of foreign DNA sequences. These sequences serve as a library to recognize and degrade potentially harmful invasive sequences. Clearly, those mutations are allowed because they increase fitness. Also note that no attempt is made to correct those mutations, like happens with polymerase proofreading.

    So, is it your claim that the cell is able to distinguish beneficial from deleterious mutations, even among those mutations that are not the result of a sophisticated system like CRISPR-Cas?

    You might be happy to use the term “mutation” for an insertion made by the CRISPR-Cas, mutations. I have made it clear that I do not like the use of the term “mutation” in such an inclusive way. I am happy with the term “point mutation” for a single genetic change brought about by some disruptive cause. In these cases, no, I do not believe cells can make the distinction between those which are beneficial and those which are deleterious. I do not believe cells target individual point mutations to either correct them or allow them to remain.

    Everything must be put in context. In multicellular organisms what is deleterious for the cell might turn out to be beneficial for the organism as a whole. And the same goes for colonies of prokaryotes. There is a balance to be maintained by allowing a level of variation and plasticity between individual cells. Total clonal rigidity leads to stasis, but living systems are by nature dynamic. From the level of cells to whole ecosystems, life thrives by maintaining a dynamic balance between growing form and dissolution.

  7. Corneel:
    CharlieM: My comment was directed to the behaviour of some people. I used to smoke and as a kid I occasionally got blisters from sunburn. Did this behaviour of mine increase my chances of getting cancer? I would say yes. I’m not allocating blame, just stating facts. Some health problems are self-inflicted and some are beyond the control of the individual. That is just a fact of life.

    Corneel: Oh nononono. You stated that excessive exposure to the sun is not merely a risk factor, but an actual cause of cancer. It is not the DNA that calls the shots; By displaying certain behaviours we are actively causing certain downstream events. You even insisted that somatic mutations are effects, not causes.

    I said exposure to the sun may have caused the cancer.

    Corneel: It is clear why that story appeals to you, because it gave you the idea of control over events that are usually attributed to unpredictable mutations of the DNA. But there is always a price to pay: if people are causing cancer by smoking a cigarette or having a sunbath, than the resulting cancer is definitely their own fault.

    I am not judging anyone, I am stating facts. Someone can develop cancer by smoke inhalation without every having smoked personally. Exposure to the sun cannot always be avoided. I’m sure we all get exposed to carcinogenic influences at times through no fault of our own.

    Corneel: So once again: is cancer caused by DNA mutations or is it caused by our own behaviour?

    I suggest you acquaint yourself with Aristotle’s four causes

    Was the Statue of David produced by the marble coming apart or was it caused by the work of Michelangelo?

  8. Corrected some HTML errors

    @ BWE

    Welcome back to TSZ. WordPress uses “less than” and “greater than” rather than bb square brackets.

    {a href=”URL address”}text for link{/a}

    Swap curly brackets for less than, greater than.

  9. CharlieM: I have made it clear that I do not like the use of the term “mutation” in such an inclusive way.

    You’re stuck with it if you want to communicate clearly.

  10. CharlieM: In multicellular organisms what is deleterious for the cell might turn out to be beneficial for the organism as a whole.

    Selection operates on the phenotype, the whole organism. Give me an example of a deleterious situation for a cell that benefits the whole organism, please, if you can.

  11. Corneel: The proximal cause of cancer is somatic mutations. Certain behaviours like smoking and exposure to the sun are sometimes called causes as well, but are more appropriately referred to as risk factors.

    These can be referred to as risk factors prior to the event. I take it you are talking about mutations that have actually happened? If you want do discuss actual cases of cancer and actual mutations then smoking or exposure to the sun become possible causes. If somebody already has cancer then they cannot be said to be at risk of getting it.

  12. Corneel:
    CharlieM: Producing variety of animal forms takes more than a bit of tinkering with DNA.

    Cornnel: See Alan’s response. To hammer this point down: most of the heritable variation in gene regulation is also encoded in the DNA.

    DNA is central to evolutionary biology in a similar way that access to a good dictionary and a knowledgeable memory of words is central to writing a novel. The creativity is produced by the way they are used.

    Corneel: Admittedly, there are some interesting effects of chromatin remodeling and position effects, but to remove DNA from its central position in evolutionary biological thought, you need to find a source of heritable variation that is not based on the transmission of polynucleotide sequences.

    Would you ask a novelist writing in the English language to get his source of words from outside of this language? DNA is the language used by living beings.

    Corneel: Your self imposed restriction to animal forms amused me BTW.

    If I was a triffid I might have composed it from its point of view. 🙂 Myself, being human, I wrote it from that perspective. You might have noticed that the topic of the op is human development and evolution. And after all we share our basic form with other animals.

  13. CharlieM,

    Leaving aside how Nodal interacts with other complexes and focusing in on how the protein itself is produced, here we can see that it consists of over 6000 nucleotides (I presume) long and is the proteolytically processed product of 3 exons. A fair bit of manipulation is required to get from the DNA to the functional protein.

    We witness complex coordination at every level.

    Hey, guess what fundamentally ensures that the same isoform is produced consistently? It’s passed from parent to child, and is the same thing that allows all manner of consistent characteristics to be attached to species. Begins with a D.

  14. CharlieM: have made it clear that I do not like the use of the term “mutation” in such an inclusive way.

    You have been calling them changes. Mutation literally translates as change. What’s the problem?

    CharlieM: In these cases, no, I do not believe cells can make the distinction between those which are beneficial and those which are deleterious. I do not believe cells target individual point mutations to either correct them or allow them to remain.

    OK, then I still have no clue what you meant when you said cells are able to retain “particular changes” while rejecting others:

    Why are these changes regarded as errors? Is it not possible that cells are organised in such a way as to allow particular changes to persist while correcting other changes.

    Do you know yourself?

  15. CharlieM: I said exposure to the sun may have caused the cancer.

    Yes you did and you continued with:

    This is what caused the mutations which lead to cancer.

    Why some conditions develop can sometimes be traced to the behaviour in the history of the organism and so mutations or changes in DNA structure are effects not causes.

    So the sunbathing is what caused the cancer mutations, which are themselves downstream effects of this behaviour. I thought that was crystal clear.

    CharlieM: I am not judging anyone, I am stating facts. Someone can develop cancer by smoke inhalation without every having smoked personally. Exposure to the sun cannot always be avoided. I’m sure we all get exposed to carcinogenic influences at times through no fault of our own.

    But I took it that you referred to situations where someone chooses from their own free will to smoke or take a sunbath. Then the resulting cancer is surely their own fault, right? Did I misunderstand?

    CharlieM: I suggest you acquaint yourself with Aristotle’s four causes

    Was the Statue of David produced by the marble coming apart or was it caused by the work of Michelangelo?

    Looks interesting, but I think the relevant question here is which is responsible for the statue? If you suggest that cancer patients have caused their disease by their behaviour, you are implicitly placing the blame on them. I advise some more caution with these kind of statements.

  16. CharlieM: DNA is central to evolutionary biology in a similar way that access to a good dictionary and a knowledgeable memory of words is central to writing a novel. The creativity is produced by the way they are used.

    Oh goodie. More analogies.

    CharlieM: Would you ask a novelist writing in the English language to get his source of words from outside of this language?

    Yes, they need to start using Dutch. The English language is just chaos.

  17. BWE:CharlieM: It’s my belief that higher consciousness is ever present

    BWE: What do you think “higher consciousness” means? A more advanced watchmaker or a being that has discovered the present?

    Hello BWE.

    Only humans make machines and devices such as watches. The type of higher consciousness I am referring to is not like that of human inventors whose inventions on being realized become separate entities. I am talking about conscious entities which are integral at a higher level, such as group intelligences. Individual organisms may not show much in the way of conscious awareness but taken together as a group they comprise highly intelligent beings. The individuals can be thought of as the organs of a higher entity.

    The present as we experience it is less real than duration. Most other animals live in the present but we humans are much more involved and aware of our past history and probabilities and possibilities for the future.

  18. Corneel:
    CharlieM: Lately the term “gene variants” has been used as a replacement for “gene mutations”. I think this is a better term.

    Corneel: I prefer “alleles”.

    CharlieM: DNA variations can be both disruptive changes from external sources or orchestrated changes from within. Why is it assumed that evolution is driven by the former? Because it fits with the narrative that life is just a fortuitous accident and that evolution proceeds by more fortuitous accidents.

    Corneel: That is just not true. We assume evolution is fueled by undirected random mutations because there is ample support that the vast majority of mutations arise in this way. You have spent enough time here at TSZ that you should be familiar with the Lederberg replica plating experiment and the Luria-Delbrück experiment. As has been conceded by several people here, mutations of the “orchestrated” type exist as well but they typically require dedicated systems (such as CRISPR-Cas) that clearly evolved themselves to support some specific task. That leads us to conclude that directed situation-appropiate mutations are the exception.

    BTW, you never answered my request to clarify yourself: Is it your claim that the cell is able to distinguish beneficial from deleterious mutations, even among those mutations that are not the result of a sophisticated system like CRISPR-Cas? What exactly is being “orchestrated”, as you put it?

    CharlieM: It is not just strings of DNA that get passed down the generations, it is living systems. The zygotes from which we have developed were fully functional living systems just as any normal prokaryote is a fully functional living system.

    This is of course true, but is not really relevant to the question how evolutionary change comes about. Evolution proceeds by change in the heritable characteristics of a population. This is why we focus on the compound we know to carry the heritable information i.e. DNA.

    We all know that undirected mutations happen all the time, but are they the main source of all the variation we see in today’s life?

    The Luria-Delbrück experiment demonstrated that viruses did not cause the bacterial immunity. Bacteria could overcome the viral invaders because they could tolerate an amount of genomic variation. The colony sampled a host of various genomic changes until it either perished or it hit on one which gave it protection against the virus. Individual bacteria are not important. The can be used as canon fodder so long as the group as a whole survive. Part of our immune system works in a similar way. Keep on sampling until the appropriate formula works.

    The DNA does not control the information that it contains. There are very many processes that take place in order to use the information stored in DNA in a contextually appropriate manner.

  19. Talking about alleles, I found this article on industrial melanism in moths.

    This is often given as an example of evolution in action so I think it warrants a closer look.

    They discuss convergent evolution of this phenomenon and focus on three species of moth. I notice there is a fair bit of speculation with the use of words such as “suggests”, “possibly”, “infer”, “imply”, “apparently”, and such like.

    It is interesting that they don’t have any data to tell if B. betularia had the melanic form prior to the industrial revolution.

    I’d appreciate more information on which specific alleles they have pinpointed as being involved. They mention a gene called “cortex”. Can anyone give me any more info on this gene or how I find out for myself? Size, number of exons, that sort of thing.

  20. I found this from “Nature”.

    Can anyone tell me how they pinpoint the insertion into the cortex gene to around 1819?

  21. CharlieM: The DNA does not control the information that it contains. There are very many processes that take place in order to use the information stored in DNA in a contextually appropriate manner.

    Nothing “controls” that information (whatever that means). Also, your description of the Luria-Delbrück experiment is straight-up evolution by natural selection.
    Now, for over a month I have been trying to get you to clarify what you meant by:

    Why are these changes regarded as errors? Is it not possible that cells are organised in such a way as to allow particular changes to persist while correcting other changes.

    All I received so far is an enormous amount of handwaving. Isn’t it time to admit that the vast majority of mutations are, in all probability, unplanned errors and that cells have absolutely no way to distinguish among them to reach some future outcome?

  22. Alan Fox:
    CharlieM: I have made it clear that I do not like the use of the term “mutation” in such an inclusive way.

    Alan Fox: You’re stuck with it if you want to communicate clearly.

    Which is more clear?:
    A mutation in the Cortex gene is implicated in the appearance of the darkened form in the peppered moth.

    or:
    The insertion of a type II transposable element into the Cortex gene is implicated in the appearance of the darkened form in the peppered moth.

    A point to consider. They don’t know how this operates to produce the darkened form or if it the only gene involved, but this gene has been hailed as the cause of industrial melanism in the peppered moth.

    Of course the process of transposition is just what Shapiro would term “natural genetic engineering”

  23. Alan Fox:
    CharlieM: In multicellular organisms what is deleterious for the cell might turn out to be beneficial for the organism as a whole.

    Alan Fox: Selection operates on the phenotype, the whole organism. Give me an example of a deleterious situation for a cell that benefits the whole organism, please, if you can.

    Apoptosis, for example. In the cells of a limb bud which will eventually produce digits because some of the cells are destined to die while others continue to multiply.

    In development selection works at the cellular level. In evolution selection works at higher levels such as that of the individual organism.. As above, so below.

  24. Allan Miller:
    CharlieM,

    Leaving aside how Nodal interacts with other complexes and focusing in on how the protein itself is produced, here we can see that it consists of over 6000 nucleotides (I presume) long and is the proteolytically processed product of 3 exons. A fair bit of manipulation is required to get from the DNA to the functional protein.

    We witness complex coordination at every level.

    Allan Miller: Hey, guess what fundamentally ensures that the same isoform is produced consistently? It’s passed from parent to child, and is the same thing that allows all manner of consistent characteristics to be attached to species. Begins with a D.

    That’s the wisdom of nature. Our bodies are composed of the same physical materials as our parents and our line of ancestors stretching back through the generations, and so it stands to reason that we use the same DNA that they used in order to produce the required proteins. And the processes that convert into functional proteins the information contained in DNA, also remains consistent through the generations. In fact these processes are extremely consistent over life as a whole.

  25. Corneel:
    CharlieM: I have made it clear that I do not like the use of the term “mutation” in such an inclusive way.

    Corneel: You have been calling them changes. Mutation literally translates as change. What’s the problem?

    The problem is the concept of “mutation” in the mind of the average layperson. A friend once told my wife that after going steady with her I had become a changed man. I don’t think she would have been very happy if she had been told she had caused me to become a mutant. 🙂

    CharlieM: In these cases, no, I do not believe cells can make the distinction between those which are beneficial and those which are deleterious. I do not believe cells target individual point mutations to either correct them or allow them to remain.

    Corneel: OK, then I still have no clue what you meant when you said cells are able to retain “particular changes” while rejecting others:

    I haven’t looked into it but I would not have thought error correction frequency is consistent when comparing different types of DNA changes. For instance between point mutations and transposon insertions. And I believe some nucleotide changes are more likely than others.

    CharlieM: Why are these changes regarded as errors? Is it not possible that cells are organised in such a way as to allow particular changes to persist while correcting other changes.

    Do you know yourself?

    My knowledge is limited, but I like to fish for answers.

  26. Corneel:
    CharlieM: I said exposure to the sun may have caused the cancer.

    Corneel: Yes you did and you continued with:

    CharlieM: This is what caused the mutations which lead to cancer.

    Why some conditions develop can sometimes be traced to the behaviour in the history of the organism and so mutations or changes in DNA structure are effects not causes.

    Corneel: So the sunbathing is what caused the cancer mutations, which are themselves downstream effects of this behaviour. I thought that was crystal clear.

    So we agree then?

    When I sad, “This is what caused the mutations which lead to cancer.”, all I was saying is that if exposure to the sun caused the mutations then this is what caused the cancer. If radiation from the sun was the cause then indeed it was the cause.

    CharlieM: I am not judging anyone, I am stating facts. Someone can develop cancer by smoke inhalation without every having smoked personally. Exposure to the sun cannot always be avoided. I’m sure we all get exposed to carcinogenic influences at times through no fault of our own.

    Corneel: But I took it that you referred to situations where someone chooses from their own free will to smoke or take a sunbath. Then the resulting cancer is surely their own fault, right? Did I misunderstand?

    Why are you so keen to apportion blame? I began smoking in my early teens. Was this my fault? Was it my parent’s fault for setting a bad influence? Was it the fault of my friends who already smoked? Was it the fault of the shopkeeper who sold the cigarettes to us? Was it the fault of society? Was it the fault of the education system? The circumstances leading to cancer are usually complex and multifarious.

    As for choosing to smoke out of free will, how free do you think my smoking was? If I started out of peer pressure, was it a free decision? And once started it becomes an addiction. Anything done out of compulsion is not done in freedom. It doesn’t matter if the compulsion was that of trying to fit in or of craving nicotine, Act performed out of external influence are the opposite of free acts.

    CharlieM: I suggest you acquaint yourself with Aristotle’s four causes

    Was the Statue of David produced by the marble coming apart or was it caused by the work of Michelangelo?

    Corneel: Looks interesting, but I think the relevant question here is which is responsible for the statue? If you suggest that cancer patients have caused their disease by their behaviour, you are implicitly placing the blame on them. I advise some more caution with these kind of statements.

    I’m sure any smoker who developed lung cancer would consider their smoking as a possible factor in its appearance. But why would I blame them for smoking if I didn’t know the circumstances which caused them to take it up in the first place?

  27. CharlieM,
    A mutation is a difference in the copied strand of DNA with respect to the template strand. That is all.

  28. CharlieM: I’d appreciate more information on which specific alleles they have pinpointed as being involved. They mention a gene called “cortex”. Can anyone give me any more info on this gene or how I find out for myself? Size, number of exons, that sort of thing.

    CharlieM: Can anyone tell me how they pinpoint the insertion into the cortex gene to around 1819?

    You can find the answers to both questions in the original paper which you can access via Pubmed. The age of the insertion was estimated from the linkage disequilibrium patterns surrounding the insert. Please report back if you discover any signs of engineering.

  29. CharlieM: The problem is the concept of “mutation” in the mind of the average layperson.

    It sure is. So go educate the average layperson.

    CharlieM: I haven’t looked into it but I would not have thought error correction frequency is consistent when comparing different types of DNA changes. For instance between point mutations and transposon insertions. And I believe some nucleotide changes are more likely than others.

    This rabbit hole just goes on and on, doesn’t it? Very well. So which of the types of mutations are NOT “errors”? What are the cell’s favourite mutations and why?

  30. CharlieM: Why are you so keen to apportion blame? I began smoking in my early teens. Was this my fault? Was it my parent’s fault for setting a bad influence? Was it the fault of my friends who already smoked? Was it the fault of the shopkeeper who sold the cigarettes to us? Was it the fault of society? Was it the fault of the education system? The circumstances leading to cancer are usually complex and multifarious.

    As for choosing to smoke out of free will, how free do you think my smoking was? If I started out of peer pressure, was it a free decision? And once started it becomes an addiction. Anything done out of compulsion is not done in freedom. It doesn’t matter if the compulsion was that of trying to fit in or of craving nicotine, Act performed out of external influence are the opposite of free acts.

    Responsibility is the flipside of having control, Charlie. Do you have it or not?

    CharlieM: I’m sure any smoker who developed lung cancer would consider their smoking as a possible factor in its appearance. But why would I blame them for smoking if I didn’t know the circumstances which caused them to take it up in the first place?

    You DON’T and you cannot know that smoking was the cause of their cancer.

  31. Alan Fox: CharlieM: Apoptosis, for example.

    Alan: Well, OK.

    Why OK? If apoptosis is deleterious to a cell, then why does it have a sophisticated system to execute it?

    Evolution does not proceed by the programmed death of organisms. Apoptosis can exist because the cells in an organism have a shared interest: The transmission of a common genome (and it’s made of DNA folks). This is not usually the case among the individual organisms in a species.

  32. Corneel,
    Sure, and it is not as if the contents of the apoptosizing (?) cell are wasted. All can be recycled.

  33. Corneel:
    CharlieM: The DNA does not control the information that it contains. There are very many processes that take place in order to use the information stored in DNA in a contextually appropriate manner.

    Corneel: Nothing “controls” that information (whatever that means).

    DNA contains the information required to produce polypeptides. Multiple orchestrated processes are necessary for this production. So I would agree with you that nothing “controls” these processes, if by “mothing” you mean no single substance.

    Corneel: Also, your description of the Luria-Delbrück experiment is straight-up evolution by natural selection.

    It is indeed.

    I know my use of analogies pleases you so here is one for you. 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: Now, for over a month I have been trying to get you to clarify what you meant by:

    (CharlieM): Why are these changes regarded as errors? Is it not possible that cells are organised in such a way as to allow particular changes to persist while correcting other changes.

    Corneel: All I received so far is an enormous amount of handwaving. Isn’t it time to admit that the vast majority of mutations are, in all probability, unplanned errors and that cells have absolutely no way to distinguish among them to reach some future outcome?

    Not all changes to the DNA are “errors”. For example crossing over during meiosis are changes which are built into the system.

    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.

  34. Alan Fox: CharlieM,
    A mutation is a difference in the copied strand of DNA with respect to the template strand. That is all.

    What do you mean by “that is all”?

    Changes to the sequence caused during the repair of a double stranded break would not count as mutations in your opinion? What about a change in chromosome number, would you count that as a mutation?

  35. Alan Fox:
    CharlieM: Apoptosis, for example.

    Alan Fox: Well, OK. But programmed cell death is ubiquitous. See Hayflick limit.

    Of course it’s ubiquitous. For example, it is a normal feature of embryonic development. And as your link makes clear cells live and die just as organisms live and die. The whole reflected in the parts.

  36. CharlieM: And as your link makes clear cells live and die just as organisms live and die.

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

  37. Corneel:
    CharlieM: I’d appreciate more information on which specific alleles they have pinpointed as being involved. They mention a gene called “cortex”. Can anyone give me any more info on this gene or how I find out for myself? Size, number of exons, that sort of thing.

    CharlieM: Can anyone tell me how they pinpoint the insertion into the cortex gene to around 1819?

    Corneel: You can find the answers to both questions in the original paper which you can access via Pubmed. The age of the insertion was estimated from the linkage disequilibrium patterns surrounding the insert.

    Thanks.

    Corneel: Please report back if you discover any signs of engineering.

    Shapiro would consider transposition to be an engineering process because it requires the use of “tools” to snip the DNA and insert transposon at the insertion. His thinking is perfectly logical even if it does use machine analogies which I am against,

    Just because one gene has been associated with melanism in the peppered moth this does not mean that darkened forms have not been around for a lot longer. Butterflies and moths have been using a wide variety of wing colouration patterns for millions of years.

    Here they tell us that dark forms are not restricted to the peppered moth:

    Principal Investigator Professor Ilik Saccheri explains: “Although many people have heard about industrial melanism in the British peppered moth, it is not widely appreciated that dark forms increased in over 100 other species of moths during the period of industrial pollution. This raises the question of whether they relied on the same or similar genetic mechanism to achieve this colour change. This was not a foregone conclusion because melanism in insects may be influenced by many different genes.”

    They continue:

    In a study published in Biology Letters, researchers from the University of Liverpool, Liverpool School of Tropical Medicine and Manchester Museum produced low coverage whole genome sequences for the pale brindled beauty and scalloped hazel species to compare with existing information about the genetics of industrial melanism in the peppered moth.

    Genetic linkage mapping using parent-offspring families shows that the mutation for melanism occurs in the same genetic region (containing the cortex gene) in all three species. Further analysis of wild samples, however, suggests that the genetic origins of melanism in the pale brindled beauty and scalloped hazel are much older than that in the British peppered moth.

    Why do they call it a mutation for melanism when a more accurate description would be an alteration of DNA sequence that is associated with melanism?

    The peppered moth might have had darkened forms in ancient times due to other DNA variables. It seems that convergent evolution abounds here.

  38. Corneel:
    CharlieM: The problem is the concept of “mutation” in the mind of the average layperson.

    Corneel: It sure is. So go educate the average layperson.

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

    CharlieM: I haven’t looked into it but I would not have thought error correction frequency is consistent when comparing different types of DNA changes. For instance between point mutations and transposon insertions. And I believe some nucleotide changes are more likely than others.

    Corneel: This rabbit hole just goes on and on, doesn’t it? Very well. So which of the types of mutations are NOT “errors”? What are the cell’s favourite mutations and why?

    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

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

    Be still, my heart.

    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.

    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.

    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.

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

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

    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 Brittain.

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

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

    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

    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?

  42. Corneel:
    CharlieM: Why are you so keen to apportion blame? I began smoking in my early teens. Was this my fault? Was it my parent’s fault for setting a bad influence? Was it the fault of my friends who already smoked? Was it the fault of the shopkeeper who sold the cigarettes to us? Was it the fault of society? Was it the fault of the education system? The circumstances leading to cancer are usually complex and multifarious.

    As for choosing to smoke out of free will, how free do you think my smoking was? If I started out of peer pressure, was it a free decision? And once started it becomes an addiction. Anything done out of compulsion is not done in freedom. It doesn’t matter if the compulsion was that of trying to fit in or of craving nicotine, Act performed out of external influence are the opposite of free acts.

    Corneel: Responsibility is the flipside of having control, Charlie. Do you have it or not?

    How long is a piece of string?

    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?

    CharlieM: I’m sure any smoker who developed lung cancer would consider their smoking as a possible factor in its appearance. But why would I blame them for smoking if I didn’t know the circumstances which caused them to take it up in the first place?

    You DON’T and you cannot know that smoking was the cause of their cancer.

    I didn’t say that smoking was the cause, I said it was a possible factor. People are always looking for simple linear cause and effect answers when in reality life is much more complex than this.

  43. Corneel:
    CharlieM: Apoptosis, for example.

    Alan: Well, OK.

    Corneel: Why OK? If apoptosis is deleterious to a cell, then why does it have a sophisticated system to execute it?

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

    Corneel: Evolution does not proceed by the programmed death of organisms.

    If organisms were not destined to have finite lifespans and to die then there could be no evolution. Senescence happens at the level of cells and at the level of organisms. The whole reflected in the parts.

    Corneel: Apoptosis can exist because the cells in an organism have a shared interest: The transmission of a common genome (and it’s made of DNA folks). This is not usually the case among the individual organisms in a species

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

    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?

  44. Alan Fox:
    to Corneel,
    Sure, and it is not as if the contents of the apoptosizing (?) cell are wasted. All can be recycled.

    Exactly. The organism can reuse the materials for its own benefit.

  45. 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?

    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?

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