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: Larry Moran […] means [is] that they disagree with much of his gene-centred view of evolution.

    I don’t think Larry Moran would consider himself a gene centrist.

    On the other hand, opposition to gene centrism seems enough for you to swallow someone’s position whole. Did you ever meet a maverick you didn’t like?

  2. Shapiro finesses this issue.
    The vast majority of the work he cites concerns unicellular organisms (my favorites, and his, are salmonella and trypanosomes — such a benevolent designer). He often uses language that obscures any germline/soma distinction.
    His examples of heritable NGE in multicellular organisms are not going to bring any joy to creationists or IDists: P-element dysgenesis is the sort of Selfish DNA warfare that would make Dawkins proud…

  3. BY way of illustration, Shapiro blogged (yeah, he does that…)

    In summary, NGE encompasses a set of empirically demonstrated cell functions for generating novel DNA structures. These functions operate repeatedly during normal organism life cycles

    linking to an impressive 58 article bibliography to support this. Well, one of these articles is about variations in somatic cells, three quarters of them are about prokaryotes and the remainder are about unicellular organisms. How many are about germline “Engineering”? Zero. Which is weird, because P-elements definitively count; perhaps they don’t represent the sort of positive, ‘erector set’-style toolkit he’s pushing.

  4. Corneel: I would have hoped it was obvious that tadpoles have strongly adapted to their habitat of shallow waters. To point out some specifics: Tadpoles have unique modifications of their mouth parts and a long gastrointestinal tract to support their grazing / suspension feeding life style. Note that adult frogs and toads, like most adult amphibians, are carnivores. Most probably that is the ancestral state.
    I do not know precisely when those adaptations evolved. Somewere after amphibians branched off from other tetrapods obviously.

    Oh I see what you are saying. You think tadpoles evolved from something else, and thus it is not that something else. So it must have new features, because its not that thing.

    There wasn’t a single bit of actual fact to that statement then, just an assumption that this must be how things happened. But you are also saying, tadpoles have been tadpoles for as long as we know. No changes to tadpoles for eons. You can’t name a single thing about tadpoles that has evolved.

    That seems to be pretty much the evolution story. Look at any animal. Go back and see what it looked like 1000 years ago. Its the same animal. Diversity of form, sure. Like terriers and poodles, and people from Turkey and people from Finland-but no, not evolved from history. Only the assumption that at some time they did.

  5. DNA_Jock,

    In correspondence and comments on some of my blogs, there have been confusions or questions as to what I mean by “natural genetic engineering” (NGE). I will use this blog to spell out what my understanding of NGE is. Then I will discuss some implications of our knowledge of NGE for thinking about how it operates in evolution, with special emphasis on where experimental and conceptual gaps need to be filled.

    For me, NGE is shorthand to summarize all the biochemical mechanisms cells have to cut, splice, copy, polymerize and otherwise manipulate the structure of internal DNA molecules, transport DNA from one cell to another, or acquire DNA from the environment. Totally novel sequences can result from de novo untemplated polymerization or reverse transcription of processed RNA molecules.

    NGE describes a toolbox of cell processes capable of generating a virtually endless set of DNA sequence structures in a way that can be compared to erector sets, LEGOs, carpentry, architecture or computer programming.

    Not sure what Neil thinks is “dubious” about this. I am sure he believes he has a better understanding of the cells functions than Shapiro. I am sure you believe you do too. I doubt anyone else believes that about you.

    Oh, but you don’t like his bibliography references. Noted. Not sure what you mean. Not at all sure that you know what you mean. But noted.

  6. phoodoo:
    Oh, but you don’t like his bibliography references.Noted.Not sure what youmean.Not at all sure that you know what you mean.But noted.

    From context, I surmise what he means is that the bibliographic references do not support what DNA-Jock thinks Shapiro is saying. From which it’s logical to conclude that either the references or the material being referenced is not understood by somebody.

  7. Flint,

    Not really.
    I think the bibliography supports what Shapiro is saying. I agree with what Shapiro is saying (in the blog post I cited). However, I am confident that many readers will come away with the mistaken belief that what Shapiro is saying has relevance for multicellular organisms. I am concerned that this misunderstanding might be intended — that he is being intentionally vague.

  8. DNA_Jock:
    Flint,

    Not really.
    I think the bibliography supports what Shapiro is saying. I agree with what Shapiro is saying (in the blog post I cited). However, I am confident that many readers will come away with the mistaken belief that what Shapiro is saying has relevance for multicellular organisms. I am concerned that this misunderstanding might be intended — that he is being intentionally vague.

    So you mean you don’t think we should draw inferences about evolution for multi-cellular life, from say experiments involving single cellular life. Again noted.

    Sorry Lenski.

  9. Flint,

    Yea, I was pretty confident no one understood what Jock was trying to say and why.

    Still not sure he does.

  10. phoodoo: Yea, I was pretty confident no one understood what Jock was trying to say and why.

    Shapiro extrapolates (or hints at extrapolation) to multicellular eukaryotes from evidence relating to prokaryotes.

    That’s my take.

  11. phoodoo: Oh I see what you are saying. You think tadpoles evolved from something else, and thus it is not that something else. So it must have new features, because its not that thing.

    Yep, that’s exactly how I phrased it: “Tadpoles of frogs and toads acquired many morphological, physi[ologi]cal and behavioural novelties not found in their ancestors.”

    phoodoo: But you are also saying, tadpoles have been tadpoles for as long as we know. No changes to tadpoles for eons. You can’t name a single thing about tadpoles that has evolved.

    I am neither a paleontologist nor a herpetologist, so you will have to forgive me for not presenting you with a detailed fossil series of tadpole evolution.

    phoodoo: That seems to be pretty much the evolution story. Look at any animal. Go back and see what it looked like 1000 years ago. Its the same animal. Diversity of form, sure. Like terriers and poodles, and people from Turkey and people from Finland-but no, not evolved from history. Only the assumption that at some time they did.

    I *believe* we also have quite some fossil series, biogeographic patterns and genetic evidence as well, but never mind that.

    Please tell me exactly when and how you believe tadpoles to have appeared. Do you believe modern amphibian species to be immutable? What happened to the species we know from fossils? I am genuinely interested.

  12. CharlieM: Everything is relative. Matter is far from passive. All matter has inner activity

    Very good; Then your views have changed. You used to argue that inner activity was limited to living substance.

    But if all matter has inner activity, then why are you so surprised that, as you so eloquently put it, “the words combine to make a meaningful story”?

  13. Corneel, correct me if i’m wrong, but you seem to believe tadpole evolution and frog evolution as somehow separate.

    Evolution is not a series of snapshots of the momentary form at a particular stage in an animal’s life. It’s about the general repetition in the descendants of the life processes in the ancestor. A complete dynamic life is repeated. It should not be forgotten that the bones and fossils that paleontologists line up were once just one part of a being that existed, not only in space but up to that point it had developed over a period of time.

    Looking back we should understand that evolution is the evolution of life histories. Frogs metamorphose from tadpoles in the same way that you or I have metamorphosed from an early embryo. A tadpole is equivalent to an embryo whose womb is the body of water in which it exists. Some frogs have no free tadpole stage in their lifecycles. In these cases the equivalent stage will be passed through within the body of the parent frog or within the egg.

    Comparing vertebrates in general the development to adulthood will always happen by metamorphosis from eggs by means of similar processes taking place in diverse environments. Because I am a mammal the development of my limb buds just happened to occur within the body of my mother, in the case of the common frog it happens within the body of water where it is living. In the case of birds this stage is passed through within the egg. The environments might vary considerably but the processes of limb development are remarkably similar in all vertebrates.

  14. Corneel:
    CharlieM: It may be a fact that no ancestor of amphibians will physically resemble a modern tadpole, but these two creatures will no doubt share particular behavioural traits, such as breathing through gills and swimming around under water.

    Corneel: The anuran tadpole stage, like the adult stage, has become adapted to its environment. Tadpoles of frogs and toads acquired many morphological, physical and behavioural novelties not found in their ancestors. Development is itself subject to evolutionary change, not a parallel of it.

    Novelties such as?

    I agree they are not parallel processes. But they both consist of change over time on different scales. The development of an individual basically repeats the development of its ancestors.

    CharlieM: I can make a reasonable guess as to the future by observing how past processes have unfolded up to the present.

    Corneel:Can we agree that your “reasonable guess” is a form of speculation?

    Yes, just as I can speculate that next Tuesday the sun will appear to move across the sky from east to west. I’m hoping it will happen that way but I can’t be totally certain that it will.

    CharlieM: The “zygote” is just a word we use to describe the initial cell. Once it begins dividing what differences are there between it and the subsequent daughter cells?

    Corneel: Humans are just collections of the zygote’s daughter cells? That’s marvelous! I propose you become president of our Reductionist Club.

    From the initial zygote there is division and subsequent differentiation. This is happening within the organism as a whole which can be considered as a unity. Holistic thinking does not ignore the parts. It considers the parts in relation to the whole.

    Corneel: Some silly people maintain that you have only reproduced once you get children.

    And why would I think otherwise?

    CharlieM: I think that scientific consensus has a lot do do with the prevailing prejudices especially when it concerns evolution.

    Corneel: Yes, I can certainly spot some prejudices, especially when it concerns evolution.

    We all have them 🙂 “Know thyself”, good advice, easy to say but hard to put into practice.

    CharlieM: The way I participate here, I don’t always read the posts that come after the one I am replying to until after I have posted my reply.

    Corneel: Don’t you think it is striking how your arguments resonate: “Have we completely resolved this and that issue?” Do you know why creationists like to say that?

    Scientists often say that all theories are tentative and outside of mathematics nothing is proven.

    CharlieM: And if you see self-consciousness slowly developing in the early stages of a baby’s life, would you consider it a pretty good prediction that if that baby continued to develop normally its self-consciousness would continue to develop further?

    Corneel: I have seen many babies, but only one human lineage so far.

    Have you ever watched a child developing into an adult and witnessed how their consciousness changes? A two week old baby has no real awareness of itself as an individual. That awareness takes time to develop.

  15. CharlieM: Have you ever watched a child developing into an adult and witnessed how their consciousness changes? A two week old baby has no real awareness of itself as an individual. That awareness takes time to develop.

    You do this a lot, Charlie. I admit I’m easy to irritate but I’m not the only one to complain (see Petrushka). Nobody is disputing any of the above statements. I dare say, if we took a straw poll, no-one would take exception. Why do you persist in stating the bleedin’ obvious as if someone did disagree?

    ETA: shoot, I missed out on using the word “banal”!

  16. petrushka:
    I was away for six months and nothing of importance was said by you or by any critic of evolution. To the extent you are not wrong, you are vacuous.

    Feel free to withdraw from the conversation at any time. While I have been active here my “vacuous” comments have invoked a host of responses from which I have learned a great deal. so you may not see any merit in them, but I am very much benefitting from being here, so I’ll selfishly carry on.

    On saying all that, it’s good to see you back, and in good health, I hope. 🙂

    petrushka: There has not been anything new or important in your corner since Paley. The only idea you have is retrospective astonishment.

    See, you have added to my knowledge. I didn’t even know I was in Paly’s corner until you enlightened me.

    Is it like being put on the naughty step? 🙂

    petrushka: Now, all you have to do to disprove my claim is to cite an example of natural genetic engineering that modifies the germ line, so that the engineered change becomes fixed in the population.

    Why would I want to disprove your claim? Maybe you think I’ve moved into Shapiro’s corner.

  17. petrushka:
    I have the “View” book and have read it. There’s nothing in it that requires changing one’s view of evolution.

    And not a single new fact or argument sincethat justifies the hoopla.

    I’ve watched this debate since about 1956, when Life Magazine came out with a series (made into books) on human evolution.

    Opponents of evolution have made no progress in that time.

    Or indeed, since Paley.

    Who are the opponents of evolution and why should I care about them?

    As I see it, many of the people in the “third way website” don’t want belief in evolution to be abandoned, they just want dogmas to be left behind and views to be broadened.

  18. Alan Fox:
    phoodoo,

    Who does that? Do you have an example?

    Well, I am glad you now admit the Lenski experiments that you have hyped so much here in the past, don’t really tell us anything at all about animal evolution. Glad we can retire that nonsense.

    Maybe you are finally waking up.

  19. petrushka: When one says, “alter one’s own heredity,” there is an implication that one’s heredity will be passed on to future generations. That is the usual understanding.

    So where is it established that this happens?

    It’s not just an implication. That is what heredity means. That which is inherited down the generations.

    An example that comes to mind is a bird such as a peahen altering her own heredity by choosing which cock to mate with. There are numerous examples in which the actions of the parents alters their heredity.

  20. CharlieM: Corneel, correct me if i’m wrong, but you seem to believe tadpole evolution and frog evolution as somehow separate.

    Obviously not; they are stages of the same individual with the same genome.
    But (hopefully) also obvious; they have very different morphology and physiology produced by stage-specific expression of that genome. That is what allows larval frogs to exploit a completely different niche than adult frogs.

    CharlieM: The development of an individual basically repeats the development of its ancestors.

    No it does not, for the reason mentioned above: the larval stage cannot be a recapitulation of the evolution of the adult phase because it is itself subject to evolutionary change.

    CharlieM: Novelties such as?

    See my answer to phoodoo. I trust that you are as fascinated by tadpoles as phoodoo is.

    CharlieM: Me: Some silly people maintain that you have only reproduced once you get children.

    Charlie: And why would I think otherwise?

    Because you claimed that the zygote has already reproduced when it reaches the blastula stage. That is very confused thinking.

    CharlieM: Have you ever watched a child developing into an adult and witnessed how their consciousness changes? A two week old baby has no real awareness of itself as an individual. That awareness takes time to develop.

    Did you ever observe a human species evolve a consciousness higher than we currently have? You keep claiming that you are just making observations, but that’s not true.

  21. DNA_Jock:
    petrushka: When one says, “alter one’s own heredity,” there is an implication that one’s heredity will be passed on to future generations. That is the usual understanding.

    So where is it established that this happens?

    DNA_Jock: Oh, it only happens in God’s most favored children. I’ll let Charlie explain.

    Thankyou.

    It all begins when a stork lands on your roof. So if someone wishes to have children, they should get a roof. The stork will be carrying a coloured basket, and…( story continues behind paywall.) 🙂

  22. petrushka: Evolution is the fixation of alleles

    Surely you would agree that evolution is much more than the fixation of alleles?

    Unless, of course, you think that fixation is synonymous with change over time.

  23. Allan Miller:
    CharlieM: I think that scientific consensus has a lot do do with the prevailing prejudices especially when it concerns evolution.

    Allan Miller: I’m seeing similar complaints from supporters of various Covid-related fringe notions. What they (and you) seem to be complaining about is that people supporting the consensus have the wrong prejudices

    All prejudices are wrong.

  24. CharlieM: As I see it, many of the people in the “third way website” don’t want belief in evolution to be abandoned, they just want dogmas to be left behind and views to be broadened.

    I eagerly await enlightenment.

    Respond to my question.

    If Shapiro’s natural engineering doesn’t change the germ line, why is it touted as a challenge to mainstream evolution?

  25. Allan Miller:
    CharlieM: Larry Moran […] means [is] that they disagree with much of his gene-centred view of evolution.

    Allan Miller: I don’t think Larry Moran would consider himself a gene centrist.

    Yes, I’m sure he’d agree with you. But I do think he believes that genes, or more specifically, changes in allele frequencies, are the prime movers of evolution.

    Allan Miller: On the other hand, opposition to gene centrism seems enough for you to swallow someone’s position whole. Did you ever meet a maverick you didn’t like?

    I must admit I preferred James Garner’s character to Roger Moore’s. Does that count? 🙂

  26. petrushka:
    CharlieM: As I see it, many of the people in the “third way website” don’t want belief in evolution to be abandoned, they just want dogmas to be left behind and views to be broadened.

    petrushka: I eagerly await enlightenment.

    Respond to my question.

    If Shapiro’s natural engineering doesn’t change the germ line, why is it touted as a challenge to mainstream evolution?

    I presume Shapiro would answer that germ cells use natural engineering to manipulate their own genomes. No need to posit any interference from outside. Control is at the cellular level not the genome level.

  27. petrushka: If Shapiro’s natural engineering doesn’t change the germ line, why is it touted as a challenge to mainstream evolution?

    You also are left with the never ending problem of explaining how it came to be.

    Those organisms with natural genetic engineering had more babies than those without it, so they had a Darwinian advantage?

    Can it get any more silly?

  28. And to prove my point, along come CharlieM and phoodoo to demonstrate that they were misled by what Shapiro was claiming.
    He would say nothing about germ cells.
    Shapiro would note that [unicellular] organisms with NGE have more progeny than [unicellular] organisms without NGE. It’s completely Darwinian.
    He would mumble the “unicellular” bit somewhat, mind you.

  29. It’s not so much that allele frequency is the mover of evolution as it is the definition of evolution.

    The interesting question is why.

    What is about genomes that make them interesting?

  30. DNA_Jock:
    And to prove my point, along come CharlieM and phoodoo to demonstrate that they were misled by what Shapiro was claiming.
    He would say nothing about germ cells.
    Shapiro would note that [unicellular] organisms with NGE have more progeny than [unicellular] organisms without NGE. It’s completely Darwinian.
    He would mumble the “unicellular” bit somewhat, mind you.

    I’m not a lawyer, so I’ll ask a question for which I don’t know the answer.

    Are changes made by NGE “intelligent”?

    That is, do they always, or frequently, improve the success of progeny? Has this question been put to a test? What would a test look like?

  31. Perhaps another way of putting my question. Suppose you had a way of stochastically increasing variation.

    How would the results look different from NGE?

    Are they known to be different?

  32. petrushka: Are changes made by NGE “intelligent”?

    Sure you’re not a lawyer?
    <ggg>
    Well, the answer’s gonna depend on how you define “intelligent”.
    The most widespread uses of NGE are different forms of antigenic variation which allow bacteria or protist parasites to evade a host’s adaptive immune response. So having a library of different surface antigens available and switching between them, either completely at random or in some form of “if stressed, switch”-type rule, is pretty bloody crafty (and the cause of much human suffering…), but easily evolvable.
    In the germline of multicellular organisms, you have some pretty baroque behavior by transposable elements, but they look more “selfish Loki” than “intelligent”.

  33. This is interesting. There is no scientific basis for rejecting the possibility that a process akin to the adaptive immune system also modifies the germ line.

    Adaptively.

    Well, nothing except the lack of evidence.

    Nothing known about biochemistry prohibits mutagenesis, but a couple of nagging questions remain. Mostly about whether engineered mutations would be differentially adaptive.

  34. So we have a red queen thing going on.

    Organisms evolved adaptive immune systems, and pathogens evolved ways to selectively increase variation.

    My first thought is that microbes come in millions and billions, and that some of them can die from self inflicted mutations, without anyone noticing. So there is no cost if the mutations are stochastic, and possibly fatal to individuals.

    There might be some interesting new science here, but I fail to see that this is anything other than a way of increasing variation. Perhaps the variation is targeted toward areas less likely to be fatal. That would be interesting.

  35. petrushka: There might be some interesting new science here, but I fail to see that this is anything other than a way of increasing variation.

    Well, you nailed it!

  36. CharlieM: All prejudices are wrong.

    All aphorisms are tedious.

    You display clear prejudices, in favour of anyone who questions the present evolutionary paradigm and against anyone who defends it. You want people in evolutionary theory to see it like you do. Else why whinge about ‘prejudice’? It is a common refrain: people only think as they do because they are locked in a mindset. They can’t possibly have come to their conclusion rationally, otherwise they’d think like you.

  37. petrushka: Nothing known about biochemistry prohibits mutagenesis, but a couple of nagging questions remain. Mostly about whether engineered mutations would be differentially adaptive.

    “Where’s the feedback” is one question that needs to be kept in consideration.

  38. I am glad to see that Shapiro on occasion responds to some of the evolution preacher barkers such as Coyne. I have read enough of Coyne to know that his positions are just ideological wishful thinking at best, and pure dogmatic bullshit at worst. I think Shapiro sets him pretty straight here:

    In a recent posting on his Why Evolution Is True website, “Jim Shapiro continues his misguided attack on neo-Darwinism,” Jerry Coyne attacks me again. Let us examine some of his arguments.

    1.

    “[I]n one of his posts he explicitly uses a creationist trope:
    The first problem with selection as the source of diversity is that selection by humans, the subject of Darwin’s opening chapter, modifies existing traits but does not produce new traits or new species. Dogs may vary widely as a result of selective breeding, but they always remain dogs.
    Given the fossil evidence of transitional forms … such a statement is simply embarrassing, and is identical to ones you’ll see in the creationist literature.
    This “guilt by association” argument (even though ID proponents call me a “crypto-Darwinist“) does not make sense; the fossil record has little to say about “selection by humans,” which was my subject.

    2.

    [W]e know of no evidence for mutations occurring nonrandomly or “adaptively”, i.e., that the occurrence of mutations is somehow biased in a direction that makes them more likely to be favorable when they arise, particularly when the environment changes in a way that requires favorable mutations to fuel adaptive evolution. There has been some controversy about the occurrence of “adaptive mutation” in bacteria, but that’s died out because there’s simply no evidence that the phenomenon occurs.

    “Adaptive mutation” is in fact alive and well in the sense that selection conditions induce (adaptive) mutagenesis carried out by well-documented natural genetic engineering agents: homologous recombination functions, mutator polymerases, and transposable elements. This has been documented in several species of bacteria and in yeast.

    3.

    In his latest columns at HuffPo, (Part 1 and Part 2), Shapiro makes the same mistake, assuming that some features of the genome — the vertebrate immune system in this case — shows that natural selection is ineffective in molding adaptive traits of organisms, and that the innate nature of the genome has really replaced the conventional view of adaptive evolution.

    I did not write about evolution of the immune system. I specifically used well-documented immune cell events to illustrate cell capacities to target and regulate genome changes, sometimes in response to intercellular signals. Neither Coyne nor I know in detail how the immune system evolved. But it certainly is a gross error to use ignorance as the basis for asserting dogmatically, as he goes on to do, that it was “molded by a combination of random mutation and natural selection.” This is yet another example of Jerry confusing his preferred theory with empirical evidence. (He repeats this unsubstantiated assertion later in his critique.)

    4.

    The amazing thing is how the body uses a small number of genes in the B cells to generate a huge variety of protective antibodies … What happens is that there are two processes, called somatic hypermutation and VJ recombination, that take the DNA sequence of the antibody-producing genes and mutate it, either creating “errors” in the DNA sequence or swapping bits within and among genes by physical recombination. This generates a large number of variable antibody proteins.

    There a few minor mistakes and one major omission here. “VJ recombination” is actually “V(D)J recombination.” Jerry forgets to mention that it is a highly targeted process of successive DNA breakage and joining events that also includes the synthesis of novel DNA sequences inserted next to the D segments. Perhaps he omitted the D region in his description because the ability of cells to generate new DNA sequences does not fit in his worldview.

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    In discussing somatic hypermutation, the aspects I highlighted were 1) its activation in immune cells following antigen binding, and 2) its specificity for sequences that encode the antigen-binding regions of the antibody without altering the rest of the molecule. Such inducible, selective, targeted mutagenesis is not included in conventional neo-Darwinian explanations of mutations as “errors” (to use Jerry’s terminology).

    Finally, Jerry does not even mention the switching of antibody classes (“class switch recombination,” or CSR). CSR was the subject that occupied the bulk of my second posting. The reason for this absence appears to be that targeting such natural genetic engineering by intercellular signals is antithetical to the “error” view of genome change.

    5.

    The key point is that there is no evidence that the evolution of the immune system in this way (by differential reproduction of individuals instead of cells) involved anything other than natural selection among individuals having randomly produced mutant variants of an ancestral immune system.

    We will examine what we know about the evolution of adaptive immune systems in vertebrates in the future. There is not space now. Let me simply note here that a number of steps already discernible from genome sequencing are not plausibly explained by “randomly produced mutant variants.”

    6.

    Note especially that in both the contingency loci of bacteria and the hypermutability loci of vertebrates, the mutations that occur are random: variants are produced regardless of whether they’d help the beleaguered vertebrate trying to destroy the antigens or the besieged bacterium trying to avoid antibodies.

    Here again, Jerry fails to recognize that variations in “contingency loci” are not in any way random mutations. Instead, they involve well-defined natural genetic engineering systems: 1) targeted homologous recombination of coding cassettes (in eukaryotic trypanosomes as well as in bacteria); 2) site-specific recombination within protein coding sequences (“shufflons”); 3) insertion and excision of DNA transposons; and 4) mutation-prone reverse transcription and cDNA reinsertion to diversify specific variable regions of phage and bacterial coding sequences (“diversity-generating retroelements”). These examples simply reinforce the message of my two immune system blogs, namely that cells of all kinds are fully competent to engineer their genomes in well-defined (i.e., non-random) ways.

    7. Although Jerry claims near the end of his diatribe that “all the facts are on my side” (always a dangerous position to hold), I think his omissions and theory-observation conflations argue differently.

    Jerry, I think you need to do better next time. Please address my real arguments, not your own mischaracterizations.

    Jock may want to take some notes.

    https://www.huffpost.com/entry/jerry-coyne-fails-to-unde_b_1411144

  39. I also like this review of Shapiros ideas on Quora, by a student named Tyke Morris:

    There seem to be a lot of evolution preachers who get their feathers ruffled by Shapiro, which tells you a lot about those preachers I reckon (one of their lame arguments is that Shapiro is a microbiologist and geneticist, not an evolutionary biologist-as if first off Shapiro doesn’t understand evolutionary biology, and second as if evolutionary biologists understand microbiology and genetics better than Shapiro. If they are not scared why do they sound so panicked about Shapiro? I could only stomach to read a few of their responses on the same page. They clearly sound worried):

    How could they not be accepted? His book has hundreds of references fully backing up every word with experiment after successful experiment. Shapiro is the unquestioned leader in the world of evolution and his book “Evolution: A View from the 21st Century” is considered to be the quintessential text on all aspects of modern evolutionary biology.

    His book comes glowingly recommended by other evolutionary giants, such as Science Medal of Honor winners Lynn Margulis (endosymbiosis) and Carl Woese (discoverer of archaea as the 3rd domain of life).

    Shapiro worked alongside Nobel Prize winner Barbara McClintock for decades, helping her demonstrate transposition, which was rejected by the Darwinian scientific community at the time. After McClintock’s discovery in the 1940’s, it was 1983 before, with Shapiro’s help, she finally won the Nobel Prize.

    Shapiro himself discovered reverse transcription, also upsetting the applecart of the Central Dogma, which saw gene to RNA to protein processes as a one-way street. Shapiro and McClintock worked together on a book about mobile genetic elements and how they work. This was not the last time Shapiro would reverse the direction of evolutionary biology.

    In 1984, Shapiro performed the world’s first induced evolution experiment, solidifying his place as the leading evolutionary biologist on the planet. Of course now everybody is doing induced evolution experiments, but the simple methodology is to place an organism in a stressed environment and see what it does in response. What he and McClintock discovered is that cells DO make intelligent, efficient and predictable responses to stress. These responses include both epigenetic controls and natural genetic engineering, a term coined by Shapiro himself.

    Shapiro was even the man who isolated the first gene, a Lac operon, just in case you get that question in a trivia game.

    So when Shapiro wrote his famous book, even though it contradicted an entrenched Darwinian orthodoxy, the scientific community had no choice but to admit it was time for evolution itself to evolve. By 2013 the word “random” was FINALLY removed from the NGSS section on mutations and in 2016, with Shapiro as a heavily applauded keynote speaker, the Royal Society publicly endorsed the death of Neo-Darwinism in favor of a more Neo-Lamarckian form of evolution.

    So the status of Shapiro’s ideas would be that the scientific community, with the exception of the marginalized atheism religious advocates, wholeheartedly support Shapiro’s version of evolution as we know it today. What remains is to re-educate the public as well as pockets of hard-headed old school college professors with dusty textbooks from the 1800’s.

    https://www.quora.com/What-is-the-status-of-James-Shapiros-theory-on-the-mechanism-of-evolution-Is-it-accepted-in-scientific-circles

  40. phoodoo,

    “His book comes glowingly recommended by other evolutionary giants, such as Science Medal of Honor winners Lynn Margulis (endosymbiosis) and Carl Woese (discoverer of archaea as the 3rd domain of life).

    Shapiro worked alongside Nobel Prize winner Barbara McClintock […]”

    That you respond favourably to such credential mongering is no surprise. Add in some fantasy that opposition to ideas betrays some deep terror and your joy is complete.

    Charlie does the same; it’s always about people rather than ideas. It is an unending theme of ID/Creationist discourse.

    Yet when it comes to the actuality of evolution (which these people accept) they are deemed to be as full of crap as the rest of those darned evolutionists. There ought to be some hint of cognitive dissonance there, though there never is.

  41. Allan Miller: Charlie does the same; it’s always about people rather than ideas.

    Wait, what?? I just gave you at least 10 paragraphs of HIS IDEAS?

    Bit early to be drinking , yea?

  42. phoodoo: Bit early to be drinking , yea?

    Said the guy who has defended Uri Geller’s ‘ability’ to bend spoons with his mind and argued that dogs can see into the future to see when their owners are coming home….

    And of course, the camps, where everyone who is there deserves to be there….

  43. phoodoo: If they are not scared why do they sound so panicked about Shapiro? I could only stomach to read a few of their responses on the same page. They clearly sound worried):

    I’m unsure what you are getting excited about here. No matter what, no matter who ‘wins’ or ‘loses’ this ‘battle’ it’s not going to suddenly turn into Intelligent Design was right all along is it?

    I’m not sure what relevance it has to you when two people are arguing details about something that you reject in its totality anyway. The immune system is not Intelligent Design in action, is it now?

  44. DNA_Jock:
    And to prove my point, along come CharlieM and phoodoo to demonstrate that they were misled by what Shapiro was claiming.
    DNA_Jock: He would say nothing about germ cells.

    He doesn’t need to. His argument is that cells in general are capable of NGE. If I said that mammals are endothermic you cannot criticize me because I said nothing about dogs.

    DNA_Jock: Shapiro would note that [unicellular] organisms with NGE have more progeny than [unicellular] organisms without NGE. It’s completely Darwinian.
    He would mumble the “unicellular” bit somewhat, mind you.

    Can you provide quotes or specific references to him saying this, so that I can get an idea of the context.

  45. CharlieM: His argument is that cells in general are capable of NGE. If I said that mammals are endothermic you cannot criticize me because I said nothing about dogs.

    A total mismatch of incomparable items. That you don’t see that is very telling.

  46. petrushka:
    It’s not so much that allele frequency is the mover of evolution as it is the definition of evolution.

    The interesting question is why.

    What is about genomes that make them interesting?

    Of course genomes are very interesting and what makes them interesting is the processes in which they are involved.

    Is “allele frequency” the definition of evolution? Is it one definition of evolution among many? Is it part of a definition of evolution? Can the reality of evolution be totally encompassed by mathematics?

    What would you say was the prime mover of evolution? And what do you think Moran sees as the prime mover in evolution?

  47. CharlieM,

    I find it truly extraordinary that Jock is suddenly so concerned about separating the concept of evolution from what happens with single celled organisms.

    Its almost as if every time one asks for examples of evolving new novel functions the ONLY thing you are ever given is NOT examples of nylon eating bacteria.

  48. petrushka:
    DNA_Jock:
    And to prove my point, along come CharlieM and phoodoo to demonstrate that they were misled by what Shapiro was claiming.
    He would say nothing about germ cells.
    Shapiro would note that [unicellular] organisms with NGE have more progeny than [unicellular] organisms without NGE. It’s completely Darwinian.
    He would mumble the “unicellular” bit somewhat, mind you.

    petrushka: I’m not a lawyer, so I’ll ask a question for which I don’t know the answer.

    Are changes made by NGE “intelligent”?

    That is, do they always, or frequently, improve the success of progeny? Has this question been put to a test? What would a test look like?

    You could have a read of this. There are hundreds of references. I’m sure they will provide some answers for you. (Although you will need to download it.)

    Here is the introduction:

    “Over the past 40 years, several books and numerous review articles have detailed the molecular mechanisms that cells utilize to alter their genomes. These “natural genetic engineering” (NGE) processes are biochemical tools that living organisms possess to make adaptive use of their DNA databases as “Read-Write Genomes”. Taking these mechanistic discoveries as established science, the goal of this review is to explore how bioinformatics has documented some of the ways that living organisms stimulate and benefit from NGE in the course of evolutionary change. Much of the relevant information will appear in lists and tables that have two objectives: To make the primary literature accessible to the reader, and to manifest how extensive the literature has become verifying that genome change in evolution results from a series of active biological processes, not from passive accidents. Previous reviews have summarized the outline of the basic arguments presented below, but this article presents each topic in greater depth and detail than earlier publications.”

  49. phoodoo: Its almost as if every time one asks for examples of evolving new novel functions the ONLY thing you are ever given is NOT examples of nylon eating bacteria.

    https://www.nature.com/articles/nrg2808
    https://link.springer.com/article/10.1007/s10709-008-9289-z
    https://www.annualreviews.org/doi/abs/10.1146/annurev-ecolsys-110411-160513
    https://www.hindawi.com/journals/ijeb/2012/821645/

    I’d be happy to chip in to help you afford access to some of these papers, if you need.

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