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. OMagain,

    Ironically he now complains that we are focused on people not ideas, 

    No, he’s complaining that I’m complaining that they are more focused on people than ideas! So we can look forward to more irritable barbs every time someone on our side so much as mentions a person, but still no discussion of ideas. It’s all gone very meta.

  2. OMagain: Ironically he now complains that we are focused on people not ideas, and yet he would never read the ideas in those papers that actually attempt to answer the question he asked!

    Rich irony indeed!

  3. phoodoo: Is that a person’s ideas?

    What’s with you evolutionists obsession with people?

    It’s a dangerous business, phoodoo, asking questions. You never know where the answers might sweep you off to.

  4. phoodoo:
    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.

    I’m not sure how or why DNA_Jock thinks that Shapiro’s NGE is insignificant in the processes of gamete formation in eukaryotes.

    Shapiro gives what he considers to be a basic NGE toolkit as follows:

    Pores for DNA mobilization across membranes
    Nucleases (cutting)
    Ligases (splicig)
    Polymerases (proof reading and error prone “mutator”)
    Exisionases (remove improper/damaged bases)
    Helicases (unwinding proteins, removed damaged oligonucleotides)
    Annealing proteins (eg recA)
    Site-specific recombinases (combined cutting and splicing)
    Reverse transcripases RNA –> DNA
    Transposases and integrases (cutting and splicing)

    How many of these molecules are used by cells in gamete production?

  5. DNA_Jock: Charlie, You continue to make my point for me.
    In response to petrushka’s critical question:

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

    You wrote:

    I presume Shapiro would answer that germ cells use natural engineering to manipulate their own genomes.

    Shapiro would (as I noted previously) avoid any statement that was as obviously wrong as this, he is careful to finesse the germ/soma distinction. This point appears to have sailed over your head. So I replied

    He would say nothing about germ cells.

    Thus your response

    He doesn’t need to.

    is a further demonstration that you are missing petrushka’s point. In a big way.

    If you want examples of Shapiro mumbling the word [unicellular], check out the exchange that phoodoo kindly posted. It is damning in the extreme, and assuming you read it, it offers further confirmation of my point that you and phoodoo have failed to spot the equivocation that Shapiro is guilty of.
    If phoodoo is willing to discuss that exchange, rather than C&P blocks o’ text, I will walk him through it. It reminds me of Behe’s mutilated table S2 from Liu et al.
    phoodoo’s citing Tyke Morris did bring me joy, though: he’s quite the authority.

    To get an idea of Shapiro’s “mumblings” you advise me to read this link in which other people argue about his views. Would it not be better to read what the man himself writes?

  6. So get the book and start

    CharlieM: Would it not be better to read what the man himself writes?

    Ironic, from someone who hasn’t read the book.

    I find nothing in it relevant to evolution.

    Get the book and show me to be wrong.

  7. CharlieM: How many of these molecules are used by cells in gamete production?

    None. Not a single one.
    [Hint: You might want to phrase your question better.]

    CharlieM: To get an idea of Shapiro’s “mumblings” you advise me to read this link in which other people argue about his views. Would it not be better to read what the man himself writes?

    Pay attention.
    I pointed you to “the exchange that phoodoo kindly posted.” which is text that Shapiro himself wrote in his attempt to rebut Moran’s critique.
    In the following comment, phoodoo posts Tyke Morris’s commentary from quora. I made fun of that, joking that Tyke Morris is ‘quite the authority‘. [He’s a “Trump was robbed” conspiracy nutter].

  8. 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.

    This is the equivocation I see. Shapiro seems to be saying mutagenesis is not random, because it is caused.

    Coyne’s point is the mutations are scattershot, and not targeted. The difference between a rifle and a hand grenade.

    What happened to the creationists who argued hand grenades couldn’t build things?

  9. It must be a real arse to go to the trouble of engineering a gamete (in the mammalian female, a process essentially complete while she’s still a foetus) to find that half your efforts (at best) are just friggin’ chucked away. Even the surviving fraction may find itself masked in the subsequent zygote. But hey, details … We can draw a massive target around that which remains and say that’s NGE, that is.

  10. I just have to ask how a designer or natural engineer knows what a changed gene will do.

    Particularly since most animal genes are regulatory rather than protein coding.

    Perhaps in organisms that are subject to attacks by immune systems, ANY non-lethal change is adaptive. But that kind of system would be kind of specialized. Not a generic driver of evolution.

  11. DNA_Jock: I made fun of that, joking that Tyke Morris is ‘quite the authority‘. [He’s a “Trump was robbed” conspiracy nutter].

    As an actual election volunteer, I certify that the elections were stolen… as they always are when you can’t even ask for an ID or challenge eligibility.

    Furthermore, in my neck of the woods, Stalin is envious…

  12. Nonlin.org: As an actual election volunteer, I certify that the elections were stolen… as they always are when you can’t even ask for an ID or challenge eligibility.

    Furthermore, in my neck of the woods, Stalin is envious…

    I understand the Republicans have taken to heart one of Stalin’s claims – that “it doesn’t matter who the people vote for, it only matters who counts the votes.”

  13. Nonlin.org: As an actual election volunteer, I certify that the elections were stolen… as they always are when you can’t even ask for an ID or challenge eligibility.

    As an actual volunteer, what did you see specifically that makes you think the election was stolen?

    Also, many previous elections were run without voter ID and eligibility challenges. Were those elections also stolen then?

  14. Nonlin.org: Furthermore, in my neck of the woods, Stalin is envious…

    So America is not back on track then? According to who? Polls shows that Bidens agenda and actions are popular, even among republicans. It’s why the GOP are reduced to its current focus on cancel-culture rather than policy – they don’t have any policies.

  15. The survey (pdf) of 1,138 likely voters across the country—conducted from April 16 to April 19 by Data for Progress on behalf of Vox—found that, when presented without partisan cues, the voting rights and election reform bill is popular with voters across party lines. Overall, 69% of the electorate supports the For the People Act, including 52% of Republicans, 70% of Independents, and 85% of Democrats.

    https://www.commondreams.org/news/2021/05/03/confirming-gop-fears-poll-shows-people-act-popular-republican-voters

    A bit like how the Affordable Care act is popular among republicans until you call it Obamacare, then they hate it. That’s because they are a bit dim.

  16. OMagain: As an actual volunteer, what did you see specifically that makes you think the election was stolen?

    Please sir!

    Was it allowing black people to vote? I mean look at Georgia!

  17. OMagain:Also, many previous elections were run without voter ID and eligibility challenges. Were those elections also stolen then?

    Yeah, Trump stole it too by that reasoning. And, every UK election ever. Thinking things through not a strong point for ’em.

    What is remarkable is how the Dems managed to mobilise so many millions to participate in this supposed fraud, precisely where it mattered.

  18. OMagain: So America is not back on track then? According to who? Polls shows that Bidens agenda and actions are popular, even among republicans. It’s why the GOP are reduced to its current focus on cancel-culture rather than policy – they don’t have any policies.

    Thanks, I was struggling to read the sign. Not seeing the connection to Stalin. Unless it’s the barbed wire around the building in the background. Is that a private prison?

    ETA: I see Flint has suggested a connection.

  19. Nonlin.org: I certify that the elections were stolen…

    There were 62 unsuccessful legal challenges claiming electoral fraud. Have you any credible evidence for your claim?

    There were as they always are when you can’t even ask for an ID or challenge eligibility.

    That’s palpable nonsense. Have you any evidence that allowing everyone who is entitled to vote in an election to do so freely (ETA*: and having that vote accurately recorded and counted) causes elections to be “stolen”? Can you not see how utterly insane your statement is?

    ETA*

  20. Allan Miller: DNA_Jock: He would say nothing about germ cells.

    Charlie: 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.

    Allan Miller: That’s poor, and betrays a weak grasp of biology. Single cells are directly invested in outcomes, because they themselves are directly ‘selected’ (yeah, let’s have another lengthy debate about what ‘selection’ means, shall we? ).

    What are you classing as single cells? Gametes are also single cells. Do you mean “free living” single cells, single cells which belong to colonies or what?

    Not that it matters because all of these cells display NGE.

    Allan Miller: Whereas germ cells are selected only by virtue of the actions of somatic cells sharing their genes, as tissues or as entire organisms that ultimately disappear to leave only those germ lines. This is another example of trying too hard to see unity.

    Perhaps you are confusing unity with uniformity.

    Shapiro writes

    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.

    So when he talks about NGE he is referring to the way that cells manipulate their compliment of DNA. Whether they be somatic cells or germ cells, they are all involved in these processes. They do this in very diverse and intricate ways, some targeted more specifically than others, and not all of the processes are designed to ensure that the cell and its genome are guaranteed to be copied and to continue the line of descent. Germ cell apoptosis is an example of the termination of continued existence.

  21. CharlieM,

    What are you classing as single cells? Gametes are also single cells. Do you mean “free living” single cells, single cells which belong to colonies or what?

    I mean organisms whose life cycle does not include a multicellular, somatic phase.

    Not that it matters because all of these cells display NGE.

    No they don’t. Ah, this assertion stuff is a feckin’ breeze!

    Allan Miller: Whereas germ cells are selected only by virtue of the actions of somatic cells sharing their genes, as tissues or as entire organisms that ultimately disappear to leave only those germ lines. This is another example of trying too hard to see unity.

    Charlie: Perhaps you are confusing unity with uniformity.

    Perhaps I’m not.

  22. CharlieM,

    So when he talks about NGE he is referring to the way that cells manipulate their compliment [sic] of DNA. 

    Rendering it utterly vacuous, as far as I can see.

  23. petrushka:
    I would summarize the discussion as follows.

    There is nothing in physics or chemistry that prevents somatic processes from altering genes, but there are no examples of this happening.

    That is a very vague statement. Genes are being continually altered in a variety of ways by somatic processes. Every time a gene is expressed it is being altered. All those sunseekers who lie sunbathing in the hot sun for any length of time will be getting genetic alterations to some of their cells. Do you think that germ cell production does not involve somatic processes?

    Those organisms that can alter their own DNA are unicellular.

    We have all been unicellular at one stage. All cells can alter their own genome.

    The alterations so far observed appear to be stochastic. The process could be called adaptive, but it is useful because the environment rewards rapid production of variation. The individual variations are not biased toward useful. There are just more variants.

    Genomic mutations appear to be stochastic from one level, but from a higher vantage point hot spots can be observed.

    I’m wondering how this comports with the concept of dysgenics. I forget the buzzword for genetic decay, but it seems opposed to the idea that deliberately increasing variation could be adaptive.

    Control of variation, not a one-sided increase of variation, is a feature of living systems. If there are laws that allow for dynamic balance there doesn’t need to be deliberation at every step of a process. Feedback mechanisms prevent runaway variation. Polarity is in evidence throughout nature and nothing happens in isolation.

  24. CharlieM: Control of variation, not a one-sided increase of variation, is a feature of living systems. If there are laws that allow for dynamic balance there doesn’t need to be deliberation at every step of a process. Feedback mechanisms prevent runaway variation. Polarity is in evidence throughout nature and nothing happens in isolation.

    WTF are you saying?

    Variation balanced by feedback sounds suspiciously like a process we’ve heard of before.

    Show me an instance of NGE making preferentially useful changes. I don’t see any in Shapiro’s book.

  25. Alan Fox:
    The dawn of multicellularity – two cell types!

    Article in Current Biology

    Thanks for that link. I’ll have a read.

    The area around Loch Torridon is a wild but beautiful place. In the 1960s my father and his team were responsible for connecting that area to the national telephone grid. The villagers were fairly isolated before then. Getting the lines in involved some blasting in remote areas. I regret that I was so young at the time and had no interest in what their excavations might have turned up. Although that area did supply me with a plentiful supply of pet slow worms. 🙂

  26. petrushka:
    Semantic or no, neutral is different than dysgenic. I seem to recall a lot of time wasted on genetic entropy, or some such garbage.

    Now, the same people are claiming, or appearing to claim, that organisms lift their genomes up by their bootstraps.

    The simplest form that every organism begins from is as a complete cell. Feel free to call that bootstrapping if you want.

    Charlie, answer my question. Are the variations produced by NGE disproportionately adaptive, or do we just see the adaptive ones, because they survive? Show your work.

    NGE is a general term for processes that cut, splice, proof read, repair, transport, unwind or otherwise manipulate DNA.

    Shapiro notes

    NGE is not an explanatory principle. In this, it differs from the use many evolutionary biologists have made of the descriptive phrase, Natural Selection, to cover gaps in their accounts of adaptive novelties. NGE is only a set of well-documented DNA change operators.

    While NGE can help in understanding the molecular details of rapid and widespread genome change, it does not tell us what makes genomic novelties come out to be useful. How natural genetic engineering leads to major new inventions of adaptive use remains a central problem in evolution science.

    You are asking a meaningless question.

  27. CharlieM: NGE is a general term for processes that cut, splice, proof read, repair, transport, unwind or otherwise manipulate DNA.

    Then that is misuse of language.

    We already have the term “crafting”, and that seems very different from “engineering”.

  28. CharlieM: How natural genetic engineering leads to major new inventions of adaptive use remains a central problem in evolution science.

    We already have a good understanding of how variation plus feedback leads to adaptive inventions.

    What Shapiro et al need to do is show something new. If the immediate products of NGE are stochastic, then it adds nothing to the understanding of evolution, other than another source of variation. Possibly a mechanism to increase variation.

    But what Shapiro’s acolytes are reading into his book is the implication that NGE variants are disproportionately adaptive. Intelligently designed.

  29. Corneel:
    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: You may want to get a bit more specific on the “particular and other changes” bit. What exactly is the difference between a “particular” and an “other” change? How does the cell tell the difference?

    BTW: I know where you want to be going with this, but you should make this explicit.

    I though I was being explicit. Genomic changes are complex. Just because we might be ignorant of all the intricacies of changes are we justified in assuming that they must be accidental? In a similar way prior to the technology that allowed us to observe the details within the cytoplasm of cells, it was generally assumed that it mainly consisted of molecules floating around waiting to bump into a suitable site.

    CharlieM: The mutations which occur in somebody who has skin cancer may be the result of excessive exposure to the sun. This is what caused the mutations which lead to cancer.

    Corneel: People do not die from “excessive exposure to the sun”. They die of cancer.

    CharlieM: 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: Very well. Then you better tell all cancer patients you meet that it is their own fault that they are dying

    Please note, it is not my logic but your logic that survivors of the likes of Hiroshima, Nagasaki and Chernobyl who contracted cancer should themselves bear the responsibility. Since when has “some” been a synonym for “all”.

  30. Corneel:
    CharlieM: I believe that biological research lays too much emphasis on the chemistry and physics of life and this will not produce a satisfactory understanding of life in itself. It’s like trying to understand a story by examining the paper and ink it is written on and the form and arrangement of letters on the page. There is a tendency to ignore anything that goes beyond physics and chemistry.

    Corneel: What nonsense!

    There is a rich and enticing narrative at all biological levels above the molecular / cellular level. You just don’t like that narrative and now you are pretending that it is incomplete. It’s not.

    You believe we have complete knowledge of biology? And I thought only God is considered to be omniscient according to believers. 🙂

  31. CharlieM: Please note, it is not my logic but your logic that survivors of the likes of Hiroshima, Nagasaki and Chernobyl who contracted cancer should themselves bear the responsibility. Since when has “some” been a synonym for “all”.

    Odd how I made the same ‘mistake’ regarding your thoughts on bad backs. Perhaps the problem is not mine or Corneel’s.

  32. What definition of accidental are we using?

    If NGE does not make targeted changes, then it is merely increasing variation.

    If the changes ARE targeted, show me an instance.

  33. Shapiro’s most grievous error is in misunderstanding the ‘Central Dogma’ of Crick. This is common – I just corrected a Wikipedia page on NGE that claimed it was ‘now partially rejected’ or some such nonsense. Proteins manipulating DNA are not violating the Central Dogma. Nor is reverse transcriptase.

    And speaking of reverse transcriptase … if a segment of a retrovirus becomes incorporated into the DNA of an organism by copying its sequence from RNA to DNA, is that NGE? Bearing in mind that the reverse transcriptase is encoded in the viral genome, not the host’s. Now compare the action of a transposon, which likewise includes the means to transpose within the sequence. It just so happens that that sequence already sits in the organism’s genome in the latter case.

    To me, these appear very similar processes, and may actually be related at a fundamental level – retrotransposons may be domesticated retroviruses, or conversely retroviruses may be escaped retrotransposons.

    Both lead to variation, of which a fraction is beneficial. One, Shapiro calls ‘NGE’, the magic wisdom of the organism. The other are the scars of infection. What – apart from the obvious – is the difference?

  34. So Shapiro is arguing, not that NGE does anything spooky, but that it exists.

    It’s another flagellum argument.

    Nineteenth century biology.

  35. Allan Miller: Proteins manipulating DNA are not violating the Central Dogma. Nor is reverse transcriptase.

    Oh what basis do you make this statement?

  36. My understanding is that the central dogma could be restated as: There is no mechanism for translating protein sequences into DNA sequences.

  37. phoodoo: Oh what basis do you make this statement?

    On the basis that the Central Dogma is referring to the transfer of sequential information. It’s not disbarring the general action of proteins on DNA, which would be an odd position to take, since they have long been known to be intimately involved in DNA manipulation.

    Naively stated, as DNA -> RNA -> protein, it might be argued that reverse transcriptase (RNA -> DNA) violates it, but it was never formulated in that way to begin with. The differences between RNA and DNA, chemically, are quite trivial, restricted to an oxygen atom per monomer and a methyl group every 2nd base. We give them different names, they operate differently in biology, but they aren’t all that different, particularly in regard to base pairing, the essence of sequential information.

  38. Allan Miller: Naively stated, as DNA -> RNA -> protein, it might be argued that reverse transcriptase (RNA -> DNA) violates it, but it was never formulated in that way to begin with.

    This is what I am talking about. What do you mean it was never formulated that way to begin with? According to you?

  39. I’ll type it out for the idle:

    “this [the Central Dogma] states that once “information” has passed into protein it cannot get out again. […] the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible, but the transfer from protein to protein, or from protein to nucleic acid, is impossible. “Information” here means the precise determination of sequence […]

  40. Allan Miller: Page 31

    Oh, I see. You mean where Crick says-“There is nothing in the evidence so far to prove that these differences between species are under the control of Mendelian genes.” Is that what you are citing?

    Or perhaps-“Our basic handicap at the moment is that we have no easy and precise technique with which to study how proteins are folded.” ?

    Or it could be you meant-“If a meal is provided which lacks an essential amino acid, it is no use trying to make up for this deficiency by providing it a few hours later.” Is that the citation you mean?

    Or maybe you meant “What sort of molecules such adapters might be is anybody’s guess.”

    Or, or….”Dounce”.???

  41. phoodoo,

    You mean where Crick says […]

    I mean where Crick formulates the ‘Central Dogma’, which you requested a citation for. Under the heading ‘Central Dogma’, which I’d thought was obvious. On page 31, which I entitled my link by way of clarification. Which I then thought I’d better type out ‘for the idle’, because I know what lazy, obtuse bastards some of my readers can be when the mood is upon them.

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