The Spiralling Flow of Life

In this series of videos Johannas Jaeger gives us some very interesting things to consider. He considers proteins to be pleomorphic assemblies not molecular machines.
Jaeger doesn’t believe in, nor feel the need to propose any extrinsic form of vitalism, but he does accept what Denis Walsh called methodological vitalism. If organisms are purposeful then it is an intrinsic purposefulness.

If we are to gain a meaningful understanding of the organism the machine metaphor will in no way suffice. Life is self-sustaining at all levels. The symbol of the caduceus is apt at so many levels, from the double helix of DNA to the movement of the solar system as it travels around the galaxy. Here is a link to a gif of the motion of the planets relative to the sun. Our hearts take on their form by the layers of muscle being laid down in a helical manner as the blood spirals onward.

The late Gerald D.BuckbergMD, professor and pioneer in cardiac surgery had this to say:

Knowledge develops through analysis, differentiation, or taking things apart. Wisdom evolves by synthesis, integration, or by putting things together, to see with the eyes of the mind.
These steps are not very helpful unless we undertake one other action, which is wholeness: to bring together diversities, to have complementary activity. I believe that we, as cardiac surgeons, are particularly fortunate because we can learn, we can understand, and we can act on the part of our patients.

There are many very intelligent people who consider dynamic processes to be more fundamental than physical matter.

D’Arcy Thompson studied living forms and their morphogenesis and did a lot of work on various animals and plants, comparing forms and applying mathematical rules to determine how one form changes into another.

From the book, “On Growth and Form”, he wrote:

The fir-cone may be looked upon as a cylindrical axis contracted at both ends, until it becomes approximately an ellipsoidal solid of revolution, generated about the long axis of the ellipse; and the semi-ellipsoidal capitulum of the teasel, the more or less hemispherical one of the thistle, and the flattened but still convex one of the sunflower, are all beautiful and successive deformations of what is typically a long, conical, and all but cylindrical stem. On the other hand, every stem as it grows out into its long cylindrical shape is but a deformation of the little spheroidal or ellipsoidal or conical surface which was its forerunner in the bud.

I would say that plant growth is expressed in varying degrees between point-wise radial forces and plane-wise peripheral forces.

To learn about the construction and growth and working of the organism he believes that the physical sciences are our only guide, but in, “On Growth and Form”, he wrote:

Matter as such produces nothing, changes nothing, does nothing; and however convenient it may afterwards be to abbreviate our nomenclature and our descriptions, we must most carefully realise in the outset that the spermatozoon, the nucleus, the chromosomes or the germ-plasm can never act as matter alone, but only as seats of energy and as centres of force.

Life does not so much consist of matter but of processes of dynamic transformations. As the human genome project demonstrated, obtaining the sequences of DNA reveals very little about life. Understanding comes only with the grasp of the movements, transformations and interactions of living forms. And this is just as true whether it is populations of organisms or intracellular molecular complexes.

Life need not and does not break any of the rules of chemistry or physics.

Goethe could see and experience the reality of dynamic, living, nature. The living world should not be thought of as a production line, manufacturing organisms as objects of nature.

In ‘Pluto’s Republic’, Peter Medawar wrote:

When scientific research is studied on the hoof, so to speak, we find that very few theories are utterly discredited in the style of which (for example) Thomas Henry Huxley demolished Goethe’s and Oken’s Vertebral Theory of the skull.

Medawar had made the mistake of attributing to Goethe the same understanding of the archetype as Owen and Oken. But Goethe’s idea of the archetype should not be thought of in the same way. His archetype is not a physical, ancestral form available to be apprehended by the senses. His archetype was an all inclusive dynamic process that does not reside within any one specific manifestation.

This piece makes clear Huxley’s view:

Huxley highlighted that method in his 1858 Croonian lecture, “On the Theory of the Vertebrate Skull,” in which he rejected a theory proposed by Johann Wolfgang von Goethe and Lorenz Oken in Germany and by Richard Owen in England that the bones of the skull and of spine in vertebrates were serial homologous.

But Goethe did not consider their relationship to be as such. For Goethe a vertebra is as much a transformed skull bone as the bone is a transformed vertebra. It is not that one has developed from the other but that they both express the archetype in their individual way. He could compare them both and picture the reciprocal transformations in his mind’s eye.

He did not examine their static form, but he could see the movement in how they took on their various shapes.

In one of Jaeger’s videos he quotes Dan Nicholson:

Living forms are the expression of a perpetual stream of matter and energy which passes the organism and at the same time constitutes it.

Perhaps he meant something like, “passes through the organism”.

Anyway  John Dupré & Daniel J. Nicholson had this to say:

When considering a particular organism, there is a general tendency to privilege or prioritise the adult stage of its life cycle (for instance, in the context of taxonomic discussions), as this is the period during which the organism most closely resembles a thing by virtue of its relative stability. But we should not forget that the organism encompasses the entire life cycle; indeed, it is the life cycle itself that constitutes the organism. Strictly speaking, it is incorrect to speak of an egg developing into a frog, as the egg is really a temporal part of the developmental trajectory that is the frog.

Nicholson continues his argument here:

It is quite remarkable to observe that, despite the enormous empirical advances that have been made since 1962, our basic theoretical picture of the cell has remained essentially unchanged (see, e.g., Bray, 2009; Danchin, 2009). The standard view nowadays is that the cell coordinates its functions by virtue of a ‘genetic program’ encoded in the DNA that directs and controls the expression of a specific set of RNAs and proteins, which assemble deterministically into stable ‘molecular machines’ that reliably and efficiently execute predetermined operations according to the mechanisms of cell division, endocytosis, signal transduction, etc. Machine analogies and metaphorical references to ‘locks’, ‘keys’, ‘gates’, ‘pumps’, ‘motors’, and ‘engines’ continue to pervade the technical literature (e.g. Piccolino, 2000; Frank, 2011), as does talk of the ‘machinery’ (e.g. Goodsell, 2009) and ‘circuitry’ (e.g. Alon, 2007) that underlies the cellular organization. The machine conception of the cell (MCC) itself is seldom explicitly defended; it has become so engrained in our minds that we simply take it for granted…
As a result, critical reviews have begun to appear that explicitly challenge the reductionistic and deterministic presuppositions of mechanicism and question the coherence of the familiar clockwork image of the cell. Notable examples include Kirschner et al. (2000), Astumian (2001), Woese (2004), Cornish-Bowden (2006), Longo and Tendero (2007), Karsenti (2008), Huang (2009), Mayer et al. (2009), Kupiec (2010), Moore (2012), Bizzarri et al. (2013), Talbott (2013), Heams (2014), Longo and Montévil (2014), Soto and Sonnenschein (2018), and a series of articles by Kurakin (2005, 2006, 2009, 2010). Drawing and building on this burgeoning body of literature, the aim of this paper is to establish the inadequacy of the MCC. From a theoretical perspective, the MCC offers a poor and rather misleading representation of biological reality—or so I will argue.

Rivers flow inexorably downwards, life flows inexorably upwards.

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464 thoughts on “The Spiralling Flow of Life

  1. Corneel:

    CharlieM: If a gene remains in the DNA of the population but is never again expressed then it is as good as lost.

    If a gene remains in the DNA of the population but is never again expressed then it will not be lost. That is what “remains” entails.

    And neither will lipid bilayers be lost.

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  2. CharlieM: And neither will lipid bilayers be lost.

    That is true. But, in case you have forgotten, the statement you are pretending to defend is this one:

    If I was looking for some molecule that remained constant over the generations I would pick polysaccharides or lipids.

    Which is remarkably silly. Your “lipid bilayer” is a mixture of a variety of different lipids, and the composition varies depending on the availability of food and (you guessed it) gene expression.
    Polysaccharides vary enormously: even the simplest two, amylose and cellulose, will vary in length, and all the myriad others vary in branching pattern and/or modifications.
    Hilariously, your “remained constant over the generations” is simply another example of your “they all look the same to me” mistake, but at a molecular level.
    [Cue creationist quoting a large block of text describing how complex mucopolysaccharides are, therefore Jesus.]
    The amazingly complex structures of polysaccharides depend on the expression of genes that direct their synthesis, modification, and digestion. See, for example, the effects of a defect in the N-sulfoglucosamine sulfohydrolase gene.

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  3. Corneel: Yes, I remember you asserting those things without a shred of evidence just like you are doing now.

    Yet you commented extensively on the evidence presented. Of course you didn’t like any, but it’s all here. Maybe you’re forgetful. Repressed memories? Lay on the couch and Dr. Fraud will be with you shortly. Better yet, just read your own comments. Last time you were explaining why it’s ok for e coli to not “evolve”.

    Yes. Good to see you too survived the virus. I hear trillions died and many more are shell shocked. Terrible war! Btw, as an expert and true believer, what’s your prediction on the “evolution” of the virus and the human race? Who will win this “evolutionary” war? Or is it a rat race? Please say “humans”. Please?

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  4. Corneel: What Alan said.

    What Alan said makes no sense. Take off your blinders.

    Corneel: Gene-like sequences that fail to make a functional product do exist and are known as pseudogenes. They tend to decay by accumulation of mutations or get deleted.

    Your appeal to “decay” is based on what?

    Pseudogenes are supposed to save Darwinism. You didn’t know?

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  5. Mung: What Alan said makes no sense.

    What I said was that selection acts on phenotypes. What is it that makes no sense to you?

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  6. Corneel: Gene-like sequences that fail to make a functional product do exist and are known as pseudogenes. They tend to decay by accumulation of mutations or get deleted.

    How long exactly does it take for something to decay and get deleted? Genes, vestigial organs, behaviors, etc? Do you still have your “inner fish”? Is it tuna? Shark? Clownfish? What about your inner fungus? Do you still have an inner athlete’s foot?

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  7. Alan Fox: What I said was that selection acts on phenotyp. What is it that makes no sense to you?

    Selection acts on what selection acts on. Who ever thought otherwise.

    If some DNA sequence has no net effect on the phenotype, selection won’t “see” it

    The “net effect” is determined by selection. Or magic.

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  8. Mung: Selection acts on what selection acts on. Who ever thought otherwise.

    The “net effect” is determined by selection. Or magic.

    The irresistible lure of obtuseness.

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  9. CharlieM:
    And neither will lipid bilayers be lost.

    Lipid bilayers are constantly replenished (by enzymes: gene products), much as water molecules are (with the distinction that the latter is more usually imported). The idea that you have a lipid bilayer at both time t1 and time t2 is not indicative of a long life for lipids, any more than the perpetual wetness of cells indicates that the water is not ‘lost’.

    The reason DNA can be metaphorically depicted as ‘immortal coils’, lost or retained according to termination or continuity of sequence in time, is not due to the conservation of a DNA molecule. The molecular contents of a cell are in a constant state of flux, with half-lives measured in hours (as I tried to illustrate with the ‘death-cap’ thought experiment). That includes DNA. But there is something about DNA – a property not shared with anything else in or around the cell – that permits the perpetuation of everything else. Which is to say: sequence.

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  10. Mung: Selection acts on what selection acts on. Who ever thought otherwise.

    Selection acts on phenotypes, individual organisms. Of course you can disagree but I am just pointing out your error.

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  11. Mung: What Alan said makes no sense.

    What Alan said is accepted by everybody, including you; There is no difference in the expected survival or reproductive success of genetically different, but otherwise identical organisms.

    Mung: Pseudogenes are supposed to save Darwinism. You didn’t know?

    I didn’t. I was under the impression that the existence of pseudogenes is an established fact. Humans have thousands of ’em. Moreover, any theory supposed to present an alternative to standard molecular evolutionary accounts is required to provide a satisfactory explanation for them.

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  12. Nonlin.org: Do you still have your “inner fish”?

    That has precisely zero relevance to the existence of pseudogenes. Did you read Neil Shubin’s book, BTW? Really recommended.

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  13. CharlieM: The heritable variations are individualized expressions of the archetype. A good question to ask regarding novelty is, how and why do birds have beaks in the first place? The beak is what I would class as a novel feature.

    And yet you link to an article that explains the evolution of avian bills as outgrowths of pre-existing structures, as a result of gene mutations in signaling pathways. That implies that archetypes somehow communicate variations to the species through inducing mutations of the DNA. Yes, the DNA.

    So now the question becomes: How do the “individualized expressions of the archetype” translate into the appropriate genetic mutations? In fact, given that purifying selection still needs to weed out forms that exceed restrictions, why do we need to suppose a source of pre-adapted forms at all?

    CharlieM: Where did I claim small changes to be “extreme forms” of the archetype?

    Here:

    And the ears of modern maize compared to teosinthe are just as predicted by Goethe. Both are indivual expressions of the archetype, the former taken to the extreme. Just as many dog breeds are extreme forms of canid.

    CharlieM: Weaker gravitational forces, something like that. In the present earthly environment, a mouse that was as big as an elephant would no longer be a mouse. The lowest standard classification is ‘species’. So let’s say ‘mouse’ applied to the genus.

    Yes, all distant future descendants of mice, including those the size of an elephant, would be classified as a mouse. Of course, Mus would no longer be genus level, but some higher classification, like Mammalia is now.

    CharlieM: Conventional evolutionary proponents speculate on ancestral relationships, yet over a large number of generations it is impossible to ascertain direct lines of descent.

    That will come as a big surprise to all taxonomists, I imagine.

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  14. CharlieM: But as evolution proceeds it is evident that organisms come to exist that show more individualistic behaviour than in previous ages. Individual prokaryotes show very little in the way of personality. In humans and higher animals the personality of individuals begins to shine from within their group behaviour. Your dog will show much more of its personality than your goldfish.

    And now you are equating individuality with personality. Do you see why that is an anthropocentric way of defining individuality?

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  15. Nonlin.org: to Corneel:

    Corneel: But lots of small changes add up and mice most certainly can in time become as big as elephants. The ancestor of all placental mammals, including elephants and blue whales, is believed to be a tiny insectivore.

    Someone believes something for sure. But is it true? Turns out, there is no evidence for it. And more precisely all evidence is against. Remember no gradualism? No divergence of character? Not even e coli is “evolving”?

    In the book, Basic Questions in Paleontology: Geologic Time, Organic Evolution, and Biological Systematics Otto H. Schindewolf, who opposed Darwinian gradualism, writes:

    The question now arises whether those miniscule mutational steps and morphological changes within an existing framework are also sufficient to explain macroevolution, the comprehensive remodeling of forms of higher taxonomic categories, which means the elaboration of new organs and structural designs.

    He did not think it was.

    Stephen Jay Gould wrote in the forward:

    Darwinism may work perfectly well, and to near exclusivity, in our observable world of lifetimes and generations. But suppose this lovely and proven mechanism cannot encompass, by extrapolation, the full scale of vastly more extensive changes that unfold during millions of years…

    Darwinian natural selection, in its essence, is a theory of trial-and-error externalism. Organisms propose (but do not direct or constrain) by presenting copious and random variation to a selecting environment. The external environment (both physical and biotic) then disposes by granting differential reproductive success to those variations fortuitously better adapted to changing local conditions. The application of this notion to all scales of macroevolution requires smooth, uniformitarian extrapolation. Gradual and adaptive changes, accumulating step by step through countless generations of competition, underlie all scales of morphological transformation and the waxing and waning of large clades.

    As can be seen from the example of the Galapagos finches, Darwinian evolution is the perfect explanation for features within a population varying around a mean, even if that mean itself changes changes over time. But features such as beaks do not just appear from nowhere. If birds really did descend from therapod dinosaurs then their beaks are just one part of a suite of changes that involved multiple orchestrated genetic changes.

    Some people say that neoteny accounts for the change from dinosaur to bird morphology. I say that this is looking at it the wrong way round. Therapod dinosaurs extended the aging process to its limits. The populations became old and died. Dinosaurs were birds that suffered the ossification, sclerosis and hardening that comes about with age. These are signs of impending death and that is indeed what happened. In any cataclysmic event it is the old and infirm that are at most risk of perishing.

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  16. Mung: to Corneel

    Corneel: If a gene remains in the DNA of the population but is never again expressed then it will not be lost. That is what “remains” entails.

    So natural selection works equally on that which is expressed and that which is not expressed?

    Godlike powers.

    Natural selection works on features which are the product of complex, intricate, genetic processes. It’s all about maintaining balance.

    You are right in that some people lie to endow it with Godlike creative powers.

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  17. Corneel: What I opposed was Charlie’s claim that IF they remain present in the population, they are “as good as lost”. No they are not. If they remain present, they remain present. That’s just common sense

    That’s why I said ‘as good as lost’ and not ‘lost’.

    The fact is that it isn’t just a gene that gets reproduced. It is the system of expression that is reroduced.

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  18. Allan Miller:

    CharlieM:
    I presume by ‘gene’ you mean a particular DNA segment?

    Generally yes, though the same applies to the molecular biologist’s gene: a segment that produces a functional transcript. The latter is still a subset of the former.

    But genes are always part of living systems. Just as one of your fingers loses its reality if it is separated from your body so the gene loses its reality if it is separated from the the transcription/translation processes.

    What is of importance between your skin cells and you son’s skin cells is the processes of gene expression.

    Doesn’t matter. The fact remains that our DNA segments are not the same molecule, but are the same sequence. This is in response to your argument that, if you were looking for a persistent molecule, you’d pick something else. I’m not arguing for molecular persistence of DNA, is the point I was getting at.

    And I’m arguing that the sequences are meaningless unless they are a part of the living processes. The processes of transcription and translation remain constant through the generations. Proteins are produced by the same means.

    Me: Gene-centrism results from a process, not a substance: replication with reciprocal recombination. It creates a competition at a subgenome level, much like those between individuals or groups.

    Charlie: Genes do not compete.

    They do. There is a finite set of loci in a population – in a diploid species, that’s twice the census size of the population. Genes compete for representation in that set, in much the same way as individuals compete for representation in the finite set represented by a population. This competition need not be direct – two individuals that never met are still in competition, in an ecological sense.

    Here in chapter 3 of ‘Dominant and recessive gene expression’, they write:

    The researchers extended their analysis to additional alleles. They made in silico predictions about the small RNA sequences and their targets by reconstructing their evolutionary history, and in so doing showed that the duplication, deletion and diversification processes of small RNAs and their targets could explain the development of a dominance network. As hypothesised, it was clear that genetic elements accumulated in different allelic lines. Some alleles have become dominant through the acquisition of small RNAs while others have become recessive through the target acquisition, almost as though they have come to a mutually beneficial agreement. It is as advantageous to be recessive as dominant; what really matters is that heterozygotes express a single allele.

    More like mutual arrangement than competition. But either way it is processes within dominance networks that determine which genes are expressed.

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  19. CharlieM: Otto H. Schindewolf

    Oh goodness me, Charlie! You bring back fond memories of Professor John A. Davison. Richard Goldschmidt and Otto Schindewolf were heroes of his (John even called his pet dachshund Otto). Saltation and Goldschmidt’s “hopeful monsters” still getting a mention after all these years makes me smile.

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  20. DNA_Jock:

    CharlieM: And neither will lipid bilayers be lost.

    That is true. But, in case you have forgotten, the statement you are pretending to defend is this one:

    If I was looking for some molecule that remained constant over the generations I would pick polysaccharides or lipids.

    I am not pretending to defend anything, but between us we are making my point.

    Which is remarkably silly. Your “lipid bilayer” is a mixture of a variety of different lipids, and the composition varies depending on the availability of food and (you guessed it) gene expression.

    How does the lipid bilayer in, say, your red blood cells differ from the lipid bilayer that is or was in the blood of your recent ancestors?

    Polysaccharides vary enormously: even the simplest two, amylose and cellulose, will vary in length, and all the myriad others vary in branching pattern and/or modifications.

    And, just as in the lipid bilayer, I was not making a comparison between any old polysaccharide, I was talking about comparing particular polysaccharides over generations.

    Hilariously, your “remained constant over the generations” is simply another example of your “they all look the same to me” mistake, but at a molecular level.
    [Cue creationist quoting a large block of text describing how complex mucopolysaccharides are, therefore Jesus.]
    The amazingly complex structures of polysaccharides depend on the expression of genes that direct their synthesis, modification, and digestion.

    And here you stress the point I was making. Gene expression is a process. And the creation of any complex structure depends on the orchestrated expression, in time and space, of multiple genes.

    See, for example, the effects of a defect in the N-sulfoglucosamine sulfohydrolase gene.

    Yes there are many horrible diseases caused by abnormal gene expression. But how did these genes get altered in the first place? It would have occurred because the copying process was not one hundred percent accurate. There are always processes behind these things.

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  21. Nonlin.org to Corneel:

    Corneel: Gene-like sequences that fail to make a functional product do exist and are known as pseudogenes. They tend to decay by accumulation of mutations or get deleted.

    How long exactly does it take for something to decay and get deleted? Genes, vestigial organs, behaviors, etc? Do you still have your “inner fish”? Is it tuna? Shark? Clownfish? What about your inner fungus? Do you still have an inner athlete’s foot?

    His “inner fish” only lasted until his mother’s waters broke. The waters have never broken for extant fish. They have not moved past this stage. They are still nourished by the ‘amniotic fluid’ of Mother Earth which are the oceans, lakes and rivers.

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  22. Allan Miller:

    CharlieM:
    And neither will lipid bilayers be lost.

    Lipid bilayers are constantly replenished (by enzymes: gene products), much as water molecules are (with the distinction that the latter is more usually imported). The idea that you have a lipid bilayer at both time t1 and time t2 is not indicative of a long life for lipids, any more than the perpetual wetness of cells indicates that the water is not ‘lost’.

    The reason DNA can be metaphorically depicted as ‘immortal coils’, lost or retained according to termination or continuity of sequence in time, is not due to the conservation of a DNA molecule. The molecular contents of a cell are in a constant state of flux, with half-lives measured in hours (as I tried to illustrate with the ‘death-cap’ thought experiment). That includes DNA. But there is something about DNA – a property not shared with anything else in or around the cell – that permits the perpetuation of everything else. Which is to say: sequence.

    To use a popular saying, DNA is necessary but not sufficient for replication and reproduction.

    As stated here cell reproduction is an intricate process:

    During division, eukaryotic cells undergo a dramatic, complex and coordinated remodelling of their cytoskeleton and membranes. For cell division to occur, chromosomes must be segregated and new cellular structures, such as the spindle apparatus, must be assembled. Pre-existing organelles, such as the nuclear envelope, endoplasmic reticulum and Golgi apparatus, must be disassembled or remodelled, distributed and reformed. Smaller organelles such as mitochondria as well as cytoplasmic content must also be properly distributed between daughter cells.

    Orthodox evolutionary theory does not rely on the immortality of DNA sequences, it relies on the opposite. It posits DNA changes as being the major cause of life diversifying.

    And in the case of individual development, if it is assumed that an organism has but one nuclear genome sequence, then what attributes does it have that causes it to produce more than one type of organism? Caterpillars and butterflies are two very distinct creatures, as are tadpoles and frogs. It is not the sequences but the way that they are manipulated that allows for this.

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  23. Corneel: That has precisely zero relevance to the existence of pseudogenes. Did you read Neil Shubin’s book, BTW?

    So I noticed you’re not answering the question. Let’s try again: “How long exactly does it take for something to decay and get deleted? ” This is a question directly related to your comment. Let’s not try to make it about something else.

    If you don’t or can’t answer, let’s agree to chalk this up to evidence against “evolution”. Depending on your answer, Neil Shubin may have (or not) lost all credibility. So what will it be?

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  24. CharlieM: As can be seen from the example of the Galapagos finches, Darwinian evolution is the perfect explanation for features within a population varying around a mean, even if that mean itself changes changes over time.

    We do not need the Darwinist crutch. “Organisms are endowed with some level of adaptation mechanisms” explains everything: the limited adaptation and the regression we see over and over.

    CharlieM: Dinosaurs were birds that suffered the ossification, sclerosis and hardening that comes about with age.

    If so, we would have seen bird fossils preceding dinosaur ones. How about no descent relationships?

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  25. CharlieM: That’s why I said ‘as good as lost’ and not ‘lost’.

    The fact is that it isn’t just a gene that gets reproduced. It is the system of expression that is reroduced.

    The ‘system of expression’ is only reproduced by virtue of genetic replication.

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  26. CharlieM:Me: Generally yes, though the same applies to the molecular biologist’s gene: a segment that produces a functional transcript. The latter is still a subset of the former.

    Charlie: But genes are always part of living systems.

    But but but. I know. I said I know back in June, again in July and August, may have mentioned it in September, now here we are in October. I know it, Dawkins knows it, as did Maynard Smith, Hamilton, Williams. This is not a cogent criticism of anything I’ve been saying regarding the evolutionary perspective they advanced, and is not made so by endless repetition.

    If you were studying for exams, you might put some effort into understanding the subject you critique. But – a common theme in such debates – it always devolves into scurrying round trying to find why something is wrong, without first troubling to comprehend it.

    Just as one of your fingers loses its reality if it is separated from your body so the gene loses its reality if it is separated from the the transcription/translation processes.

    Hello analogy, my old friend.

    Me: Doesn’t matter. The fact remains that our DNA segments are not the same molecule, but are the same sequence.
    Charlie: And I’m arguing that the sequences are meaningless unless they are a part of the living processes.

    Doesn’t matter. DNA replication does not distinguish between ‘processed’ and ‘unprocessed’ sequence. Copies of both pass to offspring, and on through the generations, via semiconservative replication. Whatever ‘meaning’ they have in physiological contexts, and any effect of that meaning on reproductive success, are irrelevant to the fundamental facts of replication.

    The processes of transcription and translation remain constant through the generations.

    Indeed they do. Yet lineages change, it seems. I wonder why? 🤔 What changes, if gene expression is constant?

    Me: They do. There is a finite set of loci in a population – in a diploid species, that’s twice the census size of the population. Genes compete for representation in that set, in much the same way as individuals compete for representation in the finite set represented by a population.
    Charlie: Here in chapter 3 of ‘Dominant and recessive gene expression’, they write:

    Not sure why you think that is relevant, or contradicts what I said. While in a diploid, a given allele will encounter either a copy or a variant of itself. But still, there are 2N loci to go at in a population of N individuals. On meiosis, they go their separate ways – and there are some interesting ‘competitions’ over occupancy of the lifeboats on that separation, too, well explained by a gene-centrist stance, but not at all by any ‘holist’.

    More like mutual arrangement than competition. But either way it is processes within dominance networks that determine which genes are expressed.

    Dominance relations are often a simple result of chemistry, rather than a ‘process’ that sits above an allele pair deciding which is used – but again, you are using physiological relations to attack an evolutionary argument. I would consider it a personal favour if you would recognise this distinction…

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  27. CharlieM: As stated here cell reproduction is an intricate process:

    Gosh, really? You live and learn.

    Orthodox evolutionary theory does not rely on the immortality of DNA sequences, it relies on the opposite. It posits DNA changes as being the major cause of life diversifying.

    This is wrong. It doesn’t ‘rely on’ either to the exclusion of the other. If there were no level of fidelity in replication, a ‘selfish gene’ would not last more than a generation, and nor would a lineage.

    Also without a degree of fidelity, phylogenetic methods would be impossible, while without markers of change, again there would be no distinguishing information. For a reductio ad absurdum, imagine trying to reconstruct the relations among a set of (i) completely scrambled genomes or (ii) identical genomes. Those are the poles of fidelity your false dichotomy imagines.

    And in the case of individual development, if it is assumed that an organism has but one nuclear genome sequence, then what attributes does it have that causes it to produce more than one type of organism?Caterpillars and butterflies are two very distinct creatures, as are tadpoles and frogs.

    Epigenetics (which is genetically-encoded; don’t get too excited). There is no particular distinction between epigenetic modifications producing different tissues, and the same basic process producing different juvenile and adult forms.

    You’d have to ask yourself why the same caterpillar always yields the same butterfly. Where is that species-level constancy encoded? It’s exactly the same question I have posed in relation to tissue-specific alternatively-spliced isoforms. You hand-wave arbitrarily at ‘something in the zygote’, but damned if you will concede that that ‘something’ is the genome.

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  28. Alan Fox: Oh goodness me, Charlie! You bring back fond memories of Professor John A. Davison. Richard Goldschmidt and Otto Schindewolf were heroes of his (John even called his pet dachshund Otto).

    Beware of anyone who can’t spell ‘minuscule’ …

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  29. Allan Miller: But – a common theme in such debates – it always devolves into scurrying round trying to find why something is wrong, without first troubling to comprehend it.

    +1

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  30. Nonlin.org: Let’s try again: “How long exactly does it take for something to decay and get deleted? ”

    How long exactly does it take for WHAT to decay and get deleted? Are you still talking about pseudogenes or have you moved on to tuna or something else completely irrelevant perhaps?

    Nonlin.org: This is a question directly related to your comment.

    How?

    Nonlin.org: If you don’t or can’t answer, let’s agree to chalk this up to evidence against “evolution”.

    Let’s not. Do your parents know you are playing with their computer?

    1+
  31. Previously I wrote

    Between the heavenly, light, peripheral plane-wise pole and the earthly, weighty, point-wise pole, birds drift towards the heavenly while elephants gravitate towards the earthly. Elephants are much more constrained by gravity than birds are.

    A closer look at feathers, especially the flight feathers of birds, indicates their relationship to this pole.

    As can be seen in this video as feathers develop the barbs grow from the tips down towards the body. this is opposite to the way hair grows in mammals. As the feather grows into its planar shape the barbs form a flowing spiral winding around the inside of the protective tube.

    And as flight feathers need to be anchored to bone, the base of the feather bud grows in towards the bone. Some birds have quill knobs on their ulnae and these begin to develop in preparation for the quill bases growing towards them. But with or without quill knobs the flight feathers need to be firmly attached to the bones in order to produce a rigid planar surface capable of withstanding the aerodynamic forces it will encounter..

    Feathers in general have a planar quality while hairs have more of a radial. line-like quality.

    In ‘Flight feather attachment in rock pigeons (Columba livia): covert feathers and smooth muscle coordinate a morphing wing’, by Tobin L. Hieronymus, there are many figures and sketches detailing of some of the muscles attached to wing feathers. I’ve attached one below. Reading this brings home just how intricate bird wings are. I look at all these muscle and tendon connections and wonder how, when a bird such as an eagle, moults its flight feathers in sequence, all the muscles must also go through a process of separating and reattaching while the bird still retains the ability to fly.

    Individual primary feather can be skilfully controlled as the bird manoeuvres in flight. But, regarding the whole wing, if you have ever played around with a birds wing you will know that they are very rigid when extended but as they fold they become very flexible and have a wide range of movement through many directions.

    Compared with a human hand the hand of a bird has been reduced and fused to the point where it has no dexterity. In the forelimb of birds the dexterity has been pushed out beyond even the extremities of the bones to the feathers. But the use this dexterity can be put to is limited, providing mastery over aerodynamics and little else. Any creative dexterity that birds possess has been transferred up from the limbs to the head. Their beaks serve a similar creative purpose to human hands. But a single beak will never achieve the level of creativity of a pair of hands.

    In their evolution, birds may have reached the heights. But the consequences of this rapid rise to fame are that as individuals they will always remain creatures and never creators.

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  32. Allan Miller,

    I confess this went over my head. But wandering into pedant’s corner for a second, I see “miniscule” has been in use since the nineteenth century and is no longer regarded as incorrect but alternative.

    What was the joke I missed BTW?

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  33. Alan Fox:
    Allan Miller,

    I confess this went over my head. But wandering into pedant’s corner for a second, I see “miniscule” has been in use since the nineteenth century and is no longer regarded as incorrect but alternative.

    Ah well. sic transit gloria mundi. Likewise one can look up synonymous usage for ‘infer’ and ‘imply’, but I will not yield, dammit! (A school classmate tried to point out the correct usage of those terms, and I resisted based upon my own dictionary, but … he was right!).

    What was the joke I missed BTW?

    Not sure what you mean!

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  34. Corneel:

    CharlieM: The heritable variations are individualized expressions of the archetype. A good question to ask regarding novelty is, how and why do birds have beaks in the first place? The beak is what I would class as a novel feature.

    And yet you link to an article that explains the evolution of avian bills as outgrowths of pre-existing structures, as a result of gene mutations in signaling pathways. That implies that archetypes somehow communicate variations to the species through inducing mutations of the DNA. Yes, the DNA.

    You are still imagining the archetype to be some external entity acting from without. When we observe a creature in space we observe its body. The body is the creature as we see it for sense perception. When we observe a creature in time we observe the archetype. The archetype is the creature as we see it for thinking perception.

    So now the question becomes: How do the “individualized expressions of the archetype” translate into the appropriate genetic mutations? In fact, given that purifying selection still needs to weed out forms that exceed restrictions, why do we need to suppose a source of pre-adapted forms at all?

    The archetype is not the ‘source’ in the way you imagine it. It is that aspect of any organism that is at first hidden from perception. It can only be revealed in an inner way through mental effort.

    CharlieM: Where did I claim small changes to be “extreme forms” of the archetype?

    Here:

    And the ears of modern maize compared to teosinthe are just as predicted by Goethe. Both are individual expressions of the archetype, the former taken to the extreme. Just as many dog breeds are extreme forms of canid.

    Sorry for the confusion. I didn’t mean extreme form of the archetype. I meant that maize as we see it has assumed extreme dimensions compared with any naturally growing teosinthe. It is like a grass that we would observe to have assumed extreme proportions.

    CharlieM: Weaker gravitational forces, something like that. In the present earthly environment, a mouse that was as big as an elephant would no longer be a mouse. The lowest standard classification is ‘species’. So let’s say ‘mouse’ applied to the genus.

    Yes, all distant future descendants of mice, including those the size of an elephant, would be classified as a mouse. Of course, Mus would no longer be genus level, but some higher classification, like Mammalia is now.

    To produce an elephant sized mouse would require a vast amount of changes in form that would have to be coordinated in such a way that permitted the descendants to remain viable. It is an interesting thought experiment.

    On the other hand every elephant that has been born, as it develops, has passed through the stage of being the size of a mouse.

    CharlieM: Conventional evolutionary proponents speculate on ancestral relationships, yet over a large number of generations it is impossible to ascertain direct lines of descent.

    That will come as a big surprise to all taxonomists, I imagine.

    I should have made it clear I was talking about groups or species. For example what would be the direct ancestor of humans or chimps, or herring gulls?

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  35. Nonlin.org:
    How long exactly does it take for something to decay and get deleted? Genes, vestigial organs, behaviors, etc?

    Varies a lot. In the case of genes, in most eukaryotes, there’s little to no selection pressure against useless pieces of DNA, so eroding the sequence to become unrecognizable, or deleted, can take quite a while. For vestigial organs it depends on whether the remaining vestiges are still useful or not. If the vestiges are useful they’ll remain. Biology is a bit complex. In case you haven’t noticed.

    Nonlin.org:
    Do you still have your “inner fish”? Is it tuna? Shark? Clownfish? What about your inner fungus? Do you still have an inner athlete’s foot?

    Obviously you haven’t bothered to understand what the book is about. Given that your main sources are misread and poorly understood wikipedia pages, I’m not too surprised.

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  36. Corneel:

    CharlieM: But as evolution proceeds it is evident that organisms come to exist that show more individualistic behaviour than in previous ages. Individual prokaryotes show very little in the way of personality. In humans and higher animals the personality of individuals begins to shine from within their group behaviour. Your dog will show much more of its personality than your goldfish.

    And now you are equating individuality with personality. Do you see why that is an anthropocentric way of defining individuality?

    I’ll take that chance.

    From here

    But why did experts until recently largely ignore the study of animal personality in the wild?

    Andrew Sih, a professor at the University of California, Davis, suggests that it is perhaps because animal personality was perceived as soft science and dangerously close to the scientific sin of anthropomorphism. Animal personality studies have crept into the field of biological sciences under various monikers, including behavioral syndromes, coping styles, animal temperament, and interindividual variation.

    Will these scientists get the same criticism?

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  37. CharlieM: The archetype is the creature as we see it for thinking perception.

    Look. This isn’t helping. I want to know how the “habits and lifestyle of a population” have made the particular aspects* of the archetype we observe today realize in actuality and not any of the others that existed in potential.

    *aspects that were at first hidden from perception and could only be revealed in an inner way through mental effort

    Do you even know?

    CharlieM: Sorry for the confusion. I didn’t mean extreme form of the archetype. I meant that maize as we see it has assumed extreme dimensions compared with any naturally growing teosinthe. It is like a grass that we would observe to have assumed extreme proportions.

    Yes, these are modest changes that have occurred in recent history. You deny that these amount to novel traits. Yet whenever I confront you with a more significant evolutionary change, you declare it impossible to have arisen by natural processes, since these require “a great deal of coordinated genetic activity”.

    But a large change is just a lot of small changes accumulating. There is no magical boundary.

    CharlieM: To produce an elephant sized mouse would require a vast amount of changes in form that would have to be coordinated in such a way that permitted the descendants to remain viable. It is an interesting thought experiment.

    It is not a “thought experiment”. This is what actually happened when elephants evolved from the common ancestor of all mammals. What prevents modern mice from growing to such proportions in a similar way? Nothing!

    CharlieM: I should have made it clear I was talking about groups or species. For example what would be the direct ancestor of humans or chimps, or herring gulls?

    Will you deny that mice and elephants have a common ancestor? If you acknowledge that mice and elephants do have a common ancestor, doesn’t it stand to reason that at least one of them has experienced a considerable change in body size?

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  38. CharlieM: Will these scientists get the same criticism?

    LOL, I know Niels Dingemanse from a PhD course we took together and have heard him present his research on animal personality in great tits. Kees van Oers was his colleague at the time at the Netherlands Institute for Ecology, participating in the same research. You’d have loved it: Kees had succeeded in artificially selecting on a personality trait in great tits (risk-taking behaviour), demonstrating a genetic component for this behaviour.

    I strongly doubt either of them would have claimed personality is the defining attribute of individuality, though.

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  39. Corneel: …have heard him present his research on animal personality in great tits.

    Corneel, your English is superb but may I suggest you use “on” instead of “in” in the sentence above. The image I got of your colleague doing his presenting was quite bizarre! 🙂

    ETA my mistake, your English is quite correct and I misread.

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  40. Alan Fox: The image I got of your colleague doing his presenting was quite bizarre!

    Oh, my word. Did the English come up with those bird names on purpose?

    0
  41. Corneel: How long exactly does it take for WHAT to decay and get deleted? Are you still talking about pseudogenes or have you moved on to tuna or something else completely irrelevant perhaps?

    Both. All. “Corneel: Gene-like sequences that fail to make a functional product do exist and are known as pseudogenes. They tend to decay by accumulation of mutations or get deleted.”

    Feel free to start with pseudogenes. Then continue with “vestigial organs”. And “vestigial behaviors”. Either reject those concepts or explain their decay process. Do you still have inner fish vestiges? If so why after all this time?

    Look, someone answered in your place. Obviously the question was not that hard. Are you losing it?

    Apparently, “there’s little to no selection pressure against useless pieces of DNA”. But is that true? We learned in evo-school that any extra work – including reproducing useless features – is in fact detrimental because of wasted resources. Did they (gasp!) lie to us in evo-school?

    Also apparently, “For vestigial organs it depends on whether the remaining vestiges are still useful or not.” This is in fact illogical as, by definition, vestigial organs cannot be useful.

    So the whole answer amounts to something wrong, plus something illogical plus “[it’s] a bit complex”. So, anything else to add?

    I also noticed that you didn’t answer the other question about Covid forecasting. No doubt because “evolution” can’t make a prediction since it isn’t real. Thanks for confirming.

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  42. Corneel,

    Google says no. Titlingur is Icelandic for sparrow apparently. Titmouse and titwillow have the same root. And tit/teat (nipple/breast) may have Dutch origins*. 🧐

    ETA* the word, not the anatomical feature.

    0
  43. Nonlin.org: …by definition, vestigial organs cannot be useful.

    Don’t know which book you are getting your information from but that’s incorrect. Consider the human appendix or an ostriches wings.

    1+
  44. Nonlin.org:
    Apparently,“there’s little to no selection pressure against useless pieces of DNA”. But is that true? We learned in evo-school that any extra work – including reproducing useless features – is in fact detrimental because of wasted resources. Did they (gasp!) lie to us in evo-school?

    Your poorly informed answers make me doubt that you’ve gone to “evo-school.” The amount of selection pressure depends on the amount of “wasted resources.” Scientists have calculated it for useless DNA segments, and eukaryotes like ourselves can carry quite a bit without any noticeable waste of resources. The reason is that these organisms do not need to duplicate their DNA too quickly or too frequently.

    Nonlin.org:
    Also apparently, “For vestigial organs it depends on whether the remaining vestiges are still useful or not.” This is in fact illogical as, by definition, vestigial organs cannot be useful.

    Vestigial, by definition, means that the organ is diminished from some prior, more noticeable, state, not that it’s useless.

    Nonlin.org:
    So the whole answer amounts to something wrong, plus something illogical plus “[it’s] a bit complex”. So, anything else to add?

    So, understanding the whole answer requires you to think like a scientist, not like a mediocre kid, like yourself, barely making it through elementary school.

    1+
  45. Nonlin.org: Apparently, “there’s little to no selection pressure against useless pieces of DNA”. But is that true? We learned in evo-school that any extra work – including reproducing useless features – is in fact detrimental because of wasted resources. Did they (gasp!) lie to us in evo-school?

    Nope. You just weren’t listening.
    Entropy noted…in most eukaryotes, there’s little to no selection pressure against useless pieces of DNA.” which is precisely what they teach in evo-school. I assume that you left off the qualifier because you did not understand its import, as I must.
    And as Alan notes, your definition of “vestigial” is wrong. You appear to have failed evo-school.

    2+

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