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. Alan Fox: Don’t know which book you are getting your information from but that’s incorrect.

    https://scienceoxford.com/vestigial-organs/#:~:text=These ‘useless’ body-parts,that function became non-existent.

    DNA_Jock: Entropy noted “…in most eukaryotes, there’s little to no selection pressure against useless pieces of DNA.”

    Strangely enough, I fully agree with you on this. But only because there’s no “selection pressure” period. Haha.

    And let’s review the history. Ignorant Darwin and dino-followers make a claim that clearly proves false once we learn a bit or two. And then the story is changed to reduce the embarrassment.

    DNA_Jock: And as Alan notes, your definition of “vestigial” is wrong.

    By this very lax definition, everything is vestigial including your brain which is clearly smaller than that of the Neanderthal. So once again, the story fails and is therefore changed to minimize embarrassment. The pattern is clear.

    And let’s go back to the original question: “How long exactly does it take for something to decay and get deleted?” Anyone up to the challenge? Because, if not, then the assertion that “They [pseudogenes, and vestigials] tend to decay by accumulation of mutations or get deleted” must be withdrawn for lack of evidence.

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  2. ROFL
    Interestingly, recent research actually suggests this organ may not be so pointless after all. “, which would be why they put ‘useless’ in quotation marks….
    So, nonlin, you might want to read the web pages that you cite. It would reduce the number of faceplants you suffer.
    Perhaps not. </Claire Foy>

    And your ‘decay’ question has already been answered: “It depends.”
    I realise that this answer may be too complex for you to understand.

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  3. Nonlin.org:
    https://scienceoxford.com/vestigial-organs/#:~:text=These ‘useless’ body-parts,that function became non-existent.

    You failed to read that for comprehension (what a surprise). The function of the original organ became non-existent, that doesn’t mean that no functions remain (did you even see those quotation marks that DNA_Jock pointed out?). The same web page mentions remnant functions of the appendix, for example.

    Also interesting that you moved out from wikipedia, probably to avoid further embarrassment. Your hypocrisy is dully noted.

    Nonlin.org:
    Strangely enough, I fully agree with you on this. But only because there’s no “selection pressure” period. Haha.

    An infantile response, as expected given that you prefer to play the idiot than admit that you did not consider that metabolic costs can be calculated.

    Nonlin.org:
    And let’s review the history. Ignorant Darwin and dino-followers make a claim that clearly proves false once we learn a bit or two. And then the story is changed to reduce the embarrassment.

    Clearly you have deep problems with reading for comprehension: the story didn’t change. You failed to consider that the amount of “wasted resources” can be calculated.

    Nonlin.org:
    By this very lax definition, everything is vestigial including your brain which is clearly smaller than that of the Neanderthal. So once again, the story fails and is therefore changed to minimize embarrassment. The pattern is clear.

    Only to an infantile mind like yours. For those who want to understand nature it’s a matter of paying attention.

    Nonlin.org:
    And let’s go back to the original question: “How long exactly does it take for something to decay and get deleted?” Anyone up to the challenge? Because, if not, then the assertion that “They [pseudogenes, and vestigials] tend to decay by accumulation of mutations or get deleted” must be withdrawn for lack of evidence.

    This was already answered. You just lack the mental prowess, and perhaps the attitude, to understand the answer.

    Finish elementary school. Pay special attention to lessons in reading for comprehension. Then come back and apologize. Nothing wrong with correcting your mistakes.

    ETA: It’s interesting that in all this time you haven’t managed to learn to read. Since you’re still uneducable, I’ll leave you to your ignorance and illiteracy.

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  4. Alan Fox:

    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.

    So do you still believe in the slow steady pace of biological evolution which mimics Lyell’s geological uniformitarianism?

    I would ask why Goldschmidt felt the need to propose ‘hopeful monsters’ in the first place.

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  5. Nonlin.org: 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?

    Did you notice this nugget of wisdom by Allan:

    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.”

    Neither pseudogenes nor vestigial organs have anything to do with your “inner fish”. Rather, the topic of the book is how aspects of our (completely functional) anatomy can be better understood by considering our evolutionary past. Read the book.

    Nonlin.org: Look, someone answered in your place.

    So they did and they were rewarded with an intellectually fulfilling exchange. Oh wait, no they weren’t. Rather, you failed to listen, resisted correction and richly sprinkled insults … again. Big incentive for me to participate.

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  6. Nonlin.org:

    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.

    Darwin was instrumental in bringing the idea of biological evolution into popular thinking. There is a vast amount of evidence disputing the claim that species first appeared in their fixed, separate forms. Life is a dynamic unity.

    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?

    It would be extremely unlikely to find ancient fossils resembling modern birds because they did not exist in that form at that time. For example, many birds would have had teeth around that time. They have found bird like tracks dated more than 200 million years old. And of course there is the controversial protoavis.

    And don’t forget the denser the bone the easier it will fossilize.

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  7. Alan Fox: And tit/teat (nipple/breast) may have Dutch origins*.

    Yep. “Tieten” is a vulgar term for breasts. We didn’t name any birds after them though.

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  8. Allan Miller:

    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

    Yes, and genetic replication is a process.

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  9. CharlieM: So do you still believe in the slow steady pace of biological evolution which mimics Lyell’s geological uniformitarianism?

    Not a question of belief. I agree with the current theory. The fact that it took nigh on two billion years for eukaryotes to emerge suggests it has not been a rapid process.

    CharlieM: I would ask why Goldschmidt felt the need to propose ‘hopeful monsters’ in the first place.

    At the time he proposed “hopeful monsters” the mechanism of inheritance was not known. One core weakness in his idea is sex. Who do monsters breed with? Cumulative small changes don’t have that problem. Phlogiston wasn’t a terrible idea for its time, either.

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  10. CharlieM: Me: The ‘system of expression’ is only reproduced by virtue of genetic replication

    Charlie: Yes, and genetic replication is a process.

    A process controlled entirely by gene sequence.

    Gee, this is fun! Do you think we can keep it up for the next 4 months?

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  11. Charlie – I repeat the challenge: identify an element of system control that does not trace back to gene sequence – one that cannot be altered by a heritable genetic change.

    It’s lame to just keep repetitiously pointing to the presence of transcription and replication enzymes (2 very similar functions: template-dependent nucleic acid polymerases in both instances) in the path from sequence to consequence. The existence of these is not in dispute. But they are genomically sourced, as is every other enzyme or functional RNA. I don’t know what else there is, and you don’t really say – fill in the blanks: it’s not specified in the genome, it’s ______.

    This is basic stuff. You need to open up your ‘holistic’ box for just a second. Just take a peek inside. It’s no good just scrawling ‘The System’ or ‘Processes’ on the box, refusing to look inside and pretending that you have provided any illumination whatsoever.

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  12. DNA_Jock: “Interestingly, recent research actually suggests this organ may not be so pointless after all. “, which would be why they put ‘useless’ in quotation marks….

    Exactly my point. The definition changes to suit the failing “theory”. Use your vestigial organ to judge for yourself. What exactly would make an organ “vestigial” as opposed to what? normal? developing? what else? And why won’t it go away after trillions and billions of years?

    DNA_Jock: And your ‘decay’ question has already been answered: “It depends.”

    Would you read the question again? For comprehension this time? Hint: “exactly”. IOW, “it depends” includes “not at all”. Perhaps that’s what you mean, only you can’t express yourself. And that would be consistent with your “inner fish” still poking its ugly head after all this time. Allegedly…

    Corneel: Neither pseudogenes nor vestigial organs have anything to do with your “inner fish”.

    False. I watched the episode and distinctly remember him claiming some people have a tiny, useless hole in their ear lobe because of their “inner fish”. Memorable as one of the stupidest thing I ever heard.

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  13. CharlieM: There is a vast amount of evidence disputing the claim that species first appeared in their fixed, separate forms. Life is a dynamic unity.

    You’re form a different planet. One utterly devoid of logic.

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  14. Allan Miller: You need to open up your ‘holistic’ box for just a second. Just take a peek inside.

    I think he’s in the box and not peeping outside!

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  15. Nonlin.org: False. I watched the episode and distinctly remember him claiming some people have a tiny, useless hole in their ear lobe because of their “inner fish”.

    I suspect you misheard. You could have a look at this Wikipedia article to refresh your memory.

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  16. Allan Miller:

    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.

    And happy to repeat for as long as need be, the most relevant common denominator is not the molecular sequence but the process.

    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.

    The purpose of my scurrying is so that i can come to a better understanding. And as we are all individuals with our own personal points of view, we are bound to have disagreements. Who knows? Our opposition may eventually reach some sort of Hegelian synthesis.

    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.

    I wouldn’t want to disappoint you 🙂

    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.

    Yes, the fact being that replication is a process.

    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?

    Lineages change for a variety of complex reasons including both environmental and integral. Sequences change, splicing changes, expression levels change, timings change. Gene are expressed using familiar processes which are constant throughout living systems, what does change is the likes of what I have just referred to above.

    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’.

    The holistic stance is inclusive of both analysis and synthesis. But while recognising the individual processes it looks at the whole and how these processes are connected. To talk of ‘competition’ is very anthropocentric, as if individual alleles were tiny homunculi within the cell.

    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…

    Yes I do recognise your complaint and I admit I do mix and match evolution and individual development.

    Things do get a bit convoluted and I do probably get a bit over-enthusiastic in trying to explain what I see as the fractal nature of life. I’m not the only one to recognise these patterns. I’ve just come across Martin G. Lockley and from a very brief reading it would seem that he has similar views in that regard at least.

    He writes:

    Organisms are homeostatic organic wholes. Their organization is understandable, and fractally repeated, from the level of the cell to whole individual organisms, through higher taxonomie groups up to the level of the biosphere. This is not fully appreciated by most biologists and paleontologists owing to emphasis on investigation of the parts (individual organs) that constitute static anatomy, rather than the dynamic morphological interrelationships. The morphodynamic approach, which is largely synonymous with a holistic heterochronic approach, also allows us to view organisms as complex systems: i.e., as manifestations of iterative or recursive fractal organization…

    ontogeny reiterates and creates phylogeny (and vice versa) in a series of fractal, recursive manifestations of form, physiology, and behavior.

    I wouldn’t mind reading some more of his writings.

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  17. CharlieM:
    And happy to repeat for as long as need be, the most relevant common denominator is not the molecular sequence but the process.

    How long? Once you’ve said it 500 times, and I’ve rejected it 500 times, what’s gained by 501? Does getting the last word make you right? (And at odds with most geneticists: the differences between organisms are not due to vague ‘process’, but ultimately to genetic sequence. ‘Process’ is actually derived from that sequence. ‘Process’ only changes when that sequence changes)

    The purpose of my scurrying is so that i can come to a better understanding.

    I don’t perceive in you a desire to understand genetics. In particular, you only go one step down the causal chain. For example, you seem to think alternative splicing is not genetically-encoded, because the same basic sequence is rearranged. But, it is.

    Me: Doesn’t matter. DNA replication does not distinguish between ‘processed’ and ‘unprocessed’ sequence.

    Charlie: Yes, the fact being that replication is a process.

    Doesn’t matter. This subdiscussion is related to molecular continuity. Saying ‘it’s a process’ evades the entire point.

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

    Charlie: Lineages change for a variety of complex reasons including both environmental

    No. Environmental changes act through conservation or elimination of modified genetic sequence, not by ‘changing’ anything (vague possibilities of epigenetic inheritance notwithstanding – the difference between mice and elephants is not due to their respective ‘experiences’, integrated from trillions of separate ancestors and unrepresented in the genome).

    … and integral. Sequences change,

    Correct

    splicing changes,

    As a result of genetic change

    expression levels change

    As a result of genetic change.

    timings change.

    As a result of genetic change.

    Gene are expressed using familiar processes which are constant throughout living systems, what does change is the likes of what I have just referred to above.

    Reducing to sequence changes, one and all.

    The holistic stance is inclusive of both analysis and synthesis. But while recognising the individual processes it looks at the whole and how these processes are connected.

    How does ‘holism’ deal with the B chromosomes of maize, the P element of Drosophila, or homing endonucleases?

    To talk of ‘competition’ is very anthropocentric, as if individual alleles were tiny homunculi within the cell.

    That’s you putting your spin on it (and a fine one to complain about metaphor!). Competition, in the sense of multiple entities constrained by a finite resource, is a perfectly respectable term in both ecology and chemistry. But if you don’t want to call it ‘competition’, that which I term ‘competition’ still happens. If there is attenuation of retention of the products in an exponential process (DNA replication is an exponential process), inevitable in a finite world, you get a ‘Darwinian competition’ for representation in the next generation. Any entity that enhances its copy number is more likely to be retained than its ‘rivals’ that produce fewer. This includes subgenome fragments, to the extent that their fates are unlinked from those of their genome-fellows during meiosis.

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  18. Alan Fox: I suspect you misheard. You could have a look at this Wikipedia article to refresh your memory.

    No. He was definitely talking about adults, not an obscure embryonic stage. It was showmanship. Obviously, he got my attention.

    DNA_Jock: “Interestingly, recent research actually suggests this organ may not be so pointless after all. “, which would be why they put ‘useless’ in quotation marks….

    Dang! You made me read more of that nonsense than I wanted. And of course you are WRONG. That is NOT why they use quotations. They make that clear when they continue, this time without quotations: “They once represented a function that evolved out of a necessity for survival, but over time that function became non-existent.

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  19. Nonlin.org: Dang! You made me read more of that nonsense than I wanted. And of course you are WRONG. That is NOT why they use quotations. They make that clear when they continue, this time without quotations: “They once represented a function that evolved out of a necessity for survival, but over time that function became non-existent.”

    That still doesn’t imply the resulting organ must have no function, doofus. It may have acquired a different one along the way.

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  20. Allan Miller:

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

    Gosh, really? You live and learn.

    Intricate dynamic processes do need to be well orchestrated and I think that over emphasis on genes down-plays this orchestration.

    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.

    I didn’t say anything which contradicts that. I said it relies on change, I didn’t mention the amount of change that can be tolerated. Even so called immortal genes can tolerate a certain amount of base changes.

    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.

    I don’t believe that there is any false dichotomy. I believe that living systems retain a balance between total order and total chaos. Natural selection maintains that balance as evolution proceeds. Genetic variety is the consequence of the process, not the cause.

    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.

    No its not ‘something in the zygote’. The genome is the source of the materials that the organism has at its disposal. How those materials are arranged, how they are constantly replaced and modified are determined by the processes at work within the organism. What gives organisms their identity is not one particular form at any given moment. What gives them their identity is the dynamically balanced, morphological processes.

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  21. Allan Miller: 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’ …

    The error their was on my part. I misspelt it whilst copying it.

    Beware of anyone who has to resort to criticising spelling or grammer; sorry, grammar. 🙂

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  22. Corneel:

    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.

    plus 1

    plus 2 🙂

    Edit – the signs have disappeared so I’ve used the word instead.
    Yet another edit – the plus signs have disappeared so I’ve used the word instead.

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  23. CharlieM:Me: Gosh, really? You live and learn.

    Charlie: Intricate dynamic processes do need to be well orchestrated and I think that over emphasis on genes down-plays this orchestration.

    No, it really doesn’t. It simply recognises where the information flow is, and what persists between generations. To use one of your expressions, a male butterfly does not pass a little homunculus on fertilisation, but a haploid genome. The fact that one may see that genome as ‘surrounded by process’ does not affect where that process is encoded. The ‘process’ surrounding a male genome does not determine what emerges: the genome does.

    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.

    Charlie: I didn’t say anything which contradicts that. I don’t believe there is any false dichotomy

    “Orthodox evolutionary theory does not rely on the immortality of DNA sequences, it relies on the opposite.” That is as near to being dichotomous as makes no difference!

    Natural selection maintains that balance as evolution proceeds. Genetic variety is the consequence of the process, not the cause.

    Natural selection reduces genetic variety, though …

    No its not ‘something in the zygote’. The genome is the source of the materials that the organism has at its disposal.

    It’s not just the source of ‘the materials’, it is also the seat of control. Name an element of control that does not trace back to a genetic sequence.

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  24. Corneel:

    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?

    As totipotent cells have the ability to produce any cell of the organism so in my opinion all animal life in the beginning had the potential to grow into self-conscious sentient individual organisms. The archetype includes all processes from initial growth and development to rational thought.

    Studying the habits and lifestyles of a population gives a good indication of how far the organisms within it have progressed.

    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”.

    I declare no such thing. There is nothing unnatural or supernatural about coordinated genetic activity in this same way that there is nothing unnatural or supernatural about the coordinated activity of social insects.

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

    But there is a difference between reversible and irreversible changes.

    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!

    Only the fact that they are very successful in filling the niche they presently occupy. Mice are rodents. Why do you think that the largest extant rodent is the capybara reaching no more than 60 plus kilograms?

    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?

    I cannot confirm nor deny that mice and elephants have a common ancestor. I can confirm that they are both mammals and the are both vertebrates because they both conform to that general plan.

    All I can do is speculate on the past. It is obvious that organisms have undergone divergent evolution, convergent evolution and parallel evolution. It is a question of how deep each of these go. Followers of orthodox evolutionary theories need divergent evolution to be the deepest in order for their theories to hold up. I don’t have such a pressing need.

    Divergence and convergence form two tracks of a spiralling path.

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  25. Corneel:

    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.

    But they do recognise that animals have personality?

    How would you describe the difference between personality and individuality?

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  26. CharlieM,

    Mystery explained. Though, as I mentioned, “miniscule” is now accepted by dictionaries (OED included) as a variant.

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  27. Nonlin.org: No. He was definitely talking about adults, not an obscure embryonic stage. It was showmanship. Obviously, he got my attention.

    Preaurical sinuses are not vestigial organs, but congenital malformations. Neither of them have anything to do with pseudogenes.

    1+
  28. CharlieM: Why do you think that the largest extant rodent is the capybara reaching no more than 60 plus kilograms?

    Me, sir!

    It’s the niche. Speciation often happens when a new (or newly vacant) niche is exploited by an invading species. Australia, New Zealand, Madagascar, for example, have extant and extinct species exploiting niches that would be occupied by different species found elsewhere if there were not geographical isolation.

    1+
  29. Alan Fox:
    CharlieM
    :

    So do you still believe in the slow steady pace of biological evolution which mimics Lyell’s geological uniformitarianism?

    Not a question of belief. I agree with the current theory. The fact that it took nigh on two billion years for eukaryotes to emerge suggests it has not been a rapid process.

    Time is relative. Do you believe the pace was constant?

    CharlieM: I would ask why Goldschmidt felt the need to propose ‘hopeful monsters’ in the first place.

    At the time he proposed “hopeful monsters” the mechanism of inheritance was not known. One core weakness in his idea is sex. Who do monsters breed with? Cumulative small changes don’t have that problem. Phlogiston wasn’t a terrible idea for its time, either.

    The mechanism wasn’t important. It was the fact that he believed that small gradual changes were not sufficient to go from micro-evolution to macro-evolution.

    And now as we are beginning to get some idea of the multifunctionality of genes and the complex, alternative ways they can be used in producing proteins, I can see why he had reasons to be sceptical even if he wasn’t aware of all the reasons.

    Blindly mucking about with the genome can have all sorts of unseen consequences as thalidomide so tragically proved.

    And it has taken 60 years of research to reach an understanding of how its effects were produced.

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  30. CharlieM,

    And now as we are beginning to get some idea of the multifunctionality of genes and the complex, alternative ways they can be used in producing proteins

    Multifunctionality, complexity and alternative splicing don’t lead to a conclusion of saltation. And, if saltation be a thing in a world of archetypes, it suggests sudden step-changes in archetypes, which isn’t very archetypical.

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  31. Allan Miller:

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

    Charlie: Yes, and genetic replication is a process.

    A process controlled entirely by gene sequence.

    The sequence does tot control the process. Sequences specify the composition of the various individual polymers involved.

    Gee, this is fun! Do you think we can keep it up for the next 4 months?

    Longer if need be 🙂

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  32. Corneel: Preaurical sinuses are not vestigial organs, but congenital malformations.

    And that’s between you and Shubin. The problem I reported is that you’re trumpeting a “trend” you can’t back up. As usual.

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  33. CharlieM: Blindly mucking about with the genome can have all sorts of unseen consequences as thalidomide so tragically proved.

    Thalidomide’s effects have nothing to do with “mucking about with the genome”. Please stay out of my lane…

    1+
  34. CharlieM: The mechanism wasn’t important.

    *Stands in amazement*
    The mechanism is crucial. If you don’t have a mechanism you can’t make a model.

    It was the fact that he believed that small gradual changes were not sufficient to go from micro-evolution to macro-evolution.

    Well, if so, he was wrong twice. Wrong that there isn’t enough time. It took two billion years or so to get to multicellular, sexually reproducing eukaryotes when all the heavy lifting is done, most biochemical pathways are established. Deuterostomes are basically doughnuts and the topological rearrangements involve regulatory changes controlling growth and development. Small regulatory changes can be large phenotypic changes. so the macro/micro barrier is an illusion. On the other hand, my objection to saltation is that single large phenotypic changes individuals will prevent mating between monsters and non-monsters – unless you want to add another layer of complexity with some kind of coordination. Occam would not be pleased.

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  35. CharlieM: Blindly mucking about with the genome can have all sorts of unseen consequences as thalidomide so tragically proved.

    As DNA_Jock noted, thalidomide affects the development of the embryo, particularly the limb buds. It has nothing to do with the genome.

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  36. Allan Miller: Charlie – I repeat the challenge: identify an element of system control that does not trace back to gene sequence – one that cannot be altered by a heritable genetic change.

    It’s lame to just keep repetitiously pointing to the presence of transcription and replication enzymes (2 very similar functions: template-dependent nucleic acid polymerases in both instances) in the path from sequence to consequence. The existence of these is not in dispute. But they are genomically sourced, as is every other enzyme or functional RNA. I don’t know what else there is, and you don’t really say – fill in the blanks: it’s not specified in the genome, it’s ______.

    I haven’t been pointing to transcription and replication enzymes, I’ve been pointing to transcription and replication processes. This involves more than just the enzymes.

    This is basic stuff. You need to open up your ‘holistic’ box for just a second. Just take a peek inside. It’s no good just scrawling ‘The System’ or ‘Processes’ on the box, refusing to look inside and pretending that you have provided any illumination whatsoever.

    I have never disputed the fact that the DNA supplies the specification for the various materials used by the organism.

    If we look into the box what do we see? We never see isolated DNA. There are no forms of life that begin from a point where there is just DNA. Initial conditions always involve multiple types of molecule. We can look at isolated DNA as much as we like, but if we want to have knowledge of function we need to study the contents of the box in its working condition, in other words, in its reality. Living systems are never static.

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  37. CharlieM: There are no forms of life that begin from a point where there is just DNA.

    Nobody is arguing that. RNA world, Charlie, where RNA is both catalyst and genome.

    0
  38. Nonlin.org: CharlieM: There is a vast amount of evidence disputing the claim that species first appeared in their fixed, separate forms. Life is a dynamic unity.

    You’re form a different planet. One utterly devoid of logic.

    Steiner was fond of relating a story about logic. Here is how he told it:

    A certain tribe of African negroes, the Felatas, have a very beautiful fable, from which much can be learned.

    Once upon a time a lion, a wolf and a hyena set out upon a journey. They met an antelope. The antelope was torn to pieces by one of the animals. The three travellers were good friends, so now the question arose as to how to divide the dismembered antelope between them. First the lion spoke to the hyena, saying, “You divide it.” The hyena possessed his logic. He is the animal who deals not with the living but with the dead. His logic is naturally determined by the measure of his courage, or rather of his cowardice. According to whether this courage is more or less, he approaches reality in different ways. The hyena said: “We will divide the antelope into three equal parts — one for the lion, one for the wolf, and one for myself.” Whereupon the lion fell upon the hyena and killed him. Now the hyena was out of the way, and again it was a question of sharing out the antelope. So the lion said to the wolf, “See, my dear wolf, now we must share it out differently. You divide it. How would you share it out?” Then the wolf said, “Yes, we must now apportion it differently; it cannot be shared out evenly as before. As you have rid us of the hyena, you as lion must get the first third; the second third would have been yours in any case, as the hyena said, and the remaining third you must get because you are the wisest and bravest of all the animals.” This is how the wolf apportioned it. Then said the lion, “Who taught you to divide in this way?” To which the wolf replied, “The hyena taught me.” So the lion did not devour the wolf, but, according to the wolf’s logic, took the three portions for himself.

    No everyone shares the same logic.

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  39. Alan Fox:

    Allan Miller: You need to open up your ‘holistic’ box for just a second. Just take a peek inside.

    I think he’s in the box and not peeping outside!

    Wouldn’t life be so much less complicated if we could put everyone in their own little box?

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  40. CharlieM: Wouldn’t life be so much less complicated if we could put everyone in their own little box?

    Indeed. But we are social animals. Box life isn’t healthy (though a short sharp session might help with the current pandemic).

    0
  41. CharlieM:Me: I haven’t been pointing to transcription and replication enzymes, I’ve been pointing to transcription and replication processes. This involves more than just the enzymes.

    Fine – still encoded by the genome. The genome does not simply provide ‘material’.

    If we look into the box what do we see? We never see isolated DNA.

    Oh, for fuck’s sake!

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  42. Nonlin.org: And that’s between you and Shubin.

    No, it’s not. YOU brought them up as examples of vestigial organs, not Neil Shubin. And YOU brought up vestigial organs and “Your Inner Fish” when I mentioned pseudogenes, not Neil Shubin.

    Here is a nice test for you: Write down, without googling, what you think pseudogenes are and what you think is believed to be the dominant mechanism that generates them. Then compare your notes to what you can find on the net. You associating them with vestigial organs suggests that you have completely the wrong idea.

    Nonlin.org: The problem I reported is that you’re trumpeting a “trend” you can’t back up. As usual.

    No, the problem is that you are promulgating on stuff you are utterly clueless about and resist correction by people who have professional expertise. As usual.

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  43. CharlieM: totipotent cells

    And we get the “evolution is like development” metaphor again. Isn’t it about time that you admit that you don’t know how it works?

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

    Charlie: But there is a difference between reversible and irreversible changes.

    I fail to see the relevance. A lot of reversible changes accumulating will also amount to a big change.

    CharlieM: Mice are rodents. Why do you think that the largest extant rodent is the capybara reaching no more than 60 plus kilograms?

    I don’t know, but I think I can hazard a guess why you are trying to switch the topic from mammals to rodents. So, can you confirm that rodents have a common ancestor? Is the rodent archetype more restrictive on size than the mammal archetype? And how can you tell, apart from the fact that there are currently no rodents the size of elephants?

    CharlieM: I cannot confirm nor deny that mice and elephants have a common ancestor.

    Then you got some ‘splaining to do. Do the cells in your body not derive from a single zygote? Perhaps you feel a bit queasy at he thought of “speculating about the past”?

    CharlieM: Followers of orthodox evolutionary theories need divergent evolution to be the deepest in order for their theories to hold up. I don’t have such a pressing need.

    It’s not “speculation” and it’s not a “need”. It’s an established fact. There is theoretical, observational and empirical proof that separated populations diverge.

    Don’t think I did not notice the “followers”. Evolutionary theory is mainstream science, not a religion. It is not on the same footing as what you are peddling here.

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  44. CharlieM: But they do recognise that animals have personality?

    Oh, certainly. As do I. You too? Not quite as much as humans, right?

    CharlieM: How would you describe the difference between personality and individuality?

    Individuality is just the sum of distinguishing features. For example, a black panther stands out as an individual. Variation in personality contributes to individuality, but is not the whole story.

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  45. CharlieM: No everyone shares the same logic.

    That’s false. Logic is what computers do. They better share the same logic or else we’re in trouble. Reason on the other hand is individual and it’s why we’re all disagreeing. Claiming “evolution” is evidence-based when no one has ever seen one iota of EXPERIMENTAL evidence, is more than a reasoning disagreement, it is indeed illogical.

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  46. Corneel: YOU brought them up as examples of vestigial organs, not Neil Shubin.

    I’m just reporting on what he said.

    Corneel: You associating them with vestigial organs suggests that you have completely the wrong idea.

    Once again you offer no proof. Why would that association suggest “wrong idea”?

    Corneel: Nonlin.org: The problem I reported is that you’re trumpeting a “trend” you can’t back up. As usual.

    No, the problem is that you are promulgating on stuff you are utterly clueless about and resist correction by people who have professional expertise.

    Not “promulgating” anything this time. Just asking inconvenient questions re your unsupported claims. Will you now tell me about “decay”? Any evidence? See? Questions, not “promulgating”!

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