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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340 thoughts on “The Spiralling Flow of Life

  1. CharlieM: I was highlighting the difference between an outer sense experience which is a momentary, subjective representation and the inner conceptual experience which is lasting, objective and real.

    Because one potentially gets more information from a movie then from a still image, the inner conceptual experience is “lasting, objective and real”? Methinks you are missing a few steps there.

    CharlieM: Your second ‘ok’ reveals that you agree some creatures are more advanced than others.

    I don’t think so. Multicellular organisms advance through development from a single celled zygote onwards, that I agree with. But it doesn’t follow that multicellular creatures are more evolutionary advanced than unicellular ones. After all, by what evolutionary measure is multicellularity to be considered progress? None, as far as I can tell.

    CharlieM: But then I could see that you were bringing to light a major distinction between humans and dandylions. How humans have such a high degree of individuality. Dandylions do not have this individuality. Their skills are group wide whereas ours are very individual.

    Yet you claim the skills of individual pilots as an accomplishment of whole mankind.

    Charlie just now: I certainly do not equate “complex” with “advanced”

    Charlie, three days ago:

    So in your opinion nervous systems which are frequently considered to be the most complex structures in the universe are no more advanced that the nervous systems of hydra?

    CharlieM: Okay, so DNA serves no purpose 🙂 But is it active? Are ribosomes active? Are cells active, are organisms active?

    Since your “inner conceptual experience” does not appear to be as lasting as you presume, now is a good time to reread KNs comment that set off this discussion.

    DNA, being a chemical substance, has certain physical properties that endow it with the capability to interact with other molecules and physical particles. These interactions are not exclusive to organic chemistry, hence there is no vital force at work.

    Animals display activity in another sense of the word. Please stop building arguments that rely on inappropriately using words in the wrong context.

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  2. Allan Miller:

    CharlieM: No. I am saying the genome lies within the control system.

    I have invited you to point to an element of control which does not root in the genome. I gave an extensive, though not exhaustive breakdown of the kinds of things I mean. All you can do in response is repeat your mantra.

    Everything you imagine ‘controlling the genome’ is actually a product of it. RNA polymerases, spliceosomes, ribosomes, all the ‘protein complexes’ you wave a hand at. All of it.

    But there is no master controller. We have seen from fruit flies that at the very point of conception they process of development is started, not from proteins that have been grown using the DNA of the newly created offspring, but form proteins directly derived from the mother. Yes I know the mother’s DNA was involved in their production, but we cannot get away from the fact that they were produced by a combined coordinated effort.

    Me: And there the similarity ends. Pursuing such analogies is fruitless. We have the actual, physical system to consider.
    Charlie: Why would we have to pursue the analogy, it is there right in front of us. Pursuing it any further would be taking it to far. I too think that the differences are far more interesting than the similarities.

    So why even mention it? DNA is different from a can of beans too.

    Because even although they are vastly different (DNA and magnetic tape that is) there is still a fundamental similarity between them.

    Cans of beans are more like cells, containers full of organic substances which organisms use for their benefit 🙂

    Me: Another dreadful analogy.

    Charlie: No just another limited analogy.

    Which is nothing like the things being analogised. Just more rabbit holes. DNA is capable of exactly the same catalytic repertoire as RNA. It just happens not to be used catalytically, in life forms that have protein enzymes and ribozymes at their disposal. The only differences between DNA and RNA are an oxygen atom and a methyl group (CH3) in roughly 50% of random base pairs in the former.

    If we trace our evolutionary waltz back through the generations from the mother fruit fly to life’s beginning we come across the RNA world scenario. All the steps since that time have involved pre-existing proteins at the conception of the offspring.

    But in the RNA world scenarion we find that:

    From an evolutionary point of view, one can identify several steps in this emerging pathway, first ‘RNA-makes-RNA’, second ‘RNA-makes-proteins’, third, “proteins make RNA” and finally “proteins-makes-DNA (from RNA)

    DNA is a product, not a producer.

    Ever since genes were equated with specific DNA sequences in the ’50s their prominence has been becoming gradually undermined by further discoveries. They are becoming regarded more and more (please excuse the metaphors) as vital contributors to a collective effort rather than as autocratic leaders.

    Nope. They were never viewed as ‘autocratic leaders’. What they are (and no discovery has undermined this) is the source of protein sequence – those proteins that you imagine ‘sit above’ the genome’ and ‘use it’ are simply its products.

    I live quite near a quarry which was the source of much of the materials used in building the city bypass. But I would not dream of saying that the quarry produced the bypass.

    Research brings new discoveries, viewpoints are developed further, they come and go. People are slowly coming round to a more holistic understanding of life.

    People always kept holism in mind. No-one studied biochemistry or genetics as if reduction were the only game in town, but in order to see how it fit together as a whole. Naive holism – thou shalt not break apart so much as a cell – is no use to anyone.

    True enough.

    No. I thought that people had overestimated the amount of knowledge that would be gained from mapping the entire genome of organisms. The context in which they are used is proving to be just as important as the sequences themselves, if not more so.

    Funnily enough, gene centrism doesn’t have much to do with mapping the genome, a point you will remain eternally impervious to. Dawkins’s ‘gene’ is not the molecular biologist’s, which we have discussed.

    I am discussing the role of DNA in development and in evolution.

    If you believe that DNA is an active participant in protein production, where is this activity?

    The sequence of RNA polymerase is held in DNA. The sequence of RNA polymerase is extracted from DNA … by RNA polymerase. Now, you may insist that the ‘actor’ here is RNA polymerase, and not its DNA sequence at all. But without that sequence, where’s RNA polymerase? It cannot come into being without its DNA sequence. So, pretty obviously, DNA sequence comes first. RNA polymerase is dependent on it for its very existence. I doubt this was the primordial state, of course. But in modern cells, that’s largely how nucleic acid ‘acts’: via protein intermediates, which it produces with the aid of protein intermediates.

    We agree that DNA is vital, but you still haven’t answered the question as to its activity. DNA is coiled, uncoiled, zipped and unzipped, packaged and repaired, cut and spliced through the activity of various complexes. There is a great deal of activity expended on DNA but I don’t see much reciprocal activity.

    Me: Utter bollocks. How do you get that from an emphasis on the evolutionary argument? You thonk evolution is deterministic? See #8

    Charlie: I meant to say ‘moving towards genetic determinism’.

    Still no. Gene centrism /= genetic determinism.

    I agree gene centrism does not equal genetic determinism.

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  3. Allan Miller:

    CharlieM:Me: I can investigate both your skeleton and your body – neither has the quality of being made-up. Archetypes, not so much.

    Charlie: So you are basing your idea of reality on what you can perceive directly through, say, vision and touch.

    I don’t think it unreasonable to regard some means of perception or detection as a requirement for accepting the reality of something. “There are these archetypes”, says Charlie. “Oh, you can’t detect them …”

    ” But if there were no archetypes, could I do this? [Holds up a dandelion]

    Yes, I agree, sense perception is a necessity. Take all the leaf-like structures in a flowering plant from the cotyledons through the leaves along the stem to the sepals, petals and parts of the flower. Imagine the movements in these forms morphing into each other. Then you have a basic idea of the archetype. This is not a static physical form, it has more in common with a process.

    If you were to understand how the projective geometry, demonstrated by people like George Adams, Olive Whicher, Lawrence Edwards and the like, related to this dynamic morphology you would have a clearer idea of what is meant by the archetypal plant.

    Certainly if it weren’t for dynamic morphology I would have little understanding of the dandylion. Through projective geometry the transformations can be understood not as a series of infinitesimal steps, but as continuous flowing movement. And life is rhythmic movement.

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  4. Allan Miller:

    CharlieM: Me: The ‘transcription complexes’ are themselves produced by DNA. Thus, DNA provides the means by which it is expressed. This is a self-replicating entity, not a ‘tape’ being played (by a machine, yet! ).

    Charlie: The self-replicating entity is the cell.

    It isn’t though. The DNA replicates; the rest of the cellular material is simply divided, typically in half. Then it grows, ultimately organised by the replicated genome.

    Here at https://www.biophysics.org they write

    What would you need to synthesize a cell de novo, or how did the first protocell come to be?

    Let’s operationally define a living cell as one that can autonomously replicate, and that is subject to Darwinian evolution.

    It needs a membrane, to keep everything together, and a biopolymer that can replicate itself (such as RNA) and hopefully also make more membrane.

    That operational definition works for me.

    Me: Perhaps you really do think you’re being profound and meaningful. I can derive no sense from it whatsoever.

    Charlie: Have you even examined projective geometry in any depth?

    No, but I’m doubtful it would shed much light on your obscurantism.

    But if you wanted to jusify your doubt, there is only one way to do it.

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  5. Corneel:

    CharlieM: I was highlighting the difference between an outer sense experience which is a momentary, subjective representation and the inner conceptual experience which is lasting, objective and real.

    Because one potentially gets more information from a movie then from a still image, the inner conceptual experience is “lasting, objective and real”? Methinks you are missing a few steps there.

    The sense experience I have of a tree is dependent on the relative position between myself and the tree. My idea of the organism that is a tree (‘idea’ not in the colloquial sense), is independent of me. It is made up of shared concepts. Concepts such as growth, life cycle, roots, branches, leaves and much more. Concepts which everyone recognises are shared by all trees.

    CharlieM: Your second ‘ok’ reveals that you agree some creatures are more advanced than others.

    I don’t think so. Multicellular organisms advance through development from a single celled zygote onwards, that I agree with. But it doesn’t follow that multicellular creatures are more evolutionary advanced than unicellular ones. After all, by what evolutionary measure is multicellularity to be considered progress? None, as far as I can tell.

    It can be considered progress through the undeniable fact that multicellular organisms in their development have been single-cellular and have passed through that stage. Would you say that cellular division and differentiation is a backward step in evolution?

    Evolution advances in the direction of individual organisms becoming more and more capable of determining their own destiny.

    CharlieM: But then I could see that you were bringing to light a major distinction between humans and dandylions. How humans have such a high degree of individuality. Dandylions do not have this individuality. Their skills are group wide whereas ours are very individual.

    Yet you claim the skills of individual pilots as an accomplishment of whole mankind.

    No, I am claiming that individual humans have the power to decide in advance on a destination they would like to reach. Humans have aims for the future which dandylion seeds do not.

    Charlie just now: I certainly do not equate “complex” with “advanced”

    Charlie, three days ago:

    So in your opinion nervous systems which are frequently considered to be the most complex structures in the universe are no more advanced that the nervous systems of hydra?

    Yes, because I am not generalising but looking at each instance individually.

    Survival does not depend on complexity. And evolution isn’t just about survival. If an organism is to advance from mere surviving to sensing in multiple ways, feeling and experiencing inward emotions, thinking and gaining knowledge through individual learning then the nervous system needs to be complex enough to allow for this. This goes beyond survival.

    The more advanced fuel control unit has become more simple but the aircraft in which they operate have become much more complex.

    Complexity and advancement can go hand in hand but that need not be the case.

    CharlieM: Okay, so DNA serves no purpose But is it active? Are ribosomes active? Are cells active, are organisms active?

    Since your “inner conceptual experience” does not appear to be as lasting as you presume, now is a good time to reread KNs comment that set off this discussion.

    DNA, being a chemical substance, has certain physical properties that endow it with the capability to interact with other molecules and physical particles. These interactions are not exclusive to organic chemistry, hence there is no vital force at work.

    Animals display activity in another sense of the word. Please stop building arguments that rely on inappropriately using words in the wrong context.

    So are we not talking about physical activity then?

    We don’t need to posit a mysterious vital force. All we need to do is to recognise that life has qualities over and above the physical/chemical and consciousness has qualities over and above life.

    There are many polarities in life between relative activity and passivity; male and female, penetrative penis and receptive vagina, motile sperm and sessile egg, active protein complexes and passive DNA.

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  6. In Chinese legend and mythology, Fu-xi and Nu-wa are the god and goddess who are said to have created humankind.

    Below is an image of the pair in the form of a double helix.

    I came across this article comparing the I Ching and genetic code. It’s too deep for me to fathom at this time, but it does take the research further than just comparing images.

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  7. CharlieM: My idea of the organism that is a tree (‘idea’ not in the colloquial sense), is independent of me. It is made up of shared concepts.

    This resonates with previous discussions you have had on ideal triangles. For the same reasons that you failed to convince anyone that ideal triangles have real objective existence outside of people’s minds, you fail to convince me that “ideal trees” exist. Do you understand why people will not accept these concepts? (It has nothing to do with thinking of matter as primal)

    CharlieM: It can be considered progress through the undeniable fact that multicellular organisms in their development have been single-cellular and have passed through that stage. Would you say that cellular division and differentiation is a backward step in evolution?

    At face value it is neither progress nor regression. Consider this: Unicellular yeasts are thought to have evolved from multicellular ancestors yet they are doing fine. The teleological view of evolution that you promote went out of fashion somewhere in the 19th century, and for good reasons.

    CharlieM: Me: Yet you claim the skills of individual pilots as an accomplishment of whole mankind.

    Charlie: No, I am claiming that individual humans have the power to decide in advance on a destination they would like to reach. Humans have aims for the future which dandylion seeds do not.

    ALL humans? So humans as a group? You don’t even realize you are doing it, do you?

    CharlieM: If an organism is to advance from mere surviving to sensing in multiple ways, feeling and experiencing inward emotions, thinking and gaining knowledge through individual learning then the nervous system needs to be complex enough to allow for this. This goes beyond survival.

    Sensing, problem solving and social skills in humans are not adaptive traits? Are you sure?

    CharlieM: We don’t need to posit a mysterious vital force. All we need to do is to recognise that life has qualities over and above the physical/chemical and consciousness has qualities over and above life.

    Well, I do recognize that. But you keep on insisting that this somehow establishes the existence of all kind of non-physical phenomena, which is nonsense.

    CharlieM: There are many polarities in life between relative activity and passivity; male and female, penetrative penis and receptive vagina, motile sperm and sessile egg, active protein complexes and passive DNA.

    Black and white. Good and bad. Them and us. No good ever came from oversimplified thinking.

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  8. CharlieM: Yes they are. Darwinian evolution should come much more easily to them with the amount of offspring they produce..

    This illustrates the lightness of your understanding of both evolutionary theory and genetics – though God forbid you should take instruction on these matters from anyone who is not a Third Wayer.

    Dandelions are asexual, so every seed is genetically identical, barring mutation. Even if they were sexual, and/ or highly mutated, there is a strong limit on the amount of genetic variation available at any site – each locus can carry a maximum of 2 variants, permuted from up to 4 in the sexual parents.
    Producing large numbers of seeds, even with mutation, is also limited in the real world by available space. In a steady state population, asexuals replace 1 for 1; sexuals 2 for 2, however many seeds are produced, while if the population is growing, ‘Darwinian’ evolution (selection) is less effective.

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  9. Allan Miller: Dandelions are asexual,

    While agreeing with the general thrust of your comment, one small correction: Dandelions in northern Europe are mostly triploid and reproduce by apomixis, but those in southern and central Europe tend to be sexual diploids.

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  10. CharlieM:Me: Everything you imagine ‘controlling the genome’ is actually a product of it. RNA polymerases, spliceosomes, ribosomes, all the ‘protein complexes’ you wave a hand at. All of it.

    Charlie: But there is no master controller.

    So?

    We have seen from fruit flies that at the very point of conception they process of development is started, not from proteins that have been grown using the DNA of the newly created offspring, but form proteins directly derived from the mother.

    For the kinds of protein you are talking about – fundamental cell cycle proteins; RNA and DNA polymerases, etc – the mother’s, father’s and zygote’s sequences are exactly the same, so it makes no difference. These were fixed deep in the history of the lineage. The differences between offspring and their parents derive from the differences between their genomes, not the identities.

    Me: Why even mention it? DNA is different from a can of beans too.

    Charlie: Because even although they are vastly different (DNA and magnetic tape that is) there is still a fundamental similarity between them.

    You are a prime example of why analogies should be avoided – because you are persuaded by ‘phantom similarities’. If the result of playing a tape in a machine were two copies of the tape, surrounded by two brand new machines, with parts determined by the contents of the tape, it might get somewhere. Since it doesn’t, imagining DNA as like a tape simply sows confusion.

    If we trace our evolutionary waltz back through the generations from the mother fruit fly to life’s beginning we come across the RNA world scenario.

    Not quite. RNA world is not (necessarily) an origin scenario, but a form of life preceding protein coding, possibly lasting many millions of years.

    All the steps since that time have involved pre-existing proteins at the conception of the offspring.

    RNA world would precede anything resembling ‘conception’ by a considerable margin.

    For someone keen on emphasising process and extension in time, you seem to prefer a static view of the relation, with each cellular instance having a discrete temporal boundary. But the relation between DNA and its products is dynamic, and transcends genome instances. It is not necessary that this cell’s proteins be produced by this cell’s DNA copy. That doesn’t undermine DNA’s primacy in the relationship.

    In a hypothetical transition from RNA organisms to protein coders, one imagines there would initially be just one protein, then a couple, then a lot, during the transition. So, in the 1-protein scenario, has ‘the system’ suddenly undergone a complete revision of relationship between genome and mode of effect? If this hypothetical protein acted upon the genome (while produced from it), would you insist “There’s no getting away from the fact that a pre-existing protein is necessary. Just one”. Suddenly, nucleic acid is ‘used by the organism’. Just because it makes a protein.

    DNA is a product, not a producer.

    Perhaps we should call the thread ‘Charlie’s spiralling argument’. What’s it a product of?

    those proteins that you imagine ‘sit above’ the genome’ and ‘use it’ are simply its products.

    Charlie: I live quite near a quarry which was the source of much of the materials used in building the city bypass. But I would not dream of saying that the quarry produced the bypass.

    Me either. Analogies, huh?

    Me: Funnily enough, gene centrism doesn’t have much to do with mapping the genome, a point you will remain eternally impervious to. Dawkins’s ‘gene’ is not the molecular biologist’s, which we have discussed.

    Charlie: I am discussing the role of DNA in development and in evolution.

    So am I, but it’s important to be aware they are two different arenas. By and large, you only ever talk of DNA in physiology.

    Me: in modern cells, that’s largely how nucleic acid ‘acts’: via protein intermediates, which it produces with the aid of protein intermediates.

    Charlie: We agree that DNA is vital, but you still haven’t answered the question as to its activity. DNA is coiled, uncoiled, zipped and unzipped, packaged and repaired, cut and spliced through the activity of various complexes.

    All of which are produced from genome sequence. It’s exactly the same issue as with RNA polymerase. Naming other proteins refutes nothing. DNA ‘acts’ via protein intermediates. It doesn’t need to catalyse directly. Its products do that.

    There is a great deal of activity expended on DNA but I don’t see much reciprocal activity.

    There doesn’t need to be.

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  11. Corneel: While agreeing with the general thrust of your comment, one small correction: Dandelions in northern Europe are mostly triploid and reproduce by apomixis, but those in southern and central Europe tend to be sexual diploids.

    Yes, I was aware of the possible objection, although Charlie and I are both firmly in the north!

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  12. Allan Miller: Yes, I was aware of the possible objection, although Charlie and I are both firmly in the north!

    The climate is changing, so it is a matter of time before the diploids will be arriving. Building a wall in the channel will not stop them.

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  13. Corneel: The climate is changing, so it is a matter of time before the diploids will be arriving. Building a wall in the channel will not stop them.

    I’m just gonna stand here and blow.

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  14. Corneel:

    CharlieM: My idea of the organism that is a tree (‘idea’ not in the colloquial sense), is independent of me. It is made up of shared concepts.

    This resonates with previous discussions you have had on ideal triangles. For the same reasons that you failed to convince anyone that ideal triangles have real objective existence outside of people’s minds, you fail to convince me that “ideal trees” exist. Do you understand why people will not accept these concepts? (It has nothing to do with thinking of matter as primal)

    The ideal triangle is not real in the sense that it is not subject to being measured. Its reality lies in the fact that every triangle perceived externally or as a mental picture partakes of it.

    CharlieM: It can be considered progress through the undeniable fact that multicellular organisms in their development have been single-cellular and have passed through that stage. Would you say that cellular division and differentiation is a backward step in evolution?

    At face value it is neither progress nor regression. Consider this: Unicellular yeasts are thought to have evolved from multicellular ancestors yet they are doing fine. The teleological view of evolution that you promote went out of fashion somewhere in the 19th century, and for good reasons.

    But as all multicellular organisms are thought to have originally evolved from single cellular organisms then it can be said that yeast has regressed to a more simplified state which will not lead to individual sentience or self awareness.

    Me: Yet you claim the skills of individual pilots as an accomplishment of whole mankind.

    Charlie: No, I am claiming that individual humans have the power to decide in advance on a destination they would like to reach. Humans have aims for the future which dandylion seeds do not.

    ALL humans? So humans as a group? You don’t even realize you are doing it, do you?

    All organisms have essential features by which they have in common with other creatures and so they can classed in a Linnaean fashion. They also have individual differences. Regarding the evolution of organisms and the development of cells, both evolution and development begin at one pole (the common group) and progress towards the other (the individual). This can be seen clearly in the development of cells in individual higher animals where there is cell division followed by cell differentiation.

    All creatures share group traits but the creatures who have attained the greatest individuality are humans. It may seem paradoxical to you but self-aware individuality is a common feature which distinguishes humans from other organisms.

    CharlieM: If an organism is to advance from mere surviving to sensing in multiple ways, feeling and experiencing inward emotions, thinking and gaining knowledge through individual learning then the nervous system needs to be complex enough to allow for this. This goes beyond survival.

    Sensing, problem solving and social skills in humans are not adaptive traits? Are you sure?

    To say that novel traits came about because they helped the organism to survive is a vast oversimplification. Organisms adapt not by gaining new traits or features but by having flexibility in the traits or features they already possess.

    CharlieM: We don’t need to posit a mysterious vital force. All we need to do is to recognise that life has qualities over and above the physical/chemical and consciousness has qualities over and above life.

    Well, I do recognize that. But you keep on insisting that this somehow establishes the existence of all kind of non-physical phenomena, which is nonsense.

    Our world of experience does not stop with what can be measured and counted. Projective geometry leads us to see the polarity between unity and multiplicity. Not a duality but a polarity.

    CharlieM: There are many polarities in life between relative activity and passivity; male and female, penetrative penis and receptive vagina, motile sperm and sessile egg, active protein complexes and passive DNA.

    Black and white. Good and bad. Them and us. No good ever came from oversimplified thinking.

    Duality divides and oversimplifies, polarity does the opposite. Plane and point are the same thing seen in different ways. The intimate connection between point, line and plane can only be perceived in movement.

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  15. Allan Miller:

    CharlieM: Yes they are. Darwinian evolution should come much more easily to them with the amount of offspring they produce..

    This illustrates the lightness of your understanding of both evolutionary theory and genetics – though God forbid you should take instruction on these matters from anyone who is not a Third Wayer.

    Dandelions are asexual, so every seed is genetically identical, barring mutation. Even if they were sexual, and/ or highly mutated, there is a strong limit on the amount of genetic variation available at any site – each locus can carry a maximum of 2 variants, permuted from up to 4 in the sexual parents.
    Producing large numbers of seeds, even with mutation, is also limited in the real world by available space. In a steady state population, asexuals replace 1 for 1; sexuals 2 for 2, however many seeds are produced, while if the population is growing, ‘Darwinian’ evolution (selection) is less effective.

    Fair enough. Dandylions are very successful plants. But from what you say they are not very good at producing variability. So they are successful in spite of the lack of variability required for Darwinian evolution.

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  16. Alan Fox: Corneel: Black and white. Good and bad. Them and us. No good ever came from oversimplified thinking.

    Catharism died out as a religion partly due to the Dualists belief that the physical world was evil and to abstain from earthly things including food was the way to salvation. (The Catholic church had a hand in the disappearance as well)

    Binary thinking gets you burned.

    We can see dualities as antagonistic and divisive or we can see them as complimentary and as aspects of an underlying unity.

    The leaders of organised religions over the centuries have a great deal to answer to because of the ‘us and them’ attitude they condoned and encouraged.

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  17. Corneel:

    Allan Miller: Dandelions are asexual,

    While agreeing with the general thrust of your comment, one small correction: Dandelions in northern Europe are mostly triploid and reproduce by apomixis, but those in southern and central Europe tend to be sexual diploids.

    Just like the dandylions taking over my garden, the plot thickens.

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  18. One important difference between living systems and machines is in the nature of their complexity. Machine complexity is solid, rigid and predictable, whereas life thrives on chaotic complexity and fluidity.

    A heart that is beating to a steady regimental rhythm is not a healthy heart. Heart rate variability (HRV), the uneven tempo of the beat signifies health.

    Heart rate variability: A new way to track well-being

    Over the past few decades, research has shown a relationship between low HRV and worsening depression or anxiety. A low HRV is even associated with an increased risk of death and cardiovascular disease.
    People who have a high HRV may have greater cardiovascular fitness and be more resilient to stress.

    Living systems do not easily submit to being measured with precision in the way that researchers would like. They harness chaos and use it to their advantage.

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  19. CharlieM:
    Fair enough. Dandylions are very successful plants. But from what you say they are not very good at producing variability. So they are successful in spite of the lack of variability required for Darwinian evolution.

    Yep. Asexuality is a good colonising ‘strategy’. However, my arguments don’t just apply to asexual species. Producing vast numbers of offspring does not of itself lead to ‘more evolution’, as one can see when considering the useful fiction of a constant population size. However many offspring you produce per individual, you end up leaving two, on average, when sexual.

    But a vast, vital and gene-centric difference is that, in the latter case, change is ‘sorted’ at locus level, not that of entire organisms. Novel alleles integrate into the genomes of future population members quasi-independently, over evolutionary time in sexuals. Even though, in any given individual, one might insist that it is ‘acting’ as an undivided whole.

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  20. Allan Miller:

    Me: Everything you imagine ‘controlling the genome’ is actually a product of it. RNA polymerases, spliceosomes, ribosomes, all the ‘protein complexes’ you wave a hand at. All of it.

    Charlie: But there is no master controller.

    So?

    The essence of life is not material substance because this comes and goes. The essence is in the processes which produce dynamic form.

    We have seen from fruit flies that at the very point of conception they process of development is started, not from proteins that have been grown using the DNA of the newly created offspring, but form proteins directly derived from the mother.

    For the kinds of protein you are talking about – fundamental cell cycle proteins; RNA and DNA polymerases, etc – the mother’s, father’s and zygote’s sequences are exactly the same, so it makes no difference. These were fixed deep in the history of the lineage. The differences between offspring and their parents derive from the differences between their genomes, not the identities.

    And the differences are produced by processes.

    Me: Why even mention it? DNA is different from a can of beans too.

    Charlie: Because even although they are vastly different (DNA and magnetic tape that is) there is still a fundamental similarity between them.

    You are a prime example of why analogies should be avoided – because you are persuaded by ‘phantom similarities’. If the result of playing a tape in a machine were two copies of the tape, surrounded by two brand new machines, with parts determined by the contents of the tape, it might get somewhere. Since it doesn’t, imagining DNA as like a tape simply sows confusion.

    I don’t believe that DNA is like a tape, I think that the tape has a very crude similarity to DNA in that information can be taken from it.

    If we trace our evolutionary waltz back through the generations from the mother fruit fly to life’s beginning we come across the RNA world scenario.

    Not quite. RNA world is not (necessarily) an origin scenario, but a form of life preceding protein coding, possibly lasting many millions of years.

    But in the scenario it is still thought to have preceded DNA.

    All the steps since that time have involved pre-existing proteins at the conception of the offspring.

    RNA world would precede anything resembling ‘conception’ by a considerable margin.

    So? First there is division and then comes differentiation. The whole reflected in the parts.

    For someone keen on emphasising process and extension in time, you seem to prefer a static view of the relation, with each cellular instance having a discrete temporal boundary. But the relation between DNA and its products is dynamic, and transcends genome instances. It is not necessary that this cell’s proteins be produced by this cell’s DNA copy. That doesn’t undermine DNA’s primacy in the relationship.

    There is nothing static the way I understand it. The action takes place through the combined unity of nucleotide, protein complexes.

    In a hypothetical transition from RNA organisms to protein coders, one imagines there would initially be just one protein, then a couple, then a lot, during the transition. So, in the 1-protein scenario, has ‘the system’ suddenly undergone a complete revision of relationship between genome and mode of effect? If this hypothetical protein acted upon the genome (while produced from it), would you insist “There’s no getting away from the fact that a pre-existing protein is necessary. Just one”. Suddenly, nucleic acid is ‘used by the organism’. Just because it makes a protein.

    In the above scenarion RNA (somehow) acted alone to produce the first protein. Where have we ever seen DNA acting alone?

    DNA is a product, not a producer.

    Perhaps we should call the thread ‘Charlie’s spiralling argument’. What’s it a product of?

    It is produced by the living process.

    Allan: those proteins that you imagine ‘sit above’ the genome’ and ‘use it’ are simply its products.

    Charlie: I live quite near a quarry which was the source of much of the materials used in building the city bypass. But I would not dream of saying that the quarry produced the bypass.

    Me either. Analogies, huh?

    The bypass was built by the construction processes.

    Me: Funnily enough, gene centrism doesn’t have much to do with mapping the genome, a point you will remain eternally impervious to. Dawkins’s ‘gene’ is not the molecular biologist’s, which we have discussed.

    Charlie: I am discussing the role of DNA in development and in evolution.

    So am I, but it’s important to be aware they are two different arenas. By and large, you only ever talk of DNA in physiology.

    The whole reflected in the parts 🙂

    Me: in modern cells, that’s largely how nucleic acid ‘acts’: via protein intermediates, which it produces with the aid of protein intermediates.

    Charlie: We agree that DNA is vital, but you still haven’t answered the question as to its activity. DNA is coiled, uncoiled, zipped and unzipped, packaged and repaired, cut and spliced through the activity of various complexes.

    All of which are produced from genome sequence. It’s exactly the same issue as with RNA polymerase. Naming other proteins refutes nothing. DNA ‘acts’ via protein intermediates. It doesn’t need to catalyse directly. Its products do that.

    The system acts as a unit. A complex unit but a unit nonetheless.

    There is a great deal of activity expended on DNA but I don’t see much reciprocal activity.

    There doesn’t need to be.

    I suppose not. Within the complex, it’s role is more passive

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  21. Corneel:

    Allan Miller: Yes, I was aware of the possible objection, although Charlie and I are both firmly in the north!

    The climate is changing, so it is a matter of time before the diploids will be arriving. Building a wall in the channel will not stop them.

    The swamin’ conquests 🙂

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  22. CharlieM: Me: So?

    Charlie: The essence of life is not material substance because this comes and goes. The essence is in the processes which produce dynamic form.

    Doesn’t really explain why ‘there is no master controller’ is any kind of refutation of anything I’m saying.

    And the differences are produced by processes.

    They aren’t produced by ‘processes’. At best, the processes extract the differences in DNA. There isn’t a different ‘DNA extraction process’ going on in you and me, nor indeed in you and an elephant. The differences lie in what is extracted, not what is doing the extracting.

    I don’t believe that DNA is like a tape, I think that the tape has a very crude similarity to DNA in that information can be taken from it.

    Super. And what can we learn from that? Zip, as far as I can see. Indeed, you refute yourself by that analogy: the difference between what comes out of two otherwise identical tape machines is entirely due to the tape, not the ‘processes’ by which tape becomes sound.

    Me: Not quite. RNA world is not (necessarily) an origin scenario, but a form of life preceding protein coding, possibly lasting many millions of years.

    Charlie: But in the scenario it is still thought to have preceded DNA.

    Chemically, DNA and RNA are practically interchangeable. As catalysis moved towards proteins, reducing the need for direct nucleic acid catalysis, a couple of minor modifications would have enabled the nucleic acid component to be stored in a more stable form, which is the main chemical consequence of 2′ deoxygenation and those methyl groups. They cause a tighter helix, in the first case by removing a steric hindrance and in the second by increasing hydrophobicity of the core. We talk of them as if they are distinct, but they are minor variants on a theme, despite their widely differing roles in modern cells.

    Me: RNA world would precede anything resembling ‘conception’ by a considerable margin.
    Charlie: So? First there is division and then comes differentiation.

    Prokaryotes don’t differentiate. One can reasonably assume that RNA organisms wouldn’t, either.

    There is nothing static the way I understand it. The action takes place through the combined unity of nucleotide, protein complexes.

    Those ‘protein complexes’ being entirely due to DNA sequence, of course. And, you are taking a static view by imposing that artificial temporal boundary. You declare a moment in time at which prior DNA copies somehow don’t count as sources for ‘process’. The protein repertoire of a given cell just somehow ‘is’, parachuted in from nowhere.

    In the above scenarion RNA (somehow) acted alone to produce the first protein. Where have we ever seen DNA acting alone?

    Like I say, ‘modern organisms don’t do x so no organism ever did x’ is not a viable argument.

    Me: Perhaps we should call the thread ‘Charlie’s spiralling argument’. What’s it a product of?

    Charlie: It is produced by the living process.

    It’s not really. It was already there. It’s replicated by the ‘living process’ – ie, by proteins it specifies the sequence of.

    Me either. Analogies, huh?

    Charlie: The bypass was built by the construction processes.

    That’s bypasses sorted, then.

    Me: So am I, but it’s important to be aware they are two different arenas. By and large, you only ever talk of DNA in physiology.

    Charlie: The whole reflected in the parts.

    No. Absolutely not. No way José, on your bike, etc etc. This is you being seduced by your analogies again. There is no analogue of the process of recombination in a single life. But this explains why you are incapable of grasping the ‘gene-centrist’ stance in evolution, I suppose.

    All of which are produced from genome sequence. It’s exactly the same issue as with RNA polymerase. Naming other proteins refutes nothing. DNA ‘acts’ via protein intermediates. It doesn’t need to catalyse directly. Its products do that.

    Charlie: The system acts as a unit. A complex unit but a unit nonetheless.

    That doesn’t make a dent in the gene-centric case, you know.

    Me: There doesn’t need to be.

    Charlie: I suppose not. Within the complex, it’s role is more passive

    Whatever semantic label you wish to ascribe to its role, it is the source of protein sequence.
    It doesn’t need to be ‘active’, since it makes proteins (via proteins!) that do the ‘acting’ for it.

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  23. CharlieM: The ideal triangle is not real in the sense that it is not subject to being measured.

    Or perhaps it cannot be measured because it is not a real thing.

    CharlieM: But as all multicellular organisms are thought to have originally evolved from single cellular organisms then it can be said that yeast has regressed to a more simplified state which will not lead to individual sentience or self awareness.

    Everybody starts a hike by leaving home, but that doesn’t mean we all travel the same path.

    CharlieM: All creatures share group traits but the creatures who have attained the greatest individuality are humans. It may seem paradoxical to you but self-aware individuality is a common feature which distinguishes humans from other organisms.

    It’s not paradoxical, it’s contradiction. You take full credit for the accomplishments of other people and then proudly proclaim that we humans can be distinguished by our great individuality. And then you praise our self awareness. If you do not understand why this amuses me no end, then there is really nothing I can say to help you.

    CharlieM: Organisms adapt not by gaining new traits or features but by having flexibility in the traits or features they already possess.

    Populations of organisms most certainly adapt by gaining new traits, in addition to increasing the frequency of existing adaptations to which you allude.

    I see you are rehashing a lot of old arguments, but I have no interest in replaying those discussions. Perhaps you should try a new tack. Do you have an inkling why your arguments fail to convince?

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  24. Allan Miller:

    CharlieM: Me: So?

    Charlie: The essence of life is not material substance because this comes and goes. The essence is in the processes which produce dynamic form.

    Doesn’t really explain why ‘there is no master controller’ is any kind of refutation of anything I’m saying.

    So you agree that DNA is not the master controller? The chromosomes residing in the nucleus are like the termite queen trapped but well protected deep within the nest producing new life which gets taken away and cared for as it matures into a useful member of the community.

    And the differences are produced by processes.

    They aren’t produced by ‘processes’. At best, the processes extract the differences in DNA. There isn’t a different ‘DNA extraction process’ going on in you and me, nor indeed in you and an elephant. The differences lie in what is extracted, not what is doing the extracting.

    There isn’t a different ‘DNA extraction process in the same way that there isn’t a different DNA layout. DNA is an aperiodic polymer with four bases in both an elephant and myself. The DNA sequences differ in their particulars and so do the steps within the processes. Cells use the same type of processes but they also use the same DNA format.

    I don’t believe that DNA is like a tape, I think that the tape has a very crude similarity to DNA in that information can be taken from it.

    Super. And what can we learn from that? Zip, as far as I can see. Indeed, you refute yourself by that analogy: the difference between what comes out of two otherwise identical tape machines is entirely due to the tape, not the ‘processes’ by which tape becomes sound.

    We learn to think about the processes with all the players that are required for successful performance. Again we learn that the whole is more than the sum of its parts. I think that a closer analogy would be that of multiple tape recorders all containing the same recording with each playing various portions of the recording at specific times to produce an overall meaningful harmonious sound over an extended period of time.

    Me: Not quite. RNA world is not (necessarily) an origin scenario, but a form of life preceding protein coding, possibly lasting many millions of years.

    Charlie: But in the scenario it is still thought to have preceded DNA.

    Chemically, DNA and RNA are practically interchangeable. As catalysis moved towards proteins, reducing the need for direct nucleic acid catalysis, a couple of minor modifications would have enabled the nucleic acid component to be stored in a more stable form, which is the main chemical consequence of 2′ deoxygenation and those methyl groups. They cause a tighter helix, in the first case by removing a steric hindrance and in the second by increasing hydrophobicity of the core. We talk of them as if they are distinct, but they are minor variants on a theme, despite their widely differing roles in modern cells.

    At the molecular level even the addition or removal of single electrons can make a vast difference to how chemicals react. Because I know how much you love analogies here is another one: DNA is to RNA as the plant kingdom is to the animal kingdom. The latter is renowned for its motile organisms the former for its sessile organisms. The latter needs the former and takes what it needs from it. That is not to say that its all one way, both need each other to a certain extent.

    Me: RNA world would precede anything resembling ‘conception’ by a considerable margin.
    Charlie: So? First there is division and then comes differentiation.

    Prokaryotes don’t differentiate. One can reasonably assume that RNA organisms wouldn’t, either.

    Which is evidence that prokaryotes have remained at a very early stage of evolution.

    There is nothing static the way I understand it. The action takes place through the combined unity of nucleotide, protein complexes.

    Those ‘protein complexes’ being entirely due to DNA sequence, of course. And, you are taking a static view by imposing that artificial temporal boundary. You declare a moment in time at which prior DNA copies somehow don’t count as sources for ‘process’. The protein repertoire of a given cell just somehow ‘is’, parachuted in from nowhere.

    DNA sequences do indeed count as sources of information. They specify particular polymers which are then used in a variety of ways in the self-organisation of the organism.

    In the above scenario RNA (somehow) acted alone to produce the first protein. Where have we ever seen DNA acting alone?

    Like I say, ‘modern organisms don’t do x so no organism ever did x’ is not a viable argument.

    And that is not my argument. We observe the processes within organisms today and we can see that the DNA is not the sole source of creativity.

    Me: Perhaps we should call the thread ‘Charlie’s spiralling argument’. What’s it a product of?

    Charlie: It is produced by the living process.

    It’s not really. It was already there. It’s replicated by the ‘living process’ – ie, by proteins it specifies the sequence of.

    And so were the RNA nucleotides already there. They have to be available to be attached, they don’t just materialise from nowhere. The process of DNA replication takes a great deal of activity. Helicases themselves spin at thousands of RPM and every day 50 to 70 billion of our cells die and new cells form. The kinetochore consists of hundreds of different proteins working together. This gives us some idea of how complex these processes are.

    And the only way to get hundreds of thousands of proteins from twenty-odd thousand genes is by the post translational manipulation of the translation products.

    Me either. Analogies, huh?

    Charlie: The bypass was built by the construction processes.

    That’s bypasses sorted, then.

    Until they begin to close lanes for maintenance. 🙂

    Me: So am I, but it’s important to be aware they are two different arenas. By and large, you only ever talk of DNA in physiology.

    Charlie: The whole reflected in the parts.

    No. Absolutely not. No way José, on your bike, etc etc. This is you being seduced by your analogies again. There is no analogue of the process of recombination in a single life. But this explains why you are incapable of grasping the ‘gene-centrist’ stance in evolution, I suppose.

    Recombination is a way of introducing greater variation into the descendants of single organisms. The introduction of the division of sexes is a way of introducing greater variation into evolution as a whole.

    All of which are produced from genome sequence. It’s exactly the same issue as with RNA polymerase. Naming other proteins refutes nothing. DNA ‘acts’ via protein intermediates. It doesn’t need to catalyse directly. Its products do that.

    You are stubbornly sticking to a linear cause and effect scenario which does not accurately reflect living systems. Living systems are fluidic, messy and full of unpredictability. And that is why, to be understood, the study of living systems needs so much more than the laws of physics

    Charlie: The system acts as a unit. A complex unit but a unit nonetheless.

    That doesn’t make a dent in the gene-centric case, you know.

    Whether selection is at the group, individual or gene level or some combination of those doesn’t affect my belief that selection is conservative rather than creative.

    Me: There doesn’t need to be.

    Charlie: I suppose not. Within the complex, it’s role is more passive

    Whatever semantic label you wish to ascribe to its role, it is the source of protein sequence.
    It doesn’t need to be ‘active’, since it makes proteins (via proteins!) that do the ‘acting’ for it.

    As we all know, DNA sequences are copied to mRNA and from the mRNA proteins get their amino acid sequences. But not directly. Protein development depends on how the peptides are arranged, and the path taken is rarely straightforward. Also cells can vary the amount of gene expression according to the needs of the moment. There is always a certain amount of flexibility depending on conditions.

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  25. Corneel:

    CharlieM: The ideal triangle is not real in the sense that it is not subject to being measured.

    Or perhaps it cannot be measured because it is not a real thing.

    That is true if you equate real with physical. It is not physically real.

    CharlieM: But as all multicellular organisms are thought to have originally evolved from single cellular organisms then it can be said that yeast has regressed to a more simplified state which will not lead to individual sentience or self awareness.

    Everybody starts a hike by leaving home, but that doesn’t mean we all travel the same path.

    True.

    CharlieM: All creatures share group traits but the creatures who have attained the greatest individuality are humans. It may seem paradoxical to you but self-aware individuality is a common feature which distinguishes humans from other organisms.

    It’s not paradoxical, it’s contradiction. You take full credit for the accomplishments of other people and then proudly proclaim that we humans can be distinguished by our great individuality. And then you praise our self awareness. If you do not understand why this amuses me no end, then there is really nothing I can say to help you.

    No contradiction. For example look at the comparison of eating habits between panda’s and humans. All pandas eat nothing but bamboo whereas human eating habits are very diverse and, where there is a choice, dependent on individual taste.

    Where have I taken credit for the accomplishments of others?

    CharlieM: Organisms adapt not by gaining new traits or features but by having flexibility in the traits or features they already possess.

    Populations of organisms most certainly adapt by gaining new traits, in addition to increasing the frequency of existing adaptations to which you allude.

    Can you give examples from existing populations?

    I see you are rehashing a lot of old arguments, but I have no interest in replaying those discussions. Perhaps you should try a new tack. Do you have an inkling why your arguments fail to convince?

    I don’t expect my arguments to convince those who disagree with what I say precisely because of our different beliefs. I’m sure there are other venues where I would get agreement. But why would I want to contribute there? I’m not here to have my views accepted, I am looking to be challenged,

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  26. CharlieM: And so were the RNA nucleotides already there. They have to be available to be attached, they don’t just materialise from nowhere.

    Talking about nucleotides, this is relevant:

    Nucleotides are some of the largest molecules synthesized by our cells, and their creation requires many substrates, many steps and huge amounts of energy. The biosynthesis of nucleotides is under very tight control since energy is wasted when making too much, and DNA replication and cellular metabolism is slowed down when making too little. Our cells are also very sensitive to the amount of free nucleotides floating within the nucleus or the cytoplasm. The cell will always choose to use the nucleotides that have already been created before synthesizing new ones. Cellular energy is conserved and DNA replication is enhanced by making sure that your cells are constantly supplied with exogenous nucleotides.

    Think of all the nucleotides required to be available within the billions of cells created daily in our bodies, not to mention those used in protein synthesis.

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  27. All living beings maintain an active dynamic balance between the life pole and the death pole.

    For example, in a review headed, ‘Dynamics of silk proteins are key to outstanding stability of spider silk as biomaterial’ they discuss the flexibility of spider silk.

    The researchers were surpirized that in some silks the high amounts of an amino acid known to produce flexible side chains was present. Why were they surprized? I’m surprized that they were surprized. In order to meet the needs of their function the substances produced by life maintain a necessary balance between rigidity and flexible motility. For example, bone consists of a polarity between lifeless, solid calcium salts necessary for rigidity and more living, pliable collagen fibres allowing for flexibility.

    Active proteins definitely belong in the vicinity of the life pole:
    Protein dynamics: Hidden, transient life of a protein between active states illuminated

    In a groundbreaking study this week in Cell, Brandeis researchers reveal for the first time computationally and experimentally the molecular pathway that a protein takes to cross the energy barrier, the “climb over the mountain.” The study reports how folded proteins can efficiently change shape while avoiding unfolding, a critical requirement for any protein in the cell.

    Mobility of form is an essential feature of living substance. Denatured proteins are proteins that have moved closer to the death pole. Intrinsically disordered proteins are becoming a popular topic of study. Chaos and order, two more poles featuring prominently in life.

    In the video, ‘Design by evolution: engineering biology in the 21st century’ The Nobel Laureate, Dr.Frances Arnold ensures us that the DNA tells the cells what to do at a particular time, how to respond to their environment. and then how to develop into an organism. She doesn’t tell us how the DNA takes charge in this way. If we want to stick with the conversational/communication metaphor I think it would more appropriate to say that cells have particular needs, they inform their genome of these needs and the genome does what it can to supply what is needed where possible. A combined, cooperative effort.

    She explains that she could type in the sequence to make a gene, send these instructions across the world and those who receive it could synthesize it. As she put it, we can play the genome but we don’t yet know how to compose it.
    She says:

    We can synthesise new code, we can insert it into cells and they will read it. .. We know the mapping code between DNA and proteins but we don’t know how it translates into the three dimensional structure of the protein.

    When she was a graduate student (in the ’70s) they told her the protein folding problem would be solved within five years. She tells us, “they lied”. And according to her an even bigger problem is in determining how the structure of the protein dictates its function, Ultimately how the DNA sequence dictates the function.

    Of course the problem is even greater than her brief explanation indicates. A DNA sequence rarely translates into a functional protein. There are usually multiple DNA sequences each coding for a single domain or just one part of a domain, several of which have to work together to make one functional protein complex. And on top of all this to talk about protein structures could give the wrong impression. This makes them sound equivalent to solid objects such as buildings. Generally proteins should be thought of as fluidic, amoeboid like forms full of living activity.

    Within earthly life classes of organisms go though the cycle of life and death, within classes individual organisms go through the cycle of life and death, within the individual organism cells go through the cycle of life and death, within cells molecular complexes go through the cycle of life and death. Spirals within spirals as in the Mandelbrot fractal image displayed below.

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  28. In the book The Secret Teachings of Plants: The Intelligence of the Heart in the Direct Perception of Nature by Stephen Harrod Buhner, he provides more details about fractals and life.

    In a section headed, Fractals, ‘Nonlinearity and Deterministic Chaos’, Buhner writes about Mandelbrot and the subject of fractals. He writes:

    The fractal shape of natural objects means they are irregular or disjoint and the word stands in opposition to algebra which comes from the Arabic al-jabr and means, “to rejoin broken parts.” (It was used originally to refer to setting broken bones.) Euclidean geometry uses algebra to measure shapes and it joins together the nonlinearity of nature by smoothing out its irregularities into something that can be understood, and supposedly controlled and predicted, with the linear mind. But fractals are not Euclidean and they are intimately related to life itself. They are not a static system of three-dimensional shapes. Fractal lines – the fractal geometry of nature – are the shapes created when life flows through physical space. They are always in flux. Looking out from our tiny and limited life span, we continually miss the fact It has never stopped. The mountain lives much slower than we do, but its shape is never static, never unchanging. It is always flowing along and between dimensions, in constantly fluctuating, never predictable ways. This understanding disturbs deeply embedded (adult, not child) preconceptions and species bias, about matter and Nature, about what what is living and what is not. For human cultures to allow scientists to dissect Nature as much as they have, Nature has to become a dead, unalive thing, otherwise no one would put up with it…
    Every property of a natural object will, when examined, display a fractal nature.

    There are no straight lines and there are no right angles in nature. In taking measurements, angles and line segment lengths, however accurate, are always approximations.

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  29. CharlieM: Where have I taken credit for the accomplishments of others?

    Wherever you have been reveling in the accomplishments of humans as a species. Like for example in the sentence immediately preceding:

    All pandas eat nothing but bamboo whereas human eating habits are very diverse […]

    How are your eating habits? More diverse than that of an individual opportunistic feeder like a crow? Do you often consume from the five main food groups of small animals, insects, grain, fruits and carrion?

    CharlieM: Me: Populations of organisms most certainly adapt by gaining new traits, in addition to increasing the frequency of existing adaptations to which you allude.

    Charlie: Can you give examples from existing populations?

    Perhaps you heard about aerobic citrate usage in Lenski’s long-term evolution experiment?

    CharlieM: I’m not here to have my views accepted, I am looking to be challenged,

    Pleased to hear it. So, do you have an inkling why your arguments fail to convince?

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  30. Corneel:

    CharlieM: Where have I taken credit for the accomplishments of others?

    Wherever you have been revelling in the accomplishments of humans as a species. Like for example in the sentence immediately preceding:

    All pandas eat nothing but bamboo whereas human eating habits are very diverse […]

    I’m not revelling in anything, I’m just stating facts.

    How are your eating habits? More diverse than that of an individual opportunistic feeder like a crow? Do you often consume from the five main food groups of small animals, insects, grain, fruits and carrion?

    You obviously didn’t get the point I was trying to make. I’m not talking about within individuals, I am talking about between individuals. Crows (and herring gulls) as a group will eat just about anything that they can squeeze into their gullet. And so will some people. But some individual humans are vegan or vegetarian and some don’t care for vegetables but they love meat. I’ve never eaten carrion but I have known one or two people who have eaten pheasants and deer that have been roadkill. And I know that insects form part of the diet of many cultures.

    If we are lucky enough we can decide individually what we eat. And I know some people whose choice of food is dependent on its health value more than the enjoyment they get out of it.

    Cows don’t eat grass because they know it is necessary for their wellbeing, they eat it because they get satisfaction from it. They have no idea of the resulting consequences.

    Me: Populations of organisms most certainly adapt by gaining new traits, in addition to increasing the frequency of existing adaptations to which you allude.

    Charlie: Can you give examples from existing populations?

    Perhaps you heard about aerobic citrate usage in Lenski’s long-term evolution experiment?

    Yes. And I’m aware of the controversy of differing interpretations. As far as I’m aware they already were able to metabolise citrate. And by a process of trial and error of various genomic configurations they were able to use the citrate that was previously unavailable to them. Bacteria may not have human-like consciousness but they are very intelligent nonetheless.

    CharlieM: I’m not here to have my views accepted, I am looking to be challenged,

    Pleased to hear it. So, do you have an inkling why your arguments fail to convince?

    Because I may be looking at things from an entirely different perspective from the people who are arguing against me?

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  31. CharlieM: Me: Doesn’t really explain why ‘there is no master controller’ is any kind of refutation of anything I’m saying.
    Charlie: So you agree that DNA is not the master controller?

    DNA is ultimately where all control resides. I don’t see it as ‘a master controller’, but that remains the case.

    The chromosomes residing in the nucleus are like …

    Are like a crap analogy.

    There isn’t a different ‘DNA extraction process in the same way that …

    In the same way that there isn’t a different DNA extraction process. Gibbering about other things that aren’t DNA extraction processes is not a refutation of this. You seem incapable of discussing the subject matter without reference to something that is not the subject matter.

    Me: Super. And what can we learn from that? Zip, as far as I can see.
    Charlie: I think that a closer analogy would be […]

    Just as useless for understanding biology.

    Me: Chemically, DNA and RNA are practically interchangeable.
    Charlie: At the molecular level even the addition or removal of single electrons can make a vast difference to how chemicals react.

    Another irrelevant analogy. You can’t have template-directed replication of ‘chemicals’ by swapping electrons, so no possibility of genetic continuity, which is the point I was getting at. You can have bidirectional copying of DNA to RNA and vice versa, because all you are doing is adding almost identical monomers.

    Because I know how much you love analogies here is another one: DNA is to RNA as the plant kingdom is to the animal kingdom.

    So you can copy the sequence of the plant kingdom to the animal, and vice versa?

    Me: Like I say, ‘modern organisms don’t do x so no organism ever did x’ is not a viable argument.

    Charlie: And that is not my argument.

    ‘Tis too:

    We observe the processes within organisms today and we can see that the DNA is not the sole source of creativity.

    And you are using that to attack the notion of pre-protein nucleic-acid-based organisms. Because we don’t see it today, it never happened.

    Charlie: And so were the RNA nucleotides already there. They have to be available to be attached, they don’t just materialise from nowhere.

    Not in the same sense. Template-based RNA and DNA polymerisation does not create sequence de novo. The replicated sequence is not ‘produced’ by the cell, but specified by the xNA template.

    The process of DNA replication takes a great deal of activity.

    No kidding

    Helicases themselves spin at thousands of RPM and every day 50 to 70 billion of our cells die and new cells form. The kinetochore consists of hundreds of different proteins working together. This gives us some idea of how complex these processes are.

    And, as I have patiently explained, this complexity in no way undermines gene-centrism (the evolutionary stance), nor the central role of DNA as source of both sequence and control.

    And the only way to get hundreds of thousands of proteins from twenty-odd thousand genes is by the post translational manipulation of the translation products.

    All of which is genetically specified. Or do you think it just happens?

    Me: No. Absolutely not. No way José, on your bike, etc etc. This is you being seduced by your analogies again. There is no analogue of the process of recombination in a single life. But this explains why you are incapable of grasping the ‘gene-centrist’ stance in evolution, I suppose.

    Charlie: Recombination is a way of introducing greater variation into the descendants of single organisms. The introduction of the division of sexes is a way of introducing greater variation into evolution as a whole.

    I’m not asking for your pet Theory Of Recombination, I’m explaining its role in gene-centred evolutionary thinking. It unchains the Selfish Gene. Without it, Dawkins’s stance (inherited as he acknowledges, from Hamilton, Williams and Maynard Smith) would gain no traction; there would be no such book. So waffling about wholes reflected in parts, or speculating on the ‘purpose’ of recombination, misses this central point.

    You are stubbornly sticking to a linear cause and effect scenario which does not accurately reflect living systems.

    It is clear that a DNA sequence must sit causally ‘upstream’ of any product its sequence specifies, be it RNA or protein.

    Whether selection is at the group, individual or gene level or some combination of those doesn’t affect my belief that selection is conservative rather than creative.

    Why can’t it be both?

    As we all know, DNA sequences are copied to mRNAand from the mRNA proteins get their amino acid sequences. But not directly. Protein development depends on how the peptides are arranged, and the path taken is rarely straightforward. Also cells can vary the amount of gene expression according to the needs of the moment. There is always a certain amount of flexibility depending on conditions.

    By and large, those ‘conditions’ depend on the developmental stage and tissue in which the cell finds itself. What happens tends to be very consistent – each individual has the same expression pattern. This is why we can identify genetic diseases, or target pharmacology. If organisms weren’t ‘repeatable’, or predictable, in this way, those things would not be possible.

    Now, a zygote doesn’t have this info in its cytoplasm. Its current cytoplasmic contents are typically a few hours old, and will be gone in a few hours more. And when the zygote has divided a few hundred times, all of that cytoplasm is long gone anyway. What remains, constant and repeated, is the genome. Now, for reasons best known to yourself, you reject this. You think that some extragenomic component has the consistency and repeatability to ensure that in tissue x at age y of every individual of organism z, derived by long division and massive dilution from that zygote, something specific happens.

    I see no need for this hypothesis. It’s the genome. Of course it’s the bloody genome! What the hell else could it be?

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  32. Allan Miller:

    CharlieM: Me: Doesn’t really explain why ‘there is no master controller’ is any kind of refutation of anything I’m saying.
    Charlie: So you agree that DNA is not the master controller?

    DNA is ultimately where all control resides. I don’t see it as ‘a master controller’, but that remains the case.

    What about when humans manipulate DNA? Where does the control reside in that situation?

    The chromosomes residing in the nucleus are like …

    Are like a crap analogy.

    Talking about crap. Right there in the process of dung production there is the polarity of cosmos and chaos, order and disorder. The growing plant forms in an orderly manner. There is predictability in the process. When a horse or cow eats the plants this order is once again returned to a chaos. In the excreted dung the form of the plant organs are no longer there. . But in this chaotic substance there are the forces which help new growth and a return to order. And thus the cycle continues. From the vastness of the universe down to tiniest organelle the same cyclic fluctuation between order and disorder is taking place. Stars and galaxies have their own metabolism.

    There isn’t a different ‘DNA extraction process in the same way that …

    In the same way that there isn’t a different DNA extraction process. Gibbering about other things that aren’t DNA extraction processes is not a refutation of this. You seem incapable of discussing the subject matter without reference to something that is not the subject matter.

    Well DNA extraction involves much more than DNA. There is a vast amount of DNA extraction going on in my cells at this moment just because I am moving my fingers across the keyboard.

    If you want to just discuss genetics then I’m sure there are plenty of expert geneticists you could argue with.

    Me: Super. And what can we learn from that? Zip, as far as I can see.
    Charlie: I think that a closer analogy would be […]

    Just as useless for understanding biology.

    I find it just the opposite. As Goethe said, nature is book to read. And if we get too focused on the details we become experts in the meaning of individual words but we lose the context of the story and context matters.

    Me: Chemically, DNA and RNA are practically interchangeable.
    Charlie: At the molecular level even the addition or removal of single electrons can make a vast difference to how chemicals react.

    Another irrelevant analogy. You can’t have template-directed replication of ‘chemicals’ by swapping electrons, so no possibility of genetic continuity, which is the point I was getting at. You can have bidirectional copying of DNA to RNA and vice versa, because all you are doing is adding almost identical monomers.

    Despite their small chemical differences, DNA and RNA differ quite dramatically in overall structure. Without the unique properties of RNA transcription would never be translated into functional proteins. The system has to work as a whole.

    Monomers get added because the system is configured to allow for it.

    Because I know how much you love analogies here is another one: DNA is to RNA as the plant kingdom is to the animal kingdom.

    So you can copy the sequence of the plant kingdom to the animal, and vice versa?

    Meaning one (DNA) is more firmly fixed in place, while the other (RNA) is more motile. It is the RNA which leaves the nucleus and travels out into the cytoplasm.

    Me: Like I say, ‘modern organisms don’t do x so no organism ever did x’ is not a viable argument.

    Charlie: And that is not my argument.

    ‘Tis too:

    We observe the processes within organisms today and we can see that the DNA is not the sole source of creativity.

    And you are using that to attack the notion of pre-protein nucleic-acid-based organisms. Because we don’t see it today, it never happened.

    Previously I wrote

    So I’m happy to accept that living entities more simple than present day cells are a possibility. If life began with RNA organisms that’s fine by me

    Like I said I’m happy to speculate that in the past organisms might have done ‘x’.

    Charlie: And so were the RNA nucleotides already there. They have to be available to be attached, they don’t just materialise from nowhere.

    Not in the same sense. Template-based RNA and DNA polymerisation does not create sequence de novo. The replicated sequence is not ‘produced’ by the cell, but specified by the xNA template.

    The template can only be of use if there is material available to populate it.

    Yes the DNA sequence is transcribed. But in many cases the transcribed sequence is only one piece of a complex consisting of multiple pieces

    The process of DNA replication takes a great deal of activity.

    No kidding

    No indeed. Well orchestrated, coordinated activity.

    Helicases themselves spin at thousands of RPM and every day 50 to 70 billion of our cells die and new cells form. The kinetochore consists of hundreds of different proteins working together. This gives us some idea of how complex these processes are.

    And, as I have patiently explained, this complexity in no way undermines gene-centrism (the evolutionary stance), nor the central role of DNA as source of both sequence and control.

    I agree that it’s the source of sequence.

    And the only way to get hundreds of thousands of proteins from twenty-odd thousand genes is by the post translational manipulation of the translation products.

    All of which is genetically specified. Or do you think it just happens?

    No. It happens due to well orchestrated, coordinated activity. 🙂

    Me: No. Absolutely not. No way José, on your bike, etc etc. This is you being seduced by your analogies again. There is no analogue of the process of recombination in a single life. But this explains why you are incapable of grasping the ‘gene-centrist’ stance in evolution, I suppose.

    Charlie: Recombination is a way of introducing greater variation into the descendants of single organisms. The introduction of the division of sexes is a way of introducing greater variation into evolution as a whole.

    I’m not asking for your pet Theory Of Recombination, I’m explaining its role in gene-centred evolutionary thinking. It unchains the Selfish Gene. Without it, Dawkins’s stance (inherited as he acknowledges, from Hamilton, Williams and Maynard Smith) would gain no traction; there would be no such book. So waffling about wholes reflected in parts, or speculating on the ‘purpose’ of recombination, misses this central point.

    The point is, where does the gene stand today in the minds of those interested parties? Here is piece on the topic. It links the discovery of Mendel’s work with the good old ‘crap’ metaphor. But not just any old crap, celestial crap. 🙂

    was the Holy Shit! moment that launched genetics’ Holy Shit! century. It seemed to explain everything. And it saved Darwin.

    The author (David Dobbs) continues:

    the selfish-gene story is so focused on the gene’s singular role in natural selection that in an age when it’s ever more clear that evolution works in ways far more clever and complex than we realise, the selfish-gene model increasingly impoverishes both scientific and popular views of genetics and evolution. As both conceptual framework and metaphor, the selfish-gene has helped us see the gene as it revealed itself over the 20th century. But as a new age and new tools reveal a more complicated genome, the selfish-gene is blinding us…

    The gene-centric view is thus ‘an artefact of history’, says Michael Eisen, an evolutionary biologist who researches fruit flies at the University of California, Berkeley. ‘It rose simply because it was easier to identify individual genes as something that shaped evolution. But that’s about opportunity and convenience rather than accuracy. People confuse the fact that we can more easily study it with the idea that it’s more important.’

    Dobbs begins this piece by telling us about grasshoppers and locusts and his surprise that they are not different species. This is no real surprise. All we need do is look at amphibia or Lepidoptera to see how the same genome can produce totally different organisms.

    Anyway there is a fair bit in this piece that I think is worth following up on.

    You are stubbornly sticking to a linear cause and effect scenario which does not accurately reflect living systems.

    It is clear that a DNA sequence must sit causally ‘upstream’ of any product its sequence specifies, be it RNA or protein.

    Not in individual development it isn’t In this case the individual’s DNA relies on external complexes supplied by the mother. Or in the case of prokaryote cell division. all the molecular complexes are already present. Prokaryote replication is never just about the DNA.

    Whether selection is at the group, individual or gene level or some combination of those doesn’t affect my belief that selection is conservative rather than creative.

    Why can’t it be both?

    It can, but this sreativity doesn’t supply any major novelties.

    As we all know, DNA sequences are copied to mRNAand from the mRNA proteins get their amino acid sequences. But not directly. Protein development depends on how the peptides are arranged, and the path taken is rarely straightforward. Also cells can vary the amount of gene expression according to the needs of the moment. There is always a certain amount of flexibility depending on conditions.

    By and large, those ‘conditions’ depend on the developmental stage and tissue in which the cell finds itself. What happens tends to be very consistent – each individual has the same expression pattern. This is why we can identify genetic diseases, or target pharmacology. If organisms weren’t ‘repeatable’, or predictable, in this way, those things would not be possible.

    Now, a zygote doesn’t have this info in its cytoplasm. Its current cytoplasmic contents are typically a few hours old, and will be gone in a few hours more. And when the zygote has divided a few hundred times, all of that cytoplasm is long gone anyway. What remains, constant and repeated, is the genome. Now, for reasons best known to yourself, you reject this. You think that some extragenomic component has the consistency and repeatability to ensure that in tissue x at age y of every individual of organism z, derived by long division and massive dilution from that zygote, something specific happens.

    I see no need for this hypothesis. It’s the genome. Of course it’s the bloody genome! What the hell else could it be?

    The extragenomic component is the pattern of activity. But it’s not really ‘extragenomic’ as you put it, as the genome is within the system of activity. For instance within all of our cells from zygote onwards there will be the activity of microtubule assembly and disassembly. Of course this involves the genetic sequences that code for the components of the microtubules and for all the other active participants. But the genes alone cannot act in isolation.

    This is quite a long post and I’d like to post it now as I’m running out of time, so I’ll apologise in advance for any formatting slip ups I might have made..

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  33. How do cells fold their genome?

    Loops within loops which rotate helically around the long axis of the chromosome.

    A nice brief explanation of the process despite the machine metaphors.

    A good example of the spiralling flow of life at the microscopic level.

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  34. CharlieM: As Goethe said…:

    *delurks*

    Goethe is widely acknowledged as Germany’s leading literary figure. His colour wheel apparently was adopted by nineteenth century painters such as Turner. But his contributions to science (apart from Goethe’s bone) have not stood the test of time and he died in 1832.

    *relurks*

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  35. CharlieM: Me: DNA is ultimately where all control resides. I don’t see it as ‘a master controller’, but that remains the case.

    Charlie: What about when humans manipulate DNA? Where does the control reside in that situation?

    This has absolutely nothing to do with it.

    Me: Are like a crap analogy.

    Charlie: Talking about crap. Right there in the process of dung production there is the polarity of cosmos and chaos, order and disorder. The growing plant […]

    Sounds like you may have been drinking reindeer piss. They like fly agarics; some people swear you get a better high that way.

    Me: In the same way that there isn’t a different DNA extraction process. Gibbering about other things that aren’t DNA extraction processes is not a refutation of this. You seem incapable of discussing the subject matter without reference to something that is not the subject matter.

    Charlie: Well DNA extraction involves much more than DNA. There is a vast amount of DNA extraction going on in my cells at this moment just because I am moving my fingers across the keyboard.

    You are a point-misser extraordinaire. This does not address, refute, or have anything to do with the fact that DNA processing is much the same in elephants and you, and the difference between elephants and you lies in differences between your DNA, not its core ‘machinery’ of expression.

    If you want to just discuss genetics then I’m sure there are plenty of expert geneticists you could argue with.

    Odd comment. If you don’t want to talk about genetics, you are free to leave the conversation.

    Me: Another irrelevant analogy. You can’t have template-directed replication of ‘chemicals’ by swapping electrons, so no possibility of genetic continuity, which is the point I was getting at. You can have bidirectional copying of DNA to RNA and vice versa, because all you are doing is adding almost identical monomers.

    Charlie: Despite their small chemical differences, DNA and RNA differ quite dramatically in overall structure.

    Quantify ‘dramatically’. DNA forms tighter helixes, is all. You can have double and single stranded forms of both, both can catalyse the full range of basic biochemical reactions (though only one does so in living forms). To equate their differences with those between neighbours in the periodic table is tripe.

    Monomers get added because the system is configured to allow for it.

    Part of that ‘configuration’ is the template. DNA can be a template for RNA polymerisation, and vice versa.

    Me: Not in the same sense. Template-based RNA and DNA polymerisation does not create sequence de novo. The replicated sequence is not ‘produced’ by the cell, but specified by the xNA template.

    Charlie: The template can only be of use if there is material available to populate it.

    Irrelevant.

    Me: No kidding

    Charlie: No indeed. Well orchestrated, coordinated activity.

    All sourced by genetic sequence. Have you come up with a non-genomic control element yet? I may have missed it.

    Me: All of which is genetically specified. Or do you think it just happens?

    Charlie: No. It happens due to well orchestrated, coordinated activity.

    Rooted in the genome.

    Me: It is clear that a DNA sequence must sit causally ‘upstream’ of any product its sequence specifies, be it RNA or protein.

    Charlie: Not in individual development it isn’t.

    Yes, in individual development. Any given DNA sequence must be causally prior to its products. It seems nonsensical to reject this, so I must assume you have misunderstood

    In this case the individual’s DNA relies on external complexes supplied by the mother.

    There you go introducing an artificial boundary, despite claiming to be all about the ‘continuous process’. In this case, products in the ‘individual’ lie downstream of DNA in ‘the mother’. My contention stands.

    Me: Why can’t it be both?

    Charlie: It can, but this sreativity doesn’t supply any major novelties.

    Why not?

    Me: I see no need for this hypothesis. It’s the genome. Of course it’s the bloody genome! What the hell else could it be?

    Charlie: The extragenomic component is the pattern of activity.

    That doesn’t really cut it. The genome ends up in every cell. The ‘pattern of activity’ in the zygote is lost, replaced from the genome as it divides into trillions of cells, each with a copy of the genome but not a preserved copy of anything else in the zygote, except as generated from the genome (by products of the genome…).

    But the genes alone cannot act in isolation.

    Good grief. That again? How many more times? Gene centrism does not postulate that genes act in isolation. I said in August that I’d said this in July …

    1+
  36. CharlieM: You obviously didn’t get the point I was trying to make. I

    I believe I did: You took credit for other people’s accomplishments to support your claim that humans have higher “individuality” than members of other species. Apart from the fact that this argument relies completely on your denial that other species display similar or higher levels of trait variation, you completely missed the irony of flaunting the individual accomplishments of other people to elevate humans as a group by virtue of our individuality. And here you do it again:

    CharlieM: But some individual humans are vegan or vegetarian and some don’t care for vegetables but they love meat. I’ve never eaten carrion but I have known one or two people who have eaten pheasants and deer that have been roadkill. And I know that insects form part of the diet of many cultures.

    Yes, other people have done that. All you have done is insisting how incredibly individual that makes us humans as a group. If you still don’t understand my point this time, I am totally giving up.

    CharlieM: Cows don’t eat grass because they know it is necessary for their wellbeing, they eat it because they get satisfaction from it. They have no idea of the resulting consequences.

    It’s true. Humans are better than cows at visualizing possible future scenario’s. I note that ALL your claims on teleology in evolution reduce to how smart we humans are. But you have never established that this is a goal of evolution, rather than having a pleasing black-and-white pattern, for example.

    CharlieM: Me: Perhaps you heard about aerobic citrate usage in Lenski’s long-term evolution experiment?

    Charlie: Yes. And I’m aware of the controversy of differing interpretations. As far as I’m aware they already were able to metabolise citrate. And by a process of trial and error of various genomic configurations they were able to use the citrate that was previously unavailable to them.

    Differing interpretation my elbow. Let’s examine this “process of trial and error of various genomic configurations” a little closer, shall we? Did you perhaps mean to refer to chance mutations in the DNA, which might increase in population frequency because of natural selection?

    Subsituting icky words does not suffice to change the “interpretation” of what has happened in that experiment.

    CharlieM: Me: Pleased to hear it. So, do you have an inkling why your arguments fail to convince?

    Charlie: Because I may be looking at things from an entirely different perspective from the people who are arguing against me?

    Quite right. Maybe you want to make sure your arguments work from our point of view? That means you probably want to steer clear of deepities. Also you might want to start using words in the same way other people understand them.

    0
  37. Allan Miller:

    Me: DNA is ultimately where all control resides. I don’t see it as ‘a master controller’, but that remains the case.

    Charlie: What about when humans manipulate DNA? Where does the control reside in that situation?

    This has absolutely nothing to do with it.

    If you want to discuss control it has everything to do with it. Every scientist who carries out gene editing is controlling genes. They consciously control the genes directly.

    Animals that eat carbohydrates are unconsciously stimulating the production of insulin. Their activity is causing particular genes to be expressed.

    Me: Are like a crap analogy.

    Charlie: Talking about crap. Right there in the process of dung production there is the polarity of cosmos and chaos, order and disorder. The growing plant […]

    Sounds like you may have been drinking reindeer piss. They like fly agarics; some people swear you get a better high that way.

    Fly agarics have fascinated me ever since I first came across them as a young boy, but I’ve never eaten them nor drunk reindeer piss. I limit myself to strong black coffee and cultivated mushrooms.

    Me: In the same way that there isn’t a different DNA extraction process. Gibbering about other things that aren’t DNA extraction processes is not a refutation of this. You seem incapable of discussing the subject matter without reference to something that is not the subject matter.

    Charlie: Well DNA extraction involves much more than DNA. There is a vast amount of DNA extraction going on in my cells at this moment just because I am moving my fingers across the keyboard.

    You are a point-misser extraordinaire. This does not address, refute, or have anything to do with the fact that DNA processing is much the same in elephants and you, and the difference between elephants and you lies in differences between your DNA, not its core ‘machinery’ of expression.

    The difference between an elephant and myself has a great deal to do with how our respective DNA is expressed. We may have only twenty odd thousand protein coding genes but we have hundreds of thousands of enhancers scattered throughout our genomes all choreographed on a scale that is beyond human understanding.

    CharlieM: If you want to just discuss genetics then I’m sure there are plenty of expert geneticists you could argue with.

    Allan: Odd comment. If you don’t want to talk about genetics, you are free to leave the conversation.

    I do want to talk about genetics and much else besides. I want to talk about life at all levels.

    Me: Another irrelevant analogy. You can’t have template-directed replication of ‘chemicals’ by swapping electrons, so no possibility of genetic continuity, which is the point I was getting at. You can have bidirectional copying of DNA to RNA and vice versa, because all you are doing is adding almost identical monomers.

    Charlie: Despite their small chemical differences, DNA and RNA differ quite dramatically in overall structure.

    Quantify ‘dramatically’. DNA forms tighter helixes, is all. You can have double and single stranded forms of both, both can catalyse the full range of basic biochemical reactions (though only one does so in living forms). To equate their differences with those between neighbours in the periodic table is tripe.

    My use of the word ‘structure’ was no doubt misleading. I did not mean by it fixed shape. I meant also how they perform dynamically over time in living organisms. More like the structure of a play than of a building.

    Monomers get added because the system is configured to allow for it.

    Part of that ‘configuration’ is the template. DNA can be a template for RNA polymerisation, and vice versa.

    And I have no problem with regarding them as templates.

    Me: Not in the same sense. Template-based RNA and DNA polymerisation does not create sequence de novo. The replicated sequence is not ‘produced’ by the cell, but specified by the xNA template.

    Charlie: The template can only be of use if there is material available to populate it.

    Irrelevant.

    You think processes are irrelevant?

    Me: No kidding

    Charlie: No indeed. Well orchestrated, coordinated activity.

    All sourced by genetic sequence. Have you come up with a non-genomic control element yet? I may have missed it.

    I’m not looking for a non genetic control element. The higher order control includes genetic elements.

    Me: All of which is genetically specified. Or do you think it just happens?

    Charlie: No. It happens due to well orchestrated, coordinated activity.

    Rooted in the genome.

    Using the genome.

    Me: It is clear that a DNA sequence must sit causally ‘upstream’ of any product its sequence specifies, be it RNA or protein.

    Charlie: Not in individual development it isn’t.

    Yes, in individual development. Any given DNA sequence must be causally prior to its products. It seems nonsensical to reject this, so I must assume you have misunderstood

    If we are focussing on the individual the source of the maternal control elements are irrelevant because they are external to the individual in question.

    In this case the individual’s DNA relies on external complexes supplied by the mother.

    There you go introducing an artificial boundary, despite claiming to be all about the ‘continuous process’. In this case, products in the ‘individual’ lie downstream of DNA in ‘the mother’. My contention stands.

    There is nothing artificial about the cell membrane of the zygote. And where did I say that processes must be continuous?

    Me: Why can’t it be both?

    Charlie: It can, but this creativity doesn’t supply any major novelties.

    Why not?

    Because in the group of entity from which it selects. it entails a reduction of variability, or a change in the proportions of the variations already present.

    Me: I see no need for this hypothesis. It’s the genome. Of course it’s the bloody genome! What the hell else could it be?

    Charlie: The extragenomic component is the pattern of activity.

    That doesn’t really cut it. The genome ends up in every cell. The ‘pattern of activity’ in the zygote is lost, replaced from the genome as it divides into trillions of cells, each with a copy of the genome but not a preserved copy of anything else in the zygote, except as generated from the genome (by products of the genome…)

    By ‘pattern of activity’ I mean the underlying processes which remain constant. For example the same pattern of transcription, translation and protein production goes on in the zygote as in a specialised cell.

    But the genes alone cannot act in isolation.

    Good grief. That again? How many more times? Gene centrism does not postulate that genes act in isolation. I said in August that I’d said this in July

    You are coming from a position of gene centrism, but I am not arguing solely against gene centrism. So we agree on the isolation point.

    I stress the point not for your benefit but for others who might read this.

    Even trying to trace the source of control through network diagrams, however convoluted and complex they look, is too much of a simplification because they do not show any meaningful representation of the dynamic time element.

    0
  38. Corneel:

    CharlieM: You obviously didn’t get the point I was trying to make.

    I believe I did: You took credit for other people’s accomplishments to support your claim that humans have higher “individuality” than members of other species. Apart from the fact that this argument relies completely on your denial that other species display similar or higher levels of trait variation, you completely missed the irony of flaunting the individual accomplishments of other people to elevate humans as a group by virtue of our individuality. And here you do it again:

    I am merely making an observation. Select any species you like and give us some examples of trait differences between individuals.

    CharlieM: But some individual humans are vegan or vegetarian and some don’t care for vegetables but they love meat. I’ve never eaten carrion but I have known one or two people who have eaten pheasants and deer that have been roadkill. And I know that insects form part of the diet of many cultures.

    Yes, other people have done that. All you have done is insisting how incredibly individual that makes us humans as a group. If you still don’t understand my point this time, I am totally giving up.

    Individuality is a distinguishing feature of humans compared to, say, herring.

    You do realise that in ‘Finding Nemo’ the fish are deliberately given human characteristics and that is not natural fish behaviour?

    CharlieM: Cows don’t eat grass because they know it is necessary for their wellbeing, they eat it because they get satisfaction from it. They have no idea of the resulting consequences.

    It’s true. Humans are better than cows at visualizing possible future scenario’s. I note that ALL your claims on teleology in evolution reduce to how smart we humans are. But you have never established that this is a goal of evolution, rather than having a pleasing black-and-white pattern, for example.

    I have said before we might be smart individually but our individual smartness, even our group smartness, pales in comparison with the smartness of, say, termites as a group.

    Me: Perhaps you heard about aerobic citrate usage in Lenski’s long-term evolution experiment?

    Charlie: Yes. And I’m aware of the controversy of differing interpretations. As far as I’m aware they already were able to metabolise citrate. And by a process of trial and error of various genomic configurations they were able to use the citrate that was previously unavailable to them.

    Differing interpretation my elbow. Let’s examine this “process of trial and error of various genomic configurations” a little closer, shall we? Did you perhaps mean to refer to chance mutations in the DNA, which might increase in population frequency because of natural selection?

    Yes I did. That is a feature of the inbuilt wisdom of the group. Natural selection just means that those individuals who were better at using the available resources prospered. The group survives by finding the right balance between order and disorder. It walks a narrow path which if it strays in either direction it will be doomed to extinction.

    Subsituting icky words does not suffice to change the “interpretation” of what has happened in that experiment.

    Interpretations are driven by prior assumptions no matter what point of view one comes from.

    Me: Pleased to hear it. So, do you have an inkling why your arguments fail to convince?

    Charlie: Because I may be looking at things from an entirely different perspective from the people who are arguing against me?

    Quite right. Maybe you want to make sure your arguments work from our point of view? That means you probably want to steer clear of deepities. Also you might want to start using words in the same way other people understand them.

    You mean everyone should have the same prior assumptions as yourself? Life is not like that. All that we are obliged to do is understand each point of view, not to agree with them.

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  39. Alan Fox: CharlieM: As Goethe said…:

    *delurks*

    Goethe is widely acknowledged as Germany’s leading literary figure. His colour wheel apparently was adopted by nineteenth century painters such as Turner. But his contributions to science (apart from Goethe’s bone) have not stood the test of time and he died in 1832.

    *relurks*

    What can I say? You give a very brief and popular account of Goethe.

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  40. CharlieM: You do realise that in ‘Finding Nemo’ the fish are deliberately given human characteristics and that is not natural fish behaviour?

    OK, I give up.

    CharlieM: I have said before we might be smart individually but our individual smartness, even our group smartness, pales in comparison with the smartness of, say, termites as a group.

    False modesty alert!

    CharlieM: That is a feature of the inbuilt wisdom of the group.

    Please note that the phenotypic changes that have been preserved first occurred as mutations in the DNA. As far as we can tell none of the changes were first introduced into the RNA or proteins. That stands to reason: any variants of RNA and protein or their regulation not encoded in the DNA would have been rapidly lost. This is why your infinite loop of “but DNA is acted upon by its products” does not fly when we are discussing evolutionary change: evolutionary novelties can only preserved if they are stably inherited.

    CharlieM: You mean everyone should have the same prior assumptions as yourself? Life is not like that. All that we are obliged to do is understand each point of view, not to agree with them.

    No, I am not asking you to uncritically accept my point of view. I am requesting you to communicate your view of things in a format that is intelligible and acceptable to others.

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  41. CharlieM:

    Allan: It is clear that a DNA sequence must sit causally ‘upstream’ of any product its sequence specifies, be it RNA or protein.

    CharlieM: Not in individual development it isn’t In this case the individual’s DNA relies on external complexes supplied by the mother

    Of course you are correct if you have used the term, ‘DNA sequence’ as shorthand for, ‘the process of attaching RNA nucleotides to the DNA sequence’. First the DNA is copied and then the RNA and protein follow from this. So I agree that the RNA is assembled according to the specifications of the DNA sequence.

    What I am alluding to is that in the case of substances such as bicoid in fruit flies, it is present in the fertilised egg before it is produced by copying the fly’s own DNA. The protein is present before it begins to be expressed through the fly’s genes.

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  42. CharlieM: What I am alluding to is that in the case of substances such as bicoid in fruit flies, it is present in the fertilised egg before it is produced by copying the fly’s own DNA. The protein is present before it begins to be expressed through the fly’s genes.

    And where, pray tell, does the information for bicoid come from? The mother’s DNA, folks.
    Have you ever heard the phrase “Maternal Effect Gene”?
    I am enjoying the reprise of Charlie’s “no animals can rival humans for their individuality” shtick.
    Lest we forget:
    Charlie:

    Anyone who thinks that all Chinese people look alike are just showing that they are not very observant in general

    Jock

    Precisely. The question then becomes: are they aware of this failing of theirs, or do they blithely rabbit on about how Caucasians show much more individual variation than the Chinese do?

    1+
  43. CharlieM: Me: This has absolutely nothing to do with it.

    Charlie: If you want to discuss control it has everything to do with it.

    Sorry, no, that’s absurd. We were talking of the situation in ‘nature’. That which occurs deep in the metaphorical forest with no-one to ‘hear’ it. You can’t dismiss that level of control by introducing the squid-ink “what about when a scientist does something?”. The metaphorical woodman’s metaphorical axe has no bearing on the fundamentals of tree development.

    Me: […] the difference between elephants and you lies in differences between your DNA, not its core ‘machinery’ of expression.

    Charlie: The difference between an elephant and myself has a great deal to do with how our respective DNA is expressed. We may have only twenty odd thousand protein coding genes but we have hundreds of thousands of enhancers scattered throughout our genomes all choreographed on a scale that is beyond human understanding.

    “Scattered throughout our genomes”. Mark that phrase well. Any tissue-specific differences in gene expression resolve to other parts of the genome.

    My use of the word ‘structure’ was no doubt misleading. I did not mean by it fixed shape. I meant also how they perform dynamically over time in living organisms. More like the structure of a play than of a building.

    They are used differently, but their instrinsic differences are slight.

    And I have no problem with regarding them as templates.

    Fair enough, but it’s important to recognise that this template is an input. And an output. It is not generated by ‘the cell’, merely replicated.

    Me: Irrelevant.

    Charlie: You think processes are irrelevant?

    No, I think it irrelevant to the point that genomes are template-replicated that the monomers have to come from somewhere.

    Me: All sourced by genetic sequence. Have you come up with a non-genomic control element yet? I may have missed it.

    Charlie: I’m not looking for a non genetic control element. The higher order control includes genetic elements.

    So you identify a set, a subset of which are ‘genetic elements’. So I’m trying to get you to identify a member of the first set which is not a member of the subset. Bet you can’t.

    Me: Rooted in the genome.
    Charlie: Using the genome.

    No, rooted. It all resolves to a genetic sequence which, if changed – mutated – would causally affect the result. You can’t change ‘that which uses the genome’ without changing the genome.

    Me: Yes, in individual development. Any given DNA sequence must be causally prior to its products. It seems nonsensical to reject this, so I must assume you have misunderstood

    Charlie: If we are focussing on the individual

    Why are we doing that?

    the source of the maternal control elements are irrelevant because they are external to the individual in question.

    You’re introducing an artificial boundary, just so you can be ‘right’.

    Me: There you go introducing an artificial boundary, despite claiming to be all about the ‘continuous process’. In this case, products in the ‘individual’ lie downstream of DNA in ‘the mother’. My contention stands.

    Charlie: There is nothing artificial about the cell membrane of the zygote.

    That’s not the boundary I mean. It’s conceptual, not physical. During female gametogenesis, a series of genetic copies is made, each if which results in a ‘new’ cell. During that series, some of the proteins in the ‘new’ cell derive not from the current DNA molecule, but from that in the prior instance. You insert a ‘hard’ boundary into this series, such that we must ignore the DNA in the antecedent cell, because it does not belong to ‘the individual’.

    And where did I say that processes must be continuous?

    That is implicit in your declaration that an evolutionary series is analogous to a developmental one. If development is ‘continuous’, then so is a long lineage (which is indeed the case). You want to import an exception to your own principle.

    Me: Why not?

    Charlie: Because in the group of entity from which it selects. it entails a reduction of variability, or a change in the proportions of the variations already present.

    New variation is continually introduced, so that isn’t a problem. Still, if that’s your basic principle, you reject selection in toto, which you claim not to.

    By ‘pattern of activity’ I mean the underlying processes which remain constant. For example the same pattern of transcription, translation and protein production goes on in the zygote as in a specialised cell.

    And, indeed, in the cells of an elephant and of you. Rendering the source of difference … ta-dah! … the genome!

    Me: Good grief. That again? How many more times? Gene centrism does not postulate that genes act in isolation. I said in August that I’d said this in July

    Charlie: You are coming from a position of gene centrism, but I am not arguing solely against gene centrism. So we agree on the isolation point.

    I stress the point not for your benefit but for others who might read this.

    I struggle to imagine anyone coming away from a reading of Dawkins et al with the notion that gene centrism demands isolated DNA, acting without mechanism. But hey, if these people need putting straight …

    0
  44. Corneel:

    CharlieM: You do realise that in ‘Finding Nemo’ the fish are deliberately given human characteristics and that is not natural fish behaviour?

    OK, I give up.

    CharlieM: I have said before we might be smart individually but our individual smartness, even our group smartness, pales in comparison with the smartness of, say, termites as a group.

    False modesty alert!

    I give up 🙂

    CharlieM: That is a feature of the inbuilt wisdom of the group.

    Please note that the phenotypic changes that have been preserved first occurred as mutations in the DNA. As far as we can tell none of the changes were first introduced into the RNA or proteins. That stands to reason: any variants of RNA and protein or their regulation not encoded in the DNA would have been rapidly lost. This is why your infinite loop of “but DNA is acted upon by its products” does not fly when we are discussing evolutionary change: evolutionary novelties can only preserved if they are stably inherited.

    The word ‘mutation’ implies an accidental change. But not all changes to the DNA are accidental. Also in the case of changes brought about by external influences there are ‘error’ correcting processes to determine which DNA changes remain and which are corrected. This may occur in a seemingly stochastic manner but the efficiency of correction allows for a limited amount of variability between individuals. This can be very beneficial for group survival as we see in cases such as the peppered moth or Darwin’s finches. Group survival takes precedence over individual survival. One hundred percent efficiency in the elimination of any changes would be detrimental to the survival of the group.

    There is wisdom in maintaining levels of imperfection.

    CharlieM: You mean everyone should have the same prior assumptions as yourself? Life is not like that. All that we are obliged to do is understand each point of view, not to agree with them.

    No, I am not asking you to uncritically accept my point of view. I am requesting you to communicate your view of things in a format that is intelligible and acceptable to others.

    I think that would probably need a bit more effort from both sides. I’m not sure if you think it’s worth the effort.

    0
  45. CharlieM: The word ‘mutation’ implies an accidental change.

    No, it doesn’t.

    CharlieM: But not all changes to the DNA […] There is wisdom in maintaining levels of imperfection.

    You have retreated to your other talking points. My arrows were aimed at your opposition to DNA as a central player in evolutionary change. Before I follow you down another rabbit hole, I’d like to see some concession from your side that succesful “group survival” by adaptation critically depends on population frequency changes of DNA variants. After that, we can discuss whether those changes are the result of “group wisdom” or known physical processes.

    CharlieM: I think that would probably need a bit more effort from both sides. I’m not sure if you think it’s worth the effort

    I thought you were looking to be challenged. That is not going to happen if you keep using your own personal lexicon.

    0
  46. DNA_Jock:

    CharlieM: What I am alluding to is that in the case of substances such as bicoid in fruit flies, it is present in the fertilised egg before it is produced by copying the fly’s own DNA. The protein is present before it begins to be expressed through the fly’s genes.

    And where, pray tell, does the information for bicoid come from? The mother’s DNA, folks.

    And where and when was the bicoid in the mother first active? It came from her mother’s DNA. And where and when was the mother’s, mother’s bicoid first active? It came from…

    The starting point of the life of any individual drosophila begins with the coordinated process involving proteins, RNA and DNA, nothing less.

    Have you ever heard the phrase “Maternal Effect Gene”?

    Yes. That is how I was able to discuss it here in the past.

    I am enjoying the reprise of Charlie’s “no animals can rival humans for their individuality” shtick.
    Lest we forget:

    Charlie:

    Anyone who thinks that all Chinese people look alike are just showing that they are not very observant in general

    Jock

    Precisely. The question then becomes: are they aware of this failing of theirs, or do they blithely rabbit on about how Caucasians show much more individual variation than the Chinese do?

    Every single person on the planet displays a complex mixture of individuality, cultural influences and racial influences. Being human is what we have in common, having a unique individual biography is what distinguishes you and everyone else on the planet as a person in your own right. The really interesting thing about bacteria is not the behaviour of the individual, it is the biography of the group as a whole.

    Where are the Confuciuses, Darwins, or Einsteins among Lenski’s populations? The one’s that, through their own efforts, stand out from the crowd? Is it because all bacteria look alike to me that I don’t see the outstanding individuals?

    0
  47. CharlieM: Where are the Confuciuses, Darwins, or Einsteins among Lenski’s populations? The one’s that, through their own efforts, stand out from the crowd? Is it because all bacteria look alike to me that I don’t see the outstanding individuals?

    And there you go again: If you define individuality as something that can only apply to humans (“through their own efforts”), then yes, only humans have it.

    That is not how other people think of individuality though.

    0
  48. CharlieM,

    Every single squirrel on the planet displays a complex mixture of individuality, cultural influences and racial influences. Being a squirrel is what they have in common, having a unique individual biography is what distinguishes them and every other squirrel on the planet as a squirrel in their own right. The really interesting thing about humans is not the behaviour of the individual, it is the biography of the group as a whole.
    You are so delightfully anthropocentric that you don’t even realize it. 😀

    0
  49. Allan Miller:

    CharlieM: Me: This has absolutely nothing to do with it.

    Charlie: If you want to discuss control it has everything to do with it.

    Sorry, no, that’s absurd. We were talking of the situation in ‘nature’. That which occurs deep in the metaphorical forest with no-one to ‘hear’ it. You can’t dismiss that level of control by introducing the squid-ink “what about when a scientist does something?”. The metaphorical woodman’s metaphorical axe has no bearing on the fundamentals of tree development.

    Where is the metaphor or analogy? Scientists do actually manipulate genomes.

    Me: […] the difference between elephants and you lies in differences between your DNA, not its core ‘machinery’ of expression.

    Charlie: The difference between an elephant and myself has a great deal to do with how our respective DNA is expressed. We may have only twenty odd thousand protein coding genes but we have hundreds of thousands of enhancers scattered throughout our genomes all choreographed on a scale that is beyond human understanding.

    “Scattered throughout our genomes”. Mark that phrase well. Any tissue-specific differences in gene expression resolve to other parts of the genome.

    The words I am using here are scattered throughout the English dictionary. So by your logic the English dictionary is the source of my creative writing.

    My use of the word ‘structure’ was no doubt misleading. I did not mean by it fixed shape. I meant also how they perform dynamically over time in living organisms. More like the structure of a play than of a building.

    They are used differently, but their instrinsic differences are slight.

    Yes ‘used’, note the word ‘used’.

    And I have no problem with regarding them as templates.

    Fair enough, but it’s important to recognise that this template is an input. And an output. It is not generated by ‘the cell’, merely replicated.

    It takes a coordinated system to replicate it.

    Me: Irrelevant.

    Charlie: You think processes are irrelevant?

    No, I think it irrelevant to the point that genomes are template-replicated that the monomers have to come from somewhere.

    I don’t think it is irrelevant. We agree that DNA provides templates, but it is important to understand how the templates are used. Context matters.

    Me: All sourced by genetic sequence. Have you come up with a non-genomic control element yet? I may have missed it.

    Charlie: I’m not looking for a non genetic control element. The higher order control includes genetic elements.

    So you identify a set, a subset of which are ‘genetic elements’. So I’m trying to get you to identify a member of the first set which is not a member of the subset. Bet you can’t.

    Genetic elements are not a subset. Every living creature on earth whether human, animal, plant, bacteria of whatever, has a genome. Genomes are a feature of the set of all organisms as are integral processes..

    Me: Rooted in the genome.
    Charlie: Using the genome.

    No, rooted. It all resolves to a genetic sequence which, if changed – mutated – would causally affect the result. You can’t change ‘that which uses the genome’ without changing the genome.

    Yes, and what causes the genome changes? There are multiple endogenous and exogenous causes of changes to the sequences.

    There are plenty of processes which have an element of control of the levels of change. For instance ‘error’ correction processes such as DNA damage response, base excision repair, nucleotide excision repair, mismatch repair, inter-strand cross-link repair, translesion synthesis, single and double stranded break repair.

    Me: Yes, in individual development. Any given DNA sequence must be causally prior to its products. It seems nonsensical to reject this, so I must assume you have misunderstood

    Charlie: If we are focussing on the individual

    Why are we doing that?

    Because you are arguing that the DNA of an individual is the root cause of her, his or its development.

    the source of the maternal control elements are irrelevant because they are external to the individual in question.

    You’re introducing an artificial boundary, just so you can be ‘right’.

    No artificial boundaries necessary.

    Me: There you go introducing an artificial boundary, despite claiming to be all about the ‘continuous process’. In this case, products in the ‘individual’ lie downstream of DNA in ‘the mother’. My contention stands.

    Charlie: There is nothing artificial about the cell membrane of the zygote.

    That’s not the boundary I mean. It’s conceptual, not physical. During female gametogenesis, a series of genetic copies is made, each if which results in a ‘new’ cell. During that series, some of the proteins in the ‘new’ cell derive not from the current DNA molecule, but from that in the prior instance. You insert a ‘hard’ boundary into this series, such that we must ignore the DNA in the antecedent cell, because it does not belong to ‘the individual’.

    Whether it is gamete cell production or somite cell production, it is the same with cell division as it is with conception of a new organism, physical boundaries are formed. The new cell receives everything it requires to exist and develop as an individual. That includes cytoplasm, organelles, proteins and nucleic acids.

    Having all this enclosed within its skin (the cell membrane) entitles it to claim them as its own. But as these cells are not in a position to stake this claim for themselves I am happy to represent them and make the claim on their behalf 🙂

    They begin their lives with enough material to enable the processes of metabolism and growth to begin.

    And where did I say that processes must be continuous?

    That is implicit in your declaration that an evolutionary series is analogous to a developmental one. If development is ‘continuous’, then so is a long lineage (which is indeed the case). You want to import an exception to your own principle.

    We are continuously regenerating body cell throughout our lives. But we still consider cells as discrete entities.

    Me: Why not?

    Charlie: Because in the group of(oops – or) entity from which it selects. it entails a reduction of variability, or a change in the proportions of the variations already present.

    New variation is continually introduced, so that isn’t a problem. Still, if that’s your basic principle, you reject selection in toto, which you claim not to.

    I don’t reject selection. It’s an observed fact. It changes the proportions of traits already present within populations.

    By ‘pattern of activity’ I mean the underlying processes which remain constant. For example the same pattern of transcription, translation and protein production goes on in the zygote as in a specialised cell.

    And, indeed, in the cells of an elephant and of you. Rendering the source of difference … ta-dah! … the genome!

    The genome and expression levels and timing and epigenetic marking.

    Me: Good grief. That again? How many more times? Gene centrism does not postulate that genes act in isolation. I said in August that I’d said this in July

    Charlie: You are coming from a position of gene centrism, but I am not arguing solely against gene centrism. So we agree on the isolation point.

    I stress the point not for your benefit but for others who might read this.

    I struggle to imagine anyone coming away from a reading of Dawkins et al with the notion that gene centrism demands isolated DNA, acting without mechanism. But hey, if these people need putting straight

    As I said, I’m arguing against a wider set of beliefs than just gene centrism.

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