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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232 thoughts on “The Spiralling Flow of Life

  1. CharlieM:Concerning the properties of letters you asked, “What properties are those?”.

    Letters are symbols for sounds that can be made by using our breath.

    True, but the ‘properties’ of those letters are far removed from those of a given molecule. One could render the letter A in daffodils, or pixels, or cut-out cardboard, or a sound. Whereas, for example, adenosine triphosphate (an RNA monomer), can only be rendered one way, as physical substance. You can make a symbolic representation of it – a 3D ball and stick model, a 2D distorted diagram of its atoms and bonds, or even the letter ‘A’ in a transcribed gene sequence. But the thing itself is not a symbol. It’s a thing! With properties, charge and shape that affect its interactions (including, as it happens, the physical parameters that cause a stack of such monomers, shorn of two of their phosphates and presented with a complementary sequence, to adopt a helical configuration).

    Isolated letters are an abstraction removed from the context of the words from which they came, and isolated DNA is an abstraction without the context of the cell to which it belongs.

    As others have pointed out, this is incorrect. If this were the case, PCR would not be possible, nor RNA probes, nor viruses. DNA is not simply informatic and symbolic. It has properties.

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  2. Allan Miller: DNA is not simply informatic and symbolic. It has properties.

    And, please note, Charlie, having a sequence of the letters A, C, D and T tells us little. It cannot be checked for information without either comparing it to known sequences or seeing what the resultant transcribed RNA or translated protein will do by synthesizing them and examining their properties in vitro and in vivo (given the current state of science).

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  3. Corneel:

    CharlieM: We can describe the act of love between two people in extreme physical detail, the movements and forces involved at all levels, but on top of this lies the emotions and thoughts of the couple of which no amount of physical laws will give an accurate description.

    I appreciate that the physical description of a coitus does not capture its emotional impact, but that does not justify you making up stuff that does not exist.

    Such as?

    CharlieM: So you see no difference between the activity of a brick and the activity of a toirtoise?

    Yes, the latter is conscious activity. My turn now: do you see no difference between the activity of DNA polymerase and the activity of a tortoise?

    Yes I do see a difference. Consciousness is not either/or. There is a range of states of consciousness between a non conscious brick and a wide awake, fully alert, human.

    CharlieM: Do you think that the activity you displayed in posting this reply was instigated from some external source or did the decision to act come from within you? Are you an automaton or do you take responsibility for your actions?

    No, I do not think of myself as an automaton. My turn now:

    Do you think the activity of a Venus flytrap capturing prey is instigated from some external source or did the decision to act come from within it? Is it an automaton or does it take responsibility for its actions?

    I think that the activity was integral to the plant, although I do not think that individual plants have the complex nervous system to be aware enough to assume personal responsibility. A human being setting a gin trap is another matter. But there are many processes that are integral to us humans that we cannot be held to be individually responsible for.

    Integral activity, awareness of that activity and responsibility for that activity, can, but need not, go together. They should be considered separately.

    I’m feeling a little vulnerable at the moment, sitting at home, surrounded by a regiment of bricks, wondering what their next move is going to be 🙂

    The Venus fly trap, another example of convergent evolution. They have developed ‘mouths’ with which to catch and digest prey, just like many animals do. A step in the direction of becoming animal-like. Plants evolve, insects evolve to feed on plants, and then in turn plants evolve to feed on insects. Nature spirals on.

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  4. Corneel:

    CharlieM: But if you observe that isolated DNA, what will it do?

    Unless you store it somewhere cold, it will degrade.

    Are you going to retract your outrageous claim that isolated DNA is an abstraction? Will you reflect on what made you say such a thing?

    Try thinking about what I am saying and do not get bogged down analysing the words. Isolated DNA is no longer living substance, it is dead matter. Without the organism it is no longer in the reality in which it belongs. It is meaningless outwith its context.

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  5. Allan Miller:

    CharlieM:Show many a person who doesn’t pepper their writings with metaphors.

    There’s an equivocation at work here. I’m betting you are well aware that there is a distinction between saddling up metaphors in pursuit of fluid prose (SWIDT?) and using them to illustrate a point about an object, concept or process, by comparison with something familiar.

    It is not just fluid prose in which metaphors are used. I would be willing to bet that most people use metaphors in their everyday speech without even thinking about it. It is quite common to refer to ‘the language of nature’, that nature can be understood as a script that can be read. All metaphors and analogies are limited and shouldn’t be taken to far, but in my opinion the machine metaphor is not just limited, it is very misleading.

    I wouldn’t expect anything other than you to disagree with most of the metaphors I use. You disagree with most of what I say directly so why should my metaphors be any different?

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  6. Allan Miller:

    CharlieM: Concerning the properties of letters you asked, “What properties are those?”.

    Letters are symbols for sounds that can be made by using our breath.

    True, but the ‘properties’ of those letters are far removed from those of a given molecule.

    I wasn’t comparing letters to molecules. I had made an analogy between letters in a book on one hand and the laws of physics in relation to life on the other. Letters are necessary features of the book just as the laws of physics are necessary constituents of life. But a book cannot be understood in terms of letters alone just as life cannot be understood by the laws of physics alone. How many murderers would be let off because the cause of death was put down to the laws of physics alone? Human rules and regulations sit on top of physical laws, they aren’t governed by physics.

    One could render the letter A in daffodils, or pixels, or cut-out cardboard, or a sound. Whereas, for example, adenosine triphosphate (an RNA monomer), can only be rendered one way, as physical substance. You can make a symbolic representation of it – a 3D ball and stick model, a 2D distorted diagram of its atoms and bonds, or even the letter ‘A’ in a transcribed gene sequence. But the thing itself is not a symbol. It’s a thing! With properties, charge and shape that affect its interactions (including, as it happens, the physical parameters that cause a stack of such monomers, shorn of two of their phosphates and presented with a complementary sequence, to adopt a helical configuration).

    Of course if we were to compare ATP with the letters in a book, another glaring difference, besides the one’s you pointed out, would be that letters do not need books to have functional relevance but ATP is dependent on life for its existence.

    I did say that isolated DNA is an abstraction, not to claim the it does not exist. My meaning was that it’s existence in this state is totally unnatural and it has been removed from where it belongs to which it must be returned if it is to used in the way it was meant to be used.

    Isolated letters are an abstraction removed from the context of the words from which they came, and isolated DNA is an abstraction without the context of the cell to which it belongs.

    As others have pointed out, this is incorrect. If this were the case, PCR would not be possible, nor RNA probes, nor viruses. DNA is not simply informatic and symbolic. It has properties.

    I did write ‘isolated DNA’. So what is isolated about this?:

    The various components required for PCR include a DNA sample, DNA primers, free nucleotides called ddNTPs, and DNA polymerase

    Nothing you refer to above would exist without cells. All of it involves the manipulation of DNA in one form or another.

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  7. CharlieM
    Try thinking about what I am saying and do not get bogged down analysing the words. Isolated DNA is no longer living substance, it is dead matter.Without the organism it is no longer in the reality in which it belongs. It is meaningless outwith its context.

    That’s a feature, not a bug, in my book. If DNA was living substance, how could it be fundamental to life? To say that life is fundamental to itself sound either circular or tautological to me

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  8. CharlieM: Me: I appreciate that the physical description of a coitus does not capture its emotional impact, but that does not justify you making up stuff that does not exist.

    Charlie: Such as?

    Inner activity, archetypes, the radial and peripheral forces, to name a few.

    CharlieM: Consciousness is not either/or. There is a range of states of consciousness between a non conscious brick and a wide awake, fully alert, human.

    CharlieM: Integral activity, awareness of that activity and responsibility for that activity, can, but need not, go together. They should be considered separately.

    Whoa, what nuance all of a sudden. A few comments ago, anyone not confining “activity” to living things was equating the activity of bricks with that of tortoises. And anyone refusing to acknowledge that living substance was possesed of inner activity must be thinking of themselves as an automaton. Could you apply this newfound sense of nuance to e.g. KNs comment that bricks are not completely passive? Or to my comment to the effect that organic molecules can go without “inner activity” but still be part of conscious beings? Thanks!

    CharlieM: Try thinking about what I am saying and do not get bogged down analysing the words.

    LOL. I cannot parse your sentences without analysing the words, Charlie.

    But I will pick on it, because I believe this is a symptom of your confusion. You once stated that you thought of subatomic particles as mathematical abstractions. Now you claim that isolated DNA is an abstraction as well. Both are of course physical entities even though we cannot observe them directly. We have learned about molecules and elementary particles because they have certain properties with which they interact with the world. It is in this sense that matter can said to be active. Acknowledging the relevance of this activity is very important to understanding our side of the argument.

    CharlieM: Isolated DNA is no longer living substance, it is dead matter. Without the organism it is no longer in the reality in which it belongs. It is meaningless outwith its context.

    Let’s hop on your train of thought to see where it leads. So you believe that “minds” have independent existence from the physical gooey inside people’s head, but OTOH you claim that DNA is drained of all its life once it is isolated from the cell. Then why can I still amplify it in a PCR and why can it still be transcribed in cell-free expression systems, I wonder? You claim that the DNA is now “meaningless outwith its context.” Well, there was plenty of meaning left, I can assure you. I did isolate it for a purpose you know 😉

    So now we are down to discussing the “meaning” of DNA. To be honest, I don’t know what you meant by that. Could you state what the “meaning” is of DNA, and how that meaning is expressed within the cell (but not without it)?

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  9. CharlieM Of course if we were to compare ATP with the letters in a book, another glaring difference, besides the one’s you pointed out, would be that letters do not need books to have functional relevance but ATP is dependent on life for its existence.

    I think letters depend on life for their existence too…

    I did say that isolated DNA is an abstraction, not to claim the it does not exist. My meaning was that it’s existence in this state is totally unnatural and it has been removed from where it belongs to which it must be returned if it is to used in the way it was meant to be used.

    Meant to be used? By whom?

    Nothing you refer to above would exist without cells. All of it involves the manipulation of DNA in one form or another.

    Yawn. And cells would not exist without nucleic acids. And round we go again.

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  10. Allan Miller,

    Yawn. And cells would not exist without nucleic acids. And round we go again.

    Let’s try something less snarky.

    Suppose that the actual state-of-affairs is that Life started out as self-replicating strings of RNA. The RNA served as both genome and catalyst for its replication. Over the course of time, by extension additional capacity arose in these genomes that assisted their survival and replication. Ultimately, protein synthesis arose, such that the genome needed a 2-stage process for its expression – rather than activity through primary transcript (a ribozyme), the transcript was further processed into a protein catalyst. The superiority of these catalysts over the ancestral ribozymes led to them being replaced in most (but not all) situations, with the original RNA organisms rendered extinct for similar reasons – they could not compete, or were consumed. The genome, meanwhile, migrates from RNA to DNA, the methylation of uracil and the removal of a 2′ oxygen rendering the molecule more stable.

    Now, you reject this as ‘mere speculation’. Even if it were the actual state-of-affairs, you would reject it, and insist that the absence of modern ribozymal organisms demands ‘something else’. Something else that you would not denigrate as ‘mere speculation’, but something you had determined from close observation: ‘Prior Intelligence’. Despite no apparent substrate for such an entity.

    Failing to find a single instance of an acellular RNA organism, in the world where they had actually existed, you would declare the minimal requirement to be a fully-fledged modern organism that ‘uses’ its genome. Your evidence that they never existed being that they don’t exist now!

    So where, in such an admittedly hypothetical progression, would the genome become subjugated to the requirements of ‘the system’ – effectively, the genome a mere tool of its products? With the first protein? The thousandth?

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  11. dazz:

    CharlieM
    Try thinking about what I am saying and do not get bogged down analysing the words. Isolated DNA is no longer living substance, it is dead matter. Without the organism it is no longer in the reality in which it belongs. It is meaningless outwith its context.

    That’s a feature, not a bug, in my book. If DNA was living substance, how could it be fundamental to life? To say that life is fundamental to itself sound either circular or tautological to me

    DNA can be living and it can be dead. It is only living when it is integrated with other substances in its natural state in a dynamic whole.

    I’m not sure where I said that life is fundamental to life. I did say in the op that some people consider dynamic processes to be more fundamental than physical matter What I would say is fundamental to reality is movement and polarity. As Heraclitus said all is in flux. He was also called ‘The Obscure’ not least because of his statements about the unity of polar opposites.

    And this is where projective geometry gives us a more realistic understanding of reality than given by Euclidean geometry. The geometry I was taught in school is to do with analysis and measurement. Take the conic section. I learned how to deal with circles, ellipses, parabolas and hyperbolas as separate shapes, their relationship seemed to be regarded as incidental. Projective geometry deals more with synthesis and dynamism in which these four figures are one and no measurements are involved.. Of course some have said, “If you can’t measure it it doesn’t exist.” Obviously I disagree.

    We learn about reality through the processes of sense perception and thinking. We could say that we perceive outwardly through sense perception and we perceive inwardly through thinking and the latter is a continuation of and gives meaning to the former.

    For our senses points are minute but finite and in the opposite direction we can picture spheres expanding only to certain finite limits. But through the inner perception of thinking, ‘points’ and ‘spheres’ become dimensionless. But they both contain each other. We cannot mentally visualise the infinity to which they belong but through thinking we ‘see’ it.

    The living substance to which DNA belongs can be perceived as having expanded from a point like source but this is only one side of its polar nature. It can also be seen as contracting from a peripheral field like expanse.

    A plane might contain an infinity of points but likewise a point contains an infinity of planes.

    I might, with some justification, be accused of rambling, but my aim is to stimulate further discussion, (preferably sensible discussion).

    Incidentally, talking about the phrase,”If you can’t measure it it doesn’t exist”, I watched a nice little TED talk by Brené Brown where her story begins with that phrase. I just thought I would link to it for anyone who wants to watch it.

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  12. CharlieM: DNA can be living and it can be dead. It is only living when it is integrated with other substances in its natural state in a dynamic whole.

    Are you sure you’re not committing the fallacy of composition here?
    You’re infamous for making stuff up as you go along and quite honestly, I don’t see the relevance of the above to my previous objection.

    CharlieM: I’m not sure where I said that life is fundamental to life

    You dismissed DNA as a possible “foundation” of life on the basis that it’s inert when isolated. That was your (made up) rule, right? I simply pointed out that presumably, you would, under your own rules, accept some other stuff that is alive when isolated. Otherwise, why bring up the isolation thing at all? But then it seems to follow that you would accept that life is fundamental to life. Does that help clarify what I meant?

    You’ve been saying that DNA is acted upon by the cell, as if it’s a passive element of the whole, now you say that it’s also alive as long as it’s doing it’s thing inside the cell… I dunno, you don’t seem to make any sense whatsoever. So is DNA alive just like the cell? Or do you mean different things when you refer to DNA as being alive vs the cell?

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  13. Corneel:

    Me: I appreciate that the physical description of a coitus does not capture its emotional impact, but that does not justify you making up stuff that does not exist.

    Charlie: Such as?

    Inner activity, archetypes, the radial and peripheral forces, to name a few.

    The blood flowing through your circulatory system, that’s inner activity. Having a nose bleed turns part of it into outer activity.

    All the varieties of plant that ever existed through all their stages of development are distinguished from each other and categorised by their differences. If you can include all these plants and along with the idea of the continuous merging of one into the other then you have the concept of the archetype.

    Centripetal and centrifugal forces are radial forces, they act along an imaginary line radiating from the centre. Surely you believe in centripetal forces at least. An example of what I consider to be a peripheral force is the sun heating the earth. It may not be a satisfactory use of the word ‘force’ for everyone but it gets across my meaning.

    CharlieM: Consciousness is not either/or. There is a range of states of consciousness between a non conscious brick and a wide awake, fully alert, human.

    CharlieM: Integral activity, awareness of that activity and responsibility for that activity, can, but need not, go together. They should be considered separately.

    Whoa, what nuance all of a sudden. A few comments ago, anyone not confining “activity” to living things was equating the activity of bricks with that of tortoises.

    I was simply looking for clarification to what, in your opinion, you considered to be the difference between the so called activities of a brick and the activity of an animal such as a tortoise. Do you see any differences between them?

    And anyone refusing to acknowledge that living substance was possesed of inner activity must be thinking of themselves as an automaton.

    No. I was referring to a specific activity. So what does cause your activity in your participation here?

    Could you apply this newfound sense of nuance to e.g. KNs comment that bricks are not completely passive?

    His application of activity to bricks is in actual fact reactivity. In the same way that one billiard ball reacts in a predictable manner when struck by another. Light falls on a brick and the brick reacts in a predictable way.

    Or to my comment to the effect that organic molecules can go without “inner activity” but still be part of conscious beings? Thanks!

    Can we say that anything at the molecular level is without inner activity?

    CharlieM: Try thinking about what I am saying and do not get bogged down analysing the words.

    LOL. I cannot parse your sentences without analysing the words, Charlie.

    So you’re a letter of the law person rather than a spirit of the law person.

    But I will pick on it, because I believe this is a symptom of your confusion. You once stated that you thought of subatomic particles as mathematical abstractions. Now you claim that isolated DNA is an abstraction as well. Both are of course physical entities even though we cannot observe them directly. We have learned about molecules and elementary particles because they have certain properties with which they interact with the world. It is in this sense that matter can said to be active. Acknowledging the relevance of this activity is very important to understanding our side of the argument.

    So do you believe that matter can be seen as active in the quantum sense while being passive in the Newtonian sense?

    CharlieM: Isolated DNA is no longer living substance, it is dead matter. Without the organism it is no longer in the reality in which it belongs. It is meaningless outwith its context.

    Let’s hop on your train of thought to see where it leads. So you believe that “minds” have independent existence from the physical gooey inside people’s head,

    No. while we exist as physical beings in this earth the mind and body are not independent

    …but OTOH you claim that DNA is drained of all its life once it is isolated from the cell. Then why can I still amplify it in a PCR and why can it still be transcribed in cell-free expression systems, I wonder? You claim that the DNA is now “meaningless outwith its context.” Well, there was plenty of meaning left, I can assure you. I did isolate it for a purpose you know

    These processes involve combining the DNA with other substances so that can be manipulated. And what is doing the manipulating? Oh yes! A functioning living being. What would have happened to that DNA if you had not performed any actions on it?

    So now we are down to discussing the “meaning” of DNA. To be honest, I don’t know what you meant by that. Could you state what the “meaning” is of DNA, and how that meaning is expressed within the cell (but not without it)?

    It meaning lies in the way it is used, in the way that information can be taken from it. Stored in some container in isolation it might as well be playdough.

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  14. dazz: dazz
    Ignored on September 28, 2020 at 3:05 pm said:

    CharlieM: DNA can be living and it can be dead. It is only living when it is integrated with other substances in its natural state in a dynamic whole.

    Are you sure you’re not committing the fallacy of composition here?
    You’re infamous for making stuff up as you go along and quite honestly, I don’t see the relevance of the above to my previous objection.

    I suppose it comes down to the fact that the most fundamental form of reproducible life we have ever witnessed is the cell. Viruses could be considered an exception but like bare DNA it cannot reproduce outside of the cell.

    CharlieM: I’m not sure where I said that life is fundamental to life

    You dismissed DNA as a possible “foundation” of life on the basis that it’s inert when isolated. That was your (made up) rule, right?

    I claimed that DNA does nothing of significance when isolated. That claim is yet to be contradicted.

    I simply pointed out that presumably, you would, under your own rules, accept some other stuff that is alive when isolated. Otherwise, why bring up the isolation thing at all? But then it seems to follow that you would accept that life is fundamental to life. Does that help clarify what I meant?

    The cell is the most basic reproducing living entity we know of.

    You’ve been saying that DNA is acted upon by the cell, as if it’s a passive element of the whole, now you say that it’s also alive as long as it’s doing it’s thing inside the cell… I dunno, you don’t seem to make any sense whatsoever. So is DNA alive just like the cell? Or do you mean different things when you refer to DNA as being alive vs the cell?

    The cell is the living entity and DNA is integral to the life of the cell. It naturally originates within cells and nowhere else.

    Within organisms some substances and structures are more passive than others. For example when we run our muscles actively move the bones of our legs. Our muscles are more active than our bones in that regard.

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  15. CharlieM,

    You keep ignoring my point, so I’m simply moving on. No problem.
    Just one more comment on this:

    CharlieM: I claimed that DNA does nothing of significance when isolated. That claim is yet to be contradicted.

    Of “significance”, yeah. And of course by that you mean “what DNA does in the cell”, right? Yawn

    Your claim is of no significance.

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  16. CharlieM: So you’re a letter of the law person rather than a spirit of the law person.

    In fact, I am an extremely easy-going person, but you have a habit of changing the meaning of words to suit your needs. For example your current treatment of “inner activity”:

    The blood flowing through your circulatory system, that’s inner activity. Having a nose bleed turns part of it into outer activity.

    Hoho, silly Corneel. What silly bugger would deny that the blood circulation exists? Well, previously you defined innner activity a bit differently:

    Having inner activity means that it is able to ingest, convert and reuse energy in order to carry out a function such as movement or growth.

    Hmmm, so NOT the blood circulation. I note that DNA doesn’t fit the bill either. And before that, you were talking about dynein nano-beings implicitly suggesting that a life force allows motor proteins to behave like tiny homunculi. It is this interpretation of “inner activity” that I strenuously deny exists.

    I note that “archetype” and “the radial and peripheral forces” received a similar treatment, miraculously transforming into innocuous descriptions of everyday phenomena. This is definitely not the way you have been using these terms up til now.

    And now you blame me for picking on your claim of isolated DNA being an abstraction. I guarantee that everybody read this as saying isolated DNA has no physical existence. If you dislike that, then use words in a way that allows other people to understand.

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  17. CharlieM: Can we say that anything at the molecular level is without inner activity?

    Even better. We can say that “inner activty”, used as a eufemism for élan vital, does not exist at all.

    The blood circulation still exists of course.

    CharlieM: So do you believe that matter can be seen as active in the quantum sense while being passive in the Newtonian sense?

    I believe you need to learn to properly use terms in context. In this way you are equivocating.

    CharlieM: Me: So you believe that “minds” have independent existence from the physical gooey inside people’s head, […]

    Charlie: No. while we exist as physical beings in this earth the mind and body are not independent

    But since you believe that it is possible to exist as something else than “physical beings in this earth”, You DO believe that minds can have independent existence from brains. Right?

    CharlieM: These processes involve combining the DNA with other substances so that can be manipulated. And what is doing the manipulating? Oh yes! A functioning living being. What would have happened to that DNA if you had not performed any actions on it?

    So you agree with me that it was MY intentions that were giving that isolated DNA a new meaning? Splendid. Was the isolated DNA still alive then?

    CharlieM: Me: Could you state what the “meaning” is of DNA, and how that meaning is expressed within the cell (but not without it)?

    CharlieM: It meaning lies in the way it is used, in the way that information can be taken from it. Stored in some container in isolation it might as well be playdough.

    But what is that meaning, I wonder?

    When I isolate and analyse DNA in order to genotype the individual it was taken from, I am definitely taking information from it. I do not understand why the DNA is dead when I utilize it, but alive when a cell does it. There must be something special about the meaning imbued by the cell, but what is it?

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  18. CharlieM: I claimed that DNA does nothing of significance when isolated. That claim is yet to be contradicted.

    No, your claim was:

    Isolated letters are an abstraction removed from the context of the words from which they came, and isolated DNA is an abstraction without the context of the cell to which it belongs.

    That claim has been contradicted multiple times. Then you changed your claim to:

    Isolated DNA is no longer living substance, it is dead matter. Without the organism it is no longer in the reality in which it belongs. It is meaningless outwith its context.

    and

    I did say that isolated DNA is an abstraction, not to claim the it does not exist. My meaning was that it’s existence in this state is totally unnatural and it has been removed from where it belongs to which it must be returned if it is to used in the way it was meant to be used.

    and now it morphed into:

    I claimed that DNA does nothing of significance when isolated.

    Leaving it up to others to find out what is the “meaning” of DNA, who determined what DNA is “meant for” and who is the arbiter of whether a molecular activity is “significant”.

    This is called “moving the goal posts”.

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  19. Just an observation for Charlie,

    Like dazz, I’m giving up on directing comments at you because if you respond at all to me it is usually to miss the point I’m trying to make. There maybe failure at communication on my part but it seems I’m far from unique in being unable to communicate with you.

    These naïve ramblings? Where are you going with this? Is your intent to get feedback or destroy us all with sheer boredom?

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  20. Allan Miller:

    CharlieM Of course if we were to compare ATP with the letters in a book, another glaring difference, besides the one’s you pointed out, would be that letters do not need books to have functional relevance but ATP is dependent on life for its existence.

    I think letters depend on life for their existence too…

    True enough. But ATP is intrinsic to the living system that contains it, this does not hold for letters.

    I did say that isolated DNA is an abstraction, not to claim the it does not exist. My meaning was that it’s existence in this state is totally unnatural and it has been removed from where it belongs to which it must be returned if it is to used in the way it was meant to be used.

    Meant to be used? By whom?

    By the organism, by the cell. Without the DNA in the cell the life of the organism has no meaning and would soon cease to live. If humans had never had the ability to use PCRs or RNA probes life would still go on.

    Nothing you refer to above would exist without cells. All of it involves the manipulation of DNA in one form or another.

    Yawn. And cells would not exist without nucleic acids. And round we go again.

    Yes cells would not exist without nucleic acids…and proteins, and lipids, and water, and energy sources,

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  21. Allan Miller:
    Allan Miller,

    Let’s try something less snarky.

    Suppose that the actual state-of-affairs is that Life started out as self-replicating strings of RNA. The RNA served as both genome and catalyst for its replication. Over the course of time, by extension additional capacity arose in these genomes that assisted their survival and replication. Ultimately, protein synthesis arose, such that the genome needed a 2-stage process for its expression – rather than activity through primary transcript (a ribozyme), the transcript was further processed into a protein catalyst. The superiority of these catalysts over the ancestral ribozymes led to them being replaced in most (but not all) situations, with the original RNA organisms rendered extinct for similar reasons – they could not compete, or were consumed. The genome, meanwhile, migrates from RNA to DNA, the methylation of uracil and the removal of a 2′ oxygen rendering the molecule more stable.

    Now, you reject this as ‘mere speculation’. Even if it were the actual state-of-affairs, you would reject it, and insist that the absence of modern ribozymal organisms demands ‘something else’. Something else that you would not denigrate as ‘mere speculation’, but something you had determined from close observation: ‘Prior Intelligence’. Despite no apparent substrate for such an entity.

    But maybe I could also speculate in a way that does not involve prior intelligence. We are all free to speculate. Your speculation involves the coming together piece by piece of physical matter. My speculation involves the coming together of matter because of field like effects. Just as iron filings will line up in the pattern of the magnetic field, or as Chladni figures on a vibrating plate. My speculation does not contradict our observations that all known life comes from life, nor that the cell is the most basic reproducing entity of life. It also satisfies the polarity of projective geometry in which matter belongs to the space pole and field-like entities belong to the counterspace pole.

    Failing to find a single instance of an acellular RNA organism, in the world where they had actually existed, you would declare the minimal requirement to be a fully-fledged modern organism that ‘uses’ its genome. Your evidence that they never existed being that they don’t exist now!

    So where, in such an admittedly hypothetical progression, would the genome become subjugated to the requirements of ‘the system’ – effectively, the genome a mere tool of its products? With the first protein? The thousandth?

    My speculation does not preclude that physical life might have started from a more simple entity than the simplest present day cell. But even this would have just been one end of a polar system.

    There has been some quite extensive work done on the relation of projective geometry to organic growth, especially plant growth and I can give references to some sources if you like.

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  22. dazz: CharlieM,

    You keep ignoring my point, so I’m simply moving on. No problem.
    Just one more comment on this:

    If you think that I’m committing the fallacy of composition you will need to be specific about where and when.

    CharlieM: I claimed that DNA does nothing of significance when isolated. That claim is yet to be contradicted.

    Of “significance”, yeah. And of course by that you mean “what DNA does in the cell”, right? Yawn

    Your claim is of no significance.

    Not sure what you mean. It’s obvious that DNA is vital to life.

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  23. CharlieM: If you think that I’m committing the fallacy of composition you will need to be specific about where and when.

    My bad, it’s more like the fallacy of division:

    A fallacy of division is the error in logic that occurs when one reasons that something that is true for a whole must also be true of all or some of its parts.

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  24. CharlieM: Me: I think letters depend on life for their existence too…

    Charlie: True enough. But ATP is intrinsic to the living system that contains it, this does not hold for letters.

    Correct. Because ATP has properties.

    Meant to be used? By whom?

    Charlie: By the organism, by the cell. Without the DNA in the cell the life of the organism has no meaning and would soon cease to live.

    That doesn’t explain what the word ‘meant’ is doing there. Here are 2 statements:
    1. DNA products are meant to be produced by the DNA.
    2. DNA is meant to be used by its products.

    On what grounds is 2 the winner?

    If humans had never had the ability to use PCRs or RNA probes life would still go on.

    So? You can’t do PCR on an abstraction, is the point.

    Yawn. And cells would not exist without nucleic acids. And round we go again.

    Charlie: Yes cells would not exist without nucleic acids…and proteins, and lipids, and water, and energy sources,

    Jeez. Your response to my reference to the Endless Repetition Game is to play the Endless Repetition Game. You know that proteins, lipids, processed energy sources are all ultimately sourced by sequence residing in DNA, don’t you? I’ve mentioned this once or twice.

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  25. CharlieM: But maybe I could also speculate in a way that does not involve prior intelligence. We are all free to speculate. Your speculation involves the coming together piece by piece of physical matter.

    You are missing my point. In a world where the RNA picture I painted was actually true, you would insist it wasn’t, through observation. You would observe modern cells and conclude that, since none of them is an RNA organism, there never were RNA organisms. That would be fallacious, would it not? Yet it’s exactly what you are doing. It’s not simply a question of “yeah, well, I can speculate an’ all”, but of recognising and addressing the logical force of a case.

    “I see no RNA organisms, therefore there must be Disembodied Intelligence” is one of the weaker syllogisms.

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  26. Corneel:

    CharlieM: So you’re a letter of the law person rather than a spirit of the law person.

    In fact, I am an extremely easy-going person, but you have a habit of changing the meaning of words to suit your needs. For example your current treatment of “inner activity”:

    The blood flowing through your circulatory system, that’s inner activity. Having a nose bleed turns part of it into outer activity.

    Hoho, silly Corneel. What silly bugger would deny that the blood circulation exists? Well, previously you defined innner activity a bit differently:

    Having inner activity means that it is able to ingest, convert and reuse energy in order to carry out a function such as movement or growth

    .

    Hmmm, so NOT the blood circulation. I note that DNA doesn’t fit the bill either.

    I think there is some confusion here because of the sloppy use of the word ‘meant’ in everyday English. I wasn’t intending ‘meant’ to be taken as a definition. Perhaps instead of, “Having inner activity means that it is able to…”, I should have written, “By means of inner activity it is able to…”.

    And before that, you were talking about dynein nano-beings implicitly suggesting that a life force allows motor proteins to behave like tiny homunculi. It is this interpretation of “inner activity” that I strenuously deny exists.

    I wasn’t giving an all inclusive definition of inner activity. Obviously e-coli doesn’t have an active blood circulation but it does have inner activity. by means of which it can function.

    Dynein complexes do not behave like homunculi they behave like minute motile creatures. There is no indication that they have anything close to human awareness.

    I note that “archetype” and “the radial and peripheral forces” received a similar treatment, miraculously transforming into innocuous descriptions of everyday phenomena. This is definitely not the way you have been using these terms up til now.

    You seem to be looking for rigid definitions while I have been indicating now, in my opinion, we might think about these concepts and their attributes and consequences.

    And now you blame me for picking on your claim of isolated DNA being an abstraction. I guarantee that everybody read this as saying isolated DNA has no physical existence. If you dislike that, then use words in a way that allows other people to understand.

    So I write something ambiguous, you argue against what you presume I mean by it, I try to clarify what I was actually trying to say, whereby I hope everyone now understands my position a little better. It may be a more convoluted route to the same end but I would hope that it encourages us to expend more thinking on it. It brings misunderstandings from both sides into focus.

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  27. Corneel:

    CharlieM: Can we say that anything at the molecular level is without inner activity?

    Even better. We can say that “inner activty”, used as a eufemism for élan vital, does not exist at all.

    The blood circulation still exists of course.

    So why confuse things by bringing up élan vital in the first plcace. We can concentrate on features of life that we can agree upon. And hopefully we can now agree that organisms have a great deal of inner activity.

    CharlieM: So do you believe that matter can be seen as active in the quantum sense while being passive in the Newtonian sense?

    I believe you need to learn to properly use terms in context. In this way you are equivocating.

    Well I am sincerely trying to be clear in what I say.

    Me: So you believe that “minds” have independent existence from the physical gooey inside people’s head, […]

    Charlie: No. while we exist as physical beings in this earth the mind and body are not independent

    But since you believe that it is possible to exist as something else than “physical beings in this earth”, You DO believe that minds can have independent existence from brains. Right?

    I believe that we can be conscious independent of brains. But I am not arguing about the rights or wrongs of my beliefs. I am trying to establish attributes of earthly life as we know it that we can mutually agree upon.

    I believe that we consist of body, soul and spirit dynamically intertwined, but that is neither here nor there. because I want to confine our discussion to things we can confidently agree do exist. My argument does not depend on the existence of soul or spirit.

    CharlieM: These processes involve combining the DNA with other substances so that can be manipulated. And what is doing the manipulating? Oh yes! A functioning living being. What would have happened to that DNA if you had not performed any actions on it?

    So you agree with me that it was MY intentions that were giving that isolated DNA a new meaning? Splendid. Was the isolated DNA still alive then?

    You give it new meaning only when it is taken out of isolation. Life and death are facts. An organism, say a zebra is alive and consists of living processes. It gets killed by lions, its life ceases. It has become dead matter. The carcase is torn to pieces and eaten. The dead matter becomes yet again part of the living, active processes within an organism.

    Me: Could you state what the “meaning” is of DNA, and how that meaning is expressed within the cell (but not without it)?

    CharlieM: It meaning lies in the way it is used, in the way that information can be taken from it. Stored in some container in isolation it might as well be playdough.

    But what is that meaning, I wonder?

    Whatever it is it will not show any signs of growing or reproducing.

    When I isolate and analyse DNA in order to genotype the individual it was taken from, I am definitely taking information from it. I do not understand why the DNA is dead when I utilize it, but alive when a cell does it. There must be something special about the meaning imbued by the cell, but what is it?

    It fulfils its reason to be by being a part of living processes. I suppose even PCRs can be classed as part of living processes even if indirectly. They are an integral part of processes performed by living human beings. In order to take information from the DNA you need to be active both inwardly and outwardly.

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  28. Corneel:

    CharlieM: I claimed that DNA does nothing of significance when isolated. That claim is yet to be contradicted.

    No, your claim was:

    Isolated letters are an abstraction removed from the context of the words from which they came, and isolated DNA is an abstraction without the context of the cell to which it belongs.

    That claim has been contradicted multiple times. Then you changed your claim to:

    Isolated DNA is no longer living substance, it is dead matter. Without the organism it is no longer in the reality in which it belongs. It is meaningless outwith its context.

    and

    I did say that isolated DNA is an abstraction, not to claim the it does not exist. My meaning was that it’s existence in this state is totally unnatural and it has been removed from where it belongs to which it must be returned if it is to used in the way it was meant to be used.

    and now it morphed into:

    I claimed that DNA does nothing of significance when isolated.

    Leaving it up to others to find out what is the “meaning” of DNA, who determined what DNA is “meant for” and who is the arbiter of whether a molecular activity is “significant”.

    This is called “moving the goal posts”

    Tell me precisely how DNA is physically active under its own steam so to speak? Apart from human interference it has never been known to have existed in isolation. So I presume that for millions of years prior to modern humans isolated DNA would have actually been an abstraction existing nowhere on earth.

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  29. Alan Fox:
    Just an observation for Charlie,

    Like dazz, I’m giving up on directing comments at you because if you respond at all to me it is usually to miss the point I’m trying to make. There maybe failure at communication on my part but it seems I’m far from unique in being unable to communicate with you.

    These naïve ramblings? Where are you going with this? Is your intent to get feedback or destroy us all with sheer boredom?

    I’m sure with a little effort misunderstandings could be cleared up. But in the end it’s your decision.

    Meanwhile I’ll just carry on with my naïve ramblings. I find the subject of projective geometry and negative Euclidean space far from boring, but each to their own.

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  30. dazz:

    CharlieM: If you think that I’m committing the fallacy of composition you will need to be specific about where and when.

    My bad, it’s more like the fallacy of division:

    A fallacy of division is the error in logic that occurs when one reasons that something that is true for a whole must also be true of all or some of its parts.

    It all depends on the specific analogy being made. Can you give me an example rather than a general accusation?

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  31. Allan Miller: CharlieM:

    Me: I think letters depend on life for their existence too…

    Charlie: True enough. But ATP is intrinsic to the living system that contains it, this does not hold for letters.

    Correct. Because ATP has properties.

    It certainly does.

    Meant to be used? By whom?

    Charlie: By the organism, by the cell. Without the DNA in the cell the life of the organism has no meaning and would soon cease to live.

    That doesn’t explain what the word ‘meant’ is doing there. Here are 2 statements:
    1. DNA products are meant to be produced by the DNA.
    2. DNA is meant to be used by its products.

    On what grounds is 2 the winner?

    You are trying to isolate components that do not belong in isolation. This is fine for analytical purposes but it is not something that is observed in reality.

    If humans had never had the ability to use PCRs or RNA probes life would still go on.

    So? You can’t do PCR on an abstraction, is the point.

    Isolated DNA does not naturally exist is the point.

    Yawn. And cells would not exist without nucleic acids. And round we go again.

    Charlie: Yes cells would not exist without nucleic acids…and proteins, and lipids, and water, and energy sources,

    Jeez. Your response to my reference to the Endless Repetition Game is to play the Endless Repetition Game. You know that proteins, lipids, processed energy sources are all ultimately sourced by sequence residing in DNA, don’t you? I’ve mentioned this once or twice.

    Run me through the processes whereby sequences source these materials.

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  32. CharlieM
    It all depends on the specific analogy being made. Can you give me an example rather than a general accusation?

    All you needed to do is check the quote in my response. I was referring to your claim that DNA is alive while inside the living cell.

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  33. CharlieM: So why confuse things by bringing up élan vital in the first plcace. We can concentrate on features of life that we can agree upon. And hopefully we can now agree that organisms have a great deal of inner activity.

    I do NOT agree with you that organisms have a great deal of “inner activity” in the sense that you have been using the word. Your view of “inner activity” differs from mine in the fact that you insist that it imbues ‘living substance’ with special properties which cannot be found in non-living matter. That corresponds precisely to how élan vital is used. So why not make this explicit?

    CharlieM: I believe that we consist of body, soul and spirit dynamically intertwined, but that is neither here nor there. because I want to confine our discussion to things we can confidently agree do exist. My argument does not depend on the existence of soul or spirit.

    But it does rely on the existence of certain unobservable non-physical entities and phenomena. If you seek attributes we can mutually agree on, then stop bringing those up.

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  34. CharlieM: You give it new meaning only when it is taken out of isolation. Life and death are facts. An organism, say a zebra is alive and consists of living processes. It gets killed by lions, its life ceases. It has become dead matter. The carcase is torn to pieces and eaten. The dead matter becomes yet again part of the living, active processes within an organism.

    Tsk tsk. Did you not read dazz’s comment?

    A fallacy of division is the error in logic that occurs when one reasons that something that is true for a whole must also be true of all or some of its parts.

    A zebra is alive. Its DNA is not.

    CharlieM: Me: But what is that meaning, I wonder?

    Charlie: Whatever it is it will not show any signs of growing or reproducing.

    The DNA I isolated was not meant to be used by the organism any more than it was meant to be used for genotyping by me. Neither did the DNA belong in a cell any more than it belongs in an eppendorf cup. Meaning and purpose is what we humans see. They are not intrinsic properties of molecules.

    CharlieM: I suppose even PCRs can be classed as part of living processes even if indirectly. They are an integral part of processes performed by living human beings. In order to take information from the DNA you need to be active both inwardly and outwardly.

    The content of an eppendorf cup in a PCR reaction is alive?!? LMAO!

    I am sorry Charlie, but this is utterly ridiculous. You are overthinking stuff. A zebra is alive. A strand of DNA is not. Not inside the zebra, nor outside it.

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  35. CharlieM to Allan: You are trying to isolate components that do not belong in isolation. This is fine for analytical purposes but it is not something that is observed in reality.

    Dude, you claimed that DNA was meant to be used by the cell. Another “sloppy use of the word” perchance?

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  36. Allan Miller:

    CharlieM: But maybe I could also speculate in a way that does not involve prior intelligence. We are all free to speculate. Your speculation involves the coming together piece by piece of physical matter.

    You are missing my point. In a world where the RNA picture I painted was actually true, you would insist it wasn’t, through observation. You would observe modern cells and conclude that, since none of them is an RNA organism, there never were RNA organisms. That would be fallacious, would it not? Yet it’s exactly what you are doing. It’s not simply a question of “yeah, well, I can speculate an’ all”, but of recognising and addressing the logical force of a case.

    “I see no RNA organisms, therefore there must be Disembodied Intelligence” is one of the weaker syllogisms

    I previously wrote

    My speculation does not preclude that physical life might have started from a more simple entity than the simplest present day cell. But even this would have just been one end of a polar system.

    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.

    You are missing my point that even an RNA form of life may have aspects that are hidden from our usual way of seeing the world. The negative polar spatial realm need not involve anything that is disembodied. Bodies are as much a part of this realm as they are a part of positive Euclidean space. No disembodiment required. Any entity that has a particulate aspect will also have a field aspect.

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  37. dazz:

    CharlieM
    It all depends on the specific analogy being made. Can you give me an example rather than a general accusation?

    All you needed to do is check the quote in my response. I was referring to your claim that DNA is alive while inside the living cell.

    So would you prefer if we were to agree that DNA is neither alive nor dead? Would you say that it was active or inactive?

    You might very well have a valid point. Are you alive? Are your organs alive? Are your cells alive? Are the organelles within your cells alive? What is the lowest point you would stop at when classing something as being alive?

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  38. Corneel:

    CharlieM: So why confuse things by bringing up élan vital in the first plcace. We can concentrate on features of life that we can agree upon. And hopefully we can now agree that organisms have a great deal of inner activity.

    I do NOT agree with you that organisms have a great deal of “inner activity” in the sense that you have been using the word. Your view of “inner activity” differs from mine in the fact that you insist that it imbues ‘living substance’ with special properties which cannot be found in non-living matter. That corresponds precisely to how élan vital is used. So why not make this explicit?

    It just means that the body works inwardly on itself to produce this inner activity.

    Here is an extract from an article at ScienceNordic:

    Why organisms aren’t machines.

    One of the most basic objections to the identification of organisms and machines is that their behaviour cannot be reduced to the activities and relations of their parts.

    In contrast to a mechanical watch, whose activity is fully determined “from the bottom up” by the activities and organisation of its parts, organisms influence the activities of their parts.

    For example, your muscles start to grow if you start to exercise. Moreover, the parts of a watch exist before the watch does. It is not the watch itself that builds its own parts.

    In contrast, organisms are self-producing in the sense that it is the organism itself that builds and maintains its parts. If synthetic biology assumes Descartes’ mechanical biology, then it might be headed to a dead end.

    And that from people who believe that all extant life is the result evolution by natural selection and that evolution is a ‘tinkerer’.

    CharlieM: I believe that we consist of body, soul and spirit dynamically intertwined, but that is neither here nor there. because I want to confine our discussion to things we can confidently agree do exist. My argument does not depend on the existence of soul or spirit.

    But it does rely on the existence of certain unobservable non-physical entities and phenomena. If you seek attributes we can mutually agree on, then stop bringing those up.

    Which certain unobservable non-physical entities did I say my argument relies on?

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  39. CharlieM: Me:
    That doesn’t explain what the word ‘meant’ is doing there. Here are 2 statements:
    1. DNA products are meant to be produced by the DNA.
    2. DNA is meant to be used by its products.

    On what grounds is 2 the winner?

    Charlie: You are trying to isolate components that do not belong in isolation.

    No I’m not. Try again.

    Me: So? You can’t do PCR on an abstraction, is the point.
    Charlie: Isolated DNA does not naturally exist is the point.

    That doesn’t make DNA an abstraction.

    Me: Jeez. Your response to my reference to the Endless Repetition Game is to play the Endless Repetition Game. You know that proteins, lipids, processed energy sources are all ultimately sourced by sequence residing in DNA, don’t you? I’ve mentioned this once or twice.

    Charlie: Run me through the processes whereby sequences source these materials.

    What, you want molecular biology lessons? I am sure you are aware of the processes of transcription and translation. You should also be aware (but it is not clear that you are) that the proteins and RNAs involved in these processes are held as DNA sequences, extracted by those very same processes. Without the sequences, the proteins cannot exist.

    So the endless refrain “you can’t extract DNA without protein” should not in fact lead to endless regress, because those protein sequences reside in DNA. Anyone who thinks they have undermined the Central Dogma by referring to protein action displays a very shaky grasp of concepts.

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  40. CharlieM: 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.

    Good. So if RNA life preceded modern protein-coding life, we can see why the notion that nucleic acids are ‘used’ by the organism might be flawed. The RNA organism is built by nucleic acids directly. In evolving protein coding, phenotype simply becomes a 2-step process, but still with nucleic acid at its centre. The organism is made of and by gene products.

    You are missing my point that even an RNA form of life may have aspects that are hidden from our usual way of seeing the world. The negative polar spatial realm need not involve anything that is disembodied. Bodies are as much a part of this realm as they are a part of positive Euclidean space. No disembodiment required. Any entity that has a particulate aspect will also have a field aspect.

    This is gibberish.

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  41. CharlieM: You might very well have a valid point. Are you alive? Are your organs alive? Are your cells alive? Are the organelles within your cells alive? What is the lowest point you would stop at when classing something as being alive?

    What about my finger nails? They never stop growing.

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  42. Corneel:

    CharlieM: You give it new meaning only when it is taken out of isolation. Life and death are facts. An organism, say a zebra is alive and consists of living processes. It gets killed by lions, its life ceases. It has become dead matter. The carcase is torn to pieces and eaten. The dead matter becomes yet again part of the living, active processes within an organism.

    Tsk tsk. Did you not read dazz’s comment?

    A fallacy of division is the error in logic that occurs when one reasons that something that is true for a whole must also be true of all or some of its parts.

    A zebra is alive. Its DNA is not.

    Fair enough. So the zebra is the living actor and DNA is one of the substances that it acts upon.

    Me: But what is that meaning, I wonder?

    Charlie: Whatever it is it will not show any signs of growing or reproducing.

    The DNA I isolated was not meant to be used by the organism any more than it was meant to be used for genotyping by me. Neither did the DNA belong in a cell any more than it belongs in an eppendorf cup. Meaning and purpose is what we humans see. They are not intrinsic properties of molecules.

    So do you think that only humans act with purpose or intent? Does purpose or intent require consciousness?

    CharlieM: I suppose even PCRs can be classed as part of living processes even if indirectly. They are an integral part of processes performed by living human beings. In order to take information from the DNA you need to be active both inwardly and outwardly.

    The content of an eppendorf cup in a PCR reaction is alive?!? LMAO!

    An Eppendorf cup is an object, it is not a process. PCRs are processes.

    I am sorry Charlie, but this is utterly ridiculous. You are overthinking stuff. A zebra is alive. A strand of DNA is not. Not inside the zebra, nor outside it.

    So there is a difference between living and non living substance? Is a zebra alive and a phagocyte in its blood stream not alive?

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  43. Corneel:

    CharlieM to Allan: You are trying to isolate components that do not belong in isolation. This is fine for analytical purposes but it is not something that is observed in reality.

    Dude, you claimed that DNA was meant to be used by the cell. Another “sloppy use of the word” perchance?

    Well it is an integral part of the cell. DNA is extensively used in cellular processes. If you believe that it is ever isolated from its cellular environment apart from as the result of purposeful human activity then let me know the circumstances.

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  44. CharlieM: Which certain unobservable non-physical entities did I say my argument relies on?

    There are several, but here is an example from your current OP:

    His archetype was an all inclusive dynamic process that does not reside within any one specific manifestation.

    If I understand your argument correctly, this is not meant as an abstraction. You believe archetypes to be ultimately real. This is most definitely not something we agree on.

    CharlieM: Fair enough. So the zebra is the living actor and DNA is one of the substances that it acts upon.

    No, the DNA is part of the zebra. The point is that you can’t transfer attributes from the whole (“the zebra is alive”) to its parts (“therefore its DNA is also alive”). In order to qualify as “alive”, certain requirements need to met. Stuff like “has a metabolism” just does not apply to molecules.

    CharlieM: So do you think that only humans act with purpose or intent? Does purpose or intent require consciousness?

    Yes. To me, purpose and intent require consciousness so are restricted to animals. Attributing meaning to something may be a uniquely human thing, not sure.

    CharlieM: An Eppendorf cup is an object, it is not a process. PCRs are processes.

    Still LMAO.

    CharlieM: So there is a difference between living and non living substance? Is a zebra alive and a phagocyte in its blood stream not alive?

    We discussed this before. “Living substance” is not a term I use.

    CharlieM: Well it is an integral part of the cell. DNA is extensively used in cellular processes.

    You are missing the point once again. You chide Allan for “trying to isolate components that do not belong in isolation”, but constantly refer to DNA being “acted upon” or “used in cellular processes”. It is only fair that Allan asked why it isn’t the other way around, yet you avoided that question.

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  45. CharlieM: So the zebra is the living actor and DNA is one of the substances that it acts upon.

    Yet DNA precedes the Zebra.

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  46. Allan Miller:
    Me: That doesn’t explain what the word ‘meant’ is doing there. Here are 2 statements:
    1. DNA products are meant to be produced by the DNA.
    2. DNA is meant to be used by its products.

    On what grounds is 2 the winner?

    Proteins are not the products of DNA. Proteins are the products of a complex process. If you were to listen to a recording on an old Walkman you would be in error if you believed the sound was being produced by the tape. What you hear is produced by the process of reading the tape and transforming the magnetic data into sound.

    It isn’t any of the substances that do the producing, it is the processes.

    Charlie: You are trying to isolate components that do not belong in isolation.

    No I’m not. Try again.

    If a prospector is lucky panning for gold will produce isolated nuggets of gold. Does DNA ever appear in such isolation in nature?

    Me: So? You can’t do PCR on an abstraction, is the point.
    Charlie: Isolated DNA does not naturally exist is the point.

    That doesn’t make DNA an abstraction.

    I never said that DNA was an abstraction. What about the time when Plato lived? Was isolated DNA an abstraction then?

    Me: Jeez. Your response to my reference to the Endless Repetition Game is to play the Endless Repetition Game. You know that proteins, lipids, processed energy sources are all ultimately sourced by sequence residing in DNA, don’t you? I’ve mentioned this once or twice.

    Charlie: Run me through the processes whereby sequences source these materials.

    What, you want molecular biology lessons? I am sure you are aware of the processes of transcription and translation. You should also be aware (but it is not clear that you are) that the proteins and RNAs involved in these processes are held as DNA sequences, extracted by those very same processes. Without the sequences, the proteins cannot exist.

    So the endless refrain “you can’t extract DNA without protein” should not in fact lead to endless regress, because those protein sequences reside in DNA. Anyone who thinks they have undermined the Central Dogma by referring to protein action displays a very shaky grasp of concepts.

    I’m happy to stop this endless refrain here and now because you have acknowledged for anything further to come from the DNA sequences, the process of transcription is essential. Processes are not a property or attribute of any single element, they are an activity of interacting, coordinated elements.

    DNA does not create proteins, cellular processes do. Proteins are not held in DNA sequences, nor are sequences of amino acids held in DNA sequences. The message is held waiting to be processed.

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  47. Allan Miller:

    CharlieM: 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.

    Good. So if RNA life preceded modern protein-coding life, we can see why the notion that nucleic acids are ‘used’ by the organism might be flawed. The RNA organism is built by nucleic acids directly. In evolving protein coding, phenotype simply becomes a 2-step process, but still with nucleic acid at its centre. The organism is made of and by gene products.

    The point is that the organism is built by inner activity.

    You are missing my point that even an RNA form of life may have aspects that are hidden from our usual way of seeing the world. The negative polar spatial realm need not involve anything that is disembodied. Bodies are as much a part of this realm as they are a part of positive Euclidean space. No disembodiment required. Any entity that has a particulate aspect will also have a field aspect.

    This is gibberish.

    Mandarin is gibberish to me.

    “There are more things in heaven and Earth…”

    Below is from an image taken from NASA’s Fermi Telescope.

    The physical matter of the galaxy can be idealised as a two dimensional spiral. Projecting out of this plane is a cone of what they describe as very energetic gamma rays. They also say, “We don’t fully understand their nature or origin.” This is a very familiar image generated by projective geometry using the polarity of point and plane..

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  48. dazz:

    CharlieM: You might very well have a valid point. Are you alive? Are your organs alive? Are your cells alive? Are the organelles within your cells alive? What is the lowest point you would stop at when classing something as being alive?

    What about my finger nails? They never stop growing.

    Good question. Why do your nails keep growing but the bones of your fingers and toes don’t?

    Easy answer which means we don’t have to worry any more about it. Because of natural selection.

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