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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338 thoughts on “The Spiralling Flow of Life

  1. Corneel:

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

    No, it doesn’t.

    It’s the impression many people get.

    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.

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

    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.

    It has and does happen.

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  2. Corneel:

    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

    Individuality is more than just a few individual differences. There has to be a certain level. Human individuality is something that we develop as we mature. I is more than just the individual differences seen in new born babies.

    I wouldn’t class squirrel individuality as being defined by living in particular tree or forest or having particular parents. Can you give me some indication from your observation of an animal such as a squirrel what would make it stand out from other squirrels of the same species? Something that would give it, not just the odd individual physical feature, but something like a behaviour or ability pointing to individuality?

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  3. CharlieM,

    Can you give me some indication from your observation of an animal such as a squirrel what would make it stand out from other squirrels of the same species? Something that would give it, not just the odd individual physical feature, but something like a behaviour or ability pointing to individuality?

    Well, since you did choose to highlight that “Every single human on the planet displays a complex mixture of individuality, cultural influences and racial influences”, I should probably warn you that I am talking about the racially diverse (22 distinct races!) Sciurus vulgaris, and not the genocidal Aryan invaders that are Sciurus carolinensis.
    Your argument still reduces to “They all look the same to me”, and trying (unsuccessfully!) to cherry-pick your criteria. This is entirely equivalent to “blithely rabbiting on about how Caucasians show much more individual variation than the Chinese do”
    Perhaps you need to get out more.

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  4. DNA_Jock: 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.

    You have transposed the words. But regarding the complex mixture of individuality, cultural influences and racial influences, are the proportions the same for squirrels as for humans? I am arguing that in humans the proportion of individuality is much higher. There is plenty of evidence of human individuality. Where is the evidence for its high level in squirrels?

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  5. DNA_Jock:

    Can you give me some indication from your observation of an animal such as a squirrel what would make it stand out from other squirrels of the same species? Something that would give it, not just the odd individual physical feature, but something like a behaviour or ability pointing to individuality?

    Well, since you did choose to highlight that “Every single human on the planet displays a complex mixture of individuality, cultural influences and racial influences”, I should probably warn you that I am talking about the racially diverse (22 distinct races!) Sciurus vulgaris, and not the genocidal Aryan invaders that are Sciurus carolinensis.
    Your argument still reduces to “They all look the same to me”, and trying (unsuccessfully!) to cherry-pick your criteria. This is entirely equivalent to “blithely rabbiting on about how Caucasians show much more individual variation than the Chinese do”

    Grey squirrels are not genocidal Aryan invaders. They lived quite happily in their native habitat. Don’t forget that it was humans that took them out of this habitat and allowed them to colonise other areas. Grey squirrels are said to have been “first introduced to Britain in the 1870s, as fashionable additions to estates”. So it seems that certain human individuals were responsible for their introduction into the U.K..

    Squirrels can’t be blamed for doing what squirrels do.

    Perhaps you need to get out more.

    When I am out and about, as I will be within the hour, I’ll possibly see some red squirrels, because, thankfully, so far grey squirrels haven’t ventured this far north.

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  6. I get the impression that my arguments for human individuality are much to close to arguments for human exceptionalism which are popular amongst intelligent design proponents and creationists. And anything that they say must be opposed at all costs, no matter how logic it may seem.

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  7. CharlieM: I am arguing that in humans the proportion of individuality is much higher. There is plenty of evidence of human individuality. Where is the evidence for its high level in squirrels?

    No, Charlie. Until you actually go out and put some serious work into measuring the ‘individuality’ in squirrels, you are not ‘arguing’ anything, you are merely asserting.
    The ascertainment bias is strong in this one.

    CharlieM: Grey squirrels are not genocidal Aryan invaders.

    Perhaps the joke went straight over your head, since it relies on seeing the silliness of applying human standards and terminology to non-human animals. Grey squirrels are not ‘Aryan’ (d’oh!), but they are rather racially homogeneous, especially when compared to the extremely diverse S. vulgaris. They ARE ‘invaders’, and they ARE ‘genocidal’, albeit not intentionally so.
    You had no comment regarding S. vulgaris. Do not for a moment think that we didn’t notice.

    CharlieM: I get the impression that my arguments for human individuality are much to close to arguments for human exceptionalism which are popular amongst intelligent design proponents and creationists. And anything that they say must be opposed at all costs, no matter how logic it may seem.

    Naah, I am not being oppositional for its own sake. Humans are pretty amazing and in certain ways unique. Creationists tend to make rather ignorant claims about humans being the acme of creation — as a molecular biologist, humans (well, vertebrates in general) are a Heath-Robinson cobbling together of miscellaneous parts. The control of splicing is a clusterfuck, pattern formation is baroque. You want ‘highly evolved’, look at bacteriophage — they are optimized.
    But you, Charlie, have ventured into a particularly unsupported claim of human exceptionalism, that is, the idea that humans display more individual variation, even when compared with dogs, horses, and pigs (!).
    This conversation should have ended the first time someone mentioned “they all look the same to me”.
    And yet we go on and on. That’s just funny.

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  8. CharlieM: It’s the impression many people get.

    You spend a lot of your time arguing against impressions people have.

    CharlieM: As I wro[t]e above, I don’t reject selection. It’s an observed fact. It changes the proportions of traits already present within populations.

    No, it does not. Natural selection changes the proportions of alleles already present within populations. Trait values will often transgress the range observed in the ancestral generation.
    Do you believe these changes are a consequence of “group wisdom” or can it be explained by physical processes?

    CharlieM: Individuality is more than just a few individual differences. There has to be a certain level.

    I am willing to bet a considerable sum of money that you cannot find a single dictionary definition that requires that individuality arises “through our own efforts” or that there “has to be a certain level”. You are adjusting the definition of the word to what you need it to mean.

    Look it up: most definitions just say it is the sum of distinguishing qualities. I appreciate that is not a welcome fact to you, but there it is.

    CharlieM: I get the impression that my arguments for human individuality are much to close to arguments for human exceptionalism which are popular amongst intelligent design proponents and creationists. And anything that they say must be opposed at all costs, no matter how logic it may seem.

    My impression is that your arguments are opposed because they do not make sense.

    It’s the impression many people get.

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  9. CharlieM:
    I get the impression that my arguments for human individuality are much to close to arguments for human exceptionalism which are popular amongst intelligent design proponents and creationists. And anything that they say must be opposed at all costs, no matter how logic it may seem.

    There are some good arguments for human exceptionalism, and some bad arguments for human exceptionalism. The problem with your view isn’t that you believe in human exceptionalism, but that your arguments are bad. That’s what everyone here is trying to point out to you.

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  10. Kantian Naturalist: The problem with your view isn’t that you believe in human exceptionalism, but that your arguments are bad.

    So bad that I had no idea that was what CharlieM was arguing for.😳

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  11. DNA_Jock:

    CharlieM: I am arguing that in humans the proportion of individuality is much higher. There is plenty of evidence of human individuality. Where is the evidence for its high level in squirrels?

    No, Charlie. Until you actually go out and put some serious work into measuring the ‘individuality’ in squirrels, you are not ‘arguing’ anything, you are merely asserting.
    The ascertainment bias is strong in this one.

    Goethean science is a science of qualities, not quantities. It leaves the work of measuring and counting to conventional science. And individuality is not a measurable feature, it’s a quality. The use of language is a good indicator of levels of individuality. My ‘bad arguments’ are my personal responsibility, I cannot blame them on race. And there are a near infinite number of ways that these arguments could be formed and from which I could develop further arguments..

    CharlieM: Grey squirrels are not genocidal Aryan invaders.

    Perhaps the joke went straight over your head, since it relies on seeing the silliness of applying human standards and terminology to non-human animals. Grey squirrels are not ‘Aryan’ (d’oh!), but they are rather racially homogeneous, especially when compared to the extremely diverse S. vulgaris. They ARE ‘invaders’, and they ARE ‘genocidal’, albeit not intentionally so.
    You had no comment regarding S. vulgaris. Do not for a moment think that we didn’t notice.

    So you claim that there are 22 races of S. vulgaris. Belonging to a distinct race is not a sign of individuality. Red squirrels are distinguished as members of a race or sub-species. Do you think that a person of Chines descent should be judged according to his or her race, or should they be judged as an individual?

    Would you judge a cat as doing wrong because it killed a bird, or would you say that this is just something cats do? You can’t blame a human for killing other humans because that’s just something humans do! To blame the individual cat, now that would be applying human standards to animals.

    CharlieM: I get the impression that my arguments for human individuality are much to close to arguments for human exceptionalism which are popular amongst intelligent design proponents and creationists. And anything that they say must be opposed at all costs, no matter how logic it may seem.

    Naah, I am not being oppositional for its own sake. Humans are pretty amazing and in certain ways unique. Creationists tend to make rather ignorant claims about humans being the acme of creation — as a molecular biologist, humans (well, vertebrates in general) are a Heath-Robinson cobbling together of miscellaneous parts. The control of splicing is a clusterfuck, pattern formation is baroque. You want ‘highly evolved’, look at bacteriophage — they are optimized.
    But you, Charlie, have ventured into a particularly unsupported claim of human exceptionalism, that is, the idea that humans display more individual variation, even when compared with dogs, horses, and pigs (!).

    I am not restricting the comparison to just physical appearance, I also include behaviour and personal histories.

    This conversation should have ended the first time someone mentioned “they all look the same to me”.
    And yet we go on and on. That’s just funny.

    It might suit your argument but physical appearance is not the only criteria.

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  12. CharlieM: I am not restricting the comparison to just physical appearance, I also include behaviour and personal histories….
    It might suit your argument but physical appearance is not the only criteria.

    Oh dear. I fully recognize that physical appearance is not the only criterion. This helps my argument: I am arguing that you do not know whether snails or squirrels display more “individuality” than humans. Consider, for example, smell: you have no clue whatsoever how much different squirrels differ in terms of their odor. You had no clue about racial variation in S. vulgaris.
    As I have noted previously, you don’t even know for your cherry-picked anthropocentric metrics:
    CharlieM:

    You think that the difference between you and your mother; likes, dislikes, physical appearance, habits and travels, etc., are on a par with the difference between the next snail you come across and its mother?

    Jock

    Yes. I think that from a snail’s perspective the differences between snails might be more glaringly varied. Speaking “objectively”, I have no idea. And neither do you. Hilariously, you don’t even know for your cherry-picked anthropocentric attributes: “habits and travels” anyone?

    When we had that interaction in May, I compared my “travels” with those of my mother. She has visited three countries that I have not (Japan, Finland and Jordan) and I have visited three that she has not (Greece, Iceland and Costa Rica). Woot. But we have both visited eighteen different countries (I’m not counting Norway, as the only time we visited we were together). So 15% different.
    Back in May, I was lacking a suitable comparator. Now that I have learned Goethean intuiting, I am able to ascertain that the snail under my porch has spent his entire life there, whereas his mother migrated across four properties to get here. That’s 300% different! That’s individuality!
    “They all look the same to me” is not merely about physical appearance: it is a shorthand way of noting that we notice differences that seem important to us, and fail to notice differences that do not seem important, such as squirrel odor.
    The hilarity continues.

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  13. I’m getting a lot of criticism for the way I am using the word, ‘individuality’ and I get the point.

    After thinking about it, I’d say it’s a matter of relativity. So I propose that individuality ranges from what I will call weak individuality to what I’ll call ultra-individuality.

    An example of weak individuality would be a grain of sand. It is a uniquely individual entity with boundaries. Humans sit at the opposite pole. We too are uniquely individual, but also, we have a part to play in shaping our personal identity as individuals. And we are able to express our individuality in outward forms through acts of will.

    So I accept the criticism which implies that ‘individuality’ is too vague a term to use when trying to make distinctions between ourselves and other natural entities.

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  14. Corneel:

    CharlieM: It’s the impression many people get.

    You spend a lot of your time arguing against impressions people have.

    CharlieM: As I wro[t]e above, I don’t reject selection. It’s an observed fact. It changes the proportions of traits already present within populations.

    No, it does not. Natural selection changes the proportions of alleles already present within populations. Trait values will often transgress the range observed in the ancestral generation.

    To take the example of Darwin’s finches and keeping to what can be observed, it is beak morphology that plays a major part in survival.

    Gene behind ‘evolution in action’ in Darwin’s finches identified

    The researchers identified HMGA2′s role by screening the genomes of medium ground finches that survived or died during the drought until they located the locus, or gene position, that had a major effect on beak size. The researchers found that the HMGA2 gene comes in two forms: one is common in finches with small beaks, while the other is common in finches with large beaks. The proportion of the two forms in the birds’ genome changed as a result of the better survival of birds with small beaks…

    The identification of HMGA2 as the determinant of beak size builds on 2015 research the Grants and Andersson’s group published in the journal Nature that singled out the gene ALX1 as the one that most influences beak shape, such as if a finch’s beak is pointed or blunt. Together, the genes could be the most prominent determinants of how Darwin’s finches adapt to their environment, said first author of the current study Sangeet Lamichhaney, a doctoral student under Andersson.

    Notice that it was more likely survival of those birds with a specific beak morphology that resulted in the change of allele frequency.

    It is obvious that beak morphology correlates to the interactions of several expressed genes in complex ways. In the end it is actual beak morphology that determines survival. The genes can be expressed in a multitude of ways to give a range of morphologies but there are limits that cannot be exceeded without affecting the viability of the bird. ‘Selection’ ensures that the correct balance is maintained over various external conditions.

    Do you believe these changes are a consequence of “group wisdom” or can it be explained by physical processes?

    As above it is the physical makeup of the whole bird that keeps the population viable. Transplant the beak of a curlew onto the head of a finch and it will not survive.

    The wisdom lies in the balanced functioning of the whole organism. If the population maintains sufficient plasticity then it will continue to thrive.

    CharlieM: Individuality is more than just a few individual differences. There has to be a certain level.

    I am willing to bet a considerable sum of money that you cannot find a single dictionary definition that requires that individuality arises “through our own efforts” or that there “has to be a certain level”. You are adjusting the definition of the word to what you need it to mean.

    Look it up: most definitions just say it is the sum of distinguishing qualities. I appreciate that is not a welcome fact to you, but there it is.

    My previous post addresses this problem.

    CharlieM: I get the impression that my arguments for human individuality are much to close to arguments for human exceptionalism which are popular amongst intelligent design proponents and creationists. And anything that they say must be opposed at all costs, no matter how logic it may seem.

    My impression is that your arguments are opposed because they do not make sense.

    It’s the impression many people get.

    I will keep on trying to refine my arguments. They must be making a bit of sense or I wouldn’t be getting all this helpful feedback.

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  15. Kantian Naturalist:

    CharlieM:
    I get the impression that my arguments for human individuality are much to close to arguments for human exceptionalism which are popular amongst intelligent design proponents and creationists. And anything that they say must be opposed at all costs, no matter how logic it may seem.

    There are some good arguments for human exceptionalism, and some bad arguments for human exceptionalism. The problem with your view isn’t that you believe in human exceptionalism, but that your arguments are bad. That’s what everyone here is trying to point out to you.

    Define ‘bad’. You mean ‘bad’ as in ‘sick’? I’m cool with that 🙂

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  16. CharlieM,

    I will keep on trying to refine my arguments. They must be making a bit of sense or I wouldn’t be getting all this helpful feedback.

    Hahaha! “If my arguments were bad, would people contest them?”.

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  17. Alan Fox:

    Kantian Naturalist: The problem with your view isn’t that you believe in human exceptionalism, but that your arguments are bad.

    So bad that I had no idea that was what CharlieM was arguing for.

    Basically I am arguing that there are progressive stages in the continuous evolution of life. Animal sentience takes the growth of plants to another level and human self-conscious individualism takes the sentience of animals to an even higher level. In humans life attains the light of consciousness. And I am saying that this is no accident, the potential was there from the start just as the potential of the butterfly is in the egg. The whole reflected in the parts. 🙂

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  18. Allan Miller:

    I will keep on trying to refine my arguments. They must be making a bit of sense or I wouldn’t be getting all this helpful feedback.

    Hahaha! “If my arguments were bad, would people contest them?”.

    Obviously you see things more in terms of black and white than I do. I hope that I have made at least some half-decent arguments amongst the bad ones.

    Anyway my comment was in reply to a specific accusation that my arguments didn’t make sense.

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  19. Allan Miller:

    CharlieM: Obviously you see things more in terms of black and white than I do.

    No, I absolutely reject that

    Of course I was saying this in reference to how good or bad my arguments are,

    But there are others more deserving of this criticism than you so maybe I shouldn’t have singled you out in this way.

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  20. DNA_Jock: as a molecular biologist, humans (well, vertebrates in general) are a Heath-Robinson cobbling together of miscellaneous parts. The control of splicing is a clusterfuck, pattern formation is baroque.

    To make such a judgement you would need to know how to produce from scratch a viable, living, developing, self-conscious, rational being, capable of perceiving, learning, remembering and making predictions about the future.

    Regarding these matters, I think your faith in your own ability to judge by far exceeds your actual ability to judge.

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  21. CharlieM: But there are others more deserving of this criticism than you so maybe I shouldn’t have singled you out in this way.

    Physician, heal thyself!

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  22. Alan Fox:

    CharlieM: But there are others more deserving of this criticism than you so maybe I shouldn’t have singled you out in this way.

    Physician, heal thyself!

    I don’t mind indulging in a bit of self-criticism, but I think you lot supply me with more than enough 🙂

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  23. CharlieM: I am arguing that there are progressive stages in the continuous evolution of life. Animal sentience takes the growth of plants to another level and human self-conscious individualism takes the sentience of animals to an even higher level. In humans life attains the light of consciousness.

    It is certainly true that this progression is one of the trends we can discern in the history of life, and this progression may be the most important with respect to certain intellectual and existential interests that we have.

    But it doesn’t follow either that this trend really is (1) the most important of all trends compared to all others or (2) this trend should be understood in terms of the teleological model of organism development.

    Your insistence on (1) and (2) indicates a rather complete lack of understanding of Darwin’s contribution to evolutionary biology. So when you claim that you accept conventional science, but are only supplementing it with “Goethean science,” we scoff because it is clear to all of us that you don’t understand “conventional science” — empirically confirmed evolutionary biology — at all.

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  24. CharlieM: Me: No, I absolutely reject that

    Charlie: Of course I was saying this in reference to how good or bad my arguments are,

    But there are others more deserving of this criticism than youso maybe I shouldn’t have singled you out in this way.

    It was intended ironically!

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  25. CharlieM: It is obvious that beak morphology correlates to the interactions of several expressed genes in complex ways. In the end it is actual beak morphology that determines survival. The genes can be expressed in a multitude of ways to give a range of morphologies but there are limits that cannot be exceeded without affecting the viability of the bird. ‘Selection’ ensures that the correct balance is maintained over various external conditions.

    Selection acts on the phenotype. That is a fact. The puzzle piece you keep missing is how this affects the genetic composition of the population.

    Consider this: All species of Galapagos finches are believed to have radiated from a single ancestral species. Do you truly believe that all different beak sizes and shapes that can be seen today were already present in the parental species? Of course not. So where did the novel forms originate?

    Darwin could see the parallel with artificial selection. Pigeon breeders have made varieties that look dramatically different from their wild ancestors. We now know that for a large part this is the result from creating novel combinations of ancestral alleles. This seems to be something you have trouble grasping. Although it is true that selection acts by weeding out less fit individuals, in doing so it changes the genetic composition of the population. As a result, the next generation might see some individuals with genotypes, and thus phenotypic traits, never seen before.

    CharlieM: As above it is the physical makeup of the whole bird that keeps the population viable. Transplant the beak of a curlew onto the head of a finch and it will not survive.

    The wisdom lies in the balanced functioning of the whole organism. If the population maintains sufficient plasticity then it will continue to thrive.

    You are confusing the survival of individual organisms with population survival. Many poorly “functioning” individual birds are dying to keep the population viable. In humans: idem dito. Many people suffer because they are born with devastating genetic diseases. Where is the wisdom in that?

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  26. Kantian Naturalist:

    CharlieM: I am arguing that there are progressive stages in the continuous evolution of life. Animal sentience takes the growth of plants to another level and human self-conscious individualism takes the sentience of animals to an even higher level. In humans life attains the light of consciousness.

    It is certainly true that this progression is one of the trends we can discern in the history of life, and this progression may be the most important with respect to certain intellectual and existential interests that we have.

    But it doesn’t follow either that this trend really is (1) the most important of all trends compared to all others or (2) this trend should be understood in terms of the teleological model of organism development.

    Without consciousness and understanding the talk of the importance of trends is totally meaningless. But it is the fact that consciousness and understanding does exist that gives it its importance. Consciousness supplies Nature with its reason to be.

    I am stating, not in incidental particular terms, but in general terms the additional attributes of each group (plants, animals, humans). Animals have life and growth in common with plants but animals, on top of this, acquired advanced motility, sentience, individual learning, and inner feelings. Humans also possess these traits of plants and animals, but we, on top of this, have developed self-consciousness, rational thought, and extremely complex language.

    Your insistence on (1) and (2) indicates a rather complete lack of understanding of Darwin’s contribution to evolutionary biology. So when you claim that you accept conventional science, but are only supplementing it with “Goethean science,” we scoff because it is clear to all of us that you don’t understand “conventional science” — empirically confirmed evolutionary biology — at all.

    Do you understand what actually has been discovered by empirically confirmed evolutionary biology? What have evolutionary biologists empirically discovered about how the spectrum of life came to be?

    Look at the Grant’s forty year finch study on the island of Daphne Major. The various ‘species’ on the island can interbreed but in general they choose not to. There are examples of crossbreeding and back, crossbreeding. They witnessed the evolution of beak sizes as an oscillatory process, not a progression towards a specialised beak.

    But imagine if it were the case that the species became totally isolated from each other. It would be the species that had the more specialised beaks that would be in danger of extinction. Any species that retained the greatest diversity. among its individual members would be at an advantage.

    It is the whole that survives and progresses at the expense of the parts. Life continues on its path precisely because it is able to shed its narrow niched, side branches. And Darwinian evolution is most suitable for an understanding of how these specialist side branches come and go. But it has nothing to say about the main trajectory. It is through unquestioning faith in the power of the theory of natural selection acting on random mutations, that it is has become such an omnipotent force in the eyes of its advocates. There is an unwillingness to admit its limitations. How much of evolutionary biology is observation and how much is speculation?

    Through the process of development the human comes to know herself/himself. Through the process of evolution Nature comes to know herself.

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  27. Corneel:

    CharlieM: It is obvious that beak morphology correlates to the interactions of several expressed genes in complex ways. In the end it is actual beak morphology that determines survival. The genes can be expressed in a multitude of ways to give a range of morphologies but there are limits that cannot be exceeded without affecting the viability of the bird. ‘Selection’ ensures that the correct balance is maintained over various external conditions.

    Selection acts on the phenotype. That is a fact. The puzzle piece you keep missing is how this affects the genetic composition of the population.

    Consider this: All species of Galapagos finches are believed to have radiated from a single ancestral species. Do you truly believe that all different beak sizes and shapes that can be seen today were already present in the parental species? Of course not. So where did the novel forms originate?

    They were already present in potential. Just as all the organs in your body were present in potential in the zygote that you were at one time. We can just speculate as to the variety of beak morphology in the original population or populations.

    But one thing is clear. The more specialised the beak the more difficulty in adapting to changing conditions.

    Darwin could see the parallel with artificial selection. Pigeon breeders have made varieties that look dramatically different from their wild ancestors. We now know that for a large part this is the result from creating novel combinations of ancestral alleles. This seems to be something you have trouble grasping. Although it is true that selection acts by weeding out less fit individuals, in doing so it changes the genetic composition of the population. As a result, the next generation might see some individuals with genotypes, and thus phenotypic traits, never seen before.

    The existence of sex means that all offspring have unique genotypes. It’s just a matter of degree.

    CharlieM: As above it is the physical makeup of the whole bird that keeps the population viable. Transplant the beak of a curlew onto the head of a finch and it will not survive.

    The wisdom lies in the balanced functioning of the whole organism. If the population maintains sufficient plasticity then it will continue to thrive.

    You are confusing the survival of individual organisms with population survival. Many poorly “functioning” individual birds are dying to keep the population viable.

    The parts being sacrificed for the whole. It’s all a matter of perspective. Life is short for the bone cell that is sacrificed in sculpting the form of the bone. Its death is necessary for a higher purpose. The population survives through changing conditions by means of the variety of individuals within it.

    In humans: idem dito. Many people suffer because they are born with devastating genetic diseases. Where is the wisdom in that?

    The wisdom is at a higher level. It’s only seen as devastating from a limited perspective that is blind to the whole.

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  28. dazz:

    CharlieM: It is the whole that survives and progresses at the expense of the parts

    The whole not reflected in the parts

    The whole, in turn, is a part of an even greater whole. T. Rex individuals perished but the species lived on. At a higher level the species became extinct but theropods lived on. The self-similar fractal nature of life.

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  29. CharlieM: part of an even greater whole. T. Rex individuals perished but the species lived on. At a higher level the species became extinct but theropods lived on. The self-similar fractal nature of life.

    As I’ve said before, it’s curious that you are so resistant to gene-centrism, then. Due to iterated recombination the whole of a genome, but for a fragment, can be lost, but the fragment lives on, like a little mini-organism that colonises genomes…

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  30. CharlieM: Me: So where did the novel forms originate?

    Charlie: They were already present in potential.

    Everything that isn’t impossible, is “present in potential”. But how did these particular potential forms actually came to be?

    CharlieM: Me: […] the next generation might see some individuals with genotypes, and thus phenotypic traits, never seen before.

    Charlie: The existence of sex means that all offspring have unique genotypes. It’s just a matter of degree.

    How does individuals being unique prevent us from identifying completely novel traits? Suppose that somewhere on this planet a purple mouse is born, or a mouse the size of an elephant. Do you think you will miss that because every mouse has a unique mixture of ancestral traits?

    CharlieM: Me: Many people suffer because they are born with devastating genetic diseases. Where is the wisdom in that?

    Charlie: The wisdom is at a higher level. It’s only seen as devastating from a limited perspective that is blind to the whole.

    So much for celebrating the individuality of human beings. When push comes to shove, individual humans are just parts that are being sacrificed for the whole.

    I fail to see the wisdom in that. In fact, I don’t want to.

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  31. Allan Miller:

    CharlieM: part of an even greater whole. T. Rex individuals perished but the species lived on. At a higher level the species became extinct but theropods lived on. The self-similar fractal nature of life.

    As I’ve said before, it’s curious that you are so resistant to gene-centrism, then. Due to iterated recombination the whole of a genome, but for a fragment, can be lost, but the fragment lives on, like a little mini-organism that colonises genomes

    If I was looking for some molecule that remained constant over the generations I would pick polysaccharides or lipids. But I am comparing processes, not substances.

    The self similarity I am discussing above is not in physical substance, but in the dynamic processes of birth, life and death. Genomes aren’t lost, they just change, but so do cells, organisms and species.

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  32. Corneel:

    Me: So where did the novel forms originate?

    Charlie: They were already present in potential.

    Everything that isn’t impossible, is “present in potential”.

    But everything is not and has never been possible for life on earth. And for living forms the potential becomes more restricted as they evolve over time. Chronos eats his own children.

    One obvious restriction that limits the size of any living form is gravity. The ancestors of blue whales may still have had the plasticity of form that allowed them to move from an aqueous to a terrestrial environment but extant whales have travelled too far down their own evolutionary trajectory to still have this potential.

    But how did these particular potential forms actually came to be?

    They are expressions of the archetypal plant or the archetypal animal as the case may be.

    To understand the archetypal plant, look at all the plants in existence and imagine them morphing into each other. Plant forms in existence are discrete, they take up definite positions in this morphing scenario. The archetype includes all plants but it also includes all the gaps that have not been realized in actuality.

    The ideal triangle give us a similar idea but it is much more simple because the time element is not a factor. That is why I am forever using the example of this ideal triangle. The number of static, physical representations of triangles ever to exist is vast and unimaginable but it is still a finite number. The ideal triangle is inclusive of an infinity of triangles.

    Me: […] the next generation might see some individuals with genotypes, and thus phenotypic traits, never seen before.

    Charlie: The existence of sex means that all offspring have unique genotypes. It’s just a matter of degree.

    How does individuals being unique prevent us from identifying completely novel traits? Suppose that somewhere on this planet a purple mouse is born, or a mouse the size of an elephant. Do you think you will miss that because every mouse has a unique mixture of ancestral traits?

    It is not unique for an animal to be purple as in the male violet-backed starling. And it isn’t unique for an animal to be the size off an elephant. You will notice that elephants are the size of elephants.

    And mice have travelled too far down their evolutionary path to ever become the size of elephants. From the image below it can be seen that their skeletons alone would have to undergo considerable coordinated transformations before they would be able to bear the weight of an animal that size. That is why, no matter how much humans fiddle with canine morphology, domestic dogs will always remain within a specific range. We are never going to see dogs the size of mice or elephants.

    Me: Many people suffer because they are born with devastating genetic diseases. Where is the wisdom in that?

    Charlie: The wisdom is at a higher level. It’s only seen as devastating from a limited perspective that is blind to the whole.

    So much for celebrating the individuality of human beings. When push comes to shove, individual humans are just parts that are being sacrificed for the whole.

    I fail to see the wisdom in that. In fact, I don’t want to.

    No, not just parts being sacrificed for the whole. Individuals who have been given the freedom to love in the true sense of the word. ‘I am in the Father and the Father is in me.’ That is what true self-consciousness, the ‘I am’, means. Generally speaking, at the present time, we are self-conscious only to a very limited degree. Evolution continues and has reached a stage where individuals can decide on their own fate. The evolution of consciousness will continue with or without us.

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  33. CharlieM: If I was looking for some molecule that remained constant over the generations I would pick polysaccharides or lipids. But I am comparing processes, not substances.

    You are looking for dynamic processes that remain constant?

    CharlieM: The self similarity I am discussing above is not in physical substance, but in the dynamic processes of birth, life and death. Genomes aren’t lost, they just change, but so do cells, organisms and species.

    Birth, life and death are “dynamic processes”, but genomes “just change”?

    I am sorry to say it, but you are still not making a lot of sense to me. Evolution is a dynamic process: it can be defined as the gradual change and diversification of all living beings. Birth-death cycles cannot explain that. Genomic changes can.

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  34. CharlieM: Me: But how did these particular potential forms actually came to be?

    Charlie: They are expressions of the archetypal plant or the archetypal animal as the case may be.

    So I understand, but how did these particular potential forms actually came to be? Why those beak shapes and not others? If evolution is like development, then what controls the “evolutionary program”?

    CharlieM: It is not unique for an animal to be purple as in the male violet-backed starling. And it isn’t unique for an animal to be the size off an elephant. You will notice that elephants are the size of elephants.

    Are you telling me that, if a purple mouse the size of an elephant were to be born, that wouldn’t strike you as a significant change?

    CharlieM: No, not just parts being sacrificed for the whole. Individuals who have been given the freedom to love in the true sense of the word. ‘I am in the Father and the Father is in me.’ That is what true self-consciousness, the ‘I am’, means. Generally speaking, at the present time, we are self-conscious only to a very limited degree. Evolution continues and has reached a stage where individuals can decide on their own fate. The evolution of consciousness will continue with or without us.

    Charlie, you are a nice guy and I like you. That’s why the “It’s only seen as devastating from a limited perspective” phrase struck me as highly uncharacteristic of you. No matter how much we value the fruits of evolution, such as our consciousness, the well being of humans must ALWAYS have priority. No good will come of this “sacrificing parts for the whole” talk.

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  35. Corneel:

    CharlieM: If I was looking for some molecule that remained constant over the generations I would pick polysaccharides or lipids. But I am comparing processes, not substances.

    You are looking for dynamic processes that remain constant?

    Yes! Just as the acceleration due to the earth’s gravity is calculated to be approximately 9.81 metres per second squared in a vacuum. Dynamic processes can have aspects which remain constant.

    CharlieM: The self similarity I am discussing above is not in physical substance, but in the dynamic processes of birth, life and death. Genomes aren’t lost, they just change, but so do cells, organisms and species.

    Birth, life and death are “dynamic processes”, but genomes “just change”?

    Genomes change because they are part of the dynamic process. Just like you and I change throughout our lives. Birth, life and death are processes which we go through.

    I am sorry to say it, but you are still not making a lot of sense to me. Evolution is a dynamic process: it can be defined as the gradual change and diversification of all living beings. Birth-death cycles cannot explain that. Genomic changes can.

    A changing genome is not an explanation, it is an observation that needs to be explained.

    I have been looking at the way B-cell genomes are changed as part of our adaptive immune system and it is very interesting.

    In this video by
    Hidde Ploegh (Boston Children’s Hospital), ‘1: Immunology: The Basics of Antibody Diversity’, he says:

    Depending on which poly-A addition site is used, the B cell either produces the secreted version or the membrane-bound version of that one-and-the-same immunoglubin. This foreshadows the important role in the B-cell receptor in perceiving antigens and allowing B-cells to expand, but also to allow that very same B cells to release immunoglobins ito the bloodstream, where they can exert their effect, for example, by neutralizing a virus. The B cell receptor also plays a key role in orchestrating the processes that I’ve just summarized. So in the absence of a heavy chain rearrangement, B cells fail to complete development. The discrete development stages are characterized by the presence of so called surrogate light chains, in this diagram depicted as VpreB and lambda-5. And only when those subunits all come together and form a properly assembled pre-B cell receptor does the B cell enable rearrangement of the missing piece, which is the light chain. So this pre-B cell receptor, depicted on the left, is a necessary condition for B cells to engage light chain rearrangement. And it’s only when all these processes are executed perfectly that we arrive at a fully assembled B cell receptor at the surface of a B lymphocyte.

    Only when the system is perfectly assembled is it ready and able to function.

    He continues:

    Viruses are masters of deception. And here’s just an example taken from herpes viruses, one class of pathogens that once you acquire them stay with you for the rest of your life. We have proteins that in…such as pp65 that involve…that interfere with ubiquitylation of possible targets. the virus that is the causative agent of mononucleosis, Epsten-Barr virus, produces a protein that renders viral products insensitive to proteolitic digestion by the proteasome. We have other herpes virus-encoded proteins that impede peptide translocation into the endoplasmic reticulum, detain class-1 molecules at the site of synthesis, or even reverse the process of membrane insertion and target those very same MHC (major histocompatibility complex) products for proteasomal degradation. The process is more complex than this. We have meanwhile figured out some of the details. This is the mating dance between the viral protein US2 and the cass-1 molecule it destroys. And in a process referred to as retrotranslocation, a newly assembled class-1 heavy chain is sent back to the cytoplasm for proteasomal degradation. This is just one example of the many tricks viruses can use to frustrate adaptive immunity. And such interference may apply to other surface proteins, cytokines released from the cell. aspects of innate immunity. I need to emphasize the fact that the constant interplay between the immune system, which exerts a selective pressure, and pathogens, which have the capacity to rapidly evolve, results in this perpetual chess game between host and pathogen.

    Much of this work enables cell biological explorations that would be difficult to achieve otherwise. And to put some molecular detail on this particular cartoon, this would be our current understanding of how this complicated ‘machine’ operates. We have this centrally positioned class-1 MHC product and a host of other cofactors that together ensure that this class-1 protein in a virus-infected cell can be extracted from the endoplasmic reticulum and ultimately targeted for proteasomal degradation.

    So, after this whirlwind tour of the immune system, let me return to where we started. We have a multi-layered immune system, of which the mechanical and innate immune defences are probably the most important on a daily basis. But once these systems fail, adaptive immunity kicks in. And the remarkable precision with which the adaptive immune system can recognize antigens has allowed the explorations which I’ve tried to summarize in the preceding thirty minutes or so.

    Key features: ability t6o distinguish between structures that differ by very little – as few as an atom, perhaps; the ability to respond rapidly; and the ability to adjust the specificity of the ensuing response to whatever the needs of the day may be.

    Videos such as this give us an idea of how these cells actually alter their genomes in the battle against invaders.

    B cell development is a good example of how random processes are used in a controlled way.
    .
    As is explained in This video, ‘Immunology: BCR/ antibody genetic diversity mechanisms’
    It’s a:

    totally random process here but very unique and very controlled, it’s chaotic and disordered but a controlled chaos and controlled disorder.

    In B cells of the adaptive immune system the genome is rearranged by a very complex set of processes which are still not entirely understood.

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  36. Corneel:

    Me: But how did these particular potential forms actually came to be?

    Charlie: They are expressions of the archetypal plant or the archetypal animal as the case may be.

    So I understand, but how did these particular potential forms actually came to be? Why those beak shapes and not others? If evolution is like development, then what controls the “evolutionary program”?

    The particular beak shapes are fashioned by the habits and lifestyle of the population. If all of a population of finches were to feed solely on hard seeds that were tough to crack then barring cross breeding all the individuals would end up with stout beaks.

    CharlieM: It is not unique for an animal to be purple as in the male violet-backed starling. And it isn’t unique for an animal to be the size off an elephant. You will notice that elephants are the size of elephants.

    Are you telling me that, if a purple mouse the size of an elephant were to be born, that wouldn’t strike you as a significant change?

    A mouse the size of an elephant would strike me as very significant. But in my opinion it becoming a reality has as much chance as the pink unicorn in my granddaughter’s bedroom coming to life.

    CharlieM: No, not just parts being sacrificed for the whole. Individuals who have been given the freedom to love in the true sense of the word. ‘I am in the Father and the Father is in me.’ That is what true self-consciousness, the ‘I am’, means. Generally speaking, at the present time, we are self-conscious only to a very limited degree. Evolution continues and has reached a stage where individuals can decide on their own fate. The evolution of consciousness will continue with or without us.

    Charlie, you are a nice guy and I like you. That’s why the “It’s only seen as devastating from a limited perspective” phrase struck me as highly uncharacteristic of you. No matter how much we value the fruits of evolution, such as our consciousness, the well being of humans must ALWAYS have priority. No good will come of this “sacrificing parts for the whole” talk.

    Thank you and I get your point. My attempt to see things objectively may seem like I am discounting the suffering that goes on all around us. I was not advising that we should seek suffering. I was trying to explain that past suffering may not be in vain. We should always avoid causing the suffering of others.

    I have heard the likes of Simon Weston actually saying that what they went through has turned out to be a blessing.

    Buddha recognised that suffering is a fact of life but he was also known for his compassion.

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

    That’s nice, but it doesn’t really address the issue. After all, a given gene copy in a cell in my skin is not the same DNA molecule as that in my son, but it is the same gene.

    But I am comparing processes, not substances.

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

    The self similarity I am discussing above is not in physical substance, but in the dynamic processes of birth, life and death. Genomes aren’t lost, they just change, but so do cells, organisms and species.

    If an organism dies without reproducing, its genome is definitely lost. On the other hand, if over the generations only a given gene remains in the population from a particular ancestor, again the rest of its genome has been ‘lost’ to the population. This seems no less in line with your ‘fractal’ principle than consideration of whole organisms and populations – except that you don’t fancy it, somewhat arbitrarily.

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  38. Allan Miller:

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

    That’s nice, but it doesn’t really address the issue. After all, a given gene copy in a cell in my skin is not the same DNA molecule as that in my son, but it is the same gene.

    I presume by ‘gene’ you mean a particular DNA segment? And if this gene is never expressed in the skin cell it is just one tiny piece of the genome occupying a space. What is of importance between your skin cells and you son’s skin cells is the processes of gene expression. All of the activity inclusive of transcription, translation and protein functions. What your son has inherited are dynamic processes.

    But I am comparing processes, not substances.

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

    Genes do not compete. They are what they are. The differing effects arise in the expression processes and these involve more than the DNA.

    The self similarity I am discussing above is not in physical substance, but in the dynamic processes of birth, life and death. Genomes aren’t lost, they just change, but so do cells, organisms and species.

    If an organism dies without reproducing, its genome is definitely lost. On the other hand, if over the generations only a given gene remains in the population from a particular ancestor, again the rest of its genome has been ‘lost’ to the population. This seems no less in line with your ‘fractal’ principle than consideration of whole organisms and populations – except that you don’t fancy it, somewhat arbitrarily.

    I have reasons for thinking differently about genes compared to cellls, organisms or populations.

    If a gene remains in the DNA of the population but is never again expressed then it is as good as lost. But if it is expressed and some function results then the unit of importance is not the bare DNA it is the active expression complex that matters. I fully agree that the DNA is a vital part of the unit.

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  39. CharlieM: The particular beak shapes are fashioned by the habits and lifestyle of the population. If all of a population of finches were to feed solely on hard seeds that were tough to crack then barring cross breeding all the individuals would end up with stout beaks.

    Yes, because of differential survival and reproduction acting on heritable variation. You have admitted as much. So where does the archetype come in?

    CharlieM: A mouse the size of an elephant would strike me as very significant. But in my opinion it becoming a reality has as much chance as the pink unicorn in my granddaughter’s bedroom coming to life.

    Whenever I bring up more modest changes you deny these are novel. You claim small changes to be “extreme forms” of the archetype and you claim that large changes do not happen. But lots of small changes add up and mice most certainly can in time become as big as elephants. The ancestor of all placental mammals, including elephants and blue whales, is believed to be a tiny insectivore.

    CharlieM: My attempt to see things objectively may seem like I am discounting the suffering that goes on all around us.

    Trust me, you are not seeing things objectively. Rather, you are a sucker for appealing narratives (I love good stories as well). But I am extremely distrustful of narratives that somehow justify group interest overriding that of the individual. Pick better stories.

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

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

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

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

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

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

    Godlike powers.

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  43. Mung: So natural selection works equally on that which is expressed and that which is not expressed?

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

    1+
  44. Mung: So natural selection works equally on that which is expressed and that which is not expressed?

    What Alan said.

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

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

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  45. Nonlin.org: Someone believes something for sure. But is it true?

    Yes it is.

    Nonlin.org: Turns out, there is no evidence for it.

    Yes, there is, gobs of it.

    Nonlin.org: And more precisely all evidence is against.

    No, no opposing evidence exists whatsoever.

    Nonlin.org: Remember no gradualism? No divergence of character? Not even e coli is “evolving”?

    Yes, I remember you asserting those things without a shred of evidence just like you are doing now. That allows me to just conveniently assert the opposite thing. What fun we have!

    Nice to see you back. I sure missed you.

    1+
  46. CharlieM:
    I presume by ‘gene’ you mean a particular DNA segment?

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

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

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

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

    Charlie: Genes do not compete.

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

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  47. Corneel:

    CharlieM: The particular beak shapes are fashioned by the habits and lifestyle of the population. If all of a population of finches were to feed solely on hard seeds that were tough to crack then barring cross breeding all the individuals would end up with stout beaks.

    Yes, because of differential survival and reproduction acting on heritable variation. You have admitted as much. So where does the archetype come in?

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

    There is some interesting information here where this question is asked.

    The beaked face of the modern bird looks distinctly different from the faces of their ancestors. How and why the birds acquired their unique craniofacial appearance?

    They add:

    The upper beak in birds is a particular challenge to understand. It is a novel structure, which forms as a result of rostral expansion of the fused premaxillary bone, which grows as two small capping elements in basal archosaurs and most dinosaurs but expands to structurally and functionally dominate the upper face in modern bird lineage.

    To get an idea of the archetypal beak, or bill if you prefer, think of all the various beaks that have existed and everything in between, that would be the archetype.

    To imagine how beaks develop from a previous condition that lacked beaks there would have been a great deal of coordinated genetic activity to bring this about. It is not just a case of tweaking a gene here or there.

    And the diversification of beak forms would require similar genetic orchestration.
    Here the article, ‘The shapes of bird beaks are highly controlled by nondietary factors’ has good video clips of illustrating changing features. It is an interesting read on the complexities of beak morphology. They write:

    However, pleiotropic associations between different skull structures can also contribute to the shape of the avian beak, and Sonic hedgehog signaling from the forebrain also relates to the spatial organization of, and changes to, face and beak shape. Furthermore, assessments of bird skull phenotypic variation suggest that beak morphology may evolve cohesively with cranial morphology.

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

    CharlieM: A mouse the size of an elephant would strike me as very significant. But in my opinion it becoming a reality has as much chance as the pink unicorn in my granddaughter’s bedroom coming to life.

    Whenever I bring up more modest changes you deny these are novel. You claim small changes to be “extreme forms” of the archetype and you claim that large changes do not happen. But lots of small changes add up and mice most certainly can in time become as big as elephants.

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

    I must admit that it would be possible for a mouse to become as big as an elephant as long as it was accompanied by a drastic change in earthly conditions. Weaker gravitational forces, something like that. In the present earthly environment, a mouse that was as big as an elephant would no longer be a mouse. The lowest standard classification is ‘species’. So let’s say ‘mouse’ applied to the genus. Rats are basically big mice, classed in the same super-family but in a different genus. As even the slightest difference between individuals (such as in Darwin’s finches) prompts classification as separate species, then I would say that elephant sized, mouse-like organisms would be classed in a separate family at least.

    Mice are are more liberated from the effects of gravity than elephants, but they are not so free as birds. Of course insects have attained an even higher level of freedom from the constraints of gravity.

    Why are these things so? Because that’s just the way they evolved, the chance way that it happened. This is a very poor answer that evokes no further thinking about the relationships within life.

    The ancestor of all placental mammals, including elephants and blue whales, is believed to be a tiny insectivore.

    And herein lies a prominent difference between the ideas of Darwin and Goethe. Darwin conceived the archetype to be an actual organism that lived, an “ancient progenitor”. Goethe idea of the archetype was a an inclusive principle that all forms throughout history conform to. Darwin thought in terms of a linear series, Goethe thought in terms of the relationship of the parts to the whole.

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

    CharlieM: My attempt to see things objectively may seem like I am discounting the suffering that goes on all around us.

    Trust me, you are not seeing things objectively. Rather, you are a sucker for appealing narratives (I love good stories as well). But I am extremely distrustful of narratives that somehow justify group interest overriding that of the individual. Pick better stories.

    There is no nice little convenient division between group behaviour and individual behaviour. But as evolution proceeds it is evident that organisms come to exist that show more individualistic behaviour than in previous ages. Individual prokaryotes show very little in the way of personality. In humans and higher animals the personality of individuals begins to shine from within their group behaviour. Your dog will show much more of its personality than your goldfish.

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