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.

464 thoughts on “The Spiralling Flow of Life

  1. Nonlin.org: I’m just reporting on what he said.

    But Neil Shubin didn’t actually say that preaurical sinuses are vestigial organs, did he? That was you.

    You offered no background. You didn’t provide a source. You couldn’t remember the name of the affliction. You even claimed incorrectly the hole appeared in the ear lobe. And to top it off you suggested that Neil Shubin claimed this to be a vestigial organ. That is not “just reporting”. That is distorting.

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

    Why on earth would I offer proof? You won’t accept any from me anyway. You really want to know? Do the test, find out for yourself:

    What are vestigial organs? How do they arise? What are pseudogenes? What is the dominant mechanism by which pseudogenes arise?

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

    Questions, right. But you already received your answers from Entropy, remember? Then you rejected his explanations because you are oblivious of selection coefficients and you don’t know what vestigial organs are. And THEN you resisted correction of your misunderstandings because you consistently refuse to learn stuff.

    What is the point of asking questions if you will not accept any answers?

  2. Allan Miller:

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

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

    So what is it that gives your body all that variety of cell types each containing the same genome? Differentiated cells are examples of how there are processes which are able to select for the needs of particular cells and their organs, from genomes that have the same sequence no matter what cell type.

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

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

    The causal chain you speak about has turned out to be a vast, convoluted causal network. All our lives began from fertilised eggs in which there are no simple, linear, causal chains.

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

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

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

    But molecular continuity also involves process continuity. It is the same processes of mitosis that are going on constantly in your cells every second of the day to allow for replication. And it is the same process of meiosis that produces every sperm cell.

    There has not been one hundred percent molecular continuity between either of your parent’s genomes and yours. There are processes which ensure that this isn’t the case.

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

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

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

    Mutations caused by external influences are environmentally induced changes. The experiences of populations will be represented in the genome, I haven’t said otherwise.

    … and integral. Sequences change,

    Correct

    splicing changes,

    As a result of genetic change

    expression levels change

    As a result of genetic change.

    timings change.

    As a result of genetic change.

    Any change is an activity, a process through which an alteration is made.

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

    Reducing to sequence changes, one and all.

    Not reducing, but involving. And as I said, any change is an activity, a process.

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

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

    Chromosomes are complex dynamic assemblages of more than just DNA. P elements and homing endonucleases only important within processes. In order to be activated, P elements rely on certain meiotic configurations.

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

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

    You said it yourself, DNA replication is a process. Processes in time are a higher level of reality than matter in space. This is the point I am trying to emphasise.

    DNA sequences are important only in the fact that they can be read, and reading is an activity in time.

  3. CharlieMSo what is it that gives your body all that variety of cell types each containing the same genome?

    Well, epigenetics, as I’ve said. All genetically based, of course.

    Let me turn that question back on you. In a zygote, there is only one instance of ‘process’. In a differentiated organism, there are trillions of cells. How does the singular ‘process’ in the zygote become the multiple and variant ‘process’ in tissues, if not via gene expression differences?

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

    Charlie: The causal chain you speak about has turned out to be a vast, convoluted causal network. All our lives began from fertilised eggs in which there are no simple, linear, causal chains.

    Neat. You flip from a ‘one-step’ view of genetic causation (genes only specify the primary product) to an ‘it’s waaaaay too complex to understand’. Well, it is complex, but not impenetrably so. In the specific matter of alternative splicing, which you believe demonstrates something ‘above’ the genome, it can be shown that splice isoforms are themselves genetically controlled – by a different part of the genome. See? 2 steps. You don’t have to go far.

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

    Charlie: But molecular continuity also involves process continuity.

    It’s not molecular continuity!.

    It is the same processes of mitosis that are going on constantly in your cells every second of the day to allow for replication. And it is the same process of meiosis that produces every sperm cell.

    The position you are arguing against here is one in which genes persist without any causal mechanism whatsoever. It is not a position anyone advances.

    There has not been one hundred percent molecular continuity between either of your parent’s genomes and yours. There are processes which ensure that this isn’t the case.

    Even so, the vast majority of my genes will be represented unchanged in my offspring (one copy or the other), your little 0.001% ‘gotcha’ notwithstanding.

    Mutations caused by external influences are environmentally induced changes.

    Aha. If a cosmic ray changes a base, then repair uses the ‘wrong’ base, is that environmental or ‘internal’? And does it matter?

    The experiences of populations will be represented in the genome, I haven’t said otherwise.

    Well, I disagree, if you mean the experiences of individuals. I wasn’t using ‘experience’ in a population-wide, metaphorical sense to represent natural selection; I was talking there of ‘Lamarckian’ mechanisms. I find the evidence unconvincing.

    Any change is an activity, a process through which an alteration is made.

    That’s stretching ‘process’ to twanging point. Mutation is a ‘process’, even if caused by a cosmic ray? That’s gene centrism defeated by a puff of logic, then! 🤣

    Me: Reducing to sequence changes, one and all.
    Charlie: Not reducing, but involving. And as I said, any change is an activity, a process.

    I meant ‘change’ in the historic sense. If a splice variant is consistently produced in the same tissue in every member of a species, that can invariably be tracked back to another genetic sequence, which ‘changed’ the prevailing historic isoform pattern in that tissue. There isn’t a continuous process of active genomic change at that level.

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

    Charlie: Chromosomes are complex dynamic assemblages of more than just DNA. P elements and homing endonucleases only important within processes. In order to be activated, P elements rely on certain meiotic configurations.

    Saying nothing; not really understanding the question. The result of all of these elements is ‘non-Mendelian’ transmission – variation from the 50/50 chance available to other autosomal DNA. There must presumably be an advantage to some entity. How does it benefit ‘the whole organism’ to undergo this distortion? Gene centrism allows identification of mechanistic reasons for the distortion – the ‘beneficiary’ is clearly the genetic sequence itself. The distorter increases in the population simply by virtue of that distortion. But you’re not having that. So …. explanation?

    You said it yourself, DNA replication is a process. Processes in time are a higher level of reality than matter in space. This is the point I am trying to emphasise.

    I am not arguing that DNA replicates without mechanism, so you are attacking a strawman.

    DNA sequences are important only in the fact that they can be read, and reading is an activity in time.

    ‘Only’? 🤣 What are they ‘read’ by? What is the source of the enzymes, and how are they regulated, non-genomically?

  4. Corneel: But Neil Shubin didn’t actually say that preaurical sinuses are vestigial organs, did he?

    That’s what I remember – some ear hole and a stupid vestigiality claim. Watch that episode.

    Corneel: Why on earth would I offer proof?

    It’s reasonable to ask for proof of your claims. If you want to be taken seriously. But never mind this time. Here’s counterproof: https://en.wikipedia.org/wiki/Human_vestigiality
    Are they also wrong to associate pseudogenes with vestigiality?

    Corneel: But you already received your answers from Entropy, remember? Then you rejected his explanations because you are oblivious of selection coefficients and you don’t know what vestigial organs are.

    No! I rejected because “it depends” is not a valid answer. If you claim a trend but can’t quantify said trend at all, it’s only logical there might not actually be a trend to speak of. Also because “vestigial yet functional” is too lax of a definition – see size of your brain. Makes sense?

    Corneel: What is the point of asking questions if you will not accept any answers?

    Not “any”. Just illogical.

  5. Nonlin.org: That’s what I remember – some ear hole and a stupid vestigiality claim. Watch that episode.

    Well, given your history of claiming that your various examples of ‘affirming the consequent’ were “direct quotations from third parties” when in fact they were lame-ass paraphrases born of your incomprehension, I think you will have to do better than this…

    [wikipedia.org/wiki/Human_vestigiality]
    Are they also wrong to associate pseudogenes with vestigiality?

    For the majority of pseudogenes, they are wrong. Corneel tried to help you out here, asking you “What is the dominant mechanism by which pseudogenes arise?” but you are so determined to faceplant that you ignored his helpful warnings.

    …No! I rejected because “it depends” is not a valid answer. If you claim a trend but can’t quantify said trend at all, it’s only logical there might not actually be a trend to speak of. Also because “vestigial yet functional” is too lax of a definition – see size of your brain. Makes sense?

    None whatsoever.
    You asked exactly how long does it take for X, or Y, or Z to decay? The only reasonable response is “It depends”. There is no concession at all that the rate cannot be measured. Similarly, competing definitions of “vestigial” do not change the evolutionary history of your appendix one iota. What is it with the map/territory confusion?

    Corneel: What is the point of asking questions if you will not accept any answers?
    Not “any”. Just illogical.

    “Illogical”, you keep using that word…

  6. Allan Miller:

    Me: Gosh, really? You live and learn.

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

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

    It is precisely the process, the activity, that determines what emerges. The cosmos, the world, life, organisms, genomes, are all processes in becoming. To think of them merely as things in space is only possible if we freeze time.

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

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

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

    But is it false?

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

    Natural selection reduces genetic variety, though …

    Biological evolution is a process whereby overall variety is produced. Natural selection restricts variety within populations. Life becomes more fragmented. It moves from unity to multiplicity. And once fragmented, there is no return to unity for physical life.

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

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

    The genome is the source in the same sense that a musical instrument can be the source of a piece of music. Genetic sequences provide the organism with the means by which it composes itself.

    The industrial age inspired the idea of life as being mechanistic and organisms as machines. Now we are well into the IT and computer age, organisms are seen as the result of software programmes encoded in the DNA. We are seen primarily as data sets. According to the EU we are “data subjects”.

    These are just passing phases.

  7. CharlieM:
    It is precisely the process, the activity, that determines what emerges.

    Nope. It’s the genome. The same basic ‘process’ of replication and gene expression takes place in elephants and mice. The difference between elephants and mice is not in that vague, obscurantist ‘process’ separately surrounding sperm and egg, but the composite diploid genome they form, expressed by ‘process’. If this is incorrect, identify the non-genomically-rooted differences in ‘process’ between the two.

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

    Charlie: But is it false?

    Yes. As I already explained. You could try reading and addressing that explanation.

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

    Charlie: The genome is the source in the same sense that a musical instrument can be the source of a piece of music…

    Oh, bloody analogies! It isn’t. That’s a terrible analogy.

    Name an element of control that does not trace back to genetic sequence.

    The industrial age inspired the idea of life as being mechanistic and organisms as machines. Now we are well into the IT and computer age, organisms are seen as the result of software programmes encoded in the DNA. We are seen primarily as data sets.

    Not by me. I prefer to avoid analogies. Life is life. It has some things in common with some other things, but I explictly reject the over-extension of metaphor. Which is precisely what you are doing. You’re grumbling that it’s not like one metaphor, it’s ‘really’ like another. ‘My metaphor’s better than your metaphor’. Forget it. Living systems are like living systems. What matters is how they operate, not how something else does.

  8. DNA_Jock: What is it with the map/territory confusion?

    It prevails in most of Nonlin’s diatribe, to the point that Nonlin herself doesn’t understand what that distinction means, and/or why it’s important. But Nonlin claims that she has “great abstraction abilities, she has been tested!” Some kindergarten, homeschooling, variety, with the test applied and marked by her mother. But who cares? A test is a test and she “aced it.”

  9. Alan Fox:

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

    Me, sir!

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

    Saying it’s a niche might satisfy your curiosity, but I would be asking a lot more questions. Such as: Why are some animals herbivores and others carnivores? Why are some generalists while others are extremely specialist.

    To explain it all by saying there was a niche to be filled is a very convenient answer that doesn’t explain what is required for an animal to reach a point where it is able to survive from its particular way of living.

  10. CharlieM: Why are some animals herbivores and others carnivores?

    Before the fall, there were no carnivores: the lion lay down with the lamb. But what did the lion eat, having neither the teeth nor the digestive system to deal with grass? At the beginning of life the niches were empty. First living organisms were chemotrophs followed by phototrophs. When you have a large biomass of phototrophs, there is the opportunity to engulf and consume them, rather than go to the trouble of having to rely on light for your energy.

    And so on. Niches all the way!

  11. CharlieM: Saying it’s a niche might satisfy your curiosity, but I would be asking a lot more questions. Such as: Why are some animals herbivores and others carnivores? Why are some generalists while others are extremely specialist.

    Would you now? You really don’t come across as being curious about the specifics. Of anything.

    To explain it all by saying there was a niche to be filled is a very convenient answer that doesn’t explain what is required for an animal to reach a point where it is able to survive from its particular way of living.

    Nobody has claimed “It’s the niche!” as a final answer. Rather it is the beginning of an exploration into such things as biogeography. As opposed to, for instance, “It’s the archetype!”, which seems to lead… nowhere.

  12. Allan Miller:

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

    Multifunctionality, complexity and alternative splicing don’t lead to a conclusion of saltation.

    No, but we do know that the pace of evolution isn’t constant. Some forms appear to have been around with little change for hundreds of millions of years while others have changed relatively rapidly and others have regressed towards earlier forms.

    And, if saltation be a thing in a world of archetypes, it suggests sudden step-changes in archetypes, which isn’t very archetypical.

    You don’t seem to understand what is meant by the Goethean archetype. Look at a plant, its growth involves a series of step changes.

    Max Leyf:

    The flower presents the most rarified organ of the plant, and therefore the ultimate expression of the light principle. From this pole, the Steigerung itself undergoes a polar inversion and the plant swings to the ultimate contraction, which culminates in the seed nestled in the dark bosom of the earth. This fact of seasonality which the plant embodies demands the recognition of another principle which we may call “rhythm,” “pulse,” or “periodicity.”

    Step changes are in evidence everywhere. The phases of matter, transitions of life from aquatic to terrestrial, metamorphosis, and many other processes involve step changes. And the dynamism inherent in the archetype encompasses all forms within it.

  13. Allan Miller:

    Me: A process controlled entirely by gene sequence.

    Charlie: The sequence does [n]ot control the process.

    Does too. Not been listening, have you?

    The sequences are used in the control processes. Regulation, remodelling and modifications are all processes.

  14. DNA_Jock:

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

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

    Whether the developers of thalidomide were aware of it or not, it’s my opinion that the drug did interfere with gene expression. Perhaps you know different in which case I am eager to read your version.

    I said that the mucking about was blind, meaning that it wasn’t direct, but that makes it even worse. It had been used to treat symptoms without any understanding of their wider effects on gene expression.

  15. CharlieM: Whether the developers of thalidomide were aware of it or not, it’s my opinion that the drug did interfere with gene expression.

    Gene expression meaning transcription? “Mucking about with the genome” is read by most of your interlocutors as changing the DNA sequence, BTW.

  16. CharlieM:Me: Multifunctionality, complexity and alternative splicing don’t lead to a conclusion of saltation.

    Charlie: No, but we do know that the pace of evolution isn’t constant. Some forms appear to have been around with little change for hundreds of millions of years while others have changed relatively rapidly and others have regressed towards earlier forms.

    That’s a long way from saltation. It’s no surprise you latch on to Goldschmidt though; seems you never met a maverick you didn’t like!

    You don’t seem to understand what is meant by the Goethean archetype. Look at a plant, its growth involves a series of step changes

    The term’s barely coherent, so no, I probably don’t understand it.

    You are arguing that the archetype exerts or represents some kind of control over form. But even if you argue for this ‘archetype’ to cover an entire life history, you’re still looking at a big change in that ‘extended archetype’ between generations. Which, as I say, is not very archetypical.

    Step changes are in evidence everywhere.

    This does not make saltation true.

    The phases of matter, transitions of life from aquatic to terrestrial, metamorphosis, and many other processes involve step changes. And the dynamism inherent in the archetype encompasses all forms within it.

    ‘The archetype’ rapidly loses all meaning, then, if it ever had any. It’s everything. There are ‘step changes’ within an archetypal unrolling of a single life, and ‘step changes’ between generational instances of archetypal individuals. Glad you cleared that up. I’m kind of sorry I mentioned it; you nearly had my eye out with all that handwaving!

  17. CharlieM:Me: Does too. Not been listening, have you?

    Charlie: The sequences are used in the control processes. Regulation, remodelling and modifications are all processes.

    No, the sequences actually control regulation. If you change the sequence – and only the sequence – regulation changes.

    Viral infection is ‘a process’ too. Does this mean that viral nucleic acid is a mere scratchpad in ‘process’, just like our own? Or is that, somehow, ‘different’? If different, how is that distinction handled by ‘process’, and why doesn’t it just ignore it?

  18. CharlieM:
    Whether the developers of thalidomide were aware of it or not, it’s my opinion that the drug did interfere with gene expression. Perhaps you know different in which case I am eager to read your version.

    Well, by degrading the transcription factor SALL4, it kind-of interfered with gene expression, but it had no effect on gene sequence. Transcription factors, though, bind to specific gene sequences. The transcription factor sequence is in the genome. The site(s) bound to also reside in the genome. This is a good example of the genome’s capacity for self-regulation, not an exception to it. Gene and binding site are both replicated, and this is what provides generational continuity, not your ‘process continuity’ of the gene expression system or its products.

    Escher’s ‘drawing hands’ is a good metaphor for this … uh … ‘process’.

    To anticipate your objection (this is about my 745th rodeo), of course SALL4 would not exist at all without the ‘process’ of transcription. But given that process, the gene for SALL4 was able to be expressed. The variation in protein repertoire does not require a different process for every instance. That variation is provided by variation in sequence alone. And thus – in an environment in which transcription exists – there is a selective competition between variant sequences.

  19. DNA_Jock: I think you will have to do better than this…

    Haha. You’re still sore from the logic lesson? And I see you’re not disputing “inner fish” is retard. Interesting!

    “Preauricular pit” – apparently not “evolution”:
    https://www.medicalnewstoday.com/articles/327106
    https://answersingenesis.org/reviews/tv/review-your-inner-fish/
    Your Inner Fish also promotes the myth of embryonic recapitulation by showing us “Molly’s gill.” Molly is a woman with a small pit in front of her ear, an inconsequential embryologic remnant that Shubin identifies as “a leftover from an ancient gill” saying, “We’re all fish,” and “Sometimes things go wrong, and when they do your inner fish can come out.”

    DNA_Jock: For the majority of pseudogenes, they are wrong.

    Oh. So now is “majority”, huh? How stupid is that defense?

    DNA_Jock: There is no concession at all that the rate cannot be measured.

    That’s what I asked for – the measure. So what is it? When will your “vestigials” completely vanish?

    DNA_Jock: Similarly, competing definitions of “vestigial” do not change the evolutionary history of your appendix one iota.

    So definitions don’t matter? When will you stop redefining for convenience?

  20. Alan Fox:

    CharlieM: The mechanism wasn’t important.

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

    It wasn’t important to Goldschmidt’s line of reasoning

    It was the fact that he believed that small gradual changes were not sufficient to go from micro-evolution to macro-evolution. For him mutations were observable features. As he wrote in the book, The Material Basis of Evolution

    In a former paper (Goldschmidt, 1933) I used the term “hopeful monster” to express the idea that mutants producing monstrosities may have played a considerable role in macroevolution. A monstrosity appearing in a single genetic step might permit the occupation of a new environmental niche and thus produce a new type in one step. A Manx cat with a hereditary concrescence of the tail vertebrae, or a comparable mouse or rat mutatant, is just a monster. But a mutant Archaeopteryx producing the same monstrosity was a hopeful monster because the resulting fanlike arrangement of the tail feathers was a great improvement in the mechanics of flying. A fish undergoing a mutation which made for a distortion of the skull carrying both eyes to one side of the body is a monster. The same mutant in a much compressed form of fish living near the bottom of the sea produced a hopeful monster, as it enabled the species to take to the life upon the sandy bottom of the ocean, as exemplified by the flounders.

    He goes on to describe mutants in terms of physiological features obvious to anyone who looked at these creatures. At that time nobody had any firm idea about the physical nature of genes or mechanisms behind these mutations.

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

    And your arguments are perfectly valid for anyone coming from a prior Darwinian type evolutionary assumption. Hopeful monsters are nigh on impossible due to accidental change, But large jumps are not impossible if any sort of guiding plan is being realised. Look at a single human development. On the whole changes are slow and steady, but at certain times, such as birth and puberty, large changes take place in a relatively short time. If there is any sort of direction to evolution then sudden jumps would be an expected feature.

  21. I was enjoying Charlie’s definition of “process”, which includes a photon mutating a nucleotide, apparently. But this has now been eclipsed by his expanding use of “blindly mucking about with the genome” to include alterations to transcription factors.
    So, when I go for a brisk walk tomorrow morning, I will be “blindly mucking around with the genome”, apud Charlie.
    I really need not have bothered with reading Old & Primrose at all…

  22. Alan Fox:

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

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

    You better have a word with Allan if you think that limb development has nothing to do with the genome.

  23. Alan Fox:

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

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

    The RNA world is speculative, not established fact. The cell is the minimum requirement for the development of all known life forms.

  24. Allan Miller:

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

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

    Creativity comes by means of expression.

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

    Oh, for fuck’s sake!

    I feel your pain 🙂

  25. CharlieM: You better have a word with Allan if you think that limb development has nothing to do with the genome.

    Read for comprehension, Charlie.

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

    Charlie: Creativity comes by means of expression.

    I guess. So do antagonism and discord. Not really relevant to anything, in terms of the primary role of sequence in both ‘product’ and ‘product control’.

  27. CharlieM: You better have a word with Allan if you think that limb development has nothing to do with the genome.

    Mmmm, the question is whether the action of thalidomide is ‘mucking with the genome’. It relates back to the death cap, that I introduced to illustrate the temporary nature of cellular ‘process’, which is perpetually refreshed from the more stable info in the genome. In this instance, thalidomide appears to wipe out the gene product SALL4, which cannot be refreshed quickly enough. In the death cap case, all gene products are terminated, so it’s a tad more detrimental.

    Now if, instead of wiping out the product, a mutagen changed the sequence of SALL4, OR its binding site, OR its UTR sequences, that would be ‘mucking about with the genome’. The change would be heritable, and feed into the ‘intergenic’ contest between rival gene sequences in the wider population. It could conceivably produce similar results to thalidomide, in which case we would expect the mutant gene to be rapidly lost. But if so, this isn’t due to any distinction of ‘process’ in the two variants, except inasmuch as process is dependent on sequence. And you could mumble ‘not naked DNA…’ to your heart’s content.

  28. Corneel:

    CharlieM: totipotent cells

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

    It’s not a metaphor, it’s a self-similar fractal. Two levels of reality, each as real as the other.

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

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

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

    Yet Darwin’s finches can still interbreed. No irreversible speciation there.

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

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

    The rodent archetype is nested within the mammal archetype.

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

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

    It would be very convenient for me to say that all animals evolved from an original, single population, just as all of our body cells derived from the single zygote. From unity to multiplicity. But how sure can I be of events that took place in such a remote past? How could I justify making such a claim?

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

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

    There is also evidence that populations converge..

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

    Followers, supporters, what’s the difference? It’s not as if Darwin does not have his followers.

    Darwin day

    International Darwin Day is looking for endorsers, supporters, and partners in our mission to establish February 12th as a globally recognized holiday! Do you represent an organization that celebrates curiosity, truth, or bravery? Are you interested in joining a global movement?

    Being on a mission, celebrating the birthday of a revered leader, proselytising. Does this remind you of anything?

  29. Corneel:

    CharlieM: But they do recognise that animals have personality?

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

    At the level of the individual, correct. An individual herring does not stand out from the crowd as individual humans do. But herrings as a group do stand out from seahorses as a group.

    Compare what you as an individual have created over your life so far with the creations of an individual herring. All the unique language compositions both aural and written, the clothing you choose to wear every day, your hairstyle, how you tend to your house and garden to give them your ‘stamp’. Do you drive? The vehicle that you choose to drive. These are just some of the examples demonstrating your personality that are not witnessed in herrings.

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

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

    In what way does a black panther stand out as an individual? It cannot consciously change its spots in the way that you can change your personal appearance. Would you say that individuality has more to do with physical attributes and personality has more to do with mental attributes?

  30. Nonlin.org:

    CharlieM: No(t) everyone shares the same logic.

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

    And by comparing human logic with computer logic you turn us into machines. Life’s logic is not as simple as adhering to the rules of logic gates. Poor logic is still logic and following the perceived most logical path will not always bring the best outcome.

    Do you agree that life is dynamic? Do you agree that trilobites once moved about in the ancient seas, but they are no longer in existence?

  31. CharlieM: It’s not a metaphor, it’s a self-similar fractal.

    Is it now? Whatever it is, it’s still time for you to admit that you don’t know how it works.

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

    Charlie: Yet Darwin’s finches can still interbreed. No irreversible speciation there.

    I strongly doubt it, but that’s irrelevant as well. A lot of small changes accumulating will still result in a big change, including reproductive isolation at some point .

    CharlieM: The rodent archetype is nested within the mammal archetype.

    So I already guessed. That doesn’t answer any of my questions.

    CharlieM: It would be very convenient for me to say that all animals evolved from an original, single population, just as all of our body cells derived from the single zygote. From unity to multiplicity. But how sure can I be of events that took place in such a remote past? How could I justify making such a claim?

    Because you just claimed that it is a self-similar fractal, remember? Apparently it is only self-similar until that is inconvenient for your argument.

    CharlieM: There is also evidence that populations converge..

    Yet birds and bats still cannot interbreed. No reversible speciation there.

  32. CharlieM: And by comparing human logic with computer logic you turn us into machines. Life’s logic is not as simple as adhering to the rules of logic gates.

    This is false. Logic is part of math. And math is what it is! Irrespective of machine, human or anything else. Most likely you continue to confuse “reason” with “logic” despite my clear explanation.

    CharlieM: Do you agree that life is dynamic?

    Sure. But if by “dynamic” you mean “evolution”, you go too far.

    Corneel: Since I have been asking repeatedly for the dominant mechanism by which pseudogenes arise, it is pretty spot on.

    Pretty not. Whatever you’ve been asking for is not my concern.

    We started this discussion by me asking you a question re one of your specific and unsupported claims, not the other way around. Go back and read.

    Corneel: Taking the blue pill, I see.

    Not necessarily. They just saved me a search. So I did remember correctly the stupid claim Shubin made. I see you’re no longer disputing that.

    On another note, you wouldn’t happen to know anything about entropy would you? Because your buddies are making a mess of it. Frankly, the level of intelligence on TSZ is not what it used to be. As bad as it was…

  33. Allan Miller:

    CharlieMSo what is it that gives your body all that variety of cell types each containing the same genome?

    Well, epigenetics, as I’ve said. All genetically based, of course.

    Do you see this base as a molecular sequence or as an active process involving many elements?

    Let me turn that question back on you. In a zygote, there is only one instance of ‘process’. In a differentiated organism, there are trillions of cells. How does the singular ‘process’ in the zygote become the multiple and variant ‘process’ in tissues, if not via gene expression differences?

    Why do you say there is only one instance of process in the zygote? The zygote is a hive of activity with metabolic processes and the processes involved in preparing for mitosis. Moving elements within and through the cell are all processes, chemical binding and dissociation are all processes, gene expression is a process. ‘Gene expression differences’ are different individual processes.

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

    Charlie: The causal chain you speak about has turned out to be a vast, convoluted causal network. All our lives began from fertilised eggs in which there are no simple, linear, causal chains.

    Neat. You flip from a ‘one-step’ view of genetic causation (genes only specify the primary product) to an ‘it’s waaaaay too complex to understand’. Well, it is complex, but not impenetrably so….

    It’s the opposite. The fact that countless figures of gene networks are readily available on the ‘net helps us to recognise and understand the complexity. And even more so, these figures are a very simplified representation of the actual processes. They don’t show the dynamic movements and molecular quantities within these networks. Neither do they show the built-in redundancies and alternative pathways that can be taken to cater for prevailing conditions.

    …In the specific matter of alternative splicing, which you believe demonstrates something ‘above’ the genome, it can be shown that splice isoforms are themselves genetically controlled – by a different part of the genome. See? 2 steps. You don’t have to go far.

    The elementary unit of control comprises a process involving nucleic acids and proteins. Control involves action.

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

    Charlie: But molecular continuity also involves process continuity.

    It’s not molecular continuity!.

    It’s more than just molecular continuity. The same types of activity continue from generation to generation.

    It is the same processes of mitosis that are going on constantly in your cells every second of the day to allow for replication. And it is the same process of meiosis that produces every sperm cell.

    The position you are arguing against here is one in which genes persist without any causal mechanism whatsoever. It is not a position anyone advances.

    I’m not arguing against that, I’m arguing for the continuity of process. Do you agree that ‘causal mechanisms’ also persist?

    There has not been one hundred percent molecular continuity between either of your parent’s genomes and yours. There are processes which ensure that this isn’t the case.

    Even so, the vast majority of my genes will be represented unchanged in my offspring (one copy or the other), your little 0.001% ‘gotcha’ notwithstanding.

    Yes there are many processes which determine the fidelity of the genome. The dynamics of evolution relies on maintaining a constant, if biased, balance between order and chaos.

    Mutations caused by external influences are environmentally induced changes.

    Aha. If a cosmic ray changes a base, then repair uses the ‘wrong’ base, is that environmental or ‘internal’? And does it matter?

    What matters is that balance is maintained.

    The experiences of populations will be represented in the genome, I haven’t said otherwise.

    Well, I disagree, if you mean the experiences of individuals. I wasn’t using ‘experience’ in a population-wide, metaphorical sense to represent natural selection; I was talking there of ‘Lamarckian’ mechanisms. I find the evidence unconvincing.

    I mean experience of populations. If a prolonged drought occurs in the Galapagos Islands this will be experience by the finch populations. Blind cave fish are as they are because populations experienced isolation in these dark caves.

    Any change is an activity, a process through which an alteration is made.

    That’s stretching ‘process’ to twanging point. Mutation is a ‘process’, even if caused by a cosmic ray? That’s gene centrism defeated by a puff of logic, then!

    Okay, externally induced mutations are not so much processes as the result of an active environment.

    Me: Reducing to sequence changes, one and all.
    Charlie: Not reducing, but involving. And as I said, any change is an activity, a process.

    I meant ‘change’ in the historic sense. If a splice variant is consistently produced in the same tissue in every member of a species, that can invariably be tracked back to another genetic sequence, which ‘changed’ the prevailing historic isoform pattern in that tissue. There isn’t a continuous process of active genomic change at that level.

    Well I agree on the consistency of the variant. But it is the splicing process that remains consistent.

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

    Charlie: Chromosomes are complex dynamic assemblages of more than just DNA. P elements and homing endonucleases only important within processes. In order to be activated, P elements rely on certain meiotic configurations.

    Saying nothing; not really understanding the question. The result of all of these elements is ‘non-Mendelian’ transmission – variation from the 50/50 chance available to other autosomal DNA. There must presumably be an advantage to some entity. How does it benefit ‘the whole organism’ to undergo this distortion? Gene centrism allows identification of mechanistic reasons for the distortion – the ‘beneficiary’ is clearly the genetic sequence itself. The distorter increases in the population simply by virtue of that distortion. But you’re not having that. So …. explanation?

    I don’t understand why being present in genomes constitutes an advantage. But they do need processes to ensure their presence.

    You said it yourself, DNA replication is a process. Processes in time are a higher level of reality than matter in space. This is the point I am trying to emphasise.

    I am not arguing that DNA replicates without mechanism, so you are attacking a strawman.

    So do you agree that processes also replicate?

    DNA sequences are important only in the fact that they can be read, and reading is an activity in time.

    ‘Only’? What are they ‘read’ by? What is the source of the enzymes, and how are they regulated, non-genomically?

    Reading is a process and of course genomes are involved. You would be as well asking me, how can I write in English non-alphabetically? The answer is, I can’t.

  34. Allan Miller:

    CharlieM:
    It is precisely the process, the activity, that determines what emerges.

    Nope. It’s the genome. The same basic ‘process’ of replication and gene expression takes place in elephants and mice. The difference between elephants and mice is not in that vague, obscurantist ‘process’ separately surrounding sperm and egg, but the composite diploid genome they form, expressed by ‘process’. If this is incorrect, identify the non-genomically-rooted differences in ‘process’ between the two.

    You say, ‘the same basic ‘process’ of replication and gene expression’. That will do for me. These processes are not vague, they are well researched and explained.

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

    Charlie: But is it false?

    Yes. As I already explained. You could try reading and addressing that explanation.

    I don’t think we have much to argue about here. If genomes never changed there would be no evolution, but if replication involved large uncontrolled changes then life would cease to continue. I thought I had made my position quite clear that life proceeds by maintaining a balance between change and remaining the same. The differences in the genomes of living creatures testifies to the fact that evolution has taken place. As far as I am aware, mutations (changes) are posited as a major driving force of evolution.

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

    Charlie: The genome is the source in the same sense that a musical instrument can be the source of a piece of music…

    Oh, bloody analogies! It isn’t. That’s a terrible analogy.

    Name an element of control that does not trace back to genetic sequence.

    Why is it a terrible analogy?

    Yes, controls rely on the existence of the genome just as your actions rely on the existence of your body. But just as when a person dies their bodies are still composed of the same materials so the genes contained in a dead cell will be the same as the genes in a living cell.

    The industrial age inspired the idea of life as being mechanistic and organisms as machines. Now we are well into the IT and computer age, organisms are seen as the result of software programmes encoded in the DNA. We are seen primarily as data sets.

    Not by me. I prefer to avoid analogies. Life is life. It has some things in common with some other things, but I explictly reject the over-extension of metaphor. Which is precisely what you are doing. You’re grumbling that it’s not like one metaphor, it’s ‘really’ like another. ‘My metaphor’s better than your metaphor’. Forget it. Living systems are like living systems. What matters is how they operate, not how something else does.

    Well how do you see my latest ‘analogy’ above? If you do not think it is apt, why not?

  35. Alan Fox:

    CharlieM: Why are some animals herbivores and others carnivores?

    Before the fall, there were no carnivores: the lion lay down with the lamb. But what did the lion eat, having neither the teeth nor the digestive system to deal with grass?

    Good question.

    At the beginning of life the niches were empty. First living organisms were chemotrophs followed by phototrophs. When you have a large biomass of phototrophs, there is the opportunity to engulf and consume them, rather than go to the trouble of having to rely on light for your energy.

    And so on. Niches all the way!

    So as the various kinds settled into their niches they received the mutations suitable for their particular lifestyles? Most niches require a whole suite of features and attributes to work in combination. Think of all the various attributes it takes to be able to survive by eating grass.

  36. DNA_Jock:

    CharlieM: Saying it’s a niche might satisfy your curiosity, but I would be asking a lot more questions. Such as: Why are some animals herbivores and others carnivores? Why are some generalists while others are extremely specialist.

    Would you now? You really don’t come across as being curious about the specifics. Of anything.

    How much do we really know each other through this medium?

    To explain it all by saying there was a niche to be filled is a very convenient answer that doesn’t explain what is required for an animal to reach a point where it is able to survive from its particular way of living.

    Nobody has claimed “It’s the niche!” as a final answer. Rather it is the beginning of an exploration into such things as biogeography. As opposed to, for instance, “It’s the archetype!”, which seems to lead… nowhere.

    Yes I agree, the ‘niche’ is a beginning, a partial explanation, a fragment, one piece of the jigsaw puzzle.

    At the opposite pole is the archetype. It does not stand at the beginning nor lead anywhere, it is that to which the senses lead us. It is a conclusion that comes into view through the fitting together of multiple sense experiences into a whole. This whole cannot be a sense experience but can only be seen in the mind’s eye. Not a static mental image but a dynamic mental reality.

  37. CharlieM: Think of all the various attributes it takes to be able to survive by eating grass.

    The most important factor is there has to be grass.

  38. Corneel:

    CharlieM: Whether the developers of thalidomide were aware of it or not, it’s my opinion that the drug did interfere with gene expression.

    Gene expression meaning transcription? “Mucking about with the genome” is read by most of your interlocutors as changing the DNA sequence, BTW.

    Well yes. As far as I’m aware transcription or any DNA binding involves interacting with the genome.

    From here

    In addition, several studies investigating molecular changes following thalidomide exposure in monkey fetuses and in human and mouse embryonic stem cells suggest changes in as many as 2000 gene expression profiles

    Are these activities not ‘rooted’ in the genome?

  39. CharlieM,

    Glad to see you admit that “It’s the archetype” is quite useless as an explanation.
    It’s like a cat falling off a slow-moving train.

    CharlieM: Are these activities not ‘rooted’ in the genome?

    What a staunchly “gene-centric” view you are suddenly taking! You would look slightly less silly if you were to just admit “I was wrong about thalidomide” but your rear-guard action here is leading you to contradict yourself.
    Still, none of these “activities” constitute “mucking about with the genome” any more than going for a brisk walk is.

  40. Allan Miller:

    Me: Multifunctionality, complexity and alternative splicing don’t lead to a conclusion of saltation.

    Charlie: No, but we do know that the pace of evolution isn’t constant. Some forms appear to have been around with little change for hundreds of millions of years while others have changed relatively rapidly and others have regressed towards earlier forms.

    That’s a long way from saltation. It’s no surprise you latch on to Goldschmidt though; seems you never met a maverick you didn’t like!

    It was Alan who brought Goldschmidt into the conversation. And he implied that if small genetic changes do result in large phenotypic changes then they would not possibly be viable because they wouldn’t be able to breed.

    You don’t seem to understand what is meant by the Goethean archetype. Look at a plant, its growth involves a series of step changes

    The term’s barely coherent, so no, I probably don’t understand it.

    It may be barely coherent from your perspective, others would disagree.

    You are arguing that the archetype exerts or represents some kind of control over form. But even if you argue for this ‘archetype’ to cover an entire life history, you’re still looking at a big change in that ‘extended archetype’ between generations. Which, as I say, is not very archetypical.

    You admit to probably not understanding the archetype and yet you can make a judgement as to what is and what isn’t archetypal.

    Step changes are in evidence everywhere.

    This does not make saltation true.

    That’s true. Even Goethe was wary of sudden jumps according to this quotation

    When I see an object before me which has come into existence, wonder about its genesis, and measure out the course of its becoming as far as I can follow it, I become aware of a series of stages which I cannot perceive next to each other, but which I must make present to myself in memory as a certain ideal whole. At first I am inclined to imagine distinct steps, but since nature makes no leaps, I am finally compelled to intuit a sequence of uninterrupted activity as a whole by sublating (aufheben) the individual parts, but without destroying the impression.

    The phases of matter, transitions of life from aquatic to terrestrial, metamorphosis, and many other processes involve step changes. And the dynamism inherent in the archetype encompasses all forms within it.

    ‘The archetype’ rapidly loses all meaning, then, if it ever had any. It’s everything. There are ‘step changes’ within an archetypal unrolling of a single life, and ‘step changes’ between generational instances of archetypal individuals. Glad you cleared that up. I’m kind of sorry I mentioned it; you nearly had my eye out with all that handwaving!

    I can see why you would think that the archetype is meaningless. It is not easy to envision through explanation and I’m probably doing a poor job at explaining. Better to access it through experience even if the initial impression is pretty vague.. A good start is if you can recognise the difference between the mental image of a triangle and everything that is contained in the concept triangle.

  41. Allan Miller:

    Me: Does too. Not been listening, have you?

    Charlie: The sequences are used in the control processes. Regulation, remodelling and modifications are all processes.

    No, the sequences actually control regulation. If you change the sequence – and only the sequence – regulation changes.

    But how are the sequences changed? Only through activity. Read you own words carefully, “if you change the sequence”.

    Viral infection is ‘a process’ too. Does this mean that viral nucleic acid is a mere scratchpad in ‘process’, just like our own? Or is that, somehow, ‘different’? If different, how is that distinction handled by ‘process’, and why doesn’t it just ignore it?

    Viral nucleic acids are just like somatic DNA, they require activity to have any effect.

  42. Allan Miller:

    CharlieM:
    Whether the developers of thalidomide were aware of it or not, it’s my opinion that the drug did interfere with gene expression. Perhaps you know different in which case I am eager to read your version.

    Well, by degrading the transcription factor SALL4, it kind-of interfered with gene expression, but it had no effect on gene sequence. Transcription factors, though, bind to specific gene sequences. The transcription factor sequence is in the genome. The site(s) bound to also reside in the genome. This is a good example of the genome’s capacity for self-regulation, not an exception to it. Gene and binding site are both replicated, and this is what provides generational continuity, not your ‘process continuity’ of the gene expression system or its products.

    Escher’s ‘drawing hands’ is a good metaphor for this … uh … ‘process’.

    To anticipate your objection (this is about my 745th rodeo), of course SALL4 would not exist at all without the ‘process’ of transcription. But given that process, the gene for SALL4 was able to be expressed. The variation in protein repertoire does not require a different process for every instance. That variation is provided by variation in sequence alone. And thus – in an environment in which transcription exists – there is a selective competition between variant sequences.

    Look at the different phenotypes between that of a ‘normal’ baby and a bay affected by thalidomide. You have explained that the genome remains the same, so what has changed? It is the way the genome has been handled that has changed. And this is the point I have been trying to make.

    Escher’s ‘drawing hands’ are indeed a good example for the genome and the associated proteins. Two halves of a single unit that cannot function when separated.

  43. DNA_Jock: I was enjoying Charlie’s definition of “process”, which includes a photon mutating a nucleotide, apparently. But this has now been eclipsed by his expanding use of “blindly mucking about with the genome” to include alterations to transcription factors.
    So, when I go for a brisk walk tomorrow morning, I will be “blindly mucking around with the genome”, apud Charlie.
    I really need not have bothered with reading Old & Primrose at all…

    Your understanding of how exercise affects gene expression will determine how blind you are to the genetic activity stimulated by it. Also I’d hope you know from experience how mild exercise affects your body, which is what matters in the end. But if you wish to imply that you’re blind to the genetic effects of giving your muscles a work out, who am I to argue? 🙂

    But this is not quite the same thing as prescribing drugs that you know will circulate in the blood and so have a fair chance of entering the cells.

  44. CharlieM: But this is not quite the same thing as prescribing drugs that you know will circulate in the blood and so have a fair chance of entering the cells.

    That’s cute, Charlie, but your original use of the phrase “mucking about with the genome” referred to heritable changes producing “hopeful monsters”.
    So drugs like thalidomide and mild exercise are in fact the same thing, in that neither of them involve “mucking about with the genome” as you originally used the term.

  45. Alan Fox:

    CharlieM: You better have a word with Allan if you think that limb development has nothing to do with the genome.

    Read for comprehension, Charlie.

    When I read that thalidomide may affect “as many as 2000 gene expression profiles”, I take that to mean it does affect the genome. And we know that it does affect limb development. These things are all linked.

    But if it makes people happy, I don’t mind revising the words, “blindly mucking about with the genome can have all sorts of unseen consequences” to “blindly mucking about with the developmental processes can have all sorts of unseen consequences.

  46. Allan Miller:

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

    Charlie: Creativity comes by means of expression.

    I guess. So do antagonism and discord.

    Antagonism and discord are features that are created. For example, within the organism normal cell growth creates harmony, cancer creates discord.

    Not really relevant to anything, in terms of the primary role of sequence in both ‘product’ and ‘product control’

    The role of the sequence is to be copied and copying is a creative process.

  47. Allan Miller:

    CharlieM: You better have a word with Allan if you think that limb development has nothing to do with the genome.

    Mmmm, the question is whether the action of thalidomide is ‘mucking with the genome’. It relates back to the death cap, that I introduced to illustrate the temporary nature of cellular ‘process’, which is perpetually refreshed from the more stable info in the genome. In this instance, thalidomide appears to wipe out the gene product SALL4, which cannot be refreshed quickly enough. In the death cap case, all gene products are terminated, so it’s a tad more detrimental.

    Now if, instead of wiping out the product, a mutagen changed the sequence of SALL4, OR its binding site, OR its UTR sequences, that would be ‘mucking about with the genome’. The change would be heritable, and feed into the ‘intergenic’ contest between rival gene sequences in the wider population. It could conceivably produce similar results to thalidomide, in which case we would expect the mutant gene to be rapidly lost. But if so, this isn’t due to any distinction of ‘process’ in the two variants, except inasmuch as process is dependent on sequence. And you could mumble ‘not naked DNA…’ to your heart’s content.

    I wasn’t arguing that thalidomide had a permanent effect on the genome. You agree that it appears to wipe out SALL4. SALL4 is a transcription factor and so losing it disrupts the normal process of transcribing a gene.

    This goes to show that drastic phenotypic changes are brought about, not by the genomic sequence but by the disruption of transcription processes.

  48. CharlieM: These are just some of the examples demonstrating your personality that are not witnessed in herrings.

    Repeat: personality is not the same as individuality. If you want to claim that differences in personality are more pronounced in humans than in herrings, then I’d concede that that sounds perfectly reasonable. But you keep insisting that this translates to higher individuality as well. This is false.

    CharlieM: Would you say that individuality has more to do with physical attributes and personality has more to do with mental attributes?

    I would say that variation in personality contributes to variation in individuality but that it is not the same thing. I really don’t see what’s so hard about this.

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.