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.
As Jock has already remarked, this use of the term renders it completely meaningless. Even eating an apple would constitute an instance of “mucking about with the genome”. But these changes are not heritable. You always forget that the changes need to be heritable in order to be evolutionary relevant (which is what we were discussing).
Yes, and I responded by trying to make you understand that you brought up an enormous heap of irrelevant stuff. Go back and read.
Yes, I am still disputing that. No, you didn’t remember correctly. Even the good Dr. Mitchell from answers in genesis didn’t call the preaurical sinuses vestigial organs. You are still wrong.
By the way, a good rule of thumb is that if people stop disputing your claims, this is not because they now agree with you, but more likely they just grew tired of explaining to you why you are mistaken.
Finally something we can agree on.
How what works? Evolution or development or both? I’m in the same boat as you and everyone else. My knowledge of these things is somewhere along a spectrum. Neither entirely ignorant nor fully knowledgeable.
Do you have any evidence to back up your strong doubt?
Are your questions geared towards understanding or is your primary concern refutation?
Yes and there are many ways in which it is self-similar. Some are obvious, but for some I can’t give a definitive answer.
Indeed they Can’t. Can you trace the origin of bats with any certainty?
The zygote is capable of producing all body cells but cells such as neurons have reached a level of specialisation where they do not naturally give rise to any other cell type. Your example of bats and birds are similar to this with regards to evolution. Self similarity in which the whole is reflected in the parts.
When we use reason we are applying logic. Your understanding of logic is very narrow.
Do you agree with evolution as in its original sense of an unrolling to reveal what is hidden within?
That’s true. Autotrophs prepare the way for heterotrophs
Just as in development growth precedes differentiation. The whole reflected in the parts.
So would you accept, “blindly mucking about with the developmental processes”?
Evolution guided by archetypes please. I am still pursuing this query:
Well, you haven’t provided a source for your claim that Galapagos finches can interbreed. But that is not the main point. There is nothing preventing populations from accumulating a lot of small changes to the point where they develop reproductive isolation. Agree?
I’d like to finally get some non-evasive answers to my question above. You are relying an awful lot on “we cannot know and experts are just speculating” while appearing certain that your view of things is correct. But whenever somebody asks for details, you just question the mainstream account. To be fair, I do not believe you have reason to be so confident.
But we disagree which are the obvious ones, and which are the ones for which you can’t provide a definitive answer. Therefore you should stop using that argument.
You claimed that divergence and convergence are on equal footing, yet it is obvious that bats and birds will never converge to the point where they can interbreed again. Therefore I maintain that divergence is a more dominant pattern in evolution than convergence.
“if you wish to imply that you’re blind to the … effects of giving your muscles a work out, who am I to argue? :)”
As you yourself noted, it’s not ‘blindly’ anything. There’s some trial and error involved, whether we are talking about diet, exercise, drug development or genetics.
I asked a simple question. It’s still unanswered with something reasonable.
Shubin did: “an inconsequential embryologic remnant that Shubin identifies as “a leftover from an ancient gill””
Don’t know. Could it be: “they don’t have a reasonable argument”? Just a hunch.
Of course we use logic in our reasoning… as well as observable evidence and assumption. Not just my understanding. Logic is what it is. And you can’t wish it into being different.
Don’t know what you mean.
It’s been addressed with a perfectly reasonable answer; you just don’t like the answer.
That’s some serious dyslexia you’ve got there if you read “a leftover from an ancient gill” as “vestigial organ”. No, congenital malformations are not vestigial organs, not even if they provide equally solid support for our evolutionary past as vestigial organs do. Also, if you believe that answers in genesis is a reliable source of information, you are pretty seriously misguided. And I am willing to bet a considerable sum of money that you STILL don’t know the dominant mechanism by which pseudogenes arise. It’s in the second sentence of the Wikipedia entry, for crying out loud!
And that is your problem: You just keep on wallowing in your ignorance like a pig in mud. I really don’t see why I should join ANOTHER thread of you resisting correction by people who are much more knowledgeable than you. Basta!
I was using the example of thalidomide to demonstrate how complex and intertwined genomic processes are. Whether it be meiosis, mitosis, transcription or any other gene related processes, it is exceedingly rare that they can be reduced to a simple case of linear cause and effect.
It doesn’t matter how tenuous the relationship are between the various actions. If we focus in on the associated processes within the genome we find multiple convoluted actions and reactions. And when we look for causal origins this does not lead us back to the genes, it inevitably leads back to an initial action.
Okay then in my opinion evolution can be seen as the move towards the personality of individual organisms from a previous condition where there was only the personality of groups.
Would you say that certain groups of animals have shared personality traits; for example rabbits are of a more nervous disposition than sloths?
Personality is a function of behaviour. Hence the more complex behavioural repertoire a species acquires, the larger the scope for individual differences becomes.
There has been an increase in behavioural complexity in metazoans, but I am still not convinced this is the goal of the entire show. Metazoans are conspicuous, but make up only a tiny fraction of the entire diversity of life.
And humans are of a more self absorbed and condescending disposition. Sure thing!
Well at the moment I am discussing causal relationships in relation to all and any genomic processes.
False, unless by ‘simple’ you intend to exclude pleiotropy, epistasis and polygenic traits. In which case, I say, “so effing what?”.
How far back are we going? Big Bang, formation of the Earth?
If we are going back anywhere between a hundred and a billion years, then its leading us to the genes.
You appear not to have followed that which you responded to. Note that SALL4 is a gene product.. Being a transcription factor, rather than an enzyme, changes nothing that I have been arguing regarding the ‘rooting’ of everything in the genome, both ‘matériel‘ and control.
You seem unable to think more than one step removed from any given sequence. You’ve made the same error regarding splice variants, methylation patterns, chromatin remodelling … if one takes a ‘peek inside the box’, rather than peeling back a corner of the cellophane and pretending, one might better appreciate what goes on.
I have read one of the Grant’s talking about the finches being incipient species rather than distinct species, but I don’t remember where I read this. I can try to find it if you wish.
I don’t doubt that divergence could result in separate species that cannot successfully interbreed. But I see this as a narrowing and reduction of their potential to evolve further.
In my opinion I have been quite open about what I consider my beliefs and what I take as knowledge. It is the admirable quality of science that it proceeds by questioning current orthodox views.
But we disagree which are the obvious ones, and which are the ones for which you can’t provide a definitive answer. Therefore you should stop using that argument.
It would be illogical to cease from arguing solely because we disagree. When we come to some sort of agreement, then we can stop arguing.
You claimed that divergence and convergence are on equal footing, yet it is obvious that bats and birds will never converge to the point where they can interbreed again. Therefore I maintain that divergence is a more dominant pattern in evolution than convergence.
I claimed that there has been divergence and I claimed that there has been convergence, I never claimed they were on an equal footing, only that they were equally observable.
If something begins from a unified state there must be divergence prior to convergence.
In order to understand evolution I find it helps to concentrate on the symbol of the caduceus so long as one does not try to force any preconceived meaning onto it. It works for me, but that’s not to say it will work for you.
We are all literally blind to the constant genetic activity within our bodies. But regarding the mind’s eye as opposed to the physical eye, we may not be so blind.
And don’t you agree that the path of logic is dependent on, and can change because of particular circumstances.
Are you also opposed to some sort of directed evolution?
So it’s all about quantity over quality?
Being self absorbed is a consequence of self conscious awareness. It involves moving beyond being confined to little more than acting on our immediate sense impressions.
That is the observation, yes. An explanation would tell us how the forms are limited by the particular circumstances in which they develop.
The link appears to be broken. The abstract doesn’t bode well.
Why do you see it like that? What would limit a mouse’s potential to grow to an elephants size?
I never said you should stop arguing. You should stop using the “evolution is like development” argument, because nobody accepts that evolution resembles development in having some goal.
Funny. That’s exactly how I read “Divergence and convergence form two tracks of a spiralling path.”
If you choose pondering the symbol of the caduceus as a means to understand evolution you are way too late to prevent forcing preconceived meaning onto it.
All non-human life is rubbish?
Thank you for this apt demonstration.
Corneel,
All you do is dodge, split hairs, and/or go silent. Because that’s all you have in support of your pseudoscience.
Since you are not disputing that particular passage, it’s only logical that Answers in Genesis is as good a source as any.
No. You’re too much of a poet.
No one calls something directed “evolution”. Not even the theistic evolutionists.
Moved a post to guano.
Rule here is don’t accuse others of lying. Another rule is moderation issues should be raised and discussed in the “moderation issues” thread. I think I’ve mentioned this before. Please take note.
Moved a post to guano.
This is a very lame excuse. If it were something simple and full of blunders, you would have jumped up and down like a happy little monkey to show your superiority. Well, tough! Silence speaks too.
And Corneel, why do you put down the piggy? Are you rejecting your own dogma of human equality with the animals?
Alan Fox,
Judge Dredd and his fine print gun…
I would exclude these, not only because they are far from simple, but because they are also non-linear.
I think you are confusing the model with reality. I’ve attached an image of pleiotropy below. It could be taken from this that there are three linear directions that this process takes. But what it doesn’t show is the coordinated effort required in the transcription process. Transcription factors and molecular complexes must work together to produce the mRNA which must then be transported out of the nucleus. They have purposely simplified the diagram below to convey the idea behind pleiotropy. The full reality is somewhat different.
No need to go that far. The extra genetic activity brought about by your brisk walk would have its initial cause in your decision to go on that walk and then acting on that decision.
And you seem unable to think even one step. Taking just one step constitutes an action. Genes do not cause effects, gene expression does. Even transcription factors need to be activated by some means. Life is rooted in activity.
Here they explain how environmental factors affect plant growth.
For example, in order to survive in a dessert a plant must be efficient in retaining water. This is reflected in its anatomy.
Sorry about that, Here it is
While looking into and thinking about evolutionary processes I have just come across this book by Maria B. O’Hare in which she provides many quotes about scaling in evolution. Such as:
There is a chapter entitled, “Of Mice and Elephants: A Matter of Scale”, in which she writes:
She writes:
The book has some interesting info on scaling. The whole reflected in the parts.
Niches are frequently referred to in discussions of evolution. And one problem with mice growing to the size of elephants that I can envision is that they are very successful in the niche they occupy. To become the size of elephants would require them to step out of their comfortable niche and traverse other already occupied niches to reach a niche which would in all probability be less successful than the niche they left.
Some people do argue that like development evolution does have a direction.
I would note that converging never brings about a return to the original position.
I didn’t concentrate on it with the intention of trying to understand evolution, that was just one of the consequences of doing so.
My answer was regarding metazoans, not humans.
Are you not self absorbed on any level?
If you could hear the ‘or’ gates clatter,
You might think differently on the matter.
(CharlieM, designated poet to the ‘zone) 🙂
The arrow of time ensures that life is moving along a course. You can believe that this course is leading somewhere like a river to the sea or you can believe that it is haphazardly meandering through the ages going nowhere in particular. Which is it?
I’m not looking for your answer, but you may want to ask yourself the question.
Following on from the book I linked to earlier, I watched a video by one of the people quoted in the book, the theoretical physicist, Geoffrey West. The video can be viewed here
When looking at highly complex systems there is a danger of neglecting their interactions and this will lead to unintentional consequences. In the video he says that, when studying highly complex systems, it must be taken into account that “these are not independent. They are all highly coupled, inter-related, multi-scale complex adaptive systems.
Further on he speaks about the scaling of organisms. He says:
There are overarching rules which set limits on the variety of life. A mouse cannot be just expanded to elephant-size in a linear manner, it would need to follow a sub-linear course.
A mouse could freefall ten times its own height and it would probably scurry away with no ill effects. On the other hand, an elephant that freefell ten times its own height would almost certainly be a dead elephant.
The idea that selection is random is flat-out wrong, so the plot result is expected.
Have you taken any courses in basic biology? The cube/square law operates at all scales from viruses and bacteria to blue whales.
You can see the graphic at 22:07 in West’s video.
The plot is log(metabolic rate, in watts) versus log(body mass, in kg).
So, before we start in with anything else, you would expect something pretty close to a straight line; to say “you would expect to see these points all over the graph” is a silly straw man.
Generally, when people want to talk about metabolic rate, they talk about watts per kg body mass which, of course, is much higher in mice than elephants. Like heart rate.
West’s point is a good one however — the correlation is very good, and the slope of the log/log plot is ~0.75, not one. That’s an “economy of scale” result.
That Charlie can watch this very educational video, and come away with his take-home message about dropping elephants is truly depressing.
That quote was from Geoffrey West, so you would need clarification from him, but I presume he was making a point in line with his belief that the evolutionary process in general had random elements, hence his vague term, ‘sort of’. He was trying to get across the consistencies and regularities within what is supposedly a directionless process.
Yes, very basic.
Yes and West is trying to explain what he and his colleagues see as a deviation from this law from the expected 2/3 to a 3/4 law.
How do you explain the tendency to correlate with multiples of the fraction one quarter in all the slopes they have calculated?
My point about mice and elephants was not a take home message from the video. It was just one personal comment. There is very much more about this research that we could discuss.
The reason that elephants cannot cope with falling from height is because they are more affected by gravity than mice. There is wisdom in their evolution in that it would be of no use to the elephant if they had a skeletal structure which could withstand much higher impact forces. It would still end up dead. Mice have overcome gravity to a greater extent than elephants, and birds in general have overcome gravity to a greater extent than mice.
This pdf has a lot of info on this topic. Here is an excerpt:
I’ve attached an image taken from the above pdf. Examples of fractal networks in which the parts are a reflection of the whole.
The above pdf was composed by the late Arthur Stinner. I only came to know of him from finding the pdf a few days ago and it looks to me as if he was a very intelligent man with a broad spectrum of knowledge. I am grateful for the work he has done and that it has been made accessible, he must have been a great and inspiring teacher.
Unsurprisingly, your judgement of other people’s motives is abysmal as well.
Why are some plants efficient in retaining water? Saying “works fine in a desert” doesn’t suffice according to this guy:
That looks familiar. I believe I once read that. The author desperately tries to save Goethe’s “dynamic typological thinking” from the dustbin of science. I don’t believe he was very succesfull.
More importantly, I do not see any attempt to explain how archetypes guide evolutionary change in their role as “organizing principles”. Could you explain why you thought the paper was pertinent to my question?
It’s called competitive exclusion. That is a principle from ecology. If I recall correctly, archetypes do not figure greatly in it. Also, it does not prevent mice from growing to the size of elephants once the appropriate niche becomes vacant, contra your claims.
True, that is because separated populations tend to diverge in most of their characters.
All non-metazoan life is rubbish?
If I am, does that establish being self absorbed as a virtue?
I mean, I am a great guy and all, but I did not realize I had become your role model.
😁
If we think of evolution as a general movement from primal to derived in the same way that individual development is also a movement from primal to derived, we can see that the more primal, precursor forms are more plastic. In other words they have the ability to produce a greater variety of subsequent forms. As an infant my body was full of growth and developmental potential. Now I am old, my body has hardened into forms that reflect the past and no longer has the fresh vigour of youth.
It is the same with evolution. Early life had a greater potential to grow and diversify. Early plants still had the ability to develop in a multitude of ways. But as their evolutionary paths became narrower they tended to stay in the rut they had made for themselves. Assuming that common ancestry is true then it would be nigh on impossible for a water lily to evolve into a cactus like plant or vice versa. But the common ancestor of both could still follow either path depending on future circumstances.
Can you give any reasons or justifications for your negative belief?
Do you mean the question about the potential of a mouse to grow to the size of an elephant?
J. B. S. Haldane had a few things to say about relative sizes:
He had some inkling of the multiple coordinated changes that would be required to transform a small animal into a massive animal.
There is a particular ratcheting effect in development and in evolution. It is much easier to transform a totipotent stem cell into a neuron than it would be to convert a neuron into a stem cell and it is the same with converting animal kinds between primal and derived.
The archetypeis no more a guide than the ideal triangle is a guide that determines the form of physical triangles. The archetype is the essence of the organism in the same way that the ideal triangle is the essence of any triangle.
Have you thought about all the necessary complex, coordinated changes that would be required in this transformation?
And just as after one circuit of the sun the earth never returns to its original position, so life spirals on.
No, just less developed.
I wasn’t making a judgement, it was a pure observation. Egoism is a double edged sword.
Well I suppose you must be because I aspire to become a great guy too 🙂
There is no more fitting demonstration of the spiralling flow of life than the mammalian heart. The concept of the heart constricting and dilating has been replaced by the reality of the observation that it twists and untwists in a spiralling motion. The videos, The Cardiac Dance, The Spirals of Life,, and The Helical Heart attest to this fairly recently discovered aspect of this remarkable organ.
During development the heart takes on its form dictated by the swirling vortices of fluids moving in the early embryo.
Everything about the cardiovascular system concerns spiralling movement.
The image below is taken from the video, Leonardo da Vinci’s theory about the heart was right. It shows the vortices created by the sinus of Valsalva and how they close the aortic valve preventing blood from flowing back into the heart.
Three-dimensional blood flow dynamics: spiral/helical laminar flow, by Peter A Stonebridge
The spiralling nature of living fluid.
I am not yet as old as you, but I definitely feel what you mean.
That would require me to accept your premise that evolution is like senescent ageing. But as with your comparison to embryonic development, I do not. Senescent ageing evolves as a consequence of the diminishing power of purifying selection with increasing age. These mechanisms do not operate above the organismal level.
This is why I told you to drop that metaphor: I know when the comparison between development and evolution makes sense and when it does not. In this case, it does not.
The paper received only a single citation in seven years. That’s even worse than my papers.
No, I am still wondering how you imagine the habits and lifestyle of a population made the particular aspects of the archetype we observe today to realize into actuality. You have avoided answering the question for quite some time now. Please don’t ask me to read another book or paper again.
We know for a fact that such transformations have taken place by the act of accumulating many small changes. Charlie being bewildered by “all the necessary complex, coordinated changes” has never stopped it thus far.