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.
I haven’t watched the videos.
I agree that talk of machines and mechanisms has limited usefulness, and is often overused.
I think I have indicated in the past that I consider myself a kind of behaviorist. But my concern is more with the behavior of processes than with the behavior of whole organisms. So you could reasonaby say that I consider dynamic processes to be more important than physical matter.
I’ll concede that, due to gravity (whatever that is 🙂 ), water generally runs downhill.
But I have no idea what the rest of the sentence is supposed to convey. Anyone able to offer clues?
I feel in my heart, nay, my very heart of hearts, that the (inexorably) Spiralling Flow of Life is deepities all the way down.
The first sentence intends to get you into familiar territory, the second is a rhetorical device building on the first so that you get all perplexed and mistake that perplexity for insight, for deep thought, for philosophical wisdom. I think this kind of device is presented in some article as “pseudo-profundity.”
You missed the alpha helix..
Anyway, you won’t find me pursuing the ‘machine metaphor’ – nor indeed any other, except on the odd occasion, in my consistent inconsistency, I feel like it. Of course organisms aren’t machines. They grow by cell division, with no analogue in the world of engineering. This division and differentiation into specialised tissues, each possessing the same genome, again has no useful analogue in the world of bolted-together parts. The lowest-level components operate under a physics which is imperceptible at the scale of assembled machines (which also renders ‘spiral’ intuitions moot: the spiralling of DNA and alpha helixes is due to completely different physical forces from those operating in spiral growth, different again in galaxies).
All that conceded, I don’t see where the ‘not machines’ argument takes us. “They are not machines therefore DNA is not where control resides” doesn’t work as a syllogism, since machines don’t have that curious feature of cellular replication, incorporating a genome copy within each instance, in any case.
I’m not surprised. There are a good few hours worth of videos there.
The Cell Is Not a Machine – Beyond Networks: The Evolution of Living Systems is what he calls the core video so you might want to take a look at that one.
I agree.
So wouldn’t you say that a whole organism has more of the attributes of a process than of an object?
Charlie, you are still evading all the challenges that have been presented to you. First, matter is not passive building material but has certain physical properties. That is what D’Arcy Wentworth Thompson’s “seats of energy” and “centres of force” alludes to, not to élan vital. I admit it is rather amusing to see you cite approvingly from “on Growth and Form”, a book that ‘helped to defeat mystical ideas of vitalism’ according to its wikipedia entry.
Secondly, human made machines do not possess the features that would allow them to evolve: trait variation, reproduction, heritability and fitness variation (differential surival and/or reproduction). Any artificial system that has those properties will evolve through natural selection. No inner activity or archetypes required.
It takes us to the ‘not a river either’ rebuttal.
Yes, it’s drawn towards the centre of the earth.
Maybe I can.
Can you not think of any way that life is flowing upwards? Think about the standard account of evolution. Some believe life to have begun in some hydro-thermal vent. Anyway, in its marine environment it began to diversify. And we know that water gravitates toward the lowest point and evolution began here. In time life begins to colonise the land which involves an upward journey. Fast forward to the present. These days there are countless multicellular organisms whizzing about in the atmosphere at heights of tens of thousands of feet. Some have reached as far as the moon. Would you not call that an upward journey?
And of course if you are looking for a more ‘profound’ answer (those who get twitchy at the hint of deepity look away now 🙂 ), you could always consider that life assumes ever higher forms of consciousness.
But you may wish to just think about the first meaning which is in no way negated by the second meaning. Hope that helps.
I didn’t miss it. Did you want me to list all the examples of helices I could find?
It’s not what you or any other scientist or expert believes. What counts is the impression made on the minds of the general public by the ubiquitous use of such machine metaphors. Especially on the impressional minds of young children. If they are taught that our cells are full of molecular machines why would they not believe what they are taught?
The helices and spiral forms that are in evidence at all these different levels might have different physical forces operating but they have the same mathematics in common. There is a common attraction towards this form.
A brick is matter. A brick is an example of passive building material.
I too disapprove of mystical ideas of vitalism.
I’ve asked my wife and she says that reproduction involves plenty of inner activity 🙂
Think of the archetype as potential dynamic form. It is not an external actor. It is that aspect of an organism which is available to the mind but not any of the standard five senses.
Why are bricks passive? In order to be visible, a brick has to be absorbing some wavelengths and reflecting others. In order have weight, a brick has to be distorting space-time to a much lesser extent than the Earth. In order to be load-bearing, a brick has to have molecular and atomic properties that involve repulsion and attraction at the quantum level.
That all seems pretty active to me!
Then you should be criticizing science educators, not scientists.
D’Arcy Thompson from, ‘On Growth and Form’
So according to Thompson living matter breaks no laws of physics. The properties of bodies can be explained purely in physical terms and that was his aim.
But there is more to life than the laws of physics, just as there is more to a story than the properties of the letters of the alphabet.
A brick will passively accept whichever light falls on it wholly explainable by the laws of physics. The effect of the light will only vary if the light varies. Shine a light on a wood louse and it will actively try to avoid it the direction in which it chooses to move is not solely determined by physics. It might choose to move up a gradient in opposition to the gravitational forces acting upon it. Light can fall on the surface of both bricks and organisms and will have similar physical effects. The difference lies in the way each one responds.
Unlike an ant a brick will not actively seek to bear a load. Any load will come upon it due to external activities. It is is not intrinsically active in the way that organisms are.
You are speculating about atomic forces about which we have no clue as to why they are the way they are. I am talking about responses we can observe directly.
I have not criticised anyone in particular. I am criticising the way that machine metaphors are used in general. Besides, I would class any scientist who publishes worthwhile research as an educator.
Fair enough.
I just happen to prefer a good few hours of not watching videos. All the more so, when your introduction failed to persuade me that they were worth watching.
deepities all the way down
Gotta love it.
Yes, we see the same pattern (spiral or whatever) in unrelated areas of the real world, but so what ? What is the connection between DNA & planetary movement ?
Completely ignoring the fact that the ’spiral’ shapes shown by the latter were entirely a side effect of the contrived manner used to display the data.
I have to agree. Indeed, I think we are approaching the point where man-made machines can design and program (and build) improved versions of themselves. If we reach that point, I would expect subsequent machine evolution to occur at a furious pace. Already we have computers producing useful outputs (predictions, diagnostics, strategies, optimizations, etc.) and we have no idea how they do it, because the programming isn’t brute force coding, it’s evolutionary in nature. The machines have taught themselves.
Flint,
If you are right, we are all doomed. 😱
Or perhaps we all get saved from ourselves.
If you redefine activity to only include the consequences of conscious decisions, then, yes only living things are active. Alas, nobody but you uses the word that way.
Hmmm, not seeing it: You have advanced some mysterious property called “inner activity” that bestows distinct qualities on the molecules in living organisms which cannot be found in non-living matter. For all intents and purposes, I cannot distinguish this “inner activity” from élan vital.
The story you are free to change to suit your preference, but the book remains what it is.
Omitted, then. Sheesh, you try and help a guy out … it is a striking structure, widely utilised and providing a number of vital features or proteins; if one is riffing upon helices, it certainly seems worth a mention.
Your descriptions of biology are absolutely stuffed with metaphors. Most of them (to use a metaphor) half-baked.
Metaphors are useful illustrations for the student. Some people – you, to pick an example at random – set far too much store by them, overextending them to a ludicrous degree. You’re actually an example of that which you oppose.
There are only so many regular arrangements in a 3D space.
Corneel,
Appreciate the effort to cheer me up but then I spotted this!
https://xkcd.com/1732/
CharlieM,
What properties are those? This is a fundamental issue with lay critiques of molecular viewpoints: atoms and molecules are not mere ‘letters’. They have properties, interactions and physical consequences; letters don’t. This was a favourite theme of physicist Mike Elzinga, a regular in the early days of TSZ.
Once again, in attacking metaphor you illustrate the problem with it, if your explanatory approach is simply to chuck out another one.
I see he’s still going strong over on The Panda’s Thumb.
Fair enough. It’s not to everyone’s taste.
The connection is mathematical. Particularly projective geometry and the polarity between space and counterspace.
They are not side effects, they are representations.
In your opinion what path does the earth take through space relative to the centre of the galaxy?
So you are saying that we are fast approaching the point where we will be able to build machines that have all the attributes of living systems. In other words they will be alive. So we reach a point where life creates life. But this is not just life creating life as in normal reproduction, it requires a high degree of conscious awareness on the part of the creators.
Do you think that these creations will have any awareness of their creators? Perhaps they will believe that they have just originated by a slow evolutionary process by which their parts just happened to assemble in an appropriate manner. “In the beginning life was simple when there were nothing but diodes and the like scattered around the earth. Then more complex entities emerged as basic multi-circuited forms developed” 🙂
You could be a modern day Noah. It’s time to start building your interplanetary ark, but you might have to wait until most of the species have become extinct. 🙂
So you see no difference between the activity of a brick and the activity of a toirtoise?
Even basic forms of life have inner activity by which they react to stimuli. How they react is not fully determined by the laws of physics even if they break none of these laws in their actions.
Do you think that the activity you displayed in posting this reply was instigated from some external source or did the decision to act come from within you? Are you an automaton or do you take responsibility for your actions?
So a book is a version of the story frozen in physical matter. The laying down of the words in the book has killed the creative potential within the story which can live on in the retelling.
We can describe the act of love between two people in extreme physical detail, the movements and forces involved at all levels, but on top of this lies the emotions and thoughts of the couple of which no amount of physical laws will give an accurate description.
And I thank you for mentioning it.
All of our everyday language is stuffed full of metaphors. And what have my cooking skills got to do with the price of fish? 🙂
Between space and counterspace the arrangements are infinite.
Thinking, feeling and willing are not physical properties although they are attributes we have by way of our physical being.
I’m not attacking metaphors only the treatment of them as if they constituted reality.
I’d be with you on that, though given that you are a bugger for peppering (yes, I am well aware …) your prose with them, you seem to sail (yes, again; I don’t just throw this stuff together) pretty close to that wind.
Defending the ‘letter’ analogy by listing other properties letters don’t have!
I don’t remember him.
Show many a person who doesn’t pepper their writings with metaphors.
Sorry, I was just putting my thoughts down without paying enough attention to your question.
Concerning the properties of letters you asked, “What properties are those?”.
Letters are symbols for sounds that can be made by using our breath. Letters point to the attributes of human beings in themselves. Words establish the relationship with the world around us. First we learn to speak and spoken language does not need to fragment words in this way.
The need to tear the words into their constituent parts only came about with the birth of written language.
Isolated letters are an abstraction removed from the context of the words from which they came, and isolated DNA is an abstraction without the context of the cell to which it belongs.
Uh no. DNA is a chemical substance and it remains so if you isolate it. I can assure you from first-hand experience.
Mike hasn’t commented at TSZ since 2014. One of his last comments:
I doubt you would have got on.
Hmm. Sometimes there’s a glimmer of self-awareness. 😏
Corneel,
I’ve already told him that.
I appreciate that the physical description of a coitus does not capture its emotional impact, but that does not justify you making up stuff that does not exist.
Yes, the latter is conscious activity. My turn now: do you see no difference between the activity of DNA polymerase and the activity of a tortoise?
No, I do not think of myself as an automaton. My turn now:
Do you think the activity of a Venus flytrap capturing prey is instigated from some external source or did the decision to act come from within it? Is it an automaton or does it take responsibility for its actions?
I fear it bears repeating several times.
But if you observe that isolated DNA, what will it do?
Unless you store it somewhere cold, it will degrade.
Are you going to retract your outrageous claim that isolated DNA is an abstraction? Will you reflect on what made you say such a thing?
There’s an equivocation at work here. I’m betting you are well aware that there is a distinction between saddling up metaphors in pursuit of fluid prose (SWIDT?) and using them to illustrate a point about an object, concept or process, by comparison with something familiar.
I get on with most people, even those with opposing views to my own, but I know what you mean.
And then I have to look away, it’s not a pretty sight 🙂
And, once isolated, what was it doing before you proceeded to manipulate it?