• apokrisis
    1.9k
    I'll repost a longer explanation I gave elsewhere that explains the basic point Hoffman makes in Life's Ratchet. It details the instability or dynamism on which life is founded.

    Biophysics finds a new substance

    This looks like a game-changer for our notions of “materiality”. Biophysics has discovered a special zone of convergence at the nanoscale – the region poised between quantum and classical action. And crucially for theories about life and mind, it is also the zone where semiotics emerges. It is the scale where the entropic matter~symbol distinction gets born. So it explains the nanoscale as literally a new kind of stuff, a physical state poised at “the edge of chaos”, or at criticality, that is a mix of its material and formal causes.

    The key finding: In brief, as outlined in this paper http://thebigone.stanford.edu/papers/Phillips2006.pdf , and in this book http://lifesratchet.com/ the nanoscale turns out to a convergence zone where all the key structure-creating forces of nature become equal in size, and coincide with the thermal properties/temperature scale of liquid water.

    So at a scale of 10^-9 metres (the average distance of energetic interactions between molecules) and 10^-20 joules (the average background energy due to the “warmth” of water), all the many different kinds of energy become effectively the same. Elastic energy, electrostatic energy, chemical bond energy, thermal energy – every kind of action is suddenly equivalent in strength. And thus easily interconvertible. There is no real cost, no energetic barrier, to turning one kind of action into another kind of action. And so also – from a semiotic or informational viewpoint – no real problem getting in there and regulating the action. It is like a railway system where you can switch trains on to other tracks at virtually zero cost. The mystery of how “immaterial” information can control material processes disappears because the conversion of one kind of action into a different kind of action has been made cost-free in energetic terms. Matter is already acting symbolically in this regard.

    This cross-over zone had to happen due to the fact that there is a transition from quantum to classical behaviour in the material world. As the micro-scale, the physics of objects is ruled by surface area effects. Molecular structures have a lot of surface area and very little volume, so the geometry dominates when it comes to the substantial properties being exhibited. The shapes are what matter more than what the shapes are made of. But then at the macro-scale, it is the collective bulk effects that take over. The nature of a substance is determined now by the kinds of atoms present, the types of bonds, the ratios of the elements.

    The actual crossing over in terms of the forces involved is between the steadily waning strength of electromagnetic binding energy – the attraction between positive and negative charges weakens proportionately with distance – and the steadily increasing strength of bulk properties such as the stability of chemical, elastic, and other kinds of mechanical or structural bonds. Get enough atoms together and they start to reinforce each others behaviour.

    So you have quantum scale substance where the emergent character is based on geometric properties, and classical scale substance where it is based on bulk properties. And this is even when still talking about the same apparent “stuff”. If you probe a film of water perhaps five or six molecules thick with a super-fine needle, you can start to feel the bumps of extra resistance as you push through each layer. But at a larger scale of interaction, water just has its generalised bulk identity – the one that conforms to our folk intuitions about liquidity.

    So the big finding is the way that contrasting forces of nature suddenly find themselves in vanilla harmony at a certain critical scale of being. It is kind of like the unification scale for fundamental physics, but this is the fundamental scale of nature for biology – and also mind, given that both life and mind are dependent on the emergence of semiotic machinery.

    The other key finding: The nanoscale convergence zone has only really been discovered over the past decade. And alongside that is the discovery that this is also the realm of molecular machines.

    In the past, cells where thought of as pretty much bags of chemicals doing chemical things. The genes tossed enzymes into the mix to speed reactions up or slow processes down. But that was mostly it so far as the regulation went. In fact, the nanoscale internals of a cell are incredibly organised by pumps, switches, tracks, transporters, and every kind of mechanical device.

    A great example are the motor proteins – the kinesin, myosin and dynein families of molecules. These are proteins that literally have a pair of legs which they can use to walk along various kinds of structural filaments – microtubules and actin fibres – while dragging a bag of some cellular product somewhere else in a cell. So stuff doesn’t float to where it needs to go. There is a transport network of lines criss-crossing a cell with these little guys dragging loads.

    It is pretty fantastic and quite unexpected. You’ve got to see this youtube animation to see how crazy this is – https://www.youtube.com/watch?v=y-uuk4Pr2i8 . And these motor proteins are just one example of the range of molecular machines which organise the fundamental workings of a cell.

    A third key point: So at the nanoscale, there is this convergence of energy levels that makes it possible for regulation by information to be added at “no cost”. Basically, the chemistry of a cell is permanently at its equilibrium point between breaking up and making up. All the molecular structures – like the actin filaments, the vesicle membranes, the motor proteins – are as likely to be falling apart as they are to reform. So just the smallest nudge from some source of information, a memory as encoded in DNA in particular, is enough to promote either activity. The metaphorical waft of a butterfly wing can tip the balance in the desired direction.

    This is the remarkable reason why the human body operates on an energy input of about 100 watts – what it takes to run a light bulb. By being able to harness the nanoscale using a vanishingly light touch, it costs almost next to nothing to run our bodies and minds. The power density of our nano-machinery is such that a teaspoon full would produce 130 horsepower. In other words, the actual macro-scale machinery we make is quite grotesquely inefficient by comparison. All effort for small result because cars and food mixers work far away from the zone of poised criticality – the realm of fundamental biological substance where the dynamics of material processes and the regulation of informational constraints can interact on a common scale of being.

    The metaphysical implications: The problem with most metaphysical discussions of reality is that they rely on “commonsense” notions about the nature of substance. Reality is composed of “stuff with properties”. The form or organisation of that stuff is accidental. What matters is the enduring underlying material which has a character that can be logically predicated or enumerated. Sure there is a bit of emergence going on – the liquidity of H2O molecules in contrast to gaseousness or crystallinity of … well, water at other temperatures. But essentially, we are meant to look through organisational differences to see the true material stuff, the atomistic foundations.

    But here we have a phase of substance, a realm of material being, where all the actual many different kinds of energetic interaction are zeroed to have the same effective strength. A strong identity (as quantum or classical, geometric or bulk) has been lost. Stuff is equally balanced in all its directions. It is as much organised by its collective structure as its localised electromagnetic attractions. Effectively, it is at its biological or semiotic Planck scale. And I say semiotic because regulation by symbols also costs nothing much at this scale of material being. This is where such an effect – a downward control – can be first clearly exerted. A tiny bit of machinery can harness a vast amount of material action with incredible efficiency.

    It is another emergent phase of matter – one where the transition to classicality can be regulated and exploited by the classical physics of machines. The world the quantum creates turns out to contain autopoietic possibility. There is this new kind of stuff with semiosis embedded in its very fabric as an emergent potential.

    So contra conventional notions of stuff – which are based on matter gone cold, hard and dead – this shows us a view of substance where it is clear that the two sources of substantial actuality are the interaction between material action and formal organisation. You have a poised state where a substance is expressing both these directions in its character – both have the same scale. And this nanoscale stuff is also just as much symbol as matter. It is readily mechanisable at effectively zero cost. It is not a big deal for there to be semiotic organisation of “its world”.

    As I say, it is only over the last decade that biophysics has had the tools to probe this realm and so the metaphysical import of the discovery is frontier stuff.

    And indeed, there is a very similar research-led revolution of understanding going on in neuroscience where you can now probe the collective behaviour of cultures of neurons. The zone of interaction between material processes and informational regulation can be directly analysed, answering the crucial questions about how “minds interact with bodies”. And again, it is about the nanoscale of biological organisation and the unsuspected “processing power” that becomes available at the “edge of chaos” when biological stuff is poised at criticality.
  • Wayfarer
    3.9k
    It's not rocket science.apokrisis

    It's actually a lot more complicated than rocket science. Rockets are simple.

    Tour pulls the usual creationist trick. Imagine the world as the sterile laboratory of the synthetic chemist where everything has been pulled apart and kept well away from anything that might let it react or develop a structure.apokrisis

    That's not what the article says, though.

    I googled James Tour, he denies being creationist, but he has been associated with The Discovery Institute. And I don't much like them. So I guess he does have a creationist axe to grind.

    But I think the question still remains. The cardinal point of any living structure is that I manifests purpose, right from the very first. There has to be that purposive action for anything to be regarded as an organism, as distinct from a mineral. That intentional ability - not conscious intention, but the ability to adapt in pursuit of the goal of survival - that is unique to living forms, is it not? And that is what seems a cardinal difference from anything in the inorganic domain.

    This is where such an effect – a downward control – can be first clearly exerted. A tiny bit of machinery can harness a vast amount of material action with incredible efficiency.apokrisis

    Downward, from what? Upward, I presume, is from physical constraints - the laws governing the interactions of particles. What imbues symbols with the power to exert 'downward control'?
  • apokrisis
    1.9k
    It's actually a lot more complicated than rocket science. Rockets are simple.Wayfarer

    Yep. That was the joke.

    I googled James Tour, he denies being creationist,Wayfarer

    I googled him too. His line is that he is a messianic jew who thinks it is important to read the Bible every morning and meditate on its meaning. He doesn't hear God literally speaking to him, but he is very aware of His presence.

    So at least he is honest about the axe he is grinding. He has strong motivation to read the state of the science a particular way.

    But I think the question still remains. The cardinal point of any living structure is that I manifests purpose, right from the very first. There has to be that purposive action for anything to be regarded as an organism, as distinct from a mineral. That intentional ability - not conscious intention, but the ability to adapt in pursuit of the goal of survival - that is unique to living forms, is it not? And that is what seems a cardinal difference from anything in the inorganic domain.Wayfarer

    Isn't that what I'm arguing? It all starts when the ontically distinct thing of information enters the world. Or rather, semiosis and "sign processing". A molecule becomes a message when it material aspects are no longer what is causal. Instead it is the function that is being executed in the name of some higher organismic purpose which is the thing.

    A cell pore is just a protein switch. You can explain how it opens and shuts due to the critical instability of its mechanical arrangement of electrostatic bonds. It just wobbles back and forth for "no good reason at all" so far as any materialist can see. Indeed, a materialist would chuck such a flaky bit of machinery in the bin as being fundamentally useless.

    But for a living system, that complex molecule exists to perform a function. It is informational in the sense that it performs a crisp logical operation. Shut or open. Them's your sharp choices. And so now the further thing of "choice" is an ontological reality of the world.

    So the material world is already busy entropifying. It already has that global thermodynamic goal. That is how the Cosmos exists and persists. It keeps running down the hill by expanding and cooling.

    Then the biological world seems to change the game by suddenly expressing a negentropic desire. It wants to live and survive. It gets this idea in its head of being an organism.

    However while that is true from a particular point of view - the usual one that evolutionary theory use to tell its story from - it misses the larger point of view which is the grand thermodynamic one.

    Now it can be seen that life and mind simply accelerate entropification locally. For some reason, entropification has got held up. Negentropy has arisen by accident in the form of the barriers preventing quick entropification. And so life and mind can get going as more purposeful and designed structure that knows how to fulfil the Second Law's desires.

    So life's desire to exist and persist is a sub-goal - a negentropic one that subserves the global entropic one. The fact that it is the very opposite seeming kind of goal is exactly what you would expect if it is to be the complementary or mutual direction of action.

    If accidental negentropy has arisen in the Cosmos - like the way fossilised plankton got trapped as petroleum in ancient sedimentary rock - then what could be more fitting than purposeful negentropy arising as the matching response. Entropification which got locally deaccelerated can be locally reaccelerated again.

    Indeed, just as we humans are doing for those languishing fossil fuel stores in our valiant bid to waste them all to heat in great big planetary-scale burst.

    Of course you will protest again that life on earth can't be so pointless and futile as all that. You feel that being human must have some special significance.

    But my argument allows humans to invent their own meanings if they like - so long as they are intelligent enough to understand the constraints that have formed their nature so far.

    Thermodynamics only sets the ground conditions. Within that space, we can freely choose what to do. Literally nothing is stopping us.

    We do have a choice over climate change and ecocide for example. But also, that choice seems quite polarised in our debates about the issue.

    Either we can be hair-shirt greens and say we have to cut down to 100 million people living off permaculture in harmony with whatever scraps of traditional ecosystems remain. Or instead, we can trust to the exponential wonder of technology, the glory of the Singularity, to make a safe transition to our next evolutionary step.

    I've always been a greeny, but it is honestly a tough call. Life delights in presenting us with polarised dilemmas - the 50/50 choices that maximise the information content of existence. Damned if you do, damned if you don't, etc.

    A bit of a diversion in the argument it might seem. Yet really, I'm still talking about the same metaphysical issue. Everything turns out to be dialectically poised in existence for good reason.

    So if you are puzzled that the Universe seems to be torn between two purposes - entropy and negentropy - well really they are only the complementary aspects of the one (pansemiotic) process needed to bring existence into existence itself.

    I stress semiosis here because the basic idea was recognised by idealists like Schelling and Hegel - as their complementary intellectual response to the Newtonian-inspired Enlightenment realists. But Naturphilosphie and the like didn't get down to the basic infodynamic mechanism like Peirce managed to do.

    So this whole thread and the many others like it want to force a hard binary choice. Either brute materialism is right or religious-style idealism is right. By now it should be obvious that - socially - each needs the other as its "other". Our culture is divided sharply because the dichotomisation of our metaphysical choices is the mechanism that drives metaphysical advance (or intellectual negentropy) itself.

    But in the end, the bigger story is how the two extremes thus created can find their resolution, their synthesis. That is where naturalism or systems thinking comes up through the middle.

    Although no-one ever notices because you still have two cultures at war producing their vast clouds of hot air, or waste heat. Entropification always wins.
  • Wayfarer
    3.9k
    His line is that he is a messianic jew who thinks it is important to read the Bible every morning and meditate on its meaningapokrisis

    Oh yeah, and also 'Tour holds more than 120 United States patents plus many non-US patents.[36] He has more than 600 research publications,[37] with an H-index = 119 (100 by ISI Web of Science) and i10 index = 484 with total citations over 67,000 (Google Scholar).' But I guess the former outweighs the latter, right? You want to be careful about the kinds of aspersions you're engaging in, though.

    It all starts when the ontically distinct thing of information enters the world.apokrisis

    The overall aim of which is: to hasten the heat death of the universe. Of course, we can entertain yourselves with other ideas whilst so doing. So it's not really ontically distinct.

    It's not lumpen materialism, but it's still materialism, insofar as the overall principle is physical, namely, entropification, which just happens to throw up apparently meaningful things, like people, in the process.

    Whereas I am sure there is an implicit dualism in the 'epistemic cut', which remains outstanding, which Howard Pattee frankly acknowledges in that paper on the physics and metaphysics of biosemiology.

    I think your model is very much what would be needed to simulate life. But it doesn't have much to say about the actual problems of philosophy, apart from deflating them or subjectivising them.
  • apokrisis
    1.9k
    But I guess the former outweighs the latter, right?Wayfarer

    Jeez, I gave Tour points for being upfront and honest about his metaphysical prejudices. I then pointed out the obvious flaw in his reasoning. Thousands of workable lipid options make abiogenesis more comprehensible, not less.

    Deal with my actual answers, don't just divert.

    And yes, any number of research patents and papers in his field of synthetic chemistry don't outweigh faulty arguments motivated by a metaphysical prejudice.

    It's not lumpen materialism, but it's still materialism, insofar as the overall principle is physical, namely, entropification, which just happens to throw up apparently meaningful things, like people, in the process.Wayfarer

    It's stronger than "just happens". I said - as a metaphysical opposite or complementary thing - it would count as "meant to happen". It is another necessary fact. We can only know entropy to be a metaphysical thing because there is its metaphysical "other" from which it can measure its own existence.

    Of course, if we are just speaking from a human point of view, I can agree that you are objectively right if you want to argue our entropic contribution to the Cosmos is infinitesimal, while our negentropic significance seems way out of scale.

    The amount of actual entropy produced by human civilisation hardly registers in the big picture. Who cares if some random planet has a sudden temperature rise of 3 or 4 degrees?

    And when it comes to negentropy, we might well be the most complex, intelligent, and creative beings ever to exist in the Universe - or at least until we went 'poof' after the short, bright flare of an anthropocene.

    So yes, I am certainly a physicalist - a naturalist seeking immanent explanation with no spooky substances of any kind. And that rules out traditional notions of material substances as well as immaterial ones, as you know.

    But it doesn't matter how often I remind you of such subtleties, you will still want to lump me as "other" - the necessary move to make some variety of idealism come out as right for you.

    Again, I am neither idealist nor realist, materialist nor dualist.

    One has the choice. Either remain trapped eternally in the standard "philosophical" culture wars - the WWE of reductionists and theists thumping chests and banging heads - or find the very small door marked exit. Walk through and discover the third option that is naturalism, organicism, systems science.
  • MikeL
    236
    At face value there appears to be some support for the idea of a thermodynamic gradient that favours the direction of life. If the logic of this holds scrutiny then this is quite a big deal. It starts a whole series of cause and effect chains after 'the hump' that tend to run away. The fact that we don't know how all the molecules or membranes in the cell came to be there is an important point, but is weakened by the observation that they could be placed on the gradient. Based solely on thermodynamics, if the arguments presented by Apokrisis hold, it is feasible at least to suggest the molecules formed naturally somewhere at some point.

    Of course this all only points in the direction of life, and says Life could be that'a'way. It does not demonstrate 'life'. So, I think a key approach at this point is to find examples of molecular and cellular interactions that do not make sense in terms of cause and effect, while also scrutinising the thermodynamic claims about life a lot closer - If we can find an apparent sentience beyond the chemistry the table is turned once more.

    The sentience of the mind is a strong fallback position as Rich has highlighted, but I also think there is plenty of stuff to work with lying around in the world of molecules and cells. It should be noted that the idea of the mind as a holographic field was first proposed by noted Quantum Mechanist David Bohm.

    One such example that might constitute evidence of a sentience would be the organelle called mitochondria inside eurkaryotes. This is commonly thought of as the battery of the cell. Theory has it that the mitrochondria, who have their own genetic code (mitochondrial DNA, as opposed to nuclear DNA), invaded our cells, but our cells trapped them in a process known as endosymbiosis.

    So we all have symbiotes inside us! Because these symbiotes have their own mtDNA (mitochondrial DNA), this means that they should be free to multiply inside us like a virus. The thing is, the expression, replication and maintenance of mtDNA is :

    " Expression, replication, and maintenance of mtDNA require factors encoded by nuclear genes. These include not only the primary machinery involved (eg, transcription and replication components) but also those in signaling pathways that mediate or sense alterations in mitochondrial function in accord with changing cellular needs or environmental conditions. " quote

    : our cells stole their machinery and enslaved them.
  • MikeL
    236
    But my argument allows humans to invent their own meanings if they like - so long as they are intelligent enough to understand the constraints that have formed their nature so far.apokrisis

    That was a good post.

    Looking further into entropy and living systems I see there is no net positive gradient toward life afterall. I must have misunderstood what was being suggested. The lowered entropic states (the bonds and concentration gradients) come at a higher entropic cost. The environment is simply flushed through the container to achieve a cause.
  • Rich
    1.7k
    But my argument allows humans to invent their own meanings if they like - so long as they are intelligent enough to understand the constraints that have formed their nature so far.
    — apokrisis

    That was a good post.
    MikeL

    There is always some magic hidden in any materialistic research explanation of life. There has to be, because there is nothing there.

    In one breathtaking leap we go from some soup of chemicals to "humans inventing their own meaning". So you have chemicals, which satisfy Big Pharm (which pretty much determined academic curriculum nowadays) and then out of no where you have humans inventing meaning?? to make it digestible for those who are experiencing life as it unfolds. What is missing from the materialist-scientific description of life is one iota of intellectual honesty. It is a game of hide and seek. Where is the mind injected in this paper?

    Ultimately it is only a packaged story designed to satisfy the intended readership - usually to raise some money. Always, we are almost there.
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