So it can be said that the topological properties of networks constrain the types of flow that pass through it, but the level of structural isomorphism is inappropriate for the analysis of the expression of particular genes or sets thereof. — fdrake

Yes. The interesting point about genomic networks is that their internal processing structure could be - in principle - uncrackable and forever hidden. Can we reconstruct the way a neural network executes its function even with full knowledge of the weights of its nodes?

If the functionality is multirealisable, then a knowledge of some particular state of task-adapted componentry does not give a simple theory of the functional dynamics of the network.

We could still hope to model genomics at a higher level. That’s why I’m thinking of a description in terms of general logical principles. Like the repetition of units (as in segmented body plans) or timing information when it comes to regulating tissue growth and developmental symmetry breakings or bifurcations.

Boy, this gets complicated. I can see - half genes from mom, half from dad. Trait A from mom, Trait B from dad. But if it's a network, that's 1/2 mom's network and 1/2 dad's network. Not even that. How do you inherit 1/2 a network? Why would it fit with the 1/2 network from the other parent? I'm not arguing against what you're saying. — T Clark

That is a good point. A big constraint on the whole gene story is that there is this strong selection for the whole damn business being evolvable too. The genome both has to regulate development and also do its best to expose individual traits to the winnowing force of selection.

So while a distributed genome behaves as a processing network, it still wants to offer up traits on an individualised basis, not the whole package.

This was the argument for why we go from the simple gene rings of bacteria to the chromosomes of multicellular life. The chromosomes, with their recombination shuffling of the gene deck, look to be a mechanism that both preserves the coherence of the developmental network and allows traits to be exposed to evolution in a suitably individualised fashion.

The evolution of sex - the separation of the immortal germ-line - is another important step. It means the genome that runs the everyday body is kept out of the evolutionary fray. The trait-level view is the specialist role played by gametes, or sperm and egg.

I'm not a biologist, and have only tertiary knowledge in developmental biology.

Yes. The interesting point about genomic networks is that their internal processing structure could be - in principle - uncrackable and forever hidden. Can we reconstruct the way a neural network executes its function even with full knowledge of the weights of its nodes?

For a specific gene network, precise estimation of parameters would be the goal. To think of a genomic network as structurally isomorphic to a neural network is probably possible, but it will remove both specificities. I doubt, though I could be wrong, that genomic networks are necessarily concerned with message passing in continuous or quasi-continuous time like neural networks are; and seem to be constructed through a correlational analysis of genes to traits and genes to genes in terms of expression. I know there are counterexamples when analysing cellular differentiation.

If the functionality is multirealisable, then a knowledge of some particular state of task-adapted componentry does not give a simple theory of the functional dynamics of the network.

I think this is a truism. But it will not diminish the analysis of a specific genomic network.

We could still hope to model genomics at a higher level. That’s why I’m thinking of a description in terms of general logical principles. Like the repetition of units (as in segmented body plans) or timing information when it comes to regulating tissue growth and developmental symmetry breakings or bifurcations.

Dynamical systems theory is already being used. Street's reference to canalisation has a link to bifurcation theory.

Edit: I would rather attempt to keep this on topic than to sidetrack the discussion into your semiotic metaphysics, though.

Our bodies and natural selection must obey the laws of physics. If it didn't then we could all fly without the proper anatomy. — Harry Hindu

Physics certainly constrains biology. But what then isn't constrained is by definition free to happen. And this freedom is what demands further modelling.

In fact, this freedom is something we have begun to generalise by talking about computation, information, negentropy, modelling relations, semiosis, etc.

So rather than biology just being some small and accidental expression of something physics failed to forbid, we are realising that it leads to a whole realm of "mind". The fact that physics creates a hard baseline of constraints in itself opens up a matchingly definite counter-possibility of a hard superstructure of rather absolute freedoms. Information becomes a real source of causality acting back on the world in evolutionary fashion.

That is why talk of genenomic networks being like neural networks in having a "separate adaptive intelligence" makes sense. A test of how much this is the case would be to consider the resilience that genomes show if you try to knock out one developmental pathway, and yet the genome can reorganise to still produce the desired functional outcome.

One super interesting thing to bring up in relation to this - I might start another thread on this down the line - is in following Robert Rosen's contention that biology is, contrary to what is commonly thought, a more general science than physics, insofar as biological systems have a richer repertoire of causal entailments than do physical ones. — StreetlightX

Yep.

To think of a genomic network as structurally isomorphic to a neural network is probably possible, but it will remove both specificities. — fdrake

That would be the research question. We do have a variety of neural network architectures as candidates. The genome could be just like of those, or something different.

I doubt, though I could be wrong, that genomic networks are necessarily concerned with message passing in continuous or quasi-continuous time like neural networks are — fdrake

Surely genomic networks would have to be very much always monitoring the state of the cell? The biophysics now makes the point that cellular machinery is always on the point of breaking down and so needing the right nudge to build itself back up.

Direct evidence that timing matters is how the most time-critical regulation - that of the respiratory chains of mitochondria - is handled right on the spot by mitochondrial genes.

So most of the mitochondria genes have migrated to the central chromosomes. The time lags are not so critical. But where fast response is needed, the genes are kept right where the reactions are taking place.

Dynamical systems theory is already being used. Street's reference to canalisation has a link to bifurcation theory. — fdrake

Of course. But this is now different if instead of the dynamics being something directly physical - the self-organising dynamics at a "chemical" level - we are talking about a dynamics-based information model.

So this is about the genome as analog computation. A dynamical description might apply. But at the level of disembodied information rather than embodied physics.

It is just the same as the problem of talking about the representation of the world in the brain. Patterns of neural activity don't just simply "look like" the physics of the world they are modelling. There is certainly some topographical relationships preserved, but also a hierarchy of functional specialisation. Activity in one small blob of the visual cortex produces our sense of colour, another that of motion.

So the old mental picture of the genome was a "flat" network at best. It was just some kind of straight transcription layer with not particular internal complexity.

Once we start talking about neural networks, we are asking just how much internal hierarchical organisation, and hence "mind-like" complexity, there is going on. A very different ball game.

The nodes in neural networks are placed there by modellers and use a message passing algorithm to update parameters linking the nodes. The nodes in gene expression networks are discovered through a kind of cluster analysis. The nodes mean different things, the nodes are generated by different things. Nevertheless if there are flows on the networks there will be general mathematical descriptions of the flows. The flows will mean very different things for the different systems.

Generally, just a great big citation needed on the material in your post.

The nodes in neural networks are placed there by modellers and use a message passing algorithm to update parameters linking the nodes. The nodes in gene expression networks are discovered through a kind of cluster analysis. — fdrake

I see a confusion here. Human-made machinery of course is engineered to be physics-free and so the hardware is completely generic in terms of its informational capacity. The network boils down to a collection of binary switches that represent a memory state. So there is a strong division between memory and processing. The divorce between the setting of weights and the dynamics of any "processing interaction with the world" is rather absolute.

From that mechanical basis, a neural network will then evolve some operational state. That can then be described in functional terms. Some collection of nodes, with their pattern of weights, will "act like a particular feature detector". We will want to point to that functional element of the internal model as a cluster that analyses. But really, that seems a heuristic rather than a properly motivated claim. A mathematically soft one, rather than a rigorously grounded one.

Then with real-life genomic networks, we can't even really claim that they even want to start with actual digital circuitry - the binary switches that enforce a strong divorce between memory states and dynamical behaviour. Genes may approach some kind of digitalism, and yet still be essentially "analog all the way down".

For me, this is still the great unsolved riddle of life and mind. Sure, mostly science presumes a digital ground - life and mind are just super-complicated machinery. But ontologically, I take the semiotic view where creativity, spontaneity and uncertainty are irreducible (even if pragmatically constrainable). And so confusion will arise if genomic networks are still imagined as having to rest on mechanically stable foundations - actual little hardware switches.

Generally, just a great big citation needed on the material in your post. — fdrake

Hah. Yep. I'm afraid I've deliberately steered clear of gene expression for the past 15 years, rather waiting for the science to sort itself out. But biophysics has suddenly got interesting, so gene regulation again becomes interesting for me as now it is easier to see what it actually has to control. And that has become much less due to the fact that molecular machinery does most of the hands-on regulation.

A cell isn't a bag of chemistry but itself a highly regulated, almost machine-like, network of entropy flow or dissipative structure.

Again, the hierarchy of control is becoming apparent. Molecular machinery is like a whole new level of regulation in itself, whereas before there was only a genetic blueprint and a chemical soup.

Now, what's philosophically interesting to me about all this is that, if I understand the implications correctly, it throws into question the specificity of life itself, or rather what does and does not count as 'alive'. — StreetlightX

The following may be somewhat tangential to your concerns, but what the hell?

In the ordinary sense we all broadly understand the distinction between "living' and 'non-living'. As per Wittgenstein; there is no determinate essence that could define the difference; rather the difference is found in the whole context of networks of "family resemblances" between phenomenal manifestations that we think of divergently as either living or non-living.

Since I have been reading his works lately Michel Henry is also much in my thoughts at the moment. He draws what he sees as an all-important distinction between Life and Being. Since Being is the always-already externalized world, life, for Henry, cannot be found there at all, but we will find only entities which do or do not manifest phenomena that we might understand to be 'life functions'.

And you're also right that this means that what matters is the evolutionary history of any particular network, such that we can't say what ought to or not belong to any particular network in advance (isn't one of the marvels of evolution it's ability to hijack or incorporate the environment into it's dynamics?). But this, I want to say, has conceptual consequences for what we understand 'life' to be, and how fragile a notion it is. — StreetlightX

So what would you say are some consequences of this idea that what matters in biology is the situatedness of the molecules and the environment in its unique historical evolutionary development?

Here's something I heard on a news bulletin today that *might* be relevant. It concerned the fact that Australia is one of the only countries where there are more boys being born than girls. This is particularly so in the ACT - the Australian Capital Territory, where the Australian Federal Capital is situated. There, the ratio is close to 110 boys born for every 100 girls - thus lending weight to researchers' theory that more boys are born where mothers believe that their financial prospects are good. Story is here. (I just loved this story.)

That's what I meant. Teleological language is useful to paraphrase stuff like that. — fdrake

Language isn't teleological. It's that most of human minds are, and they project that onto reality in how they use a language. There are others that try to avoid that, and in so doing, recognize the faults of the language and attempt to create new terms to use that doesn't lead to one simply paraphrasing, but actually getting at what it is that we are talking about independent of any subjective projections.

Physics certainly constrains biology. But what then isn't constrained is by definition free to happen. And this freedom is what demands further modelling.

In fact, this freedom is something we have begun to generalise by talking about computation, information, negentropy, modelling relations, semiosis, etc. — apokrisis

That isn't freedom. Computers are designed to perform many different functions - from creating a document and printing it, to surfing the internet, to playing 3D games. This wide range of things that computers do doesn't mean that they are free to do something they weren't designed to do, like fly off your desk and make you breakfast.

Think. Universal Turing computation.

Imagine at some future time there was a complete list of all the things which could influence the expression of an arbitrary assemblage of genes. Call this collection P. At any time before this collection is made, there will be a subset Q(t) of P that represents the current list of all influences on genetic expressions. — fdrake

Hm, there's a bit of an ambiguity here, I think, already at the level of formulation: any genomic network is already a space of possibilities, such that some parts of the network may be active in any particular process of expression, while other parts may not be - and just which parts are and are not may be dependent on certain (regulatory) genetic and epigenetic conditions. This means, further, that what even counts as 'a' network is not fixed, and individuation is itself dependent on the parameters of any one investigation - what we count as belonging or not belonging to 'a' network (the space of possibilities), and by extention, what we count as 'a' network to begin with, is itself not something fixed in advance. Of course this is just the scientific process: fix the boundaries of the phenomena you want to study, hold all else equal, then poke around. When you ask then:

Can we tell at any time whether the set of properties is exhaustive, and that we have provided a spanning partition of P generated by the properties? If the set of studied gene expressions were fixed and finite, in principle this would be possible.

- The problem, it seems to me, is that even if we could get around the combinatoric issues, any exhaustive list of properties would be in some sense only so by fiat. And if so, I'm not sure how much we can milk the distinction between P and Q(t) to really speak about any demarcation between the biotic and the abiotic.

The other, intimately related, conceptual issue I see is that because genomic networks are complex, the activation or deactivation of certain parts of the network (via regulation) may alter the very possibility space itself: what was once an 'influence' which would never have been able to play a role in the expression of a certain trait, becomes an influence, or vice versa. And this change may have knock-on effects with respect to other 'possible influences' as well; things get confusing, I think, because at stake are second-order possibilities: 'possible possibilities', as it were. And again, at this point, I'm not sure how stable any distinction between P and it's subset Q(t) might be...

In the ordinary sense we all broadly understand the distinction between "living' and 'non-living'. As per Wittgenstein; there is no determinate essence that could define the difference; rather the difference is found in the whole context of networks of "family resemblances" between phenomenal manifestations that we think of divergently as either living or non-living. — Janus

Sure, sure, but the question is what kind of licence developmental biology allows us when it comes to speaking about life in the terms it provides. The context here is quite rigoursly defined, and is not at odds with Witty's insights.

Since I have been reading his works lately Michel Henry is also much in my thoughts at the moment. He draws what he sees as an all-important distinction between Life and Being. Since Being is the always-already externalized world, life, for Henry, cannot be found there at all, but we will find only entities which do or do not manifest phenomena that we might understand to be 'life functions'. — Janus

Yeah, I'm familiar with Henry - I think he's an absolute genius - but I also think his conception of 'Life' qua self-affecting, pathic 'Subjectivity' is - there's no nice way to put this - entirely vacuous. I wrote a long, multipost thread in the old forum about this - on his conception of immanence in particular - which is lost to time now, but yeah, I've never found his mobilization of the concept of 'Life' very - if at all - useful, unfortunately.

Computers are designed to perform many different functions - from creating a document and printing it, to surfing the internet, to playing 3D games. This wide range of things that computers do doesn't mean that they are free to do something they weren't designed to do, like fly off your desk and make you breakfast. — Harry Hindu

Think. Universal Turing computation. — apokrisis

Think. Can a Universal Turing computer fly off the desk and make you breakfast?

Now, what's philosophically interesting to me about all this is that, if I understand the implications correctly, it throws into question the specificity of life itself, or rather what does and does not count as 'alive'. That is, if we think in terms of networks, how is it possible to think the specificity of life itself, insofar as the dynamics of genome networks are defined as much by extra-biological factors as they are biological ones? Because extra-biological factors are as just as important as biological factors in the process of gene expression, it becomes very hard to draw any kind of hard diving line between the two. This also follows, as a matter of principle, from the fact that networks are simply indifferent to the 'content' of the nodes which constitute them: it's all just a matter of the organization and threshold levels. — StreetlightX

How does this issue have implications for our thoughts about "what does and does not count as alive"?

It's not news that organisms like us need oxygen to stay alive. That gives us no reason to speak as though oxygen is alive.

The fact that the boundary between an organism and its environment is fuzzy and permeable doesn't mean there's no difference between the organism and its environment, and doesn't mean there's no difference between animate and inanimate objects.

Sure, sure, but the question is what kind of licence developmental biology allows us when it comes to speaking about life in the terms it provides. The context here is quite rigoursly defined, and is not at odds with Witty's insights. — StreetlightX

Of course, developmental biology will add to our stock of "phenomenal manifestations that we think of divergently as either living or non-living" and may even change our minds as to whether we think of particular phenomena as living or non-living. It may even lead some thinkers to dissolve the distinction altogether which is what you and fdrake seem to have been alluding to in some of your comments.

but I also think his conception of 'Life' qua self-affecting, pathic 'Subjectivity' is - there's no nice way to put this - entirely vacuous. — StreetlightX

It doesn't surprise me that you would think that given the presuppositions that are inherent in your approach. In a way I agree; life, as conceived by Henry is vacuous from the viewpoint of the determinate world of "ek-static phenomena". However, it is anything but vacuous in terms of living affection; which is really Henry's point.

It may even lead some thinkers to dissolve the distinction altogether which is what you and fdrake seem to have been alluding to in some of your comments. — Janus

It's not so much the goal to 'dissolve' the distinction as to 'denaturalize' it, to make it an object less of scientific analysis than political and ethical judgement.

It doesn't surprise me that you would think that given the presuppositions that are inherent in your approach. In a way I agree; life, as conceived by Henry is vacuous from the viewpoint of the determinate world of "ek-static phenomena". However, it is anything but vacuous in terms of living affection; which is really Henry's point. — Janus

But Life is not vacuous from the ek-static point of view: as Henry is everywhere at pains to point out, Life is the quite literally the essence of manifestation; Henry's critique of the whole phenomenological tradition before him is that time and time again, it comes across Life, only to end up ignoring it. The problem, if anything, is the other way around - it's the Henry's own philosophy is almost entirely uncritical, in the Kantian sense - Life is the essence of manifestation, but it cannot, ironically, account for the manifestation of the ek-static phenomena which it everywhere underlies. This is not an original critique, and has been pointed out time and time again by many commentators of Henry's work - and entirely rightly, I think.

Here is Renaud Barbaras: "Although he discovers auto-affection at the heart of aIl givenness at a distance, Henry never heads down the opposite path to discover how auto-affection leads into intentionality, how we can go from immanence to transcendence.... Henry cannot provide answers to these questions precisely because he argues that they concern two completely impenetrable regimes of appearance. " (Barbaras, The Essence of Life: Desire or Drive?); and Dan Zahavi: "Henry operates with the notion of an absolutely self-sufficient, non-ekstatic, irrelational self-manifestation, but he never presents us with a convincing explanation of how a subjectivity essentially characterized by such a complete self-presence can simultaneously be in possession of an inner temporal articulation; how it can simultaneously be directed intentionally toward something different from itself; how it can be capable of recognizing other subjects (being acquainted with subjectivity as it is through a completely unique self-presence); how it can be in possession of a bodily exteriority; and finally how it can give rise to the self-division found in reflection:" (Zahavi, Subjectivity and Immanence in Michel Henry). See also Ray Brassier's devastating reading of Henry in his Alien Theory, which I won't quote here.

Finally, your own point that Life isn't vacuous form the point of view of Life is... well, just a tautology. But again, this is all very off-topic!

It's not news that organisms like us need oxygen to stay alive. That gives us no reason to speak as though oxygen is alive. — Cabbage Farmer

Because the topology between 'inside' and 'outside' at stake here is different: it's not just that there are 'organisms' on the one side and 'oxygen' on the other; it's that epigenetic and environmental influences are already 'on the side' of life, or rather the organism, to begin with. That's the whole point of focusing on networks: whether the nodes in a genomnic network are biotic or abiotic is a matter of sheer indifference from the point of view of the network, which can only 'see' relations, topologies, and threshold values. While it's true, as others have pointed out, there is a kind of specificity provided by the spatio-temporal dynamics of the cellular environment itself, this only serves, as I've argued, to worsen the ambiguity because those dynamics themselves also cannot be neatly parsed along biotic/abiotic lines.

The problem is that life traverses both 'sides' in the manner of a mobius strip or klein bottle, where the distinction between inside and outside cannot really, be made:

Because the topology between 'inside' and 'outside' at stake here is different: it's not just that there are 'organisms' on the one side and 'oxygen' on the other; it's that epigenetic and environmental influences are already 'on the side' of life, or rather the organism, to begin with. That's the whole point of focusing on networks: whether the nodes in a genomnic network are biotic or abiotic is a matter of sheer indifference from the point of view of the network, which can only 'see' relations, topologies, and threshold values. While it's true, as others have pointed out, there is a kind of specificity provided by the spatio-temporal dynamics of the cellular environment itself, this only serves, as I've argued, to worsen the ambiguity because those dynamics themselves also cannot be neatly parsed along biotic/abiotic lines.

The problem is that life traverses both 'sides' in the manner of a mobius strip or klein bottle, where the distinction between inside and outside cannot really, be made: — StreetlightX

I still don't see what difference you're suggesting.

So far it seems perhaps you're mistaking an abstract mathematical representation of some interactions in a physical system, for the physical system itself.

It's a matter of indifference, "from the point of view" of a geometrical abstraction, what the abstraction is an abstraction of. It's no surprise if a geometrical representation of complex physical interactions omits a great deal of information, and no surprise if distinctions that are relevant to us in some contexts are not relevant in the framework of that geometrical representation.


The organism ends at its own fuzzy boundary, but the environment does not. Organisms are interwoven with their environments, and are entirely composed of material from their environments over time. The material we're made of is only borrowed for a while.

That material is organized into a physically coherent structure in space and time, so the organism is distinguishable in its environment according to principles of biological organization; but it remains in constant physical interaction with a local physical context, in a continuous exchange of matter and energy.

Given a particular "set of genes", which may be characterized physically; and a range of possible environmental factors, which can be characterized as distinct sets of physical factors; there corresponds a range of phenotypical outcomes, which can be characterized as distinct sets of physical states or physically determined capacities or "traits" of the organism. The organism, its genes, its environment, and its traits all have concrete physical existence in space and time, and can be distinguished accordingly.

Now you say some mathematician comes along to represent those concrete physical relations abstractly by sketching beautiful geometrical topographies in his notebook. And in that abstract mathematical representation, perhaps, "it is a matter of indifference" whether the nodes are biotic or abiotic.

Does that mean anything more than that, once you abstract from real physical context, and represent complex physical features of an environment as mathematical "nodes", you may lose sight of the complex physical features, and forget to look back and forth between the enchanting sketch and the real world it is designed to represent?

Depending on what sort of representation we're discussing, I suppose it may also be a matter of indifference whether the organisms and traits and environmental factors represented in the diagram are actual or only possible -- such maps may represent relations of sets of possible genetic codes, possible environmental factors, possible traits -- and not a single real thing in the world. In fact there's a difference between my genes, my traits, and the environments I've actually passed through over time, on the one hand, and all the environments I could possibly have passed through in a mathematician's dream, and all the traits I might have had if things had gone otherwise, on the other hand.

That may be "a matter of indifference from the point of view of the representation", too. But it's not a matter of indifference to real organisms that suffer real environments.

It's not so much the goal to 'dissolve' the distinction as to 'denaturalize' it, to make it an object less of scientific analysis than political and ethical judgement. — StreetlightX

OK, but that leaves me wondering what criteria the political and ethical judgements will ideally be based upon.

But Life is not vacuous from the ek-static point of view: as Henry is everywhere at pains to point out, Life is the quite literally the essence of manifestation; Henry's critique of the whole phenomenological tradition before him is that time and time again, it comes across Life, only to end up ignoring it. — StreetlightX

You seem to have misunderstood what I was alluding to. I wasn't trying to suggest that Henry wants to stress that life is vacuous "from the ek-static point of view". Of course every phenomenon is a manifestation of life for Henry. The point is that life cannot be analyzed from the ek-static point of view; an intentional account of it cannot be given, and no account of life can be inter-subjectively corroborated. It is on account of this that I said life (I probably should have that the idea of life is vacuous instead, because obviously life, however you conceive it cannot be vacuous in itself) is vacuous from the perspective of "the truth of the world". and I think this is pretty much behind what you are saying when you say that

his conception of 'Life' qua self-affecting, pathic 'Subjectivity' is - there's no nice way to put this - entirely vacuous. — StreetlightX

Thanks for the other references, anyway, but, really I am just beginning to explore Henry's ideas, and I would much rather flounder my way to a creative misreading, if that's what it is to come to; than be 'corrected' by 'expert' secondary opinions.

The point is that life cannot be analyzed from the ek-static point of view; an intentional account of it cannot be given, and no account of life can be inter-subjectively corroborated. — Janus

Ah fair enough, that makes more sense.

Thanks for the other references, anyway, but, really I am just beginning to explore Henry's ideas, and I would much rather flounder my way to a creative misreading, if that's what it is to come to; than be 'corrected' by 'expert' secondary opinions. — Janus

Heh, that's fine too, and despite my critical take on Henry, I still think he's an absolutely incredible philosopher who deserves to be widely studied and read. I think his intitutions regarding intentionality are absolutely right, even if I think his 'solution' is entirely wrong! Glad you're reading him nonetheless.

OK, but that leaves me wondering what criteria the political and ethical judgements will ideally be based upon. — Janus

Man, that's a whole other kettle of fish, but, at a minimum, I'd say that part of the challenge of both ethics and politics - the myriad differences between them notwithstanding - is that there can be no ideal criteria, only criteria immanent to the context(s) of judgement in which judgement must be exercised. But again, that's outside the scope fo this thread.

. The organism, its genes, its environment, and its traits all have concrete physical existence in space and time, and can be distinguished accordingly. — Cabbage Farmer

But I'm talking about a process: the process of gene expression, and the question of how this process, which necessarily traverses both biotic and abiotic elements, entails an inability to situate life clearly on the side of the biotic. If anything, the abstraction lies in breaking down the process into it's analytic elements and ignoring its holistic aspects. If, on the other hand, I speak about the process in terms of a network, it is because network thinking best brings out the processual nature of what is at stake. It is no use, as such, in simply speaking of individual entities like 'organism', 'environment', etc - none of these capture of processual specificity of what is at stake here.

It is no use, as such, in simply speaking of individual entities like 'organism', 'environment', etc - none of these capture of processual specificity of what is at stake here. — StreetlightX

I think perhaps this is a mountain out of a molehill. While there are some processes that are abiotic mixed in with the biotic (like the networks with biotic molecules and environment), this does not mean that we cannot distinguish abiotic and biotic processes altogether. Biotic processes are ones that have a mix BUT have the known constituent parts that comprise biological molecules. Thus if ATP is going, DNA sequencing, etc. etc. then more than likely this is biological. As we discussed biology is not just the networks abstracted but instantiated in the very evolutionary way it has "solved" the problems of the environment. This is something that has not been replicated and can perhaps be mapped, but mapping it in abstraction is not the same thing.

Biotic processes are ones that have a mix BUT have the known constituent parts that comprise biological molecules. — schopenhauer1

But this would include say, ecosystems and river catchments. In any case I'm not arguing that we can't distinguish between biotic and abiotic processes: my point is rather that life itself traverses both such that life cannot be defined in strictly biotic terms. And to be extra clear, I'm also not arguing that we can't distinguish between life and not-life, only that such a distinction cannot be 'read off' the phenomena themselves in any straightforward way, if only because what exactly would and would not count as 'a' phenomena is precisely what is in question: a question of individuation.

It's easy make the distinction of life and non-life when talking about a giraffe and a cup. But what about when talking about a virus, or the beginnings of life that scientists theorize about that were simply self-replicating molecules? Is a DNA molecule alive? What about a liver in a jar?

But this would include say, ecosystems and river catchments. In any case I'm not arguing that we can't distinguish between biotic and abiotic processes: my point is rather that life itself traverses both such that life cannot be defined in strictly biotic terms. And to be extra clear, I'm also not arguing that we can't distinguish between life and not-life, only that such a distinction cannot be 'read off' the phenomena themselves in any straightforward way, if only because what exactly would and would not count as 'a' phenomena is precisely what is in question: a question of individuation. — StreetlightX

Again though, biological systems are a series of networks that are hierarchical. They are relational, and if some important components of the "nodes" are taken away, the system stops functioning. However, the core constituents and their evolutionary development are what matters here to distinguish it from any old system.

biological systems are a series of networks that are hierarchical. They are relational, and if some important components of the "nodes" are taken away, the system stops functioning. — schopenhauer1

This description would apply to literally any complex system, living or not. And besides, to repeat for the third time, the question is not whether or not we have a criteria for a living system or not, but whether one can discern whether or not such a criteria would apply to begin with. If you keep ignoring the fact that at issue is a question of individuation (what does and does not count as 'a' system), you'll miss what I'm trying to say.

This description would apply to literally any complex system, living or not. — StreetlightX

I don't think so because you are forgetting the part about biological constituents with the unique evolutionary ways that the organism uses to solve problems in the environment.

but whether one can discern whether or not such a criteria would apply to begin with. If you keep ignoring the fact that at issue is a question of individuation (what does and does not count as 'a' system), you'll miss what I'm trying to say. — StreetlightX

I think though these two problems are related in the case of your problem. Where are the limits of biological systems? Should there be limits to any system which is open and sharing some form of information? Do you accept that there can be discrete units that relate with other discrete units? As i said there is a hierarchy for each discrete unit of organism.