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. — StreetlightX

Really interesting. You, Apokrisis, fdrake, and a few others are often discourteous enough to try to tie the simplifications we play with in philosophy to the irreducibly complex real world.

This is not exactly the same thing, but what you've written reminded me of something I read in an essay by Stephen J. Gould. He wrote that the most important genes in terms of impact on the organism are often those that control the rate or sequence of expression of other genes. That made a lot of sense to me - that it is a network of interactions that you can't just hold in your mind as one piece as opposed to a stacking of bricks in a wall.

Also, can you describe the "extra-biological factors" you're talking about.

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.

There's alot more to say, but as usual, I'm going to stop before I go on too long. — StreetlightX

Have you not heard of biosemiosis yet? I am sure @apokrisis can explain this. I am not even being facetious here, this seems like a great example of how this fits into the biosemiosis framework.

Really interesting. You, Apokrisis, fdrake, and a few others are often discourteous enough to try to tie the simplifications we play with in philosophy to the irreducibly complex real world. — T Clark

Come now! Philosophy is no more or less rich than the 'real world' of which it speaks - you give it too little credit!

He wrote that the most important genes in terms of impact on the organism are often those that control the rate or sequence of expression of other genes. — T Clark

Yeah, Gould was among the greatest champions of those who were dissatisfied with the 'gene-centrism' of biology, but even then, he hewed closely to the idea that genes were nonetheless the only units of heredity relevant to organisms, when this is more and more no longer thought to be the case.

Yeah, Gould was among the greatest champions of those who were dissatisfied with the 'gene-centrism' of biology, but even then, he hewed closely to the idea that genes were nonetheless the only units of heredity relevant to organisms, when this is more and more no longer thought to be the case. — StreetlightX

The network approach really kicks sociobiology in the balls, which I'm sure Gould would have loved.

In terms of evolution, this matters because understood as such, the 'unit' of evolutionary variation can no longer be thought to be single genes, but rather, the an entire genomic network — StreetlightX

Where do ‘species’ fit in? Surely they rate a mention at least as ‘nodes’ in the network?

Yeah, biosemiosis fits into this insofar as signs serve to regulate the dynamics of both development and evolution and helps us to speak of 'directedness' in both, but I'm unsure how to triangulate that with the question of life posed in the OP.

Yep, the less sociobiological pseudoscience, the better.

Yeah, biosemiosis fits into this insofar as signs serve to regulate the dynamics of both development and evolution and helps us to speak of 'directedness' in both, but I'm unsure how to triangulate that with the question of life posed in the OP. — StreetlightX

Doesn't it have to do with something like negentropy? Life appears to go against the Second Law of Thermodynamics, but it really isn't because its an open system that takes in free energy from its surroundings and produces heat and entropy back. Life is what is a negentropic open system.

I guess that may be more at the biophysics level of definition. But, are you asking whether life needs to have some sort of material substance like genetic material, to be considered life or is it more about the arrangement of the material? And if it is the arrangement of the material, what makes it different from any other arrangement of material? I'm just wondering if you can break down your post into a succinct question as far as the question of life you are proposing.

That is, if we think in terms of networks, how is it possible to think the specificity of life itself — StreetlightX

The problem I see here is you seem to be arguing that network topologies force their organisation on biological structure in a rather crystalline fashion. So something brute about possible topological arrangements would impose itself on biology and greatly restrict the variety of body structure that genes could encode.

But the argument is that genes are organised like neural networks and so embody a plastic intelligence. As you say, the genetic information would be distributed as a pattern of network weights. Yet in being a neural network, the network topology wouldn’t simply impose its own crystalline structure on the biology. Instead, the network could represent any kind of biological design as the “image it holds in mind”.

So just as a neural network can be trained to recognise any pattern, gene expression would be the same in reverse - the capacity to output any learnt pattern. The same intelligence of course helps to explain how the genome can recognise the current state of the body so as to respond appropriately in the first place. So really the genome is a pattern matching system.

And as such, there doesn’t seem any strong reason to suggest that the genome would be limited in the variety of states it could choose to represent. The limits such as they are would be more the logical ones - like the rules to generate bilateral symmetry and the repetition of segments - than topological ones. And that in itself is evidence that the gene networks must be operating at an intelligent level - actually relying on logic-like operations to switch and direct body development.

Where do ‘species’ fit in? Surely they rate a mention at least as ‘nodes’ in the network? — Wayfarer

The OP is mostly concerned with developmental dynamics rather than evolutionary dynamics (despite the thread title!), so at this point the 'scale' of the discussion is limited to individual ontogeny rather than species-level phylogeny. There is, of course, the stupidly interesting question of former influences the latter, but that's probably a bit outside the bounds of the OP itself. I will say though, that one can think of a species as itself an individual (that is, subject to processes of individuation), which can itself populate a node among a larger ecological network.

Doesn't it have to do with something like negentropy? Life appears to go against the Second Law of Thermodynamics, but it really isn't because its an open system that takes in free energy from its surroundings and produces heat and entropy back. Life is what is a negentropic open system. — schopenhauer1

The problem is that negentropy defines any type of organization, from whirlpools to star systems. That is, negentropy isn't specific to life, even as life counts as among the most magnificent examples of negentropic organization.

I guess that may be more at the biophysics level of definition. But, are you asking whether life needs to have some sort of material substance like genetic material, to be considered life or is it more about the arrangement of the material? And if it is the arrangement of the material, what makes it different from any other arrangement of material? I'm just wondering if you can break down your post into a succinct question as far as the question of life you are proposing. — schopenhauer1

I guess the basic issue I'm grappling with is this: a genomic network is essentially indiscriminate with respect to what it counts as among its nodes - from a network perspective, whether a node is a biological element (say, DNA) or not is more or less irrelevant. All a network 'sees' is relations, structure, and threshold values. Of course, genes are necessary to, well, gene expression. But on the other hand, genes are also entirely inert, and they would in fact do and be nothing without the extra-biological scaffolding which enables that expression to take place in the first place. Consider this expanded, mirrored version of Waddington's epigenetic landscape:



Here it's more clear that life takes place 'in between' gene and environment, or the biological and the non-biological, which makes its exact specification very hard to place. Perhaps I can put it this way: if one can't identify the biological alone with life (insofar as there can be no such thing, strictly speaking, as 'biology alone'), then how exactly are we to situate 'life?'. I don't think, by the way, that this question can be answered categorically. I ultimately think that this is a political and even ethical question, rather than a strictly empirical one, but I want to specify, on the side of the empirical, as it were, why this would be the case.

I think your OP's missing a step @StreetlightX, you go straight from the influence of abiogenic factors on gene expression without mentioning their mediated relationship through cellular differentiation - which is determined both by systematic/topological factors of a specific cell's cellular environment but also the standing of the differentiating cell within its environment (specific, point-like values that realise the network to a specific context). So the developmental process is always-already specific since it articulates the developmental trajectories of cells in accordance with things that generally condition them.

Further, networks are individuated by more then their topological properties - you can have two networks with graph isomorphism: this states, roughly, that the relevance structure of the system is the same but have both different nodes (rendering the graph specific and individuated from its topological equivalents precisely because they are indexed to different genes) and also different flows on the network (more than one way to 'pass a current of information' through the graph). 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.

The specificity comes in the application of general principles (like generating co-expression networks of specific genes) to individual gene clusters - discovering the clusters the process -. Specificity is always-already part of the developmental process for a given organism, but not necessarily part of the methodology of its analysis.

Perhaps I can put it this way: if one can't identify the biological alone with life (insofar as there can be no such thing, strictly speaking, as 'biology alone'), then how exactly are we to situate 'life?'. I don't think, by the way, that this question can be answered categorically. I ultimately think that this is a political and even ethical question, rather than a strictly empirical one, but I want to specify, on the side of the empirical, as it were, why this would be the case. — StreetlightX

The problem I have is with the idea of "biology alone". Biology is not a self-contained set of substrates, but a fluid dynamic between certain macromolecules and the environment in a series of physical processes- some described probabilistically, some perhaps more straightforward (and all of it it perhaps biosemiotically). Thus it isn't just DNA, but the networks that they produce to create more complex processes. The networks that you describe may be analogous, if we were to isolate it in a network mapping way, but it is its situatedness, along with other biological substrates like DNA, cells, proteins and generally all the macromolecules that are found in lifeforms, that make it biological. The evolutionary history of how these networks came about and its unique way of solving problems using its structural constituents to influence its growth and development is what matters here.

In terms of evolution, this matters because understood as such, the 'unit' of evolutionary variation can no longer be thought to be single genes, but rather, the an entire genomic network (one consequence of this is that one can no longer talk about DNA as a simple 'blueprint' for life. — StreetlightX

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.

Can a network change without a change in any specific gene? What establishes the network? Other genes? That would mean the network establishes the network. What mutates? I guess this type of genetic network would make the whole structure more stable, since everything's tied to everything else. As a civil engineer I say that the reason wood framed houses hold up so well is that there are thousands of nails and hundreds of pieces of wood all tied together.

Crap - you've given me more stuff to add to my reading list. I'm not as fast a reader as you guys.

The idea is that there are multiple 'ropes' which underlie the expression of any one trait, and cutting one, or even rearranging the organization of the ropes, may or may not affect the final outcome. Only by understanding the network and the interactions among it, may we understand how gene expression takes place — StreetlightX

If you cut one, or rearrange the organization of a set, and it doesn't affect the outcome (the expression of that trait), then it would be safe to say that that particular gene that was removed, or that particular arrangement of sets of genes that was rearranged, doesn't affect the expression of that trait. That is to say that there isn't a causal connection between that gene or arrangement of genes and that particular trait.

Biology is beholden to the laws of physics. You can't have the findings of two different fields contradict each other. Biology is just a sub-discipline of physics. Humans tend to put things into little boxes, including fields of science, which is ultimately an explanation of the world as a whole.

@Harry Hindu

Biology is beholden to the laws of physics. You can't have the findings of two different fields contradict each other. Biology is just a sub-discipline of physics. Humans tend to put things into little boxes, including fields of science, which is ultimately an explanation of the world as a whole. — Harry Hindu

Really? The types of question appropriate in biology are a lot different from the types in physics. There are differences on the entities concerned, the relevant explanatory frameworks and the types of experiment conducted. That a biological system does not contradict any physical laws is one of the least interesting features of a biological system: the interesting ones concern its biology.

A reduction of biology to physics methodologically is pointless, philosophically a reduction of the living to the non-living is interesting though. Perhaps it's useful to say that the living is composed by the non-living in some manner, however.

'it's all made of particles!'
'is the tendency of negatively charged particles to repulse negatively charged particles made of particles?'
'no, it's something the particles do'

That a biological system does not contradict any physical laws is one of the least interesting features of a biological system: the interesting ones concern its biology. — fdrake

I don't understand the distinction. It is all interesting to me, or at least the part I want to know about at any given moment. I could get all the biological explanations I wanted to, but it would all be without any foundation without physics. Even after answering every "biological" question, you'd still be left with asking, "What governs biology?"

It seems to me that two different domains of investigation that ask different questions and end up NOT contradicting each other is what is really interesting.

A reduction of biology to physics methodologically is pointless, philosophically a reduction of the living to the non-living is interesting though. Perhaps it's useful to say that the living is composed by the non-living in some manner, however. — fdrake

Again, I don't see the distinction you are making. If a reduction of biology to physics is pointless, then so to is reducing the living to the non-living. Our bodies and natural selection must obey the laws of physics. If it didn't then we could all fly without the proper anatomy.

'it's all made of particles!'
'is the tendency of negatively charged particles to repulse negatively charged particles made of particles?'
'no, it's something the particles do' — fdrake

Which is to say that the particle has a particular feature or property (it's negativity) that makes it do what it does. You seem to be implying that negativity could exist independent of particles. If it could, then why did you use the term, "particle" at all?

That a biological system doesn't contradict the laws of physics doesn't tell you much about the biological system. As you pointed out, stuff like air-resistance and aerodynamics enables things to fly; but doesn't make an incentive for things to fly. I meant the reduction of biology as a field of study to physics as a field of study is pointless - they're concerned about different things and use different methods. The ontological reduction from the living to the non-living might still be informative though.

I didn't intend to imply that the interaction of charges could exist independent of particles (requires charged particles and carrier particles). Just that it's something particles do, not something that they are. This was meant to highlight that the ontological reduction of stuff to particles doesn't even help much in describing what particles do (other than as an enabling condition for the study of particle behaviour); as an analogy to the reduction of biology as a field of study to physics as a field of study.

I'd rather keep the discussion related to what 'the reduction of the living to the non-living' suggests, rather than attempting to subordinate fields of study to each other. Just because I think the subordination of fields of study to each other is a different type of question, and is largely irrelevant, to answering and posing questions about life and the specificity of living organisms.

Awesome reply. Yeah, you're totally right that I've almost entirely ignored the cytoplasmic and intercellular contribution to the processes of gene expression, and that these things too, with all their myriad mechanisms, also have a deep and important role to play. But while you've refined the analysis so that we can be more specific about the genomic network itself - at this point one perhaps should simply call it a developmental network - the question about life which motivates the OP still, I think, remains unanswered. In fact I think it's rendered even worse! For while the OP operates with a very (much too) simplistic distinction between gene and 'environment', bringing the cellular context into it brings out the ambiguity of just what is meant by environment here: it is everything other than DNA? Or is it the cytoplasm? Or does it stop at the skin? In some sense, this question cannot be answered in the abstract: what counts as environment depends on the kind of investigation we want to carry out.

But just here is where the ambiguity over what then defines the boundary between life and not-life also enters into play, insofar as the topology between inside and outside (and this has nothing to do with the network topology we are talking about) becomes impossible to define (again, in the abstract). All you have, once again, is a developmental network largely indifferent to any boundaries that might be imposed form the top-down, as it were. Of course at this point it's tempting to do the scientific thing and simply follow the contours of the network itself: what does and doesn't make a difference to it in such and such cases? But then you get limit-cases like viruses which don't have the translation machinery for their DNA or RNA and need to hijack that of its host cells, or even - at the opposite end of the spectrum - life-support tech to sustain the body would would otherwise be unable to survive 'by itself'.

But because there's no a priori way to specify the limits of the biological here (one can only 'follow the system'), there's also no a priori way to rule out or in what should or shouldn't belong to any particular network. Life becomes not a problem of finding the right definition, but of finding the right 'application'. The question isn't "it this alive?', but 'it is fair to count this as an individual to which what we call life would or would not apply in the first place'? This is where one leaves behind the empirical and enters the realm of the ethical and the political. Evelyn Fox Keller gets at some of what I'm trying to bring out when she asks: "These terms are themselves ambiguous: what exactly is a gene, and what does it do? Even more troublesome is the ambiguity of the term environment. Do we mean it to refer to everything other than DNA, to the milieu in which the fertilized ovum develops, or to the factors beyond the organism that affect its development? Finally, there is also the question, contributions to what?" (Fox-Keller, The Mirage of a Space Between Nature and Nurture).

Yep, these are supremely important questions, and what I'm trying to argue is that they cannot be answered in the abstract - one can only follow the developmental and evolutionary history of... whatever unit of analysis one would like to fix. One work that really helped me to get to grips with some of the conceptual issues at stake here was Susan Oyama's The Ontogeny of Information, which, honestly, everyone currently arguing in the 'Information' thread ought to be reading.

The problem I have is with the idea of "biology alone". Biology is not a self-contained set of substrates, but a fluid dynamic between certain macromolecules and the environment in a series of physical processes- some described probabilistically, some perhaps more straightforward (and all of it it perhaps biosemiotically). Thus it isn't just DNA, but the networks that they produce to create more complex processes. The networks that you describe may be analogous, if we were to isolate it in a network mapping way, but it is its situatedness, along with other biological substrates like DNA, cells, proteins and generally all the macromolecules that are found in lifeforms, that make it biological. The evolutionary history of how these networks came about and its unique way of solving problems using its structural constituents to influence its growth and development is what matters here. — schopenhauer1

I agree! I spoke of 'biology alone' precisely in order to render the notion a bit ridiculous; that was the point of the expanded Waddington diagram, to show that it is impossible to speak, in any coherent way, of biology alone with respect to life. 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.

If you cut one, or rearrange the organization of a set, and it doesn't affect the outcome (the expression of that trait), then it would be safe to say that that particular gene that was removed, or that particular arrangement of sets of genes that was rearranged, don't affect the expression of that trait. — Harry Hindu

May I introduce you to genetic redundency and genetic robustness, or more specifically canalisation, if we're talking about genes alone. They're dear friends, be nice to them.

That a biological system does not contradict any physical laws is one of the least interesting features of a biological system: the interesting ones concern its biology. — fdrake

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. Physical systems thus being a more limited field of study, even if they qualitatively make up more of the universe. This is one of those lovely thoughts, I think, that spurred me to study biology in some depth - want to know physics? Study biology! :D

I remember how much you hate possible world semantics for modal logic, but I think some idea of possibility/necessity modality is useful here to sharpen the claim that a demarcation criterion between the biotic and abiotic is impossible - at least as it concerns the generating processes of organisms.

I assume that a demarcation criterion is largely an epistemological device, and nature would not care about the distinction between the divided factors apart from differences in generalised processes that influence them.

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.

Considering the structure of Q(t), there are likely to be subclasses that are united by shared properties - generalities in genomic networks indexed to sets of co-expressing genes. 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. Not in practice however, there is an absurd combinatorial explosion whenever you're dealing with genome subunits, nevermind sets of genome subunits paired with genome subunits...

One way to represent P would be the set of all common expression properties, represented by their network bearers. In order to decide that we have all the properties that constitute P we would need a demarcation between factors that influence the development of genes and those that do not. Specifically, we would need to be able to infer from some particular Q(t) that there are no more possible types of gene expression influencing entities or processes - that we truly have a spanning partition of P, even if we do not know all its elements.

Evolution conditions Q(t) and the generated property list approximating P, since there will always be novel environmental scenarios. In particular, this ensures that novel categorisations are always indexed with a set of environmental parameters, at least insofar as the development of developmental processes is concerned. The indexing role the environment would play in this kind of study would ensure that environmental conditions are in some sense dense - ubiquitously represented and always very 'close' in the sense of accompaniment and foundation to accounts of changes in developmental biology- within the study of developmental processes as they relate to their environments. However, it is also likely that the environment is conceived as that set of things 'outwith' the 'biological' constituents of the developmental process. Despite the environment's ubiquity (denseness) within the analytic concepts of the development of developmental biology. This operationally equates the concepts of environmentality and exogeny. (You can observe the converse happening in ecology btw, the equation of an ecology with its interiority to description)

Whether the demarcation problem for the biotic and the abiotic is decideable within or using information from these theories would then depend on the extent to which the abiotic is operationally defined as the biologically exogenous, and whether it is operationally necessary to treat it as such.

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. Physical systems thus being a more limited field of study, even if they qualitatively make up more of the universe. This is one of those lovely thoughts, I think, that spurred me to study biology in some depth - what to know physics? Study biology! :D

Responding with quote from a physicist friend: "I'm uncomfortable with science that deals with anything that isn't a state variable. (temperature, pressure)"

Ahaha, love it. Also because the book of Rosen's that I took that from has an entire chapter devoted to explaining just how limiting state variables are, lol (Life Itself). Will reply to your post about PWS (*shudder*) tomorrow. Need sleep.

I don't see how any of that disagrees with what I said. A physical trait or behavior is a different outcome than redundancy. Redundancy has its components that if you take away one, then redundancy can longer be the outcome.

As you pointed out, stuff like air-resistance and aerodynamics enables things to fly; but doesn't make an incentive for things to fly. — fdrake

I don't see incentive as part of the equation. Things behave in certain ways as a result of how they were designed. There was no incentive prior to, or the cause of, flight. Flight occurred as a result of natural selection acting on genetic mutations over eons. By saying there is an incentive is projecting your own purposes onto reality, as if reality has reasons, or incentives, to design things. It doesn't. "Design" isn't even an appropriate term to use to describe what natural selection does, as there is no incentive, purpose, reason, or goal that natural selection has prior to the process itself taking place.

I didn't intend to imply that the interaction of charges could exist independent of particles (requires charged particles and carrier particles). Just that it's something particles do, not something that they are. This was meant to highlight that the ontological reduction of stuff to particles doesn't even help much in describing what particles do (other than as an enabling condition for the study of particle behaviour); as an analogy to the reduction of biology as a field of study to physics as a field of study. — fdrake

Then if it wasnt implied that negativity was a separate feature of a particle, then it must be that it is an integral feature of that particle. Repelling other particles is what that particle does as a result of its negativity. If it didn't repel other particles then we couldn't say that possessed negativity.

Everything that something does is limited by and determined by its shape and the laws of physics. Incentives are still limited by the laws of physics.

I don't see incentive as part of the equation. Things behave in certain ways as a result of how they were designed. There was no incentive prior to, or the cause of, flight. Flight occurred as a result of natural selection acting on genetic mutations over eons. By saying there is an incentive is projecting your own purposes onto reality, as if reality has reasons, or incentives, to design things. It doesn't. "Design" isn't even an appropriate term to use to describe what natural selection does, as there is no incentive, purpose, reason, or goal that natural selection has prior to the process itself taking place.

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

. By saying there is an incentive is projecting your own purposes onto reality, as if reality has reasons, or incentives, to design things. — Harry Hindu

It's relative, not absolute purpose. For a phenotypic variation to be differentially replicated,* it must provide some survival or reproductive advantage relative to other members of the population. Surviving and reproducing is not an absolute purpose, but it's how the game is played.

I remember seeing an episode of NOVA or something where they were testing chickens as part of a theory that wing flapping might evolve as a sort of turbo boost for running-- that is, helps you survive which helps you reproduce.

* That sounds like it could be a TMBG song about evolution.