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. — schopenhauer1

But this is just circular then: biological systems are systems with biological constituents...

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? — schopenhauer1

I don't understand what you're asking with these questions. Could you be more specific?

But this is just circular then: biological systems are systems with biological constituents... — StreetlightX

I don't think so, do other systems reproduce, metabolize, using the same unique set of tools (biological molecular parts)? Do other systems evolve in the unique way biological systems do? No and no, and thus we start making distinctions between this system versus other systems. But I know, this is not what you thread is supposed to be about.

I don't understand what you're asking with these questions. Could you be more specific? — StreetlightX

It sounds like you're asking things like "What makes an ecosystem different than an organism?" and I wanted to see what your thoughts were about what makes an organism an organism.

I don't think so, do other systems reproduce, metabolize, using the same unique set of tools (biological molecular parts)? — schopenhauer1

But this is the first time you've mentioned metabolism or reproduction. You previously spoke simply of hierarchical networked systems, that were, in a way not yet specified, biological.You seem to be filling in your definition as you go along. But - and this is about the fourth time I'm making this point, and I'm afraid I will not make it again - whether or not you do have an adequate definition of the living is not in question. It is a question of application, which is why I spoke about limit cases like viruses or life-support systems with fdrake, and which even Harry mentioned. Further, I never once asked 'what makes an ecosystem different than an organism', because I have been quite clear that I've been speaking about processes, and not 'units' of things. You seem to keep going over ground that is not relevant to what is being addressed. Perhaps I have not been clear, but it is tiring trying to correct for viewpoints I do not hold.

I think this is a bit unfair being that you indeed seemed to be talking about life based on your last paragraph there, but if your topic is different than I guess I misinterpreted what you were aiming at with your OP. Here is what you said (I bolded what I took most important):

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

But I am talking about life, and quite specifically the question of 'what does and does not count as 'alive'. The emphasis is on the counting-as: a question of the applicability of criteria and the individuation of what, precisely, is at issue. And I was quite clear in the opening paragraph of the OP that I was concerned precisely with the process of gene expression - I even italicized the word in that paragraph - and what this process entails for thinking about what counts as life.

Perhaps I can put it this - not super precise - way: the question is not 'what is alive?', but 'what is alive?'. This latter is the question of individuation, of what counts-as a-life, a question which I think is opened by a reflection on the process of gene expression.

I have been quite clear that I've been speaking about processes, and not 'units' of things. — StreetlightX

Perhaps I can put it this - not super precise - way: the question is not 'what is alive?', but 'what is alive?'. This latter is the question of individuation, of what counts-as a-life, a question which I think is opened by a reflection on the process of gene expression. — StreetlightX

I think the first quote there makes it difficult for some of us to understand what approach is suggested by the second quote. You seem to rule out exactly what most of us would be doing if we set out either to choose a criterion for life or apply it. It makes it look as though you want to ask, not whether something that eats is living, but whether eating is living, and that can't be what you're saying.

Is the connection that an organism is "composed" of such processes?

The analogy that came to my mind was the relation between phonemes and morphemes. Morphemes, as the smallest units of semantic content, are by definition made of parts that do not have semantic content. As such, it's no use looking to the phonemes to determine whether a given object is a morpheme; there is in a sense nothing special, nothing directly related to semantics about phonemes. You can't read off morpheme-hood. (You can do some things, given more rules: say what could be a morpheme in a given language, etc.)

But now I seem to be doing the sort of thing the first quote would discourage; and the second quote suggests that the issue is what a unit of semantic content could possibly be, given that the unit is composed of non-semantic units.

Am I at all close to understanding your point?

:)

To try and square the circle you’ve pointed out: one thing that I wanted to bring out with the focus on gene expression is that, to the degree that we take expression to be an exemplar of a living process, life itself must be thought of in processual terms. This is a fairly uncontroversial point in-itself, I hope: life is not a ‘thing’ but a process - or, in a less ‘dualizing’ approach: life is a ‘thing’ composed of processes (the language here is strained). But, and this is the crux, the peculiarity of the process is that it is neither biotic nor abiotic, but is, as it were, continuous between the two realms - in fact, such is the continuity that to speak of ‘two realms’ is already something of an after-the-fact projection: the process itself ‘doesn’t care’ about the rather arbitrary labels imposed upon the ‘elements’ involved. In principle, one could map the causal dynamics involved in gene expression without parsing the constituent elements into biotic and abiotic and do so without any loss of information.

This indifference, I think, opens up a fascinating speculative possibility: that life itself can be entirely divorced from the biotic. To pursue this thought in a different register, consider the following line of speculation from the evolutionary biologists Eva Jablonka and Marion Lamb, who envisage a possible future in which the DNA inheritance system is altogether replaced by higher-order one - and that, not only could this possibly happen, but that something like it might have already happened with respect to our already existing DNA system:

"In existing organisms, which all have a nucleic acid–based inheritance system, it is inconceivable that the DNA inheritance system will be eliminated by another one that operates at a higher level. But theoretically it is possible that one heredity system can replace another. It may well have happened at an early stage in the evolution of life, during the murky period between chemical and biological evolution. Many theorists suggest that heredity during these early stages was not based on nucleic acids, and that the nucleic acid systems came later and replaced the primitive heredity systems. Maybe such a replacement will also occur in the distant future— if we create intelligent, reproducing, and evolving robots, they may eventually eliminate us. This would be equivalent to the elimination of one heredity system by another”. (Jablonka and Lamb, Evolution in Four Dimensions)

J+L are here not talking of course, about gene expression but inheritance systems in evolution more generally, but the principle is the same: that life itself may be considered as something entirely separate from the biotic. Life would thus be a formal principle rather than a material one: so long as the process and its organisation are kept in place, the exact ‘instantiation’ of the formal principle is - from a very specific perspective - a matter of sheer indifference (I take inspiration also from Robert Rosen and Nicholas Rashevsky’s imperative to "throw away the matter and keep the underlying organisation”, when speaking about biological systems).

The final step here is to see that formal systems, by definition, do not provide an index of their own applicability. That is, they simply say: ‘anything that meets these organisational criteria belong to the class of systems so named living’. But what does and does not count as ‘a’ thing here is not something that can be read off the phenomena itself: someone on a life support system might be said to be structurally coupled to that system, without which they would die: but the individuation of what counts and does not count here is a matter of judgement, not a matter of empirical study - hence the moral dilemmas we face when, in some circumstances, we decide on turning off a life support system or removing an breathing tube. Again, I’ve gone on too long and there’s still lots to say. But hope this fills out some possible gaps.

Got it. I believe I am following you, and sometime tomorrow I will move on to thinking about it.

Cool. To provoke/frame a little more, I guess part of what's at stake is an 'anti-descriptivist' approach to 'life'. In fact I'd suggest the kinds of problems at work here at equally at work in all forms of nomination, whether it be life or - to crib from Kripke - Kurt Godel.

I think you need to remove the ambiguity from your categories of "process" to understand the criticism which has been directed at your approach.

First, we understand in general, "processes". Then we have the more particular "living processes". It would appear like we would have some principles, whereby we distinguish living processes, as a particular type of process. Classically one would refer to a living being as carrying out the process, and this would determine a living process.

You have removed this living thing, which is assumed to carry out the living process, so from my perspective you have no means for distinguishing living processes from other processes. Now it makes no sense to classify a process as a living process because there is no basis for distinguishing a living process from a non-living process.

It appears like what you are trying to do, and this would be a real challenge, is to make living processes into the more general category. In this case, all processes would be distinguished in relation to being alive. Sub-categories, different types of processes, would all be related to each other through what you call what counts as alive. Here I can see three categories, was alive, is alive, and will be alive.

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.

Don`t see anything to pick at here. So long as the problem space for the demarcation of life and not-life is the space of possible genomic networks, rather than specific ones. Not that this space of possibilities is independent of the considerations relevant to the networks.

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.

I don`t understand why you would think it would be by fiat, since the construction, or discovery, of genomic networks is a fortiori the conceptual space for that demarcation at least as far as this thread is concerned. Rather, the inclusion of types of factors in them is the conceptual space. This isn`t a criticism of what you said, rather to elicit more information. Why at any given point would it be by fiat?

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...

I don't think that this is a particularity of genomic networks, they only instantiate the problems that epigenetics rises for the distinction of life. Inclusion in a specific genomic network requires that a node is a gene, the more general picture you raise of the epigenetic landscape is the appropriate space of concepts for tracing the implications for the demarcation of biotic and abiotic factors.

I also think it's likely that abiotic and biotic factors are likely to have an operational definition within the study of genomic networks that doesn't coincide completely with the (supposedly) philosophical distinction between life and not-life.

The appropriate conceptual space for this argument is something like genomic networks as a problem instantiation of epigenetics for the demarcation between life and not-life, so decisions (subarguments) should be considering the scope of genomic networks and how their internal distinctions relate to life and not-life, and further how this relates to epigenetic effects - then how that counterfactual space of concepts (study of genomic networks -> epigenetic effects) relates to the demarcation problem for life.

It looks to me, though I may be misreading you, that you are committing something of a category error (at least if the above typology of the space of problems is accurate), confusing the inclusion within specific genomic networks and its formal undecideability with respect to the biotic and the abiotic with the general features of the study of genomic networks (which is where epigenetics comes in). This paper incorporates this distinction methodologically.

Edit: I see you addressed some of this in response to @Srap Tasmaner

J+L are here not talking of course, about gene expression but inheritance systems in evolution more generally, but the principle is the same: that life itself may be considered as something entirely separate from the biotic. Life would thus be a formal principle rather than a material one: so long as the process and its organisation are kept in place, the exact ‘instantiation’ of the formal principle is - from a very specific perspective - a matter of sheer indifference (I take inspiration also from Robert Rosen and Nicholas Rashevsky’s imperative to "throw away the matter and keep the underlying organisation”, when speaking about biological systems). — StreetlightX

Are there any known philosophies that DO think that biological constituents must be in the picture along with the process and its organization (i.e. contra Rosen perhaps)? If so, what is their reasoning? I'm just trying to kick off a dialectic to ensure you are not overlooking counter-examples.

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. — StreetlightX

What is there in this world that isn't a process, or in process, or the abstract result of some process?

The process of being alive involves biotic and abiotic materials: At any time in which a living organism exists, there are materials currently integrated as the organism, materials in the process of being integrated into the organism, materials in the process of being disintegrated from the organism, and materials that are not, are not being, and have not been integrated with the organism. The boundary of the organism's integrity is not the same as the generic boundary of biotic and abiotic organization: There's a great deal of recycling of material from each organism to others.

How does this sort of account "ignore the holistic aspects" of the relation between organism and environment, or the holistic aspects of the process of living?

It's still not clear to me why you seem to think everyone's been in the dark about the porousness of the relation between organism and environment. It's still not clear to me how abstract representation of features of the relation of genetic code, environment, and traits in terms of mathematical networks and topologies is supposed to be a remedy for the alleged misconception.


Of course life is a process. Of course the organism changes over time in constant interaction and exchange with the rest of its environment. Recent investigation into the way "traits" result from various combinations of genetic material and environmental factors is a welcome refinement of our view of that interaction. Perhaps it's especially valuable as a correction of a too-narrow misconception of the relation between genetic code and traits. But the idea that external factors -- like the quantity and quality of food, water, sunlight, air, and company -- influence the path of an organism's development seems a very old idea indeed.

Note, just so there's no confusion - this is a response to a discussion that took place 6 months ago. It was one of my favorites. Reading on the web, I came across the linked article which I think is interesting and relevant.

https://www.quantamagazine.org/how-many-genes-do-cells-need-maybe-almost-all-of-them-20180419/