This is great. The way Glen frames the up-in-the-air parts is IMO the direction to a great program of questions. Many of them don’t seem to have been well addressed in general terms, but there is a ton of lovely casework (particularly by developmental biologists), giving some part of the variety we need to include, and suggesting how diverse it can get.
> On Apr 9, 2026, at 0:03, glen <[email protected]> wrote: > > I feel like I'm going to regret this post. But what the hell, eh? > > I was down with an unordered: > • collection of features > • measurement method > • successive execution of the method > • relative rates of change > > So at the end of EricS' post, including the parse of "cause", I felt like I > was stable. But then EricC goes on about "animals change", "species change", > and "organisms". OK, to be fair, EricS did use "generations" and > "reproductive". So there's an implicit ... what? ... unit, atom, ... thing in > there that we all agree is doing the _generating_ [⛧]. And it's common for > that sort of thing to be entirely latent, occult. But I took EricS' primary > criticism as pointing out that it *is* occult, and speculation about the > generator(s) has to take a particular form (namely relative frequency and > rates of change of the features given the measurement method). I.e. any > conjecture about the generator has to be grounded in that. I think there are two things going on here, one fairly ordinary, and the other a direction for real novelty. The ordinary part was my hedgy way of talking about frequency of features. I did that, in space too brief to say anything clearly, to wave at the fact that, at the end of the day, all of these statistical estimators of amplification-rate have to be defined on _sets_ of individuals (or of whatever). That means we have to commit to some way to partition things, and to treat members within any set in the partition as equivalent, and those in different sets as distinct, in defining what it means for the degree of amplification to differ “by type”. So all that falls to the details of what signal you are trying to test for and what question you want to answer. The much more interesting thing is all the rest of Glen’s paragraph above. On this, I think there is a simple way to sketch a program, which will hold up even though I don’t have interesting things to say about almost-any of the solution to it. 0. It seems silly, but like number theorists who always want to start by defining zero, I think the best place to start is with the partition between pattern-forming in equilibrium systems, and pattern-forming that _must_ come from non-equilibrium. Here, “equilibrium” means that the inventory of allowed elementary events and of whatever governs their probabilities are symmetric under reversal between forward-time and reverse-time indexing, and moreover, that all waiting times for any barriers are surpassed. The reason this is a good division is that it reduces the first step in our ontology to dimension-counting. If all waiting-times are surpassed, then all the parameters that set them become unable to impact the collection of possible patterns formed. (To be more concrete, for example, this means we keep molecule “free energies of formation” in chemistry, but we discard “kinetics” describing reaction rates.) Clearly there is less information defining equilibrium systems, and so less variety available to make distinct patterns. So, first list all the patterns that _can_ form in such equilibrium settings. 0.a. It is useful to note that the attraction to equilibrium outcomes defines what one will later need to mean by “things fall apart”. (The usual habit of the public is to go on and on about maximization of entropy etc., but I think Yeats keeps us better focused on the very non-occult meaning, whereas if you say “entropy” half the room goes mystical.) 1. Then, we look at all the other patterns that can _only_ be formed in systems driven away from equilibrium, where the driving boundary conditions interact with the remaining barrier-parameters in some ways. Because any extra-equilibrium patterns are always (by definition) tending to fall apart, they exist only by the grace of some kind of amplification, and this is where we get to the need to define the right amplification and attenuation rate-parameters. Generally, it is the non-uniformity in these sets of parameters that will make concrete whatever we want to mean by “selection”. 1.a. Now, at this point, there is a fun debate with Michael Lachmann. He wants _everything_ in this category 1 to be called “evolution through selection”, because he doesn’t see any single bright line that sets one sub-category within it apart from the others. I fully understand him, but I won’t choose his practice, because I think we already have a name for non-equilibrium pattern formation, which entails everything in the bullet 1 above, and I would rather reserve any new terms, such as evolution-through-selection, for more restricted sub-classes, and generally those in the general direction of things we see in biology, which were the exemplars when the terms were brought into this usage. Michael and I have no trouble talking across this difference of choice, of course, and one can see it both ways. 1.b. The things I want to cordon off with my narrower evolution-through-selection are all those in which the states at single times, and their connections across times, become characterized by all sorts of other structure. For this we have lots of wonderful terms, even just within biology: organism, genome, species, genotype, pan-genome, reproduction, lifecycle, etc. The new snow, as I see it, is to ask: How is it that this driven-patterning world brings into existence forms of order that want (meaning, justify the use of) these names, and how do the different ones come about? That question is open-ended, and the developmental biologists, ecologists, and others, are our guides in how to do it. 2. I think, even at this very early level, there is lots of clarity that can be laid out. Here, some suggested definitions, and these are meant to respond to Glen’s question about “what? units?…” which I think reflects _exactly_ the right level of reservedness against pre-registration. 2.a. An “organism” will be roughly whatever we want to describe as something individual, of which many can be gathered into populations, and which has an associated life-course and lifecycle. All this, of course, to be formalized carefully per-case. 2.b. A “genome” is (in our biosphere) an integrated collection of elements capable of carrying the operating system for the lifecycle of some organism. It is that integration that makes those elements into “genes” as we will later call them, so a lot goes into how genomes come into the world and why. A nice feature is that genomes are governed by things like Chris Kempes’s allometric scaling laws, somehow connecting them to cell sizes, lifecycle times, domain type, and so forth. 2.c. A “lifecycle” is whatever sequence the operating system of the genome takes organisms through, as different forms are built up, shed, recombined or reworked, etc. May not be a simple “cycle”; the so-called “minor taxa” of things like brown algae show us what a menagerie of active and environment-responsive management this can be. “Reproduction” is the choreographed event-sequence that carries out a lifecycle. It is like the event-dual to the object-state of the organisms in any of the lifecycle stages of the corresponding species. 2.d. Fascinatingly, the notation of the pan-genome — which will typically (or at least often) be about an order of magnitude larger in its gene inventory than what is found in any actual realized genome — is somehow the resource-cloud that we want to connect with notions of “genotype” and “species”. It seems that punting things out of most genomes, so that they are only carried by somebody rarely-attested in the population, to maintain the “pan-genome”, and then pulling them back in when needed, is a very active and regulated process. The “genotype” is the thing that “breeds true” in a species, and that tells what can or can’t ever be in the genome of some actual organism of that species. So, roughly, its actively managed part defines the scope of the pan-genome for the species. Clearly, all this gets cloudy and overlapping. Genetic elements can be in the pan-genomes of more than one species, and so forth. The degree of overlap often correlates strongly with the degree of relatedness of different clades. So we have to learn what is the right mathematical structure to use to describe the actual world faithfully. But there do seem to be major modes of organization that justify these terms. As far as I know, the above draft-meanings are idiosyncratic to me, though I think they reflect the broad usage by the different biology-groups that own them. I have spent time talking to people on each of these terms, to check that they find my picture above concordant with their own sense of the phenomena, and I think I am not violating anything with this way of putting things. I think one could do work within this framework, Eric .- .-.. .-.. / ..-. --- --- - . .-. ... / .- .-. . / .-- .-. --- -. --. / ... --- -- . / .- .-. . / ..- ... . ..-. ..- .-.. 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