I have lots of homework to do. But I wanted to remark off the bat that the
rocks rolling down hills thing reminded me of [McShea and Brandon's Biology's
First Law](https://doi.org/10.1111/evo.13735)
"ZFEL (general formulation): In any evolutionary system in which there is variation
and heredity, there is a tendency for diversity and complexity to increase, one that is
always present but may be opposed or augmented by natural selection, other forces, or
constraints acting on diversity or complexity."
And that triggered a confusion about the structure of the rocks and the hill. If it's a stream of
diverse hard rocks dropped on a soft hill, we have a kind of "heredity" in the canals.
But if it's just one "generation" like a landslide, then mortality (or coming to rest at
the bottom) can be the only operator. Regardless, it's kinda fun to warp yourself into it. I need
to read the 3 links to see if I have anything constructive to say.
Re (2): capturing/defending territory - You're likely right about this. In
fact, I have a friend who, in the heat of a face-to-face conversation, will
speculate with a claim for exploration. But then as the discussion goes on, he
gets more defensive about his speculation, even admitting that he doesn't put
much stock in it. But because it's face-to-face, his physiology isn't prone to
detached exploration. So F2F can work against detachment, at least in his case.
Thanks much for your indulgence.
On 4/12/26 6:29 PM, Santafe wrote:
Sorry to drop; I also wanted to do a little looking for materials.
On Apr 11, 2026, at 0:43, glen <[email protected]> wrote:
Very cool. Thanks for continuing this. I have 2 requests if you can answer off
the top of your head:
1. One or two good citations for the 2 classes of the out of equilibrium
patterns. I'm at a loss for an example pattern Lachman might include, but you
exclude.
I can give you an idea how widely Michael wants to scope. But for the example I will mention, I can’t find any publication where he built this out, or even a podcast where he discusses it. Probably because it would be hard to find buyers. So these are just things he used as examples in working conversations (maybe even 6 or 7 years ago now? I’m not sure). Michael wanted to treat rocks rolling down hills at different rates as an equally good exemplar of selection. Take lifecycles and everything biological out of the picture entirely. This isn’t a terrible math-analogy for how mortality selection works, if we think of death as regression toward the equilibrium of a Gibbs chemical ensemble. (In other ways, that’s a terrible mangling of categories, but for the tiny bit of math that is left in this case, it works out the same way.) Michael’s limiting case, though, lacks any amplification step or anything like a lifecycle. So there can’t really be anything like fecundity
selection, and there isn’t persistent non-equilibrium patterning. (One could go into the direction of erosion, and look for some kind of amplification, to produce a limited analogue to fecundity selection. But that is still only surfing the shoulder of a transient, so it isn’t a good model for true patterned persistent states in other ways.)
As the other side, where there is differential amplification and attenuation,
but in highly structured systems, a standard layout would be the one I always
trot out by Michael Lynch, as a summary of the population-geneticsts’
abstraction:
The frailty of adaptive hypotheses for the origins of organismal complexity
<https://www.pnas.org/doi/10.1073/pnas.0702207104>
pnas.org <https://www.pnas.org/doi/10.1073/pnas.0702207104>
pnas.2007.104.issue-suppl_1.cover.gif
<https://www.pnas.org/doi/10.1073/pnas.0702207104>
<https://www.pnas.org/doi/10.1073/pnas.0702207104>
Now, I generally put Lynch up as a foil, because he lays out a set of systems, arguing that they are all-and-everything you need, to belittle and attack those who try to put up further “evolutionary syntheses” or their equivalent. However, the formalisms that Lynch is actually offering only apply properly to the abstractions of the replicating genes of Williams and Dawkins. Then, without happening to comment on the fact that he is changing the subject, he goes on to shout “of course selection takes place at the level of genotypes” etc. Yet, where there is relational information that _makes_ genotypes genotypes, he has said nothing about the system of accounting that characterizes how such information is retained and propagated, in his earlier “all-and-everything”. And of course, it was the wish to deal with all that relational information (and other kinds, like symbiotic dependencies in communities) that motivated a lot of the extended syntheses that he mocks and
criticizes. I do often find that his technical criticisms of the extended syntheses are appropriate, because many of them don’t seem anchored in really well-formed principles. But to criticize the argument that something is needed seems misguided to me. I can imagine things that go along the lines of conceptual clarity of the way Fisher worked, but that pick up the many interesting questions that were not in play in Fisher’s day.
I don’t know the literature on pan-genomes well, so much of what I have of them
is from meetings. I did want to mention Jay Lennon, from this meeting here:
Microbial communities: Energetics and dynamics across space and time
<https://www.nitmb.org/microbial-communities-workshop>
nitmb.org <https://www.nitmb.org/microbial-communities-workshop>
95c3c6_6fcd4e52c85c426b8bc99314e9f0a8c4~mv2.png
<https://www.nitmb.org/microbial-communities-workshop>
<https://www.nitmb.org/microbial-communities-workshop>
as someone interesting, whom I heard recently enough that I can remember the
source. I don’t have a paper that seems to exactly cover the scope of his
talk, which had lots of inter-related things and off-hand comments that reflect
the breadth of intuitive appreciation that a worker often has of an area,
beyond what ever makes it into papers. But, from the angle of sporulation, he
does give some discussion of how dormant phases can be reservoirs of genetic
capabilities, which can be actively and selectively re-activated, here:
pmc-card-share.jpg
Evolution with a seed bank: The population genetic consequences of microbial dormancy
<https://pmc.ncbi.nlm.nih.gov/articles/PMC5748526/>
nlm.nih.gov <https://pmc.ncbi.nlm.nih.gov/articles/PMC5748526/>
<https://pmc.ncbi.nlm.nih.gov/articles/PMC5748526/>
Somebody else, who does very-long-term starvation phenotypes on E. coli, and
shows that the whole genome and cell form undergo radical metamorphoses, was
the first person who really got my attention on the dynamic and intentional
characteristics of pan-genomes. But I don’t remember who it was. (Oddly, I
have some synesthetic image of the room I was sitting in watching, but I
couldn’t tell you what meeting or what year it was in.) He is somebody
well-known for this.
2. I'm assuming you and Lachman's ability to grok and play along with each
others' preferences is *because* you work in the same physical location and can
talk informally back and forth. Is that true? Or do you think you could come to
the same facile donning-doffing of each perspective if you *only* communicated
by electronic means ... or through publication letters and such?
It’s a good question. Probably equal amounts of both.
My impulse — being someone given to abstraction — is to suggest that the main
driver is temperament. Neither Michael nor I is out to capture or defend
territory. We also share taking no enjoyment in “conversations” that go in
circles forever because the interlocutors talk past each other and
misunderstand each other’s claims. Michael is, in general, a much more
easy-going and tolerant person than I am, so he doesn’t tend to the immediate
impatience and annoyance with such conversations that I have. But he never
drifts into that direction, so there is never needless upstream swimming to do.
He is also very clear with his categories. Since we both enjoy and are
looking for questions that are actually about something, then, it is
almost-always pretty systematic to see where a misunderstanding has happened,
and figure out how to unravel it to get to a meaningful question we can try to
puzzle out.
But equally much, being in a room has mattered. For a long time now, it has been several years at a time between my path-crossings with Michael. However, it does turn out to be invaluable that I can trudge a half-hour across town in the snow, to sit for an afternoon in a room with him, to try to hash through something. The counterexample that shows this is probably essential is that he makes certain statements to the effect that Hector Zenil’s information-theoretic criticisms of Walker and Cronin’s Assembly Theory are “wrong”. While there is a lot of Zenil’s screed in his blog posts that is unhelpul — but which reviewers and editors were largely able to get him to cut out when he got a few papers on this published — there is a core of his assertion, that the Assembly Index is a certain version of a compression index, that seems correct to me. I am sure that Michael speaks in good faith, and also that he knows what he is talking about. And I am a semi-tourist in these
algorithmic information things, not an essential worker. But for all that, I don’t understand just what Michael is claiming in detail, and probably won’t until I have a couple hours with him for which that is the main topic to sort out. I have felt the lack of that as a kind of exposure, because I worry where I am missing something.
It’s all interesting,
Eric
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