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Biology

Entomology

Ants

Ants & Media

Development, Ecology, Evolution

4/22 with John Harland discussion

Jere

Interfaces

Observer who is doing the experiment — not just the Subject itself.

Here it may be relevant to explore

Active Inference⁠

2022 Textbook,

Figure 9.1⁠

⁠

Within the dashed line we have the map/model of the

How to explain

Biology⁠

Quantum⁠

Physicists, in 10 minutes?

Starting with large swamp of microbial lifeforms. Complex changing system, e.g. 10E18 bacterial, 10E6 DNA basepairs, with reproduction on hours-days, and spontaneous mutational rate 10E-9. — Do the math! It is an enormously powerful biological mechanism; the singular nucleotide polymorphisms as well as e.g. recombination, structural events, conjugation, viral activity, etc. — there are many creative events, the hypotheses unfolded by the biological system.

Biological systems just want to have fun.

What came first, the chicken or the egg? Cheggan.

John

Biological mechanisms can be quite complex, some of the most complex. Physics and

Maths⁠

can work on simpler systems.

We have all viewed the previous conversation with AK & JH.

Upper Triangularity of certain systems — with a Matrix, how can there can be effect/flow across parts of the system.

What are living systems? What do they have in common?

Input/Output. Sense/Action.

Unitary evolution. Self-Adjoint operations. Can things that make sense in one direction, also make sense in other direction.

Discrete Dynamical system — Matrix M.

Time evolution of the system is given by u_t

Self-adjoined matricies — e_t=e^(imt)

The question is about what the right hand side means, it can be calculated though with infinite series.

We don’t know how to write down the time evolution of Universe, what are the states, we don’t know the big picture, just small pictures.

We are talking about the smaller piece of biological system, nested in bigger dynamical system.

⁠

? may be 0.

S2 smaller environment, affects upwards. However if ?=0 then there is no downwards causation from S1

This is a “perfect niche”

What does it mean to Evolve?

Quantum⁠

Meaning just Change? Change in observations, hidden states?

Biology⁠

Sometimes meant as simply change in the multiscale

Development, Ecology, Evolution⁠

And/or the “Evolution by Natural Selection” conditions?

⁠

Where and how might

Quantum⁠

inform the

Biology⁠

inquiry?

Mechanistic

⁠

Quantum⁠

phenomena in Biological systems —

Electromagnetic fields

Microtubules

Instrumental-Statistical

Using Quantum methods and statistics within a single scale of analysis, for e.g. psychology, decision-making.

Quantum Bayes —

Realism and instrumentalism in Bayesian cognitive science⁠

— using QBism for cognitive science, with or without appeal to an electronic-scale mechanism (←) or the multiscale topological nesting (→).

⁠

Connecting the free energy principle with quantum cognition⁠

(2022)

While free energy minimization, which incorporates Bayesian inference, leads to a Boolean lattice of propositions (classical logic), quantum cognition, which seems to be very dissimilar to Bayesian inference, leads to an orthomodular lattice of propositions (quantum logic). Thus, we address this challenging issue to bridge and connect the free energy minimization principle with the theory of quantum cognition.

Multiscale theoretical

Using scale-free formalism (e.g. see

Chris Fields 2023 course⁠

Topological control flows⁠

quantum neural networks⁠

) to better scaffold

Development, Ecology, Evolution⁠

⁠

_____?

⁠

M4W Emails⁠

—

https://www.freelists.org/post/math4wisdom/April-24-Wednesday-Evolution-in-Biology-and-Physics-and,1⁠

[math4wisdom] Re: April 24, Wednesday, Evolution in Biology and Physics and...

“Also, as I mentioned, the three minds in this context are like adding 1 dimension or 2 dimensions or 3 dimensions, respectively.”

From a Quantum

Active Inference⁠

(

Chris Fields 2023 course⁠

) — the Classical holographic screen/interface/blanket is the one with the reduced dimensionality/bandwidth. The Cognitive System (Agent, Mind) adds at least 1 more dimension (if it didn’t add a dimension, it would not be a mind at all, it would just be like a passthrough conduit but not cognitive/computational/processural element).

To add 3 dimensions here from a single dimensional input (e.g. to reconstitute/rehydrate 3 more cognitive state spaces/dimensions from the single-channel Telephone wire) is the most dimensionally-sophisticated cognitive process. Within the types/classes of cognitive things that add 1, 2, 3 (more?) dimension (the minds),

Category Theory⁠

helps with mapping/accounting.

From a

Synergetics⁠

perspective — geometry of thinking — let’s work from the idea that that a minimal (cognitive) system is a Tetrahedron, 4-fold at minimum. Speculatively:

The most reflexive mind, takes 3 external points & adds in the 4th single perspective.

⁠

This is Blake’s “single vision”, or Newton’s Sleep (like the nightmare of uniperspectival scientific inquiry)

https://blakesociety.org/single-vision-and-newtons-sleep/⁠

https://www.jvascsurg.org/article/S0741-5214(97)70119-8/fulltext⁠

: * Now I a fourfold vision see, * And a fourfold vision is given to me * Tis fourfold in my supreme delight * And three fold in soft Beulahs night * And twofold Always. May God us keep * From Single vision & Newtons sleep

The most deliberative mind takes the single observation (anything else would be a non-observation), and adds 3 dimensions (bringing the most contextualization possible from the inner semiotic process).

This “arrival of the 3” from the cognitive system, may also reflect e.g. Mind/Body/Spirit, or in

Active Inference⁠

particular partition the Internal/Action/Sense states constituting the Thing/Agent. So it can represent “showing up fully” to the observation (which may even be a counterfactual observation, or a stigmergic niche modification).

Could this connect with

Wondrous Wisdom⁠

4 questions? e.g. Whether/What/How/Why, and which of the 4 are brought forth into the total cognitive Tet, from the niche & from the agent (3+1, 2+2, 1+3) — if it is (4+0), then the other system across that interface/blanket is not contributing to the cognitive setting at all. Could that have to do with 4-ness, 8’s, Bott Periodicity (”Bott periodicity says that the "actual" dimension may grow indefinitely but nobody outside will be the wiser for it because the n+8 dimensional system, in terms of its external relationships, functions just like an n dimensional system.”),

Jitterbug? Resetting in a new/different way within a cycle that comes/ranges with values like (-4,0) through (0,4) in some/all of the possible adjacencies (which are the statespace-modifying “symmetry breaks”) since this is a more generalized space than e.g. “femur length” (which will always be a centimeter value with quite limited empirical bounds).

⁠

— How/when does the threesome get nested? E.g. for multiscale concurrency (policy selection and taking stands at the scale of cell, tissue, organism, group, etc).

As for

A Variational Synthesis of Evolutionary and Developmental Dynamics⁠

(the

formalisms for that paper in Latex⁠

⁠

— Here is the nested Bayes graph representation. The Action-Perception loop of the worm (intra-life dynamics) is nested within the ensemble of the population scale slower nested engagement with the populations & the deeper/slower niche.

⁠

— Here is the Renormalization Group with the R and G (splitting and lumping) operators. I know that Renormalization is used in Physics and in

Quantum⁠

(e.g. “Renormalization Group and Quantum Information” (

Gaite 2006⁠

) “The renormalization group is a tool that allows one to obtain a reduced description of systems with many degrees of freedom while preserving the relevant features. In the case of quantum systems, in particular, one-dimensional systems defined on a chain, an optimal formulation is given by White's "density matrix renormalization group".”

There is the key motif of adding (cognitive) dimensions (projecting up into latent dimensions, more Quantum), in contrast with the dimensional reduction/projection.

From the Variational paper: “Although not developed here, the renormalisation group construction means that we can apply the same arguments to autonomous kinds—i.e., agents—at the slow scale. In other words, on average, the extended genotype of internal kinds comes to encode Bayesian beliefs about external kinds, while active kinds will look as if they are trying to realise those beliefs, via niche construction [

77⁠

103⁠

104⁠

105⁠

]. In virtue of the minimisation of variational free energy, we have an implicit maximum entropy principle, which brings us back to [

21⁠

22⁠

] via [

49⁠

].”

21 — Campbell, J.O. Universal Darwinism As a Process of Bayesian Inference. Front. Syst. Neurosci. 2016, 10, 49. [

Google Scholar⁠

] [

CrossRef⁠

] [

PubMed⁠

] [

Green Version⁠

⁠

22 — Ramírez, J.C.; Marshall, J.A.R. Can natural selection encode Bayesian priors? J. Theor. Biol. 2017, 426, 57–66. [

Google Scholar⁠

] [

CrossRef⁠

]

49 — Friston, K. A free energy principle for a particular physics. arXiv 2019, arXiv:1906.10184. [

Google Scholar⁠

]

“In verbalization, words could have "possible" meanings that get "culled" as we work towards the "real" meanings. Similarly, with argumentation. In a sense, this is all about making sense of death, how it fits within the big picture, what it is all about.” — in the video and in the emails, I was very curious about Why this 1/2 culling? What could that represent the state space of? E.g. if the femur was [10 +/- 1 cm], are we talking about a 1/2 pruning in variance/extremes/values, does the measurement/existence of the femur itself constitute some kind of reduction from a latent higher/extra-dimension space of “what it could be”?

However in reading this example about Words and

Language⁠

, I am thinking about the 1/2 like in terms of Time (e.g. arrow flowing one way OR another). Specifically for words in sentences, there is a sequence to all-but-palindromic sentences. The multiscale interpretation of words is in the context/terms of previous sequences and appearances of prior words. So at least in terms of the Semiotic event, there is semantic (ir)reversibility because the sentence/program/equation would read/operate differently backwards (unless constructed to be mirrored or redundant in other ways, things we do see in biological systems). There is a 1/2 pruning, in terms of the arrow/hand of time, “sweeping the rug” one way and not another (”ringing & unringing a bell” came up a lot in our leadup to

Livestream #054.0⁠

discussing

Active Inference⁠

and

Category Theory⁠

with Toby St. Clere Smithe). Does this retain/discover/trace certain consistent configurations? What does this mean for

Quantum⁠

and for

Biology⁠

consistency? Is consistency for a biological organism/system persistence, and/or something else?

I invite us all to watch part or all of John Harland's video about his research program, "Extradynamical Evolutionary Foundation for Physics".

https://www.youtube.com/watch?v=wIVgraRnr5c⁠

You might skip around towards the end. We'll be discussing evolution from our perspectives as thinkers in biology and physics.

DAF: I have watched the video. Overall I am excited to learn more about John’s work on this.

Wonderful! DAF, great to see you writing out your thoughts. I was going to ask if you could create a page here on Evolution but I see that this is the page! I will link to this page from the M4W header. Take a look. Cool!

I made

Development, Ecology, Evolution⁠

if you want to use it. Or

Biology⁠

is good. Thanks! Ya I am looking forward to preparing for it.

⁠

Peter Turney wrote "Conditions for Major Transitions in Biological and Cultural Evolution". I exchanged a few brief letters with him.

https://arxiv.org/abs/1806.07941⁠

He notes the usual three conditions for evolution - variation, heredity, natural selection - and adds three more for open-ended evolution - fission, fusion, cooperation.

Awesome.

I would also like to take a look at this paper that Dave Gray suggested months ago, by Stuart Kauffman and Andrea Roli, "A Third Transition in Science?"

https://royalsocietypublishing.org/doi/pdf/10.1098/rsfs.2022.0063⁠

⁠

Yes. From the paper: “We can neither define nor deduce the evolving phase space: we can use no mathematics based on set theory to do so. We cannot write or solve differential equations for the diachronic evolution of ever-new adaptations in a biosphere” — This is sometimes referred to as, Un-pre-statability. There is a primary unprestatability in that probabilistic events cannot be justifiably pre-stated beyond the statistically optimal (e.g. MaxEnt, FreeEnergyMin) distribution. Then there is a deeper sense that the states spaces themselves have an unfolding (e.g. a

Questions⁠

taken up by “

Physics of creation - Symmetry breaking, (en)active inference, and unfolding statespaces⁠

“ from an

Active Inference⁠

/ Free Energy Principle perspective. Also I believe that “We can neither define nor deduce the evolving phase space” is too strong of a claim, and can be taken/deployed in an almost scientifically-demoralizing fashion. I would say in the grand scheme, in terms of Bits of uncertainty reduction, for many state spaces over many timescales, we can do quite well (e.g. “

The Unreasonable Effectiveness of Mathematics in the Natural Sciences⁠

”, by Eugene Wigner, who was

mentioned in the email⁠

). Whether this within- and among-state space anticipation can be done at all, is a weird/moot question — it can be done, it must be done, and it is being done (in our maps &

Symbolic Formalism⁠

s for

Biology⁠

complex systems

“we can use no mathematics based on set theory” — Perhaps

Category Theory⁠

can be used? #YonedaLemma #CatNotSet

⁠

Figure 1 may be interesting to explore with

Category Theory⁠

These cognitive schema can be described and implemented using

agent-based frameworks for modeling epistemic ecosystem⁠

⁠

Selection “acts on the Kantian whole”.

⁠

https://www.jstor.org/stable/26370801⁠

Kant’s Concept of Organism Revisited: A Framework for a Possible Synthesis between Developmentalism and Adaptationism? Philippe Huneman (2017).

⁠

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8904326/⁠

The Kantian account of mechanical explanation of natural ends in eighteenth and nineteenth century biology (2022)

From the

Ants⁠

and

Ants & Media⁠

Ento-Linguistic Domains⁠

perspective — it is interesting about the “SuperOrganism” concept

https://en.wikipedia.org/wiki/Superorganism⁠

. This implies that the nestmate is the organism, and the colony is the “super” organism. We even see this tension in the naming/ambiguity of the Social, Eu-Social (good? true? social), for example “The Molecular and Evolutionary Genetic Implications of Being Truly Social for the Social Insects” (

Linksvayer 2015⁠

) — how are

Ants⁠

and other

Entomology⁠

“truly” social? What is truly the social?

Whereas the classical citation

https://onlinelibrary.wiley.com/doi/10.1002/jmor.1050220206⁠

of WM Wheeler 1911 is “The ant-colony as an organism” — in the Kantian sense. However

This idea of

Biology⁠

as a “2nd person, social” science came up in the end of the discussion on

GuestStream #078.1⁠

What could come before time? Intertwining affectivity and temporality at the basis of intentionality⁠

⁠

What is the relationship between multiscale ecological-selective dynamics (which appear to have contingency, punctuated multi-stabilities, times of plenty/scarcity/stasis/change etc. — and this “always pruning by 1/2” notion from

Quantum⁠

What state space is it that is getting reduced, in Biology?

Can we connect to the information geometry of e.g. Fisher’s Geometry Model and diffusion/paths in multivariate phenotypic spaces?

Can the

Symbolic Formalism⁠

for multiscale phenotypic systems be useful enough to enable compositional high-throughput empirical inquiry?

e.g. to set up all the API’s & LLMs &

Category Theory⁠

so we can dispatch the request for “Do analysis X on the

tissue-specific transcriptomics⁠

for all ant species where we have 3 or more sightings in Y location & ...”.

⁠

5/7/2024 KU

⁠

Tunnel to Wwwanderers Group (PDX)⁠

⁠

6/7/2024

⁠

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