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The Deep Stack of Existence
Seeing Life and its Substrates as Richly Connected Layers
Saturn close to occlusion by
Dark Si...
A Taste of History
A series of online history seminars
with Tony Birch, Gary Foley and Jacqui Katona
Gary Foley: For those...
Too Funny for Words
Abstractions, Category Errors,
Epistemic Cuts
Life on an Active Planet The Two-edged Sword
Multiple Pa...
The Deep Stack of Existence
Seeing Life and its Substrates as Richly Connected Layers
0. Uncertain Preconditions
for Cosmo...
0. Uncertain Preconditions for Cosmogenesis
Schematic was good enough to use at 2007 Philosophy of Complexity
workshop in ...
1. Light Matter on Dark Background
Big Bang inflationary moment of creation
Potentials revealed in aftermath, physical laws...
Making sense of quantum
physics can be a challenge.
Video of Laughlin’s Linus
Pauling Memorial Lecture
https://www.youtube...
2. One solar system is our backyard
In round figures the moon is ten circumnavigations of Earth away, Venus is
more than 10...
The Formation of the Moon May Have
Stretched the Earth Into a Potato
by Joel Hruska, 15 April 2020
https://www.extremetech...
3. Explorations of prokaryotic chemistry
We can defer some of this to Bill Hall’s promised presentation on
origins in ligh...
Fig. 2 (A-E): Syntrophic
amino acid utilization. In
Imachi, H., Nobu, M.K.,
Nakahara, N. et al.
Isolation of an archaeon
a...
The Deep Stack of Existence
Seeing Life and its Substrates as Richly Connected Layers
Two central points, as we cross the ...
4. Replicating dynamically encoded knowledge
Everything needs a dissipating gradient to feed on, plus convertibles
Autocat...
The calcified parts of Cambrian and later fossils
have long been vital to dating geological strata,
the period names often ...
5. Collective benefits for multicellular eukaryotes
Lynn Margulis identified the role of symbioses between prokaryote lineag...
Tuesday’s overdose of confirmation bias fulfilment
I’ve been arguing for a while from a systems analyst perspective, armed
w...
Default insistence
that humans are
more evolved
than other
species don’t pass
the pub test.
We have a
generation time
in d...
6. Keeping current against mediated fixations
Building on Bill Hall’s Application HolyWars, Lynne Kelly’s PhD research that...
Final Cause*
The Uses to Which Things Are Put
Humans obsess over our tools,
failing to recognise all the tools
provided by...
Reflections! Questions?
Next month: Going Over the Cliff
Existential urgency of transitioning from
Ecosystem Decline to Eco...
The Deep Stack of Existence: Seeing Life and its Substrates as Richly Connected Layers
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The Deep Stack of Existence: Seeing Life and its Substrates as Richly Connected Layers

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A key point summary of deep history through a complex systems lens with emphasis on connectivity and contingency, within the context of our Supervenience Project's envisaged chapters Towards Healthy General Knowledge and Life on an Active Planet, with late focus on recent neurological research confirming the breadth of common heritage of mobile animals.

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The Deep Stack of Existence: Seeing Life and its Substrates as Richly Connected Layers

  1. 1. The Deep Stack of Existence Seeing Life and its Substrates as Richly Connected Layers Saturn close to occlusion by Dark Side of the Moon 4 August 2014 Tony Smith Melbourne Emergence Meetup 13 August 2020
  2. 2. A Taste of History A series of online history seminars with Tony Birch, Gary Foley and Jacqui Katona Gary Foley: For those who are genuinely interested in the proposed online Winter School on the history and politics of the Black Resistance with Tony Birch, myself and Jacqui Katona you may register your interest on the link below and when we have made a decision on when it will happen and other details, we will contact you. https://goori2.aidaform.com/templates-en-event-registration-form
  3. 3. Too Funny for Words Abstractions, Category Errors, Epistemic Cuts Life on an Active Planet The Two-edged Sword Multiple Paths to Emergence Constraints and Degrees of Freedom Birds and Others Interweb to Facebook Better than Out of Control Information, Maps and Territories Urban Hydrology out of Sight Going Down with the Egg Basket Self-organising, Adaptive Codification and Communication Exploiting a Dissipating Gradient: creaming, trickle down Dystopian Utopias and Science Fiction Towards Healthy General Knowledge The Inside View: knowing when you're dreaming Verbal Blindness Accepting Cosmological Responsibility
  4. 4. The Deep Stack of Existence Seeing Life and its Substrates as Richly Connected Layers 0. Uncertain Preconditions for Cosmogenesis 5. Collective benefits for multicellular eukaryotes 2. One solar system is our backyard 1. Light Matter on Dark Background 3. Explorations of prokaryotic chemistry 4. Replicating dynamically encoded knowledge 6. Keeping current against mediated fixations
  5. 5. 0. Uncertain Preconditions for Cosmogenesis Schematic was good enough to use at 2007 Philosophy of Complexity workshop in Stellenbosch, Western Cape. Our hippocampus-enabled spatial mapping evolved to function in conservative 3D space does not make it easy to see possibilities beyond the event horizon, nor the microstructure facilitating physics, the complications of which we step through at length in the next section. The Deep Stack of Existence is context, complexity and connectedness all the way down, so we cannot expect Preconditions for Cosmogenesis to be any less complex. What we can know with confidence is that the Weak Anthropic Principle tells us all we can know from finding ourselves in a multiverse and on a planet which facilitates our momentary existence. Uncertainty continues in all that follows, with lines drawn in the sand where closer inspection would most likely reveal smudged gradients.
  6. 6. 1. Light Matter on Dark Background Big Bang inflationary moment of creation Potentials revealed in aftermath, physical laws emerging? Excess of baryons (protons, neutrons, not anti-~) Hydrogen, helium (𝛼) and dark matter/mass Gravitational amplification of density fluctuations Neutral atoms, transparency, cosmic microwave background First generation “population III” stars, nucleosynthesis Yes we have no beryllium, 𝛼+𝛼 doesn't go But 3𝛼/carbon and 4𝛼/oxygen do and catalyse cycle Binding energy valley of iron and nickel Biggest stars have shortest lives, supernovae, remnants Electron orbitals, chemical bonding, molecules, dust to dust Second generation “population II” star formation is different Mergers between remnants create heavier elements Cosmic ray collisions fill low end gaps Life uses relatively rare phosphorus, boron, molybdenum Galaxy clusters, voids, central black holes Planetary accretion disks, exoplanet observation biases
  7. 7. Making sense of quantum physics can be a challenge. Video of Laughlin’s Linus Pauling Memorial Lecture https://www.youtube.com/ watch?v=0qCSpWjsAiE provided an even clearer picture than his book did, but still one standout lesson about the precision of crystal grid alignments is not the centrepiece. Rodney A Brooks makes the case that Quantum Field Theory is a better way of understanding than Quantum Mechanics though they produce equivalent results, with problems arising when philosophers place too much weight on local uncertainty, ignoring the stronger implications of universal connectedness between diverse histories.
  8. 8. 2. One solar system is our backyard In round figures the moon is ten circumnavigations of Earth away, Venus is more than 100x further than the moon, Neptune more than 100xVenus, Alpha Centauri is near 10,000x Neptune, a billion times that circumnavigation. Earlier speculations notwithstanding, there is no doubt that formation of an accretion disk of gas and dust is a normal component of star formation and that the adhesive nature of dust particles can build planets relatively quickly, the latter steps clearing out individual planetary orbits involve big collisions. Isotope ratios and other data indicate that Earth and moon are survivors of a major mixing event that models suggest involved not just a final impactor the size of Mars, retrospectively named Theia, but a particular collision geometry which David Waltham rates as the most critical factor in Earth’s uniqueness. This left Earth rotating rapidly, tidal action transferring angular momentum to the moon by expanding its orbit, a process expected to continue to tidal lock. It took half a billion years for the surface to solidify, widely thought to follow a heavy bombardment due to movement of outer planets triggering asteroids. Plate tectonics assembled and dissembled continents as Life started to leave traces in sediments, invented photosynthesis with its highly combustible waste product, oxygen, changing planetary chemistry and serving as an energy store to fuel a massive diversification of Life following extreme glaciation events.
  9. 9. The Formation of the Moon May Have Stretched the Earth Into a Potato by Joel Hruska, 15 April 2020 https://www.extremetech.com/extreme/309361-the-formation- of-the-moon-may-have-stretched-the-earth-into-a-potato MIT: ‘Snowball Earth’ Came From Huge Drop in Sunlight by Ryan Whitwam, 30 July 2020 https://medium.com/extremetech-access/mit-snowball-earth- came-from-huge-drop-in-sunlight-e6acf326b4a3 via
  10. 10. 3. Explorations of prokaryotic chemistry We can defer some of this to Bill Hall’s promised presentation on origins in light of viral interest that will benefit from his expertise in evolutionary biology and his more rigorous academic processes. Here we should restrict ourselves to an overview of Earth’s middle 3.5 billion years of self-organising, adaptive chemical complexity; drawing initially on Bill’s alert to a 2020 paper by Imachi et al on an archaeon presumed close to the prokaryote–eukaryote boundary. Stuart Kauffman’s pioneering theoretical research on autocatalytic sets still influences ongoing work on the origins of metabolism. There is no consensus on how complex metabolism got enclosed in lipid membranes, let alone with a genetic reproduction system, though deep rock pores provide limitless hydrated test tubes while our laboratories demand cellular cultures near room temperature. Biochemistry employs common building blocks like Lego, such as adenosine attaching phosphates as a safe cellular energy source or in RNA codon chains for ribosomal translation into amino acids. While the slow release of the heat of planetary formation powers geologic and deep life processes, Life’s discovery of photosynthesis had the surface adapting poisonous oxygen to energising services, multiplying interaction potentials for symbiosis to form eukaryotes.
  11. 11. Fig. 2 (A-E): Syntrophic amino acid utilization. In Imachi, H., Nobu, M.K., Nakahara, N. et al. Isolation of an archaeon at the prokaryote– eukaryote interface. Nature 577, 519–525 (2020). 15 January 2020, https://doi.org/10.1038/ s41586-019-1916-6 The take home point is that this is representative of the metabolic mapping which has become a key tool beyond the internal workings of cells to study the interdependence of prokaryotic communities as producers/consumers in metabolic clusters at unexpected depths.
  12. 12. The Deep Stack of Existence Seeing Life and its Substrates as Richly Connected Layers Two central points, as we cross the Ediacaran boundary into the more familiar riches of our multi-cellular world: The physics of condensed matter allows traces of past events to be retained until degraded on varying timetables. Life actively maintains such traces in ways that engage processes for pattern persistence, replication and evolution. The view from the Razorback Lookout, Brachina Trail, looking SW towards the ABC Ranges and Wilpena Pound, taking in the entire Cryogenian to upper Ediacaran sedimentary sequence from the Trezona Fm. at left, to the Rawnsley Quartzite (tips of the hills in the far distance). Ediacara, as seen from Nilpena, one of the world’s most striking Ediacaran fossil localities, with multiple bedding surfaces excavated and re-constituted on the hillsides, each covered in hundreds of well-preserved impressions of Ediacara biota.
  13. 13. 4. Replicating dynamically encoded knowledge Everything needs a dissipating gradient to feed on, plus convertibles Autocatalytic sets use some components to generate others, recursively Metabolism knows how to control its reactions via self-limiting processes Porous membranes know which pores are soluble, how to grow and bud Ribosomes know how to make proteins coded for by tRNA and assemble Prokaryotes know to associate with complementary sources and sinks Knowledge thrives and replicates when and where it works, otherwise dies New knowledge is acquired by chance with great risks and great rewards Genetic knowledge is shared cannibalistically by bacteria, via viruses or sex Knowledge is naturally encoded in biochemistry’s combinatorial explosions Developmental pathway knowledge is in eggs, seeds, spores and genomes DNA provides persistent genetic knowledge, still only expressed in cells Patterns of intercellular communication facilitate contingent knowledge Mycorrhizal networking of vegetation roots informs forests and grasslands Networks of neurons facilitate essential behaviours of mobile animals Beyond chemical and positional knowledge, senses monitor sound and light All Life applies knowledge to sensory inputs in determining next actions Shared knowledge facilitates collaboration, continuity and adaptation
  14. 14. The calcified parts of Cambrian and later fossils have long been vital to dating geological strata, the period names often reflecting the place where a particular assemblage was first characterised, but with even the vital transition of the Ediacaran not yet making it into traditional compilations. With advances in science and technology, much more information can nowadays be gleaned from traces left in the microstructure, from chemical residues to pollen and burrows. Fossilisation is far from a uniform process.Traces left and the fraction resurfacing depend on place, time and local conditions, then, now and between. Stones to me are the objects that parallel all life, more so than trees or mortal things because stones are almost immortal.They know things learned over deep time. Stone represents earth, tools and spirit; it conveys meaning through its use and through its resilience to the elements.At the same time it ages, cracking and eroding as time wears it down, but it is still there, filled with energy and spirit. Tasmanian Max quoted by TysonYunkaporta
  15. 15. 5. Collective benefits for multicellular eukaryotes Lynn Margulis identified the role of symbioses between prokaryote lineages in establishing the first eukaryotic cells which was only part way to the complex multicellular taxa that now dominate our thinking, despite her further work on the importance of a lot more symbionts, including gut microbiomes. Recent molecular research supports the impression that most mobile animals share a common central nervous system architecture with rich diversification and behavioural flexibility to exploit new opportunities and diversity further. The interplay of unrelated taxa taking complementary roles in geographically constrained ecosystems opens up even more possibilities, from pollination and seed dispersal to the reprocessing of dead wood, dead bodies, and dead shits. Many animals live some or all of the time in large gatherings of their own kind, briefly for mass matings or to pass on found shells as they grow, safer seasonal migration or breeding, daily roosting, or building reefs, cities of eusocial insects or mad apes.Trees, vines and more make jungles, grasses and forbs savannahs. Within species there can be cultural divides which can become a prelude to speciation, from the divergent feeding strategies of many lineages of Orcas to the Congo dividing our closest cousins on their preference for love or war.
  16. 16. Tuesday’s overdose of confirmation bias fulfilment I’ve been arguing for a while from a systems analyst perspective, armed with observation and digital recording across diverse settings, that there has to be an extensive basic set of functionality achieved by some early common ancestor of much of animalia.Then on 11 August 2020 two reports landed with different lines of evidence of ancient commonalities. Ancestral regulatory mechanisms specify conserved midbrain circuitry in arthropods and vertebrates Jessika C. Bridi, Zoe N. Ludlow, Benjamin Kottler, Beate Hartmann, Lies Vanden Broeck, Jonah Dearlove, Markus Göker, Nicholas J. Strausfeld, Patrick Callaerts, and Frank Hirth PNAS August 11, 2020 117 (32) 19544-19555 https://doi.org/10.1073/pnas.1918797117 Inside the mind of an animal Neuroscientists are scrutinizing huge piles of data to learn how brains create emotions and other internal states such as aggression and desire. Alison Abbott Illustration by Karol Banach Nature 584, 182-185, 11 August 2020 https://www.nature.com/articles/d41586-020-02337-x
  17. 17. Default insistence that humans are more evolved than other species don’t pass the pub test. We have a generation time in decades, nowadays an artificially high rate of surviving to reproductive age, and barely a handful of extant related species; while many other species reproduce in months, their seeds and larvae are significant food sources, and often have many thousands of seemingly similar species, each with its own ecological role.
  18. 18. 6. Keeping current against mediated fixations Building on Bill Hall’s Application HolyWars, Lynne Kelly’s PhD research that was a bridge for us, my recent Quietening Timelessness presentation, and misrepresentations of the Anthropocene as a geological epoch rather than a transition; when the train became a runaway is a question for historians. As a crude hypothesis lets play with the transition from oral language and artistic representation to written language, though what really mattered was the ability to infuse permanency/timelessness into prescriptive texts which could be isolated from ongoing revalidation of living knowledge. Yes, most serious systems for maintaining textual knowledge bases have processes for maintaining currency, but, in this age of ever faster sharing, they are more vulnerable to rumours spreading faster than corrections. Today there are too many circumstances which grant authority to textual representations regardless of obvious observations of the living world, administration pulling rank on essential work regardless of viral lessons. While overdependence on text only roughly correlates with the rise of oppressive empires, the worst of regimes still fuss over keeping records. Meanwhile self-proclaimed Fundamentalists call on impossibly literal interpretations of ancient texts to bludgeon dissenters into silence, inspiring law makers and law enforcers to assume similar immunities.
  19. 19. Final Cause* The Uses to Which Things Are Put Humans obsess over our tools, failing to recognise all the tools provided by Life before metallic lustre grabbed our attention. But it may be the additional uses found for tools with an assumed purpose which are interesting. Audio communication has been adapted way beyond listening for signals from the world, notably for echo location involving major secondary enhancements. Being alive is about learning and adapting.When that stops you’re as dead as any collapsed system. *There is a sad consensus that oversimplified notions of cause and affect are an some kind of advance on Aristotle’s 4 causes. Ebook release day delivery: Thursday, 3 September 2020
  20. 20. Reflections! Questions? Next month: Going Over the Cliff Existential urgency of transitioning from Ecosystem Decline to Ecosystem Regeneration

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