Novel assays for complex systems: a review
Abstract
Recent developments in quantum biology, epigenetics, complexity theory, network analysis, and artificial intelligence (among other fields) suggest that familiar assumptions about the mechanisms of biological interaction may not be justified. Specifically: quantum algebras that assume forms of entanglement, coherence, and superposition may apply at a wide range of scales of living systems; such systems (including but not limited to the familiar typology of cells and organisms) are generally characterized by complex far-from-equilibrium metastabilities, not susceptible to linear perturbation theoretical tools; and the increasing scope and extent of industrial economies, which reinforce certain forms of deterministic, separable, linear dynamics, may introduce a previously unrecognized bias into experimental explorations of life behaviors (and contribute significantly to disruptive feedbacks loops in local and earth-wide homeostatic regimes). We will discuss potential consequences of such revised assumptions on theoretical and experimental research programs, and offer possible next steps.
Background
Scientists now know that linear systems susceptible of analytic solutions -- even approximate ones -- are a small component of the phase space of the universe, and especially of life.
Quantum algebras
Classical algebras assume local realism. Quantum algebras assume, instead, that elements of a system can be interlinked in specific ways. Such algebras can emerge from classical dynamics, or from quantum mechanics.
Photosynthesis
Experimental evidence for, and theoretical elaboration of, noise-amplified quantum coherence at biologically relevant timescales.
Ongoing questions include whether such coherence is adaptive or coincidental, and specifics such as whether vibronic or electronic excitations are the cause of observed quantum beats resulting from self-interference.
Olfaction
"Key and lock" models of protein geometry-mediated signalling suffer because the same receptors discriminate between many biomolecules. Perhaps receptors use quantum resonance at various sites, rather than simple morphology.
Magnetoreception
Birds, bats, and other species see magnetic fields (especially inclination) in their eyes. One favored potential mechanism involves spin-entangled
Evolution
Quantum evolution assumes that at least in some circumstances, an ensemble of heritable phenotypes may remain in superposition until a crisis, thus sampling the entire allowed space and reducing to the most adaptive phenotype upon collapse of the ensemble wavefunction.
Cell-cell communication
Cell communication may exceed the traditional modes of biomolecular import/export. If entire cells become even partially entangled, whether through exchange of biophotons, traditional molecules, or in other ways, then their behaviors will be linked on different timescales and potentially across longer distances.
Cognitive studies / linguistics
We think as if parts of speech are all present, even when we talk about things sequentially.
Ecologies
Both individuals and populations can behave as if coherent.
Trends and possibilities
If living systems are assumed to be nontrivially nonclassical in either or both emergent or microscopic ways, then a wide range of heretofore out-of-bounds research becomes immediately interesting.
Epigenetics
Genetic determinism is no longer capable of describing the extremely contingent, history-dependent diversity among cells, and even organism-level phenotypes.
"Evo-devo"
A new field recognizing that development of the organism involves not only recapitulation of evolutionary histories at organismal level, but adaptive selection among diverse cells as the very process of differentiation and structure-development.
Transcriptome diversity and stochastic proteins
Cell-level assays of familiar model organisms reveals an extraordinary diversity of transcriptomes, both between differentiated cells, and among stem cells before differentiation -- and even among neighboring cells within tissues. This implies that cells with slughtly differing boundary conditions can mobilize identical genomes to produce profoundly different assortments of proteins -- and moreover, that these same proteins can participate in greatly differing pathways depending on location, history, and potentially other switching mechanisms.
Holobiont
Organisms in general include a very wide diversity of "species" of cell, which are crucial to metabolic pathways and even complex behaviors (including cognition on humans).
Generational memory
Mice remember foods their grandparents learned to prefer. Indigenous people remain somatically stimulated by genocidal traumas after seven generations.
What is evolving?
40 years ago it was imagined that evolution works on genes. But perhaps whole ecosystems evolve, as much as species, and cells within organisms (or populations within holobionts).
Competition, cooperation: coherence?
Competition and cooperation have traditionally been seen as competing or even exclusive categories. But what if quantum logics encourage us to consider that nested layers of systems are evolving in relation with internal and external environments that are interconnected, in which multiple elements that appear on one level to be in competition are ultimately part of a coherent whole that is cooperating to find a new and richer metastable pattern? And vice versa -- cooperative ecologies are in competition.
Trends and possibilities
How do we explore living systems of which humans are a part? Using analogies with systems smaller than us to outline ways to recognize multi-level evolutionary adaptation, stochastic development, and nondeterministic coherence in the complex system including human social structures, industrial land tenure, and changing ecologies.
Artificial complex systems
AI is developing more quickly in practice than in theory.
Neural nets: deep learning vs. algorithms
AI cannot be understood. Evolutionary learning outcompetes analytical (intelligible) algorithms.
AI and God
AI has raised a host of formerly theological questions. Most prominently: if strong AI is possible, then simulations should far exceed base reality, and we are almost certainly created by an external being with potentially infinite power over our reality. How could we know? What qualifies as evidence? How might we communicate with such a creator?
Information and existence
Are octonions, the quantum foam of the vacuum spacetime, and holographic cosmologies evidence that we are, indeed, simulated life? Is "existence" fully described by information (ie. quantum numbers, vectors in phase space, etc.)?
Are we already part of an AI?
Strong AI is typically thought of as intentionally constructed. Recently, some fear that existing "passive" AIs will accidentally jailbreak their servers and begin acting on themselves (and the world) in runaway deep learning with unpredictable (terrifying) consequences. However, what if the already-existing tech-mediated interactions between humans are considered the nodes of a neural net? Could we already be becoming a global cyborg AI? If so, how could we tell -- and how could we communicate with it?
Prediction, meaning, and neural interfaces
We tend to imagine that statements have meaning if they have a (statistically) predictable structure to their interactions with the world. But what if such statements are connected with the "world" not directly, but by how a larger system (such as an AI) grows through them? Then predictability might indicate not the truth of the statement considered internally, but the success of its use by the larger structure. And vice versa.
Secondly, predictability might require a separability that limits human capacity for participation in quantum algebra-dependant living systems. Neural links, if classical in character, might amplify this limitation.
Trends and possibilities
AI is upon us, ready or not. We may have to consider many possible sources of structure to the data we gather, especially digitally, especially socially. How do we learn to communicate with intelligences we can't understand? (How, perhaps, have humans been doing so for a very long time?)
Research strategies
Rigid boundaries between disciplines and regimes of knowing may no longer be adequate to the rapidly changing situation. What are potential resources for linking sciences and ways of knowing towards deeper insight and potential collective action?
Fieldwork and nonreplicable experiments
Fieldwork sciences -- from botany to anthropology -- have for 200 years been considered inferior to lab sciences because their research was not able to remove the subjectivity of the researcher and the contingency of the researched by replicating effectively identical measurements by different scientists in different places and times. But that's precisely what we need: skills for making meaningful observations and honing useful forms of communication with complex systems, which are always changing and whose variables cannot be controlled.
Human psyche as complexity-grokking instrument
Neurophysiology leads to the conclusion that human sensory apparatus, memory, and language is an evolutionarily-honed tool for relating to complex systems outside of itself in timely and adaptive ways. This is most familiar in the context of other humans. How can it be applied to other systems? How has it been already, within other social structures?
Animism, ceremony, and indigineity
It is commonplace to consider animisms -- ie. cosmologies that treat nonhuman systems as persons -- as antithetical to science. What if they are an enormous store of crucial skills for mobilizing the person-grokking capacities of the human brain towards interactions with other forms of life? What if we understand ceremony as a set of practices for modulating and calibrating the human psyche for this end? What if indigenous peoples can be understood as adaptive social systems that rely on these practices to weave humans and more-than-human ecologies into coherence?
Humility and power
Knowledge is (or has been considered) power. But to interact with widespread quantum logics, we may need to recognize mutually exclusive data as plausibly simultaneously real. This recognition may operate at multiple levels, from the details of research practice to a renewed humility with which we hold scientific knowledge in the context of other ways of knowing -- in order to have and use a different kind of power.
Climate change
We face existential crisis. Scientists have reinforced a self-contradictory narrative that the climate, a complex system, can be simply understood. This has limited the effectiveness of interventions into political arenas. What are other ways the complexity of the life-system, and its dangerously rapid changes (not only climatic, but biodiversity, habitat, pollutants, etc.), can interface with political phase transition?
Bioethics
"Knowledge is neutral; it's what you do with it that matters." No one believes this anymore. If the process of science itself is a powerful part of the life system that is transforming the planet, and if how it operates matters, then what can scientists do that makes a difference?
References
Lots and lots of them. 500 at least. Go baby go!