1
|
Clark KB. Ownership psychology as a "cognitive cell" adaptation: A minimalist model of microbial goods theory. Behav Brain Sci 2023; 46:e330. [PMID: 37813404 DOI: 10.1017/s0140525x23001498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Microbes perfect social interactions with intuitive logics and goal-directed reciprocity. These multilevel, cognition-resembling adaptations in Dictyostelid cellular molds enable individual-to-group viability through public/private bacterial farming and dynamic marketspaces. Like humans and animals, Dictyostelid livestock-ownership depends on environmental sensing, cooperation, and competition. Moreover, social-norm policing of cosmopolitan colonies coordinates farmer decisions, phenotypes, and ownership identities with bacteria herding, privatization, and consumption.
Collapse
Affiliation(s)
- Kevin B Clark
- Cures Within Reach, Chicago, IL, USA ; www.linkedin.com/pub/kevin-clark/58/67/19a; https://access-ci.org
- Felidae Conservation Fund, Mill Valley, CA, USA
- Expert Network, Penn Center for Innovation, University of Pennsylvania, Philadelphia, PA, USA
- Network for Life Detection (NfoLD), NASA Astrobiology Program, NASA Ames Research Center, Mountain View, CA, USA
- Multi-Omics and Systems Biology & Artificial Intelligence and Machine Learning Analysis Working Groups, NASA GeneLab, NASA Ames Research Center, Mountain View, CA, USA
- Frontier Development Lab, NASA Ames Research Center, Mountain View, CA, USA
- SETI Institute, Mountain View, CA, USA
- Peace Innovation Institute, Netherlands & Stanford University, Palo Alto, CA, USA
- Shared Interest Group for Natural and Artificial Intelligence (sigNAI), Max Planck Alumni Association, Berlin, Germany
- Biometrics and Nanotechnology Councils, Institute for Electrical and Electronics Engineers, New York, NY, USA
| |
Collapse
|
2
|
Clark KB. Neural Field Continuum Limits and the Structure-Function Partitioning of Cognitive-Emotional Brain Networks. BIOLOGY 2023; 12:352. [PMID: 36979044 PMCID: PMC10045557 DOI: 10.3390/biology12030352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/07/2023] [Accepted: 02/13/2023] [Indexed: 02/25/2023]
Abstract
In The cognitive-emotional brain, Pessoa overlooks continuum effects on nonlinear brain network connectivity by eschewing neural field theories and physiologically derived constructs representative of neuronal plasticity. The absence of this content, which is so very important for understanding the dynamic structure-function embedding and partitioning of brains, diminishes the rich competitive and cooperative nature of neural networks and trivializes Pessoa's arguments, and similar arguments by other authors, on the phylogenetic and operational significance of an optimally integrated brain filled with variable-strength neural connections. Riemannian neuromanifolds, containing limit-imposing metaplastic Hebbian- and antiHebbian-type control variables, simulate scalable network behavior that is difficult to capture from the simpler graph-theoretic analysis preferred by Pessoa and other neuroscientists. Field theories suggest the partitioning and performance benefits of embedded cognitive-emotional networks that optimally evolve between exotic classical and quantum computational phases, where matrix singularities and condensations produce degenerate structure-function homogeneities unrealistic of healthy brains. Some network partitioning, as opposed to unconstrained embeddedness, is thus required for effective execution of cognitive-emotional network functions and, in our new era of neuroscience, should be considered a critical aspect of proper brain organization and operation.
Collapse
Affiliation(s)
- Kevin B. Clark
- Cures Within Reach, Chicago, IL 60602, USA;
- Felidae Conservation Fund, Mill Valley, CA 94941, USA
- Campus and Domain Champions Program, Multi-Tier Assistance, Training, and Computational Help (MATCH) Track, National Science Foundation’s Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support (ACCESS), https://access-ci.org/
- Expert Network, Penn Center for Innovation, University of Pennsylvania, Philadelphia, PA 19104, USA
- Network for Life Detection (NfoLD), NASA Astrobiology Program, NASA Ames Research Center, Mountain View, CA 94035, USA
- Multi-Omics and Systems Biology & Artificial Intelligence and Machine Learning Analysis Working Groups, NASA GeneLab, NASA Ames Research Center, Mountain View, CA 94035, USA
- Frontier Development Lab, NASA Ames Research Center, Mountain View, CA 94035, USA & SETI Institute, Mountain View, CA 94043, USA
- Peace Innovation Institute, The Hague 2511, Netherlands & Stanford University, Palo Alto, CA 94305, USA
- Shared Interest Group for Natural and Artificial Intelligence (sigNAI), Max Planck Alumni Association, 14057 Berlin, Germany
- Biometrics and Nanotechnology Councils, Institute for Electrical and Electronics Engineers (IEEE), New York, NY 10016, USA
| |
Collapse
|
3
|
Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective. Int J Mol Sci 2021; 22:ijms222111311. [PMID: 34768741 PMCID: PMC8582858 DOI: 10.3390/ijms222111311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
Bioluminescence, the emission of light catalysed by luciferases, has evolved in many taxa from bacteria to vertebrates and is predominant in the marine environment. It is now well established that in animals possessing a nervous system capable of integrating light stimuli, bioluminescence triggers various behavioural responses and plays a role in intra- or interspecific visual communication. The function of light emission in unicellular organisms is less clear and it is currently thought that it has evolved in an ecological framework, to be perceived by visual animals. For example, while it is thought that bioluminescence allows bacteria to be ingested by zooplankton or fish, providing them with favourable conditions for growth and dispersal, the luminous flashes emitted by dinoflagellates may have evolved as an anti-predation system against copepods. In this short review, we re-examine this paradigm in light of recent findings in microorganism photoreception, signal integration and complex behaviours. Numerous studies show that on the one hand, bacteria and protists, whether autotrophs or heterotrophs, possess a variety of photoreceptors capable of perceiving and integrating light stimuli of different wavelengths. Single-cell light-perception produces responses ranging from phototaxis to more complex behaviours. On the other hand, there is growing evidence that unicellular prokaryotes and eukaryotes can perform complex tasks ranging from habituation and decision-making to associative learning, despite lacking a nervous system. Here, we focus our analysis on two taxa, bacteria and dinoflagellates, whose bioluminescence is well studied. We propose the hypothesis that similar to visual animals, the interplay between light-emission and reception could play multiple roles in intra- and interspecific communication and participate in complex behaviour in the unicellular world.
Collapse
|
4
|
Unpredictable homeodynamic and ambient constraints on irrational decision making of aneural and neural foragers. Behav Brain Sci 2019; 42:e40. [PMID: 30940238 DOI: 10.1017/s0140525x1800184x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Foraging for nutritional sustenance represents common significant learned/heritable survival strategies evolved for phylum-diverse cellular life on Earth. Unicellular aneural to multicellular neural foragers display conserved rational or irrational decision making depending on outcome predictions for noise-susceptible real/illusory homeodynamic and ambient dietary cues. Such context-dependent heuristic-guided foraging enables optimal, suboptimal, or fallacious decisions that drive organismal adaptation, health, longevity, and life history.
Collapse
|
5
|
Clark KB. Insight and analysis problem solving in microbes to machines. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:183-93. [DOI: 10.1016/j.pbiomolbio.2015.08.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/12/2015] [Indexed: 10/23/2022]
|
6
|
Westerhoff HV, Brooks AN, Simeonidis E, García-Contreras R, He F, Boogerd FC, Jackson VJ, Goncharuk V, Kolodkin A. Macromolecular networks and intelligence in microorganisms. Front Microbiol 2014; 5:379. [PMID: 25101076 PMCID: PMC4106424 DOI: 10.3389/fmicb.2014.00379] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/05/2014] [Indexed: 11/13/2022] Open
Abstract
Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of information and communication technology (ICT): they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity - particularly activity of the human brain - with a phenomenon we call "intelligence." Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as "human" and "brain" out of the defining features of "intelligence," all forms of life - from microbes to humans - exhibit some or all characteristics consistent with "intelligence." We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo.
Collapse
Affiliation(s)
- Hans V. Westerhoff
- Department of Molecular Cell Physiology, Vrije Universiteit AmsterdamAmsterdam, Netherlands
- Manchester Centre for Integrative Systems Biology, The University of ManchesterManchester, UK
- Synthetic Systems Biology, University of AmsterdamAmsterdam, Netherlands
| | - Aaron N. Brooks
- Institute for Systems BiologySeattle, WA, USA
- Molecular and Cellular Biology Program, University of WashingtonSeattle, WA, USA
| | - Evangelos Simeonidis
- Institute for Systems BiologySeattle, WA, USA
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | | | - Fei He
- Department of Automatic Control and Systems Engineering, The University of SheffieldSheffield, UK
| | - Fred C. Boogerd
- Department of Molecular Cell Physiology, Vrije Universiteit AmsterdamAmsterdam, Netherlands
| | | | - Valeri Goncharuk
- Netherlands Institute for NeuroscienceAmsterdam, Netherlands
- Russian Cardiology Research CenterMoscow, Russia
- Department of Medicine, Center for Alzheimer and Neurodegenerative Research, University of AlbertaEdmonton, AB, Canada
| | - Alexey Kolodkin
- Institute for Systems BiologySeattle, WA, USA
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| |
Collapse
|
7
|
Clark KB. Basis for a neuronal version of Grover's quantum algorithm. Front Mol Neurosci 2014; 7:29. [PMID: 24860419 PMCID: PMC4029008 DOI: 10.3389/fnmol.2014.00029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/31/2014] [Indexed: 11/25/2022] Open
Abstract
Grover's quantum (search) algorithm exploits principles of quantum information theory and computation to surpass the strong Church–Turing limit governing classical computers. The algorithm initializes a search field into superposed N (eigen)states to later execute nonclassical “subroutines” involving unitary phase shifts of measured states and to produce root-rate or quadratic gain in the algorithmic time (O(N1/2)) needed to find some “target” solution m. Akin to this fast technological search algorithm, single eukaryotic cells, such as differentiated neurons, perform natural quadratic speed-up in the search for appropriate store-operated Ca2+ response regulation of, among other processes, protein and lipid biosynthesis, cell energetics, stress responses, cell fate and death, synaptic plasticity, and immunoprotection. Such speed-up in cellular decision making results from spatiotemporal dynamics of networked intracellular Ca2+-induced Ca2+ release and the search (or signaling) velocity of Ca2+ wave propagation. As chemical processes, such as the duration of Ca2+ mobilization, become rate-limiting over interstore distances, Ca2+ waves quadratically decrease interstore-travel time from slow saltatory to fast continuous gradients proportional to the square-root of the classical Ca2+ diffusion coefficient, D1/2, matching the computing efficiency of Grover's quantum algorithm. In this Hypothesis and Theory article, I elaborate on these traits using a fire-diffuse-fire model of store-operated cytosolic Ca2+ signaling valid for glutamatergic neurons. Salient model features corresponding to Grover's quantum algorithm are parameterized to meet requirements for the Oracle Hadamard transform and Grover's iteration. A neuronal version of Grover's quantum algorithm figures to benefit signal coincidence detection and integration, bidirectional synaptic plasticity, and other vital cell functions by rapidly selecting, ordering, and/or counting optional response regulation choices.
Collapse
Affiliation(s)
- Kevin B Clark
- Research and Development Service, Veterans Affairs Greater Los Angeles Healthcare System Los Angeles, CA, USA ; Complex Biological Systems Alliance North Andover, MA, USA
| |
Collapse
|
8
|
Clark KB. Ciliates learn to diagnose and correct classical error syndromes in mating strategies. Front Microbiol 2013; 4:229. [PMID: 23966987 PMCID: PMC3746415 DOI: 10.3389/fmicb.2013.00229] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 07/28/2013] [Indexed: 01/06/2023] Open
Abstract
Preconjugal ciliates learn classical repetition error-correction codes to safeguard mating messages and replies from corruption by “rivals” and local ambient noise. Because individual cells behave as memory channels with Szilárd engine attributes, these coding schemes also might be used to limit, diagnose, and correct mating-signal errors due to noisy intracellular information processing. The present study, therefore, assessed whether heterotrich ciliates effect fault-tolerant signal planning and execution by modifying engine performance, and consequently entropy content of codes, during mock cell–cell communication. Socially meaningful serial vibrations emitted from an ambiguous artificial source initiated ciliate behavioral signaling performances known to advertise mating fitness with varying courtship strategies. Microbes, employing calcium-dependent Hebbian-like decision making, learned to diagnose then correct error syndromes by recursively matching Boltzmann entropies between signal planning and execution stages via “power” or “refrigeration” cycles. All eight serial contraction and reversal strategies incurred errors in entropy magnitude by the execution stage of processing. Absolute errors, however, subtended expected threshold values for single bit-flip errors in three-bit replies, indicating coding schemes protected information content throughout signal production. Ciliate preparedness for vibrations selectively and significantly affected the magnitude and valence of Szilárd engine performance during modal and non-modal strategy corrective cycles. But entropy fidelity for all replies mainly improved across learning trials as refinements in engine efficiency. Fidelity neared maximum levels for only modal signals coded in resilient three-bit repetition error-correction sequences. Together, these findings demonstrate microbes can elevate survival/reproductive success by learning to implement classical fault-tolerant information processing in social contexts.
Collapse
Affiliation(s)
- Kevin B Clark
- Research and Development Service, Veterans Affairs Greater Los Angeles Healthcare System Los Angeles, CA, USA
| |
Collapse
|