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Fields C. The free energy principle induces intracellular compartmentalization. Biochem Biophys Res Commun 2024; 723:150070. [PMID: 38896995 DOI: 10.1016/j.bbrc.2024.150070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 06/21/2024]
Abstract
Living systems at all scales are compartmentalized into interacting subsystems. This paper reviews a mechanism that drives compartmentalization in generic systems at any scale. It first discusses three symmetries of generic physical interactions in a quantum-theoretic description. It then shows that if one of these, a permutation symmetry on the inter-system boundary, is spontaneously broken, the symmetry breaking is amplified by the Free Energy Principle (FEP). It thus shows how compartmentalization generically results from permutation symmetry breaking under the FEP. It finally notes that the FEP asymptotically restores the broken symmetry, showing that the FEP can be regarded as a theory of fluctuations away from a permutation-symmetric boundary, and hence from an entangled joint state of the interacting systems.
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Affiliation(s)
- Chris Fields
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA.
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Hartl B, Risi S, Levin M. Evolutionary Implications of Self-Assembling Cybernetic Materials with Collective Problem-Solving Intelligence at Multiple Scales. ENTROPY (BASEL, SWITZERLAND) 2024; 26:532. [PMID: 39056895 PMCID: PMC11275831 DOI: 10.3390/e26070532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024]
Abstract
In recent years, the scientific community has increasingly recognized the complex multi-scale competency architecture (MCA) of biology, comprising nested layers of active homeostatic agents, each forming the self-orchestrated substrate for the layer above, and, in turn, relying on the structural and functional plasticity of the layer(s) below. The question of how natural selection could give rise to this MCA has been the focus of intense research. Here, we instead investigate the effects of such decision-making competencies of MCA agential components on the process of evolution itself, using in silico neuroevolution experiments of simulated, minimal developmental biology. We specifically model the process of morphogenesis with neural cellular automata (NCAs) and utilize an evolutionary algorithm to optimize the corresponding model parameters with the objective of collectively self-assembling a two-dimensional spatial target pattern (reliable morphogenesis). Furthermore, we systematically vary the accuracy with which the uni-cellular agents of an NCA can regulate their cell states (simulating stochastic processes and noise during development). This allows us to continuously scale the agents' competency levels from a direct encoding scheme (no competency) to an MCA (with perfect reliability in cell decision executions). We demonstrate that an evolutionary process proceeds much more rapidly when evolving the functional parameters of an MCA compared to evolving the target pattern directly. Moreover, the evolved MCAs generalize well toward system parameter changes and even modified objective functions of the evolutionary process. Thus, the adaptive problem-solving competencies of the agential parts in our NCA-based in silico morphogenesis model strongly affect the evolutionary process, suggesting significant functional implications of the near-ubiquitous competency seen in living matter.
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Affiliation(s)
- Benedikt Hartl
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA;
- Institute for Theoretical Physics, Center for Computational Materials Science (CMS), TU Wien, 1040 Wien, Austria
| | - Sebastian Risi
- Digital Design, IT University of Copenhagen, 2300 Copenhagen, Denmark;
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA;
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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McMillen P, Levin M. Collective intelligence: A unifying concept for integrating biology across scales and substrates. Commun Biol 2024; 7:378. [PMID: 38548821 PMCID: PMC10978875 DOI: 10.1038/s42003-024-06037-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/11/2024] [Indexed: 04/01/2024] Open
Abstract
A defining feature of biology is the use of a multiscale architecture, ranging from molecular networks to cells, tissues, organs, whole bodies, and swarms. Crucially however, biology is not only nested structurally, but also functionally: each level is able to solve problems in distinct problem spaces, such as physiological, morphological, and behavioral state space. Percolating adaptive functionality from one level of competent subunits to a higher functional level of organization requires collective dynamics: multiple components must work together to achieve specific outcomes. Here we overview a number of biological examples at different scales which highlight the ability of cellular material to make decisions that implement cooperation toward specific homeodynamic endpoints, and implement collective intelligence by solving problems at the cell, tissue, and whole-organism levels. We explore the hypothesis that collective intelligence is not only the province of groups of animals, and that an important symmetry exists between the behavioral science of swarms and the competencies of cells and other biological systems at different scales. We then briefly outline the implications of this approach, and the possible impact of tools from the field of diverse intelligence for regenerative medicine and synthetic bioengineering.
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Affiliation(s)
- Patrick McMillen
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Michael Levin
- Department of Biology, Tufts University, Medford, MA, 02155, USA.
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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Kaufmann R. Three sketches of life in (not flat) Earth: Comment on "Path integrals, particular kinds, and strange things" by K. Friston et al. Phys Life Rev 2024; 48:3-7. [PMID: 38007925 DOI: 10.1016/j.plrev.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/28/2023]
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Tung A, Sperry MM, Clawson W, Pavuluri A, Bulatao S, Yue M, Flores RM, Pai VP, McMillen P, Kuchling F, Levin M. Embryos assist morphogenesis of others through calcium and ATP signaling mechanisms in collective teratogen resistance. Nat Commun 2024; 15:535. [PMID: 38233424 PMCID: PMC10794468 DOI: 10.1038/s41467-023-44522-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024] Open
Abstract
Information for organismal patterning can come from a variety of sources. We investigate the possibility that instructive influences for normal embryonic development are provided not only at the level of cells within the embryo, but also via interactions between embryos. To explore this, we challenge groups of embryos with disruptors of normal development while varying group size. Here, we show that Xenopus laevis embryos are much more sensitive to a diverse set of chemical and molecular-biological perturbations when allowed to develop alone or in small groups, than in large groups. Keeping per-embryo exposure constant, we find that increasing the number of exposed embryos in a cohort increases the rate of survival while incidence of defects decreases. This inter-embryo assistance effect is mediated by short-range diffusible signals and involves the P2 ATP receptor. Our data and computational model emphasize that morphogenesis is a collective phenomenon not only at the level of cells, but also of whole bodies, and that cohort size is a crucial variable in studies of ecotoxicology, teratogenesis, and developmental plasticity.
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Affiliation(s)
- Angela Tung
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Megan M Sperry
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Wesley Clawson
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Ananya Pavuluri
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Sydney Bulatao
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Michelle Yue
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Ramses Martinez Flores
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Vaibhav P Pai
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Patrick McMillen
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Franz Kuchling
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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Seifert G, Sealander A, Marzen S, Levin M. From reinforcement learning to agency: Frameworks for understanding basal cognition. Biosystems 2024; 235:105107. [PMID: 38128873 DOI: 10.1016/j.biosystems.2023.105107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/17/2023] [Accepted: 12/17/2023] [Indexed: 12/23/2023]
Abstract
Organisms play, explore, and mimic those around them. Is there a purpose to this behavior? Are organisms just behaving, or are they trying to achieve goals? We believe this is a false dichotomy. To that end, to understand organisms, we attempt to unify two approaches for understanding complex agents, whether evolved or engineered. We argue that formalisms describing multiscale competencies and goal-directedness in biology (e.g., TAME), and reinforcement learning (RL), can be combined in a symbiotic framework. While RL has been largely focused on higher-level organisms and robots of high complexity, TAME is naturally capable of describing lower-level organisms and minimal agents as well. We propose several novel questions that come from using RL/TAME to understand biology as well as ones that come from using biology to formulate new theory in AI. We hope that the research programs proposed in this piece shape future efforts to understand biological organisms and also future efforts to build artificial agents.
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Affiliation(s)
- Gabriella Seifert
- Department of Physics, University of Colorado, Boulder, CO 80309, USA; W. M. Keck Science Department, Pitzer, Scripps, and Claremont McKenna College, Claremont, CA 91711, USA
| | - Ava Sealander
- Department of Electrical Engineering, School of Engineering and Applied Sciences, Columbia University, New York, NY 10027, USA; W. M. Keck Science Department, Pitzer, Scripps, and Claremont McKenna College, Claremont, CA 91711, USA
| | - Sarah Marzen
- W. M. Keck Science Department, Pitzer, Scripps, and Claremont McKenna College, Claremont, CA 91711, USA.
| | - Michael Levin
- Department of Biology, Tufts University, Medford, MA 02155, USA; Allen Discovery Center at Tufts University, Medford, MA 02155, USA
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Stano P, Nehaniv C, Ikegami T, Damiano L, Witkowski O. Autopoiesis: Foundations of life, cognition, and emergence of self/other. Biosystems 2023; 232:105008. [PMID: 37619925 DOI: 10.1016/j.biosystems.2023.105008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy.
| | - Chrystopher Nehaniv
- Department of Systems Design Engineering, University of Waterloo, Waterloo, ON, Canada.
| | - Takashi Ikegami
- The Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
| | - Luisa Damiano
- Research Group on the Epistemology of the Sciences of the Artificial, Department of Communication, Arts and Media, IULM University, Milan, Italy.
| | - Olaf Witkowski
- Cross Labs, The University of Tokyo, Tokyo Institute of Technology, Tokyo, Japan.
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Matsuno K. Semiosis as a Source of Providing Empirical Phenomena with a New Type of Cohesion. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1173. [PMID: 37628203 PMCID: PMC10453632 DOI: 10.3390/e25081173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/01/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023]
Abstract
Embodying the indexical signs is vital to semiosis as a cohesive material agency mediating between consequents and antecedents. One unique factor of biology compared with standard physics and chemistry is the cohesion enabling the biological components, codes and organizations to accommodate themselves with a specific material embodiment. Every individual body is uniquely biological and requires a specific cohesion of material origin for its own sake that could not be found in the non-living material world. The relevant cohesion comes from the exchange interaction of the atomic quantum particles, such as the carbon atoms, which is far greater than the electrons as a common exchange mediator adopted for the spatial cohesion ubiquitous in physics and chemistry. What is specific to the temporal cohesion latent in the atomic exchange is the immutable identity of the individual quantum particle surviving only over a limited time, while being constantly alternated with the new ones of the same kinds in a successive manner. Semiosis is supported by the underlying teleonomic cohesion, such that the preceding temporal cohesion may constantly induce the succeeding similar one ad infinitum.
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Affiliation(s)
- Koichiro Matsuno
- Department of Bio-Engineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
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