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Newman SA. Form, function, mind: What doesn't compute (and what might). Biochem Biophys Res Commun 2024; 721:150141. [PMID: 38781663 DOI: 10.1016/j.bbrc.2024.150141] [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: 10/24/2023] [Revised: 03/07/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing animal (metazoan) tissues, a non-computational modality, but cell differentiation, which utilizes chromatin-based revisable memory banks and program-like function-calling, via the developmental gene co-expression system unique to the metazoans, has a quasi-computational basis. Multi-attractor dynamical models are argued to be misapplied to global properties of development, and it is suggested that along with computationalism, classic forms of dynamicism are similarly unsuitable to accounting for cognitive phenomena. Proposals are made for treating brains and other nervous tissues as novel forms of excitable matter with inherent properties which enable the intensification of cell-based basal cognition capabilities present throughout the tree of life. Finally, some connections are drawn between the viewpoint described here and active inference models of cognition, such as the Free Energy Principle.
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2
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Pio-Lopez L, Levin M. Aging as a loss of morphostatic information: A developmental bioelectricity perspective. Ageing Res Rev 2024; 97:102310. [PMID: 38636560 DOI: 10.1016/j.arr.2024.102310] [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: 11/05/2023] [Revised: 02/21/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
Abstract
Maintaining order at the tissue level is crucial throughout the lifespan, as failure can lead to cancer and an accumulation of molecular and cellular disorders. Perhaps, the most consistent and pervasive result of these failures is aging, which is characterized by the progressive loss of function and decline in the ability to maintain anatomical homeostasis and reproduce. This leads to organ malfunction, diseases, and ultimately death. The traditional understanding of aging is that it is caused by the accumulation of molecular and cellular damage. In this article, we propose a complementary view of aging from the perspective of endogenous bioelectricity which has not yet been integrated into aging research. We propose a view of aging as a morphostasis defect, a loss of biophysical prepattern information, encoding anatomical setpoints used for dynamic tissue and organ homeostasis. We hypothesize that this is specifically driven by abrogation of the endogenous bioelectric signaling that normally harnesses individual cell behaviors toward the creation and upkeep of complex multicellular structures in vivo. Herein, we first describe bioelectricity as the physiological software of life, and then identify and discuss the links between bioelectricity and life extension strategies and age-related diseases. We develop a bridge between aging and regeneration via bioelectric signaling that suggests a research program for healthful longevity via morphoceuticals. Finally, we discuss the broader implications of the homologies between development, aging, cancer and regeneration and how morphoceuticals can be developed for aging.
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Affiliation(s)
- Léo Pio-Lopez
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA; Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA.
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3
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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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4
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Levin M. Bioelectric networks: the cognitive glue enabling evolutionary scaling from physiology to mind. Anim Cogn 2023; 26:1865-1891. [PMID: 37204591 PMCID: PMC10770221 DOI: 10.1007/s10071-023-01780-3] [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: 11/28/2022] [Revised: 04/12/2023] [Accepted: 04/24/2023] [Indexed: 05/20/2023]
Abstract
Each of us made the remarkable journey from mere matter to mind: starting life as a quiescent oocyte ("just chemistry and physics"), and slowly, gradually, becoming an adult human with complex metacognitive processes, hopes, and dreams. In addition, even though we feel ourselves to be a unified, single Self, distinct from the emergent dynamics of termite mounds and other swarms, the reality is that all intelligence is collective intelligence: each of us consists of a huge number of cells working together to generate a coherent cognitive being with goals, preferences, and memories that belong to the whole and not to its parts. Basal cognition is the quest to understand how Mind scales-how large numbers of competent subunits can work together to become intelligences that expand the scale of their possible goals. Crucially, the remarkable trick of turning homeostatic, cell-level physiological competencies into large-scale behavioral intelligences is not limited to the electrical dynamics of the brain. Evolution was using bioelectric signaling long before neurons and muscles appeared, to solve the problem of creating and repairing complex bodies. In this Perspective, I review the deep symmetry between the intelligence of developmental morphogenesis and that of classical behavior. I describe the highly conserved mechanisms that enable the collective intelligence of cells to implement regulative embryogenesis, regeneration, and cancer suppression. I sketch the story of an evolutionary pivot that repurposed the algorithms and cellular machinery that enable navigation of morphospace into the behavioral navigation of the 3D world which we so readily recognize as intelligence. Understanding the bioelectric dynamics that underlie construction of complex bodies and brains provides an essential path to understanding the natural evolution, and bioengineered design, of diverse intelligences within and beyond the phylogenetic history of Earth.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, 200 Boston Ave., Suite 4600, Medford, MA, 02155, USA.
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
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Blackiston D, Kriegman S, Bongard J, Levin M. Biological Robots: Perspectives on an Emerging Interdisciplinary Field. Soft Robot 2023; 10:674-686. [PMID: 37083430 PMCID: PMC10442684 DOI: 10.1089/soro.2022.0142] [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] [Indexed: 04/22/2023] Open
Abstract
Advances in science and engineering often reveal the limitations of classical approaches initially used to understand, predict, and control phenomena. With progress, conceptual categories must often be re-evaluated to better track recently discovered invariants across disciplines. It is essential to refine frameworks and resolve conflicting boundaries between disciplines such that they better facilitate, not restrict, experimental approaches and capabilities. In this essay, we address specific questions and critiques which have arisen in response to our research program, which lies at the intersection of developmental biology, computer science, and robotics. In the context of biological machines and robots, we explore changes across concepts and previously distinct fields that are driven by recent advances in materials, information, and life sciences. Herein, each author provides their own perspective on the subject, framed by their own disciplinary training. We argue that as with computation, certain aspects of developmental biology and robotics are not tied to specific materials; rather, the consilience of these fields can help to shed light on issues of multiscale control, self-assembly, and relationships between form and function. We hope new fields can emerge as boundaries arising from technological limitations are overcome, furthering practical applications from regenerative medicine to useful synthetic living machines.
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Affiliation(s)
- Douglas Blackiston
- Department of Biology, Allen Discovery Center at Tufts University, Medford, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- Institute for Computationally Designed Organisms, Massachusetts and Vermont, USA
| | - Sam Kriegman
- Institute for Computationally Designed Organisms, Massachusetts and Vermont, USA
- Center for Robotics and Biosystems, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
| | - Josh Bongard
- Institute for Computationally Designed Organisms, Massachusetts and Vermont, USA
- Department of Computer Science, University of Vermont, Burlington, Vermont, USA
| | - Michael Levin
- Department of Biology, Allen Discovery Center at Tufts University, Medford, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- Institute for Computationally Designed Organisms, Massachusetts and Vermont, USA
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Levin M. Darwin's agential materials: evolutionary implications of multiscale competency in developmental biology. Cell Mol Life Sci 2023; 80:142. [PMID: 37156924 PMCID: PMC10167196 DOI: 10.1007/s00018-023-04790-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/10/2023]
Abstract
A critical aspect of evolution is the layer of developmental physiology that operates between the genotype and the anatomical phenotype. While much work has addressed the evolution of developmental mechanisms and the evolvability of specific genetic architectures with emergent complexity, one aspect has not been sufficiently explored: the implications of morphogenetic problem-solving competencies for the evolutionary process itself. The cells that evolution works with are not passive components: rather, they have numerous capabilities for behavior because they derive from ancestral unicellular organisms with rich repertoires. In multicellular organisms, these capabilities must be tamed, and can be exploited, by the evolutionary process. Specifically, biological structures have a multiscale competency architecture where cells, tissues, and organs exhibit regulative plasticity-the ability to adjust to perturbations such as external injury or internal modifications and still accomplish specific adaptive tasks across metabolic, transcriptional, physiological, and anatomical problem spaces. Here, I review examples illustrating how physiological circuits guiding cellular collective behavior impart computational properties to the agential material that serves as substrate for the evolutionary process. I then explore the ways in which the collective intelligence of cells during morphogenesis affect evolution, providing a new perspective on the evolutionary search process. This key feature of the physiological software of life helps explain the remarkable speed and robustness of biological evolution, and sheds new light on the relationship between genomes and functional anatomical phenotypes.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, 200 Boston Ave. 334 Research East, Medford, MA, 02155, USA.
- Wyss Institute for Biologically Inspired Engineering at Harvard University, 3 Blackfan St., Boston, MA, 02115, USA.
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Bongard J, Levin M. There’s Plenty of Room Right Here: Biological Systems as Evolved, Overloaded, Multi-Scale Machines. Biomimetics (Basel) 2023; 8:biomimetics8010110. [PMID: 36975340 PMCID: PMC10046700 DOI: 10.3390/biomimetics8010110] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic view. Such a view dissolves the contingent dichotomies driven by human cognitive biases (e.g., a tendency to oversimplify) and prior technological limitations in favor of a more continuous view, necessitated by the study of evolution, developmental biology, and intelligent machines. Form and function are tightly entwined in nature, and in some cases, in robotics as well. Thus, efforts to re-shape living systems for biomedical or bioengineering purposes require prediction and control of their function at multiple scales. This is challenging for many reasons, one of which is that living systems perform multiple functions in the same place at the same time. We refer to this as “polycomputing”—the ability of the same substrate to simultaneously compute different things, and make those computational results available to different observers. This ability is an important way in which living things are a kind of computer, but not the familiar, linear, deterministic kind; rather, living things are computers in the broad sense of their computational materials, as reported in the rapidly growing physical computing literature. We argue that an observer-centered framework for the computations performed by evolved and designed systems will improve the understanding of mesoscale events, as it has already done at quantum and relativistic scales. To develop our understanding of how life performs polycomputing, and how it can be convinced to alter one or more of those functions, we can first create technologies that polycompute and learn how to alter their functions. Here, we review examples of biological and technological polycomputing, and develop the idea that the overloading of different functions on the same hardware is an important design principle that helps to understand and build both evolved and designed systems. Learning to hack existing polycomputing substrates, as well as to evolve and design new ones, will have massive impacts on regenerative medicine, robotics, and computer engineering.
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Affiliation(s)
- Joshua Bongard
- Department of Computer Science, University of Vermont, Burlington, VT 05405, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, 200 Boston Ave., Suite 4600, Medford, MA 02155, USA
- Correspondence: ; Tel.: +(617)-627-6161
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Libanori A, Soto J, Xu J, Song Y, Zarubova J, Tat T, Xiao X, Yue SZ, Jonas SJ, Li S, Chen J. Self-Powered Programming of Fibroblasts into Neurons via a Scalable Magnetoelastic Generator Array. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206933. [PMID: 36468617 PMCID: PMC10462379 DOI: 10.1002/adma.202206933] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Developing scalable electrical stimulating platforms for cell and tissue engineering applications is limited by external power source dependency, wetting resistance, microscale size requirements, and suitable flexibility. Here, a versatile and scalable platform is developed to enable tunable electrical stimulation for biological applications by harnessing the giant magnetoelastic effect in soft systems, converting gentle air pressure (100-400 kPa) to yield a current of up to 10.5 mA and a voltage of 9.5 mV. The platform can be easily manufactured and scaled up for integration in multiwell magnetoelastic plates via 3D printing. The authors demonstrate that the electrical stimulation generated by this platform enhances the conversion of fibroblasts into neurons up to 2-fold (104%) and subsequent neuronal maturation up to 3-fold (251%). This easily configurable electrical stimulation device has broad applications in high throughput organ-on-a-chip systems, and paves the way for future development of neural engineering, including cellular therapy via implantable self-powered electrical stimulation devices.
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Affiliation(s)
- Alberto Libanori
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jennifer Soto
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jing Xu
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Yang Song
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jana Zarubova
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Trinny Tat
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xiao Xiao
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Shou Zheng Yue
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Pediatrics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Steven J Jonas
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Pediatrics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Children's Discovery and Innovation Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Song Li
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jun Chen
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Shreesha L, Levin M. Cellular Competency during Development Alters Evolutionary Dynamics in an Artificial Embryogeny Model. ENTROPY (BASEL, SWITZERLAND) 2023; 25:e25010131. [PMID: 36673272 PMCID: PMC9858125 DOI: 10.3390/e25010131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/23/2022] [Accepted: 12/29/2022] [Indexed: 05/25/2023]
Abstract
Biological genotypes do not code directly for phenotypes; developmental physiology is the control layer that separates genomes from capacities ascertained by selection. A key aspect is cellular competency, since cells are not passive materials but descendants of unicellular organisms with complex context-sensitive behavioral capabilities. To probe the effects of different degrees of cellular competency on evolutionary dynamics, we used an evolutionary simulation in the context of minimal artificial embryogeny. Virtual embryos consisted of a single axis of positional information values provided by cells' 'structural genes', operated upon by an evolutionary cycle in which embryos' fitness was proportional to monotonicity of the axial gradient. Evolutionary dynamics were evaluated in two modes: hardwired development (genotype directly encodes phenotype), and a more realistic mode in which cells interact prior to evaluation by the fitness function ("regulative" development). We find that even minimal ability of cells with to improve their position in the embryo results in better performance of the evolutionary search. Crucially, we observed that increasing the behavioral competency masks the raw fitness encoded by structural genes, with selection favoring improvements to its developmental problem-solving capacities over improvements to its structural genome. This suggests the existence of a powerful ratchet mechanism: evolution progressively becomes locked in to improvements in the intelligence of its agential substrate, with reduced pressure on the structural genome. This kind of feedback loop in which evolution increasingly puts more effort into the developmental software than perfecting the hardware explains the very puzzling divergence of genome from anatomy in species like planaria. In addition, it identifies a possible driver for scaling intelligence over evolutionary time, and suggests strategies for engineering novel systems in silico and in bioengineering.
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Affiliation(s)
- Lakshwin Shreesha
- UFR Fundamental and Biomedical Sciences, Université Paris Cité, 75006 Paris, France
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA
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10
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Hazan H, Levin M. Exploring the Behavior of Bioelectric Circuits Using Evolution Heuristic Search. Bioelectricity 2022. [DOI: 10.1089/bioe.2022.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hananel Hazan
- Allen Discovery Center at Tufts University, Medford, Massachusetts, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts, USA
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Fields C, Levin M. Competency in Navigating Arbitrary Spaces as an Invariant for Analyzing Cognition in Diverse Embodiments. ENTROPY (BASEL, SWITZERLAND) 2022; 24:819. [PMID: 35741540 PMCID: PMC9222757 DOI: 10.3390/e24060819] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/26/2022] [Accepted: 06/08/2022] [Indexed: 12/20/2022]
Abstract
One of the most salient features of life is its capacity to handle novelty and namely to thrive and adapt to new circumstances and changes in both the environment and internal components. An understanding of this capacity is central to several fields: the evolution of form and function, the design of effective strategies for biomedicine, and the creation of novel life forms via chimeric and bioengineering technologies. Here, we review instructive examples of living organisms solving diverse problems and propose competent navigation in arbitrary spaces as an invariant for thinking about the scaling of cognition during evolution. We argue that our innate capacity to recognize agency and intelligence in unfamiliar guises lags far behind our ability to detect it in familiar behavioral contexts. The multi-scale competency of life is essential to adaptive function, potentiating evolution and providing strategies for top-down control (not micromanagement) to address complex disease and injury. We propose an observer-focused viewpoint that is agnostic about scale and implementation, illustrating how evolution pivoted similar strategies to explore and exploit metabolic, transcriptional, morphological, and finally 3D motion spaces. By generalizing the concept of behavior, we gain novel perspectives on evolution, strategies for system-level biomedical interventions, and the construction of bioengineered intelligences. This framework is a first step toward relating to intelligence in highly unfamiliar embodiments, which will be essential for progress in artificial intelligence and regenerative medicine and for thriving in a world increasingly populated by synthetic, bio-robotic, and hybrid beings.
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Affiliation(s)
- Chris Fields
- Allen Discovery Center at Tufts University, Science and Engineering Complex, 200 College Ave., Medford, MA 02155, USA;
| | - Michael Levin
- Allen Discovery Center at Tufts University, Science and Engineering Complex, 200 College Ave., Medford, MA 02155, USA;
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA
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12
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Levin M. Technological Approach to Mind Everywhere: An Experimentally-Grounded Framework for Understanding Diverse Bodies and Minds. Front Syst Neurosci 2022; 16:768201. [PMID: 35401131 PMCID: PMC8988303 DOI: 10.3389/fnsys.2022.768201] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/24/2022] [Indexed: 12/11/2022] Open
Abstract
Synthetic biology and bioengineering provide the opportunity to create novel embodied cognitive systems (otherwise known as minds) in a very wide variety of chimeric architectures combining evolved and designed material and software. These advances are disrupting familiar concepts in the philosophy of mind, and require new ways of thinking about and comparing truly diverse intelligences, whose composition and origin are not like any of the available natural model species. In this Perspective, I introduce TAME-Technological Approach to Mind Everywhere-a framework for understanding and manipulating cognition in unconventional substrates. TAME formalizes a non-binary (continuous), empirically-based approach to strongly embodied agency. TAME provides a natural way to think about animal sentience as an instance of collective intelligence of cell groups, arising from dynamics that manifest in similar ways in numerous other substrates. When applied to regenerating/developmental systems, TAME suggests a perspective on morphogenesis as an example of basal cognition. The deep symmetry between problem-solving in anatomical, physiological, transcriptional, and 3D (traditional behavioral) spaces drives specific hypotheses by which cognitive capacities can increase during evolution. An important medium exploited by evolution for joining active subunits into greater agents is developmental bioelectricity, implemented by pre-neural use of ion channels and gap junctions to scale up cell-level feedback loops into anatomical homeostasis. This architecture of multi-scale competency of biological systems has important implications for plasticity of bodies and minds, greatly potentiating evolvability. Considering classical and recent data from the perspectives of computational science, evolutionary biology, and basal cognition, reveals a rich research program with many implications for cognitive science, evolutionary biology, regenerative medicine, and artificial intelligence.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, United States
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Cambridge, MA, United States
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13
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Grodstein J, Levin M. Stability and robustness properties of bioelectric networks: A computational approach. BIOPHYSICS REVIEWS 2021; 2:031305. [PMID: 38505634 PMCID: PMC10903393 DOI: 10.1063/5.0062442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/07/2021] [Indexed: 03/21/2024]
Abstract
Morphogenesis during development and regeneration requires cells to communicate and cooperate toward the construction of complex anatomical structures. One important set of mechanisms for coordinating growth and form occurs via developmental bioelectricity-the dynamics of cellular networks driving changes of resting membrane potential which interface with transcriptional and biomechanical downstream cascades. While many molecular details have been elucidated about the instructive processes mediated by ion channel-dependent signaling outside of the nervous system, future advances in regenerative medicine and bioengineering require the understanding of tissue, organ, or whole body-level properties. A key aspect of bioelectric networks is their robustness, which can drive correct, invariant patterning cues despite changing cell number and anatomical configuration of the underlying tissue network. Here, we computationally analyze the minimal models of bioelectric networks and use the example of the regenerating planarian flatworm, to reveal important system-level aspects of bioelectrically derived patterns. These analyses promote an understanding of the robustness of circuits controlling regeneration and suggest design properties that can be exploited for synthetic bioengineering.
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Affiliation(s)
- Joel Grodstein
- Department of Electrical and Computer Engineering, Tufts University, Medford, Massachusetts 02155, USA
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Cervera J, Levin M, Mafe S. Morphology changes induced by intercellular gap junction blocking: A reaction-diffusion mechanism. Biosystems 2021; 209:104511. [PMID: 34411690 DOI: 10.1016/j.biosystems.2021.104511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/14/2021] [Indexed: 02/07/2023]
Abstract
Complex anatomical form is regulated in part by endogenous physiological communication between cells; however, the dynamics by which gap junctional (GJ) states across tissues regulate morphology are still poorly understood. We employed a biophysical modeling approach combining different signaling molecules (morphogens) to qualitatively describe the anteroposterior and lateral morphology changes in model multicellular systems due to intercellular GJ blockade. The model is based on two assumptions for blocking-induced patterning: (i) the local concentrations of two small antagonistic morphogens diffusing through the GJs along the axial direction, together with that of an independent, uncoupled morphogen concentration along an orthogonal direction, constitute the instructive patterns that modulate the morphological outcomes, and (ii) the addition of an external agent partially blocks the intercellular GJs between neighboring cells and modifies thus the establishment of these patterns. As an illustrative example, we study how the different connectivity and morphogen patterns obtained in presence of a GJ blocker can give rise to novel head morphologies in regenerating planaria. We note that the ability of GJs to regulate the permeability of morphogens post-translationally suggests a mechanism by which different anatomies can be produced from the same genome without the modification of gene-regulatory networks. Conceptually, our model biosystem constitutes a reaction-diffusion information processing mechanism that allows reprogramming of biological morphologies through the external manipulation of the intercellular GJs and the resulting changes in instructive biochemical signals.
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Affiliation(s)
- Javier Cervera
- Dept. Termodinàmica, Facultat de Física, Universitat de València, E-46100, Burjassot, Spain.
| | - Michael Levin
- Dept. of Biology and Allen Discovery Center at Tufts University, Medford, MA, 02155-4243, USA
| | - Salvador Mafe
- Dept. Termodinàmica, Facultat de Física, Universitat de València, E-46100, Burjassot, Spain
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15
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Abstract
Increased control of biological growth and form is an essential gateway to transformative medical advances. Repairing of birth defects, restoring lost or damaged organs, normalizing tumors, all depend on understanding how cells cooperate to make specific, functional large-scale structures. Despite advances in molecular genetics, significant gaps remain in our understanding of the meso-scale rules of morphogenesis. An engineering approach to this problem is the creation of novel synthetic living forms, greatly extending available model systems beyond evolved plant and animal lineages. Here, we review recent advances in the emerging field of synthetic morphogenesis, the bioengineering of novel multicellular living bodies. Emphasizing emergent self-organization, tissue-level guided self-assembly, and active functionality, this work is the essential next generation of synthetic biology. Aside from useful living machines for specific functions, the rational design and analysis of new, coherent anatomies will greatly increase our understanding of foundational questions in evolutionary developmental and cell biology.
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Affiliation(s)
- Mo R. Ebrahimkhani
- Department of Pathology, School of Medicine, University of Pittsburgh, A809B Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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16
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Bioelectric signaling: Reprogrammable circuits underlying embryogenesis, regeneration, and cancer. Cell 2021; 184:1971-1989. [PMID: 33826908 DOI: 10.1016/j.cell.2021.02.034] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/08/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022]
Abstract
How are individual cell behaviors coordinated toward invariant large-scale anatomical outcomes in development and regeneration despite unpredictable perturbations? Endogenous distributions of membrane potentials, produced by ion channels and gap junctions, are present across all tissues. These bioelectrical networks process morphogenetic information that controls gene expression, enabling cell collectives to make decisions about large-scale growth and form. Recent progress in the analysis and computational modeling of developmental bioelectric circuits and channelopathies reveals how cellular collectives cooperate toward organ-level structural order. These advances suggest a roadmap for exploiting bioelectric signaling for interventions addressing developmental disorders, regenerative medicine, cancer reprogramming, and synthetic bioengineering.
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Pezzulo G, LaPalme J, Durant F, Levin M. Bistability of somatic pattern memories: stochastic outcomes in bioelectric circuits underlying regeneration. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190765. [PMID: 33550952 PMCID: PMC7935058 DOI: 10.1098/rstb.2019.0765] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2020] [Indexed: 02/06/2023] Open
Abstract
Nervous systems' computational abilities are an evolutionary innovation, specializing and speed-optimizing ancient biophysical dynamics. Bioelectric signalling originated in cells' communication with the outside world and with each other, enabling cooperation towards adaptive construction and repair of multicellular bodies. Here, we review the emerging field of developmental bioelectricity, which links the field of basal cognition to state-of-the-art questions in regenerative medicine, synthetic bioengineering and even artificial intelligence. One of the predictions of this view is that regeneration and regulative development can restore correct large-scale anatomies from diverse starting states because, like the brain, they exploit bioelectric encoding of distributed goal states-in this case, pattern memories. We propose a new interpretation of recent stochastic regenerative phenotypes in planaria, by appealing to computational models of memory representation and processing in the brain. Moreover, we discuss novel findings showing that bioelectric changes induced in planaria can be stored in tissue for over a week, thus revealing that somatic bioelectric circuits in vivo can implement a long-term, re-writable memory medium. A consideration of the mechanisms, evolution and functionality of basal cognition makes novel predictions and provides an integrative perspective on the evolution, physiology and biomedicine of information processing in vivo. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.
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Affiliation(s)
- Giovanni Pezzulo
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome, Italy
| | - Joshua LaPalme
- Allen Discovery Center, Tufts University, Medford, MA, USA
| | - Fallon Durant
- Allen Discovery Center, Tufts University, Medford, MA, USA
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, USA
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18
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Gene regulatory networks exhibit several kinds of memory: quantification of memory in biological and random transcriptional networks. iScience 2021; 24:102131. [PMID: 33748699 PMCID: PMC7970124 DOI: 10.1016/j.isci.2021.102131] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/09/2020] [Accepted: 01/26/2021] [Indexed: 02/08/2023] Open
Abstract
Gene regulatory networks (GRNs) process important information in developmental biology and biomedicine. A key knowledge gap concerns how their responses change over time. Hypothesizing long-term changes of dynamics induced by transient prior events, we created a computational framework for defining and identifying diverse types of memory in candidate GRNs. We show that GRNs from a wide range of model systems are predicted to possess several types of memory, including Pavlovian conditioning. Associative memory offers an alternative strategy for the biomedical use of powerful drugs with undesirable side effects, and a novel approach to understanding the variability and time-dependent changes of drug action. We find evidence of natural selection favoring GRN memory. Vertebrate GRNs overall exhibit more memory than invertebrate GRNs, and memory is most prevalent in differentiated metazoan cell networks compared with undifferentiated cells. Timed stimuli are a powerful alternative for biomedical control of complex in vivo dynamics without genomic editing or transgenes. Gene regulatory networks' dynamics are modified by transient stimuli GRNs have several different types of memory, including associative conditioning Evolution favored GRN memory, and differentiated cells have the most memory capacity Training GRNs offers a novel biomedical strategy not dependent on genetic rewiring
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19
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Life, death, and self: Fundamental questions of primitive cognition viewed through the lens of body plasticity and synthetic organisms. Biochem Biophys Res Commun 2020; 564:114-133. [PMID: 33162026 DOI: 10.1016/j.bbrc.2020.10.077] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/25/2020] [Accepted: 10/28/2020] [Indexed: 12/16/2022]
Abstract
Central to the study of cognition is being able to specify the Subject that is making decisions and owning memories and preferences. However, all real cognitive agents are made of parts (such as brains made of cells). The integration of many active subunits into a coherent Self appearing at a larger scale of organization is one of the fundamental questions of evolutionary cognitive science. Typical biological model systems, whether basal or advanced, have a static anatomical structure which obscures important aspects of the mind-body relationship. Recent advances in bioengineering now make it possible to assemble, disassemble, and recombine biological structures at the cell, organ, and whole organism levels. Regenerative biology and controlled chimerism reveal that studies of cognition in intact, "standard", evolved animal bodies are just a narrow slice of a much bigger and as-yet largely unexplored reality: the incredible plasticity of dynamic morphogenesis of biological forms that house and support diverse types of cognition. The ability to produce living organisms in novel configurations makes clear that traditional concepts, such as body, organism, genetic lineage, death, and memory are not as well-defined as commonly thought, and need considerable revision to account for the possible spectrum of living entities. Here, I review fascinating examples of experimental biology illustrating that the boundaries demarcating somatic and cognitive Selves are fluid, providing an opportunity to sharpen inquiries about how evolution exploits physical forces for multi-scale cognition. Developmental (pre-neural) bioelectricity contributes a novel perspective on how the dynamic control of growth and form of the body evolved into sophisticated cognitive capabilities. Most importantly, the development of functional biobots - synthetic living machines with behavioral capacity - provides a roadmap for greatly expanding our understanding of the origin and capacities of cognition in all of its possible material implementations, especially those that emerge de novo, with no lengthy evolutionary history of matching behavioral programs to bodyplan. Viewing fundamental questions through the lens of new, constructed living forms will have diverse impacts, not only in basic evolutionary biology and cognitive science, but also in regenerative medicine of the brain and in artificial intelligence.
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20
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Levin M. The Biophysics of Regenerative Repair Suggests New Perspectives on Biological Causation. Bioessays 2020; 42:e1900146. [PMID: 31994772 DOI: 10.1002/bies.201900146] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/03/2019] [Indexed: 12/13/2022]
Abstract
Evolution exploits the physics of non-neural bioelectricity to implement anatomical homeostasis: a process in which embryonic patterning, remodeling, and regeneration achieve invariant anatomical outcomes despite external interventions. Linear "developmental pathways" are often inadequate explanations for dynamic large-scale pattern regulation, even when they accurately capture relationships between molecular components. Biophysical and computational aspects of collective cell activity toward a target morphology reveal interesting aspects of causation in biology. This is critical not only for unraveling evolutionary and developmental events, but also for the design of effective strategies for biomedical intervention. Bioelectrical controls of growth and form, including stochastic behavior in such circuits, highlight the need for the formulation of nuanced views of pathways, drivers of system-level outcomes, and modularity, borrowing from concepts in related disciplines such as cybernetics, control theory, computational neuroscience, and information theory. This approach has numerous practical implications for basic research and for applications in regenerative medicine and synthetic bioengineering.
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Affiliation(s)
- 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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21
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Fields C, Levin M. Scale-Free Biology: Integrating Evolutionary and Developmental Thinking. Bioessays 2020; 42:e1900228. [PMID: 32537770 DOI: 10.1002/bies.201900228] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/24/2020] [Indexed: 12/16/2022]
Abstract
When the history of life on earth is viewed as a history of cell division, all of life becomes a single cell lineage. The growth and differentiation of this lineage in reciprocal interaction with its environment can be viewed as a developmental process; hence the evolution of life on earth can also be seen as the development of life on earth. Here, in reviewing this field, some potentially fruitful research directions suggested by this change in perspective are highlighted. Variation and selection become, for example, bidirectional information flows between scales, while the notions of "cooperation" and "competition" become scale relative. The language of communication, inference, and information processing becomes more useful than the language of causation to describe the interactions of both homogeneous and heterogeneous living systems at any scale. Emerging scale-free theoretical frameworks such as predictive coding and active inference provide conceptual tools for reconceptualizing biology as the study of a unified, multiscale dynamical system.
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Affiliation(s)
- Chris Fields
- 23 Rue des Lavandieres, 11160 Caunes Minervois, France
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
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22
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Tung A, Levin M. Extra-genomic instructive influences in morphogenesis: A review of external signals that regulate growth and form. Dev Biol 2020; 461:1-12. [PMID: 31981561 DOI: 10.1016/j.ydbio.2020.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 12/18/2022]
Abstract
Embryonic development and regeneration accomplish a remarkable feat: individual cells work together to create or repair complex anatomical structures. What is the source of the instructive signals that specify these invariant and robust organ-level outcomes? The most frequently studied source of morphogenetic control is the host genome and its transcriptional circuits. However, it is now apparent that significant information affecting patterning also arrives from outside of the body. Both biotic and physical factors, including temperature and various molecular signals emanating from pathogens, commensals, and conspecific organisms, affect developmental outcomes. Here, we review examples in which anatomical patterning decisions are strongly impacted by lateral signals that originate from outside of the zygotic genome. The endogenous pathways targeted by these influences often show transgenerational effects, enabling them to shape the evolution of anatomies even faster than traditional Baldwin-type assimilation. We also discuss recent advances in the biophysics of morphogenetic controls and speculate on additional sources of important patterning information which could be exploited to better understand the evolution of bodies and to design novel approaches for regenerative medicine.
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Affiliation(s)
- Angela Tung
- Department of Biology and Allen Discovery Center at Tufts University, Medford, MA, USA
| | - Michael Levin
- Department of Biology and Allen Discovery Center at Tufts University, Medford, MA, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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23
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24
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Fields C, Bischof J, Levin M. Morphological Coordination: A Common Ancestral Function Unifying Neural and Non-Neural Signaling. Physiology (Bethesda) 2020; 35:16-30. [DOI: 10.1152/physiol.00027.2019] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nervous systems are traditionally thought of as providing sensing and behavioral coordination functions at the level of the whole organism. What is the evolutionary origin of the mechanisms enabling the nervous systems’ information processing ability? Here, we review evidence from evolutionary, developmental, and regenerative biology suggesting a deeper, ancestral function of both pre-neural and neural cell-cell communication systems: the long-distance coordination of cell division and differentiation required to create and maintain body-axis symmetries. This conceptualization of the function of nervous system activity sheds new light on the evolutionary transition from the morphologically rudimentary, non-neural Porifera and Placazoa to the complex morphologies of Ctenophores, Cnidarians, and Bilaterians. It further allows a sharp formulation of the distinction between long-distance axis-symmetry coordination based on external coordinates, e.g., by whole-organism scale trophisms as employed by plants and sessile animals, and coordination based on body-centered coordinates as employed by motile animals. Thus we suggest that the systems that control animal behavior evolved from ancient mechanisms adapting preexisting ionic and neurotransmitter mechanisms to regulate individual cell behaviors during morphogenesis. An appreciation of the ancient, non-neural origins of bioelectrically mediated computation suggests new approaches to the study of embryological development, including embryological dysregulation, cancer, regenerative medicine, and synthetic bioengineering.
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Affiliation(s)
- Chris Fields
- 23 Rue des Lavandières, Caunes Minervois, France
| | - Johanna Bischof
- Allen Discovery Center at Tufts University, Medford, Massachusetts
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, Massachusetts
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25
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Levin M. The Computational Boundary of a "Self": Developmental Bioelectricity Drives Multicellularity and Scale-Free Cognition. Front Psychol 2019; 10:2688. [PMID: 31920779 PMCID: PMC6923654 DOI: 10.3389/fpsyg.2019.02688] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/14/2019] [Indexed: 12/12/2022] Open
Abstract
All epistemic agents physically consist of parts that must somehow comprise an integrated cognitive self. Biological individuals consist of subunits (organs, cells, and molecular networks) that are themselves complex and competent in their own native contexts. How do coherent biological Individuals result from the activity of smaller sub-agents? To understand the evolution and function of metazoan creatures' bodies and minds, it is essential to conceptually explore the origin of multicellularity and the scaling of the basal cognition of individual cells into a coherent larger organism. In this article, I synthesize ideas in cognitive science, evolutionary biology, and developmental physiology toward a hypothesis about the origin of Individuality: "Scale-Free Cognition." I propose a fundamental definition of an Individual based on the ability to pursue goals at an appropriate level of scale and organization and suggest a formalism for defining and comparing the cognitive capacities of highly diverse types of agents. Any Self is demarcated by a computational surface - the spatio-temporal boundary of events that it can measure, model, and try to affect. This surface sets a functional boundary - a cognitive "light cone" which defines the scale and limits of its cognition. I hypothesize that higher level goal-directed activity and agency, resulting in larger cognitive boundaries, evolve from the primal homeostatic drive of living things to reduce stress - the difference between current conditions and life-optimal conditions. The mechanisms of developmental bioelectricity - the ability of all cells to form electrical networks that process information - suggest a plausible set of gradual evolutionary steps that naturally lead from physiological homeostasis in single cells to memory, prediction, and ultimately complex cognitive agents, via scale-up of the basic drive of infotaxis. Recent data on the molecular mechanisms of pre-neural bioelectricity suggest a model of how increasingly sophisticated cognitive functions emerge smoothly from cell-cell communication used to guide embryogenesis and regeneration. This set of hypotheses provides a novel perspective on numerous phenomena, such as cancer, and makes several unique, testable predictions for interdisciplinary research that have implications not only for evolutionary developmental biology but also for biomedicine and perhaps artificial intelligence and exobiology.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
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26
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Emmons-Bell M, Durant F, Tung A, Pietak A, Miller K, Kane A, Martyniuk CJ, Davidian D, Morokuma J, Levin M. Regenerative Adaptation to Electrochemical Perturbation in Planaria: A Molecular Analysis of Physiological Plasticity. iScience 2019; 22:147-165. [PMID: 31765995 PMCID: PMC6881696 DOI: 10.1016/j.isci.2019.11.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/01/2019] [Accepted: 11/05/2019] [Indexed: 12/29/2022] Open
Abstract
Anatomical homeostasis results from dynamic interactions between gene expression, physiology, and the external environment. Owing to its complexity, this cellular and organism-level phenotypic plasticity is still poorly understood. We establish planarian regeneration as a model for acquired tolerance to environments that alter endogenous physiology. Exposure to barium chloride (BaCl2) results in a rapid degeneration of anterior tissue in Dugesia japonica. Remarkably, continued exposure to fresh solution of BaCl2 results in regeneration of heads that are insensitive to BaCl2. RNA-seq revealed transcriptional changes in BaCl2-adapted heads that suggests a model of adaptation to excitotoxicity. Loss-of-function experiments confirmed several predictions: blockage of chloride and calcium channels allowed heads to survive initial BaCl2 exposure, inducing adaptation without prior exposure, whereas blockade of TRPM channels reversed adaptation. Such highly adaptive plasticity may represent an attractive target for biomedical strategies in a wide range of applications beyond its immediate relevance to excitotoxicity preconditioning. Exposure to BaCl2 causes the heads of Dugesia japonica to degenerate Prolonged exposure to BaCl2 results in regeneration of a BaCl2-insensitive head Ion channel expression is altered in the head to compensate for excitotoxic stress TRPMa is upregulated in BaCl2-treated animals; blocking TRPM prevents adaptation
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Affiliation(s)
- Maya Emmons-Bell
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA; Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Fallon Durant
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA; Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Angela Tung
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA; Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Alexis Pietak
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
| | - Kelsie Miller
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
| | - Anna Kane
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Devon Davidian
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA; Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Junji Morokuma
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA; Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA; Department of Biology, Tufts University, Medford, MA 02155, USA.
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27
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Mehta AS, Singh A. Insights into regeneration tool box: An animal model approach. Dev Biol 2019; 453:111-129. [PMID: 30986388 PMCID: PMC6684456 DOI: 10.1016/j.ydbio.2019.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 12/20/2022]
Abstract
For ages, regeneration has intrigued countless biologists, clinicians, and biomedical engineers. In recent years, significant progress made in identification and characterization of a regeneration tool kit has helped the scientific community to understand the mechanism(s) involved in regeneration across animal kingdom. These mechanistic insights revealed that evolutionarily conserved pathways like Wnt, Notch, Hedgehog, BMP, and JAK/STAT are involved in regeneration. Furthermore, advancement in high throughput screening approaches like transcriptomic analysis followed by proteomic validations have discovered many novel genes, and regeneration specific enhancers that are specific to highly regenerative species like Hydra, Planaria, Newts, and Zebrafish. Since genetic machinery is highly conserved across the animal kingdom, it is possible to engineer these genes and regeneration specific enhancers in species with limited regeneration properties like Drosophila, and mammals. Since these models are highly versatile and genetically tractable, cross-species comparative studies can generate mechanistic insights in regeneration for animals with long gestation periods e.g. Newts. In addition, it will allow extrapolation of regenerative capabilities from highly regenerative species to animals with low regeneration potential, e.g. mammals. In future, these studies, along with advancement in tissue engineering applications, can have strong implications in the field of regenerative medicine and stem cell biology.
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Affiliation(s)
- Abijeet S Mehta
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA; Premedical Program, University of Dayton, Dayton, OH, 45469, USA; Center for Tissue Regeneration and Engineering at Dayton (TREND), University of Dayton, Dayton, OH, 45469, USA; The Integrative Science and Engineering Center, University of Dayton, Dayton, OH, 45469, USA; Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA.
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28
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Miller WB, Torday JS, Baluška F. The N-space Episenome unifies cellular information space-time within cognition-based evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:112-139. [PMID: 31415772 DOI: 10.1016/j.pbiomolbio.2019.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/26/2019] [Accepted: 08/09/2019] [Indexed: 02/08/2023]
Abstract
Self-referential cellular homeostasis is maintained by the measured assessment of both internal status and external conditions based within an integrated cellular information field. This cellular field attachment to biologic information space-time coordinates environmental inputs by connecting the cellular senome, as the sum of the sensory experiences of the cell, with its genome and epigenome. In multicellular organisms, individual cellular information fields aggregate into a collective information architectural matrix, termed a N-space Episenome, that enables mutualized organism-wide information management. It is hypothesized that biological organization represents a dual heritable system constituted by both its biological materiality and a conjoining N-space Episenome. It is further proposed that morphogenesis derives from reciprocations between these inter-related facets to yield coordinated multicellular growth and development. The N-space Episenome is conceived as a whole cell informational projection that is heritable, transferable via cell division and essential for the synchronous integration of the diverse self-referential cells that constitute holobionts.
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Affiliation(s)
| | - John S Torday
- Department of Pediatrics, Harbor-UCLA Medical Center, USA.
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29
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Manicka S, Levin M. The Cognitive Lens: a primer on conceptual tools for analysing information processing in developmental and regenerative morphogenesis. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180369. [PMID: 31006373 PMCID: PMC6553590 DOI: 10.1098/rstb.2018.0369] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2018] [Indexed: 12/31/2022] Open
Abstract
Brains exhibit plasticity, multi-scale integration of information, computation and memory, having evolved by specialization of non-neural cells that already possessed many of the same molecular components and functions. The emerging field of basal cognition provides many examples of decision-making throughout a wide range of non-neural systems. How can biological information processing across scales of size and complexity be quantitatively characterized and exploited in biomedical settings? We use pattern regulation as a context in which to introduce the Cognitive Lens-a strategy using well-established concepts from cognitive and computer science to complement mechanistic investigation in biology. To facilitate the assimilation and application of these approaches across biology, we review tools from various quantitative disciplines, including dynamical systems, information theory and least-action principles. We propose that these tools can be extended beyond neural settings to predict and control systems-level outcomes, and to understand biological patterning as a form of primitive cognition. We hypothesize that a cognitive-level information-processing view of the functions of living systems can complement reductive perspectives, improving efficient top-down control of organism-level outcomes. Exploration of the deep parallels across diverse quantitative paradigms will drive integrative advances in evolutionary biology, regenerative medicine, synthetic bioengineering, cognitive neuroscience and artificial intelligence. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.
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Affiliation(s)
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA
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30
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Cervera J, Manzanares JA, Mafe S, Levin M. Synchronization of Bioelectric Oscillations in Networks of Nonexcitable Cells: From Single-Cell to Multicellular States. J Phys Chem B 2019; 123:3924-3934. [PMID: 31003574 DOI: 10.1021/acs.jpcb.9b01717] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological networks use collective oscillations for information processing tasks. In particular, oscillatory membrane potentials have been observed in nonexcitable cells and bacterial communities where specific ion channel proteins contribute to the bioelectric coordination of large populations. We aim at describing theoretically the oscillatory spatiotemporal patterns that emerge at the multicellular level from the single-cell bioelectric dynamics. To this end, we focus on two key questions: (i) What single-cell properties are relevant to multicellular behavior? (ii) What properties defined at the multicellular level can allow an external control of the bioelectric dynamics? In particular, we explore the interplay between transcriptional and translational dynamics and membrane potential dynamics in a model multicellular ensemble, describe the spatiotemporal patterns that arise when the average electric potential allows groups of cells to act as a coordinated multicellular patch, and characterize the resulting synchronization phenomena. The simulations concern bioelectric networks and collective communication across different scales based on oscillatory and synchronization phenomena, thus shedding light on the physiological dynamics of a wide range of endogenous contexts across embryogenesis and regeneration.
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Affiliation(s)
- Javier Cervera
- Departament de Termodinàmica, Facultat de Física , Universitat de València , E-46100 Burjassot , Spain
| | - José Antonio Manzanares
- Departament de Termodinàmica, Facultat de Física , Universitat de València , E-46100 Burjassot , Spain
| | - Salvador Mafe
- Departament de Termodinàmica, Facultat de Física , Universitat de València , E-46100 Burjassot , Spain
| | - Michael Levin
- Allen Discovery Center at Tufts University, Department of Biology , Tufts University Medford , Massachusetts 02155-4243 , United States
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31
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Levin M, Pietak AM, Bischof J. Planarian regeneration as a model of anatomical homeostasis: Recent progress in biophysical and computational approaches. Semin Cell Dev Biol 2019; 87:125-144. [PMID: 29635019 PMCID: PMC6234102 DOI: 10.1016/j.semcdb.2018.04.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 12/22/2022]
Abstract
Planarian behavior, physiology, and pattern control offer profound lessons for regenerative medicine, evolutionary biology, morphogenetic engineering, robotics, and unconventional computation. Despite recent advances in the molecular genetics of stem cell differentiation, this model organism's remarkable anatomical homeostasis provokes us with truly fundamental puzzles about the origin of large-scale shape and its relationship to the genome. In this review article, we first highlight several deep mysteries about planarian regeneration in the context of the current paradigm in this field. We then review recent progress in understanding of the physiological control of an endogenous, bioelectric pattern memory that guides regeneration, and how modulating this memory can permanently alter the flatworm's target morphology. Finally, we focus on computational approaches that complement reductive pathway analysis with synthetic, systems-level understanding of morphological decision-making. We analyze existing models of planarian pattern control and highlight recent successes and remaining knowledge gaps in this interdisciplinary frontier field.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, United States; Biology Department, Tufts University, Medford, MA 02155, United States.
| | - Alexis M Pietak
- Allen Discovery Center at Tufts University, Medford, MA 02155, United States
| | - Johanna Bischof
- Allen Discovery Center at Tufts University, Medford, MA 02155, United States; Biology Department, Tufts University, Medford, MA 02155, United States
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Kamm RD, Bashir R, Arora N, Dar RD, Gillette MU, Griffith LG, Kemp ML, Kinlaw K, Levin M, Martin AC, McDevitt TC, Nerem RM, Powers MJ, Saif TA, Sharpe J, Takayama S, Takeuchi S, Weiss R, Ye K, Yevick HG, Zaman MH. Perspective: The promise of multi-cellular engineered living systems. APL Bioeng 2018; 2:040901. [PMID: 31069321 PMCID: PMC6481725 DOI: 10.1063/1.5038337] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/18/2018] [Indexed: 12/31/2022] Open
Abstract
Recent technological breakthroughs in our ability to derive and differentiate induced pluripotent stem cells, organoid biology, organ-on-chip assays, and 3-D bioprinting have all contributed to a heightened interest in the design, assembly, and manufacture of living systems with a broad range of potential uses. This white paper summarizes the state of the emerging field of "multi-cellular engineered living systems," which are composed of interacting cell populations. Recent accomplishments are described, focusing on current and potential applications, as well as barriers to future advances, and the outlook for longer term benefits and potential ethical issues that need to be considered.
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Affiliation(s)
- Roger D. Kamm
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Rashid Bashir
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
| | - Natasha Arora
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Roy D. Dar
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
| | | | - Linda G. Griffith
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Melissa L. Kemp
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | | | | | - Adam C. Martin
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | | | - Robert M. Nerem
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Mark J. Powers
- Thermo Fisher Scientific, Frederick, Maryland 21704, USA
| | - Taher A. Saif
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
| | - James Sharpe
- EMBL Barcelona, European Molecular Biology Laboratory, Barcelona 08003, Spain
| | | | | | - Ron Weiss
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Kaiming Ye
- Binghamton University, Binghamton, New York 13902, USA
| | - Hannah G. Yevick
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
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Ferenc NN, Levin M. Effects of Ivermectin Exposure on Regeneration of D. dorotocephala Planaria: Exploiting Human-Approved Ion Channel Drugs as Morphoceuticals. Macromol Biosci 2018; 19:e1800237. [PMID: 30485697 DOI: 10.1002/mabi.201800237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 10/22/2018] [Indexed: 01/19/2023]
Abstract
Transformative applications in regenerative medicine await increased control of processes implementing repair and remodeling of complex living structures. Recent work reveals ion channel drugs as a powerful toolkit for modulating endogenous bioelectric circuits that control growth and form in vivo and in vitro. It is therefore especially important to develop assays in model systems that will enable the testing of these "morphoceuticals"-compounds with predictable effects on anatomical structure. The regenerative planaria are an ideal model system for this purpose. Several studies have shown a role for bioelectric signaling in planarian regeneration, but these have focused on Dugesia japonica and Schmidtea mediterranea. It is not known how the alterations of ion channel activity would affect regeneration in other species of planaria-an important aspect of building robust computational models of bioelectric circuits. Here, the effect of ivermectin (IVM), a chloride channel opener drug commonly used to combat heartworm is tested, on regeneration in a new species of planaria: Dugesia dorotocephala. Exposure to IVM during regeneration results in patterning abnormalities, such as bifurcated tails with partial heads, as well as delayed regeneration. These data extend our understanding of the effects of human-approved ion channel drugs on regenerative processes.
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Affiliation(s)
- Nina N Ferenc
- Chemistry Department, Westfield High School, Chantilly, VA, 20151, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, 200 Boston Ave., Medford, MA, 02155, USA
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Bioelectrical coupling in multicellular domains regulated by gap junctions: A conceptual approach. Bioelectrochemistry 2018; 123:45-61. [DOI: 10.1016/j.bioelechem.2018.04.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 12/16/2022]
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35
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Pietak A, Levin M. Bioelectrical control of positional information in development and regeneration: A review of conceptual and computational advances. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 137:52-68. [PMID: 29626560 PMCID: PMC10464501 DOI: 10.1016/j.pbiomolbio.2018.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 12/16/2022]
Abstract
Positional information describes pre-patterns of morphogenetic substances that alter spatio-temporal gene expression to instruct development of growth and form. A wealth of recent data indicate bioelectrical properties, such as the transmembrane potential (Vmem), are involved as instructive signals in the spatiotemporal regulation of morphogenesis. However, the mechanistic relationships between Vmem and molecular positional information are only beginning to be understood. Recent advances in computational modeling are assisting in the development of comprehensive frameworks for mechanistically understanding how endogenous bioelectricity can guide anatomy in a broad range of systems. Vmem represents an extraordinarily strong electric field (∼1.0 × 106 V/m) active over the thin expanse of the plasma membrane, with the capacity to influence a variety of downstream molecular signaling cascades. Moreover, in multicellular networks, intercellular coupling facilitated by gap junction channels may induce directed, electrodiffusive transport of charged molecules between cells of the network to generate new positional information patterning possibilities and characteristics. Given the demonstrated role of Vmem in morphogenesis, here we review current understanding of how Vmem can integrate with molecular regulatory networks to control single cell state, and the unique properties bioelectricity adds to transport phenomena in gap junction-coupled cell networks to facilitate self-assembly of morphogen gradients and other patterns. Understanding how Vmem integrates with biochemical regulatory networks at the level of a single cell, and mechanisms through which Vmem shapes molecular positional information in multicellular networks, are essential for a deep understanding of body plan control in development, regeneration and disease.
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Affiliation(s)
| | - Michael Levin
- Allen Discovery Center at Tufts, USA; Center for Regenerative and Developmental Biology, Tufts University, Medford, MA, USA
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36
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Mathews J, Levin M. The body electric 2.0: recent advances in developmental bioelectricity for regenerative and synthetic bioengineering. Curr Opin Biotechnol 2018; 52:134-144. [PMID: 29684787 PMCID: PMC10464502 DOI: 10.1016/j.copbio.2018.03.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/23/2018] [Indexed: 12/18/2022]
Abstract
Breakthroughs in biomedicine and synthetic bioengineering require predictive, rational control over anatomical structure and function. Recent successes in manipulating cellular and molecular hardware have not been matched by progress in understanding the patterning software implemented during embryogenesis and regeneration. A fundamental capability gap is driving desired changes in growth and form to address birth defects and traumatic injury. Here we review new tools, results, and conceptual advances in an exciting emerging field: endogenous non-neural bioelectric signaling, which enables cellular collectives to make global decisions and implement large-scale pattern homeostasis. Spatially distributed electric circuits regulate gene expression, organ morphogenesis, and body-wide axial patterning. Developmental bioelectricity facilitates the interface to organ-level modular control points that direct patterning in vivo. Cracking the bioelectric code will enable transformative progress in bioengineering and regenerative medicine.
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Affiliation(s)
- Juanita Mathews
- Biology Department, and Allen Discovery Center at Tufts University, Medford, MA 02155, United States
| | - Michael Levin
- Biology Department, and Allen Discovery Center at Tufts University, Medford, MA 02155, United States.
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Silver BB, Nelson CM. The Bioelectric Code: Reprogramming Cancer and Aging From the Interface of Mechanical and Chemical Microenvironments. Front Cell Dev Biol 2018; 6:21. [PMID: 29560350 PMCID: PMC5845671 DOI: 10.3389/fcell.2018.00021] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/15/2018] [Indexed: 12/12/2022] Open
Abstract
Cancer is a complex, heterogeneous group of diseases that can develop through many routes. Broad treatments such as chemotherapy destroy healthy cells in addition to cancerous ones, but more refined strategies that target specific pathways are usually only effective for a limited number of cancer types. This is largely due to the multitude of physiological variables that differ between cells and their surroundings. It is therefore important to understand how nature coordinates these variables into concerted regulation of growth at the tissue scale. The cellular microenvironment might then be manipulated to drive cells toward a desired outcome at the tissue level. One unexpected parameter, cellular membrane voltage (Vm), has been documented to exert control over cellular behavior both in culture and in vivo. Manipulating this fundamental cellular property influences a remarkable array of organism-wide patterning events, producing striking outcomes in both tumorigenesis as well as regeneration. These studies suggest that Vm is not only a key intrinsic cellular property, but also an integral part of the microenvironment that acts in both space and time to guide cellular behavior. As a result, there is considerable interest in manipulating Vm both to treat cancer as well as to regenerate organs damaged or deteriorated during aging. However, such manipulations have produced conflicting outcomes experimentally, which poses a substantial barrier to understanding the fundamentals of bioelectrical reprogramming. Here, we summarize these inconsistencies and discuss how the mechanical microenvironment may impact bioelectric regulation.
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Affiliation(s)
- Brian B Silver
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Celeste M Nelson
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States
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Sullivan KG, Levin M. Inverse Drug Screening of Bioelectric Signaling and Neurotransmitter Roles: Illustrated Using a Xenopus Tail Regeneration Assay. Cold Spring Harb Protoc 2018; 2018:pdb.prot099937. [PMID: 29437995 DOI: 10.1101/pdb.prot099937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Xenopus embryos and larvae are an ideal model system in which to study the interplay between genetics, physiology, and anatomy in the control of structure and function. An important emerging field is the study of bioelectric signaling, the exchange of ion- and neurotransmitter-mediated messages among all types of cells (not just nerve and muscle cells), in the regulation of growth and form during embryogenesis, regeneration, and cancer. To facilitate the mechanistic investigation of bioelectric events in vivo, it is necessary to identify the endogenous signaling machinery involved in any patterning process of interest. This protocol uses the tail regeneration assay in Xenopus to perform an inverse drug screen; tiers of known compounds are used to probe the involvement of increasingly specific classes of bioelectric and neurotransmitter machinery. By using a hierarchical approach, large classes of targets are ruled out in early rounds, focusing attention on progressively narrower sets of proteins. Such a screen avoids many of the limitations of a molecular-genetic targeting approach and provides a rapid and efficient way to focus on specific targets. Usually, <10 experiments are needed to determine whether bioelectrics and/or neurotransmitter signaling are involved in the process of interest. This protocol describes the strategy in the context of a semiquantitative analysis of tail regeneration but can be applied to any assay in Xenopus or other small aquatic model system (e.g., zebrafish). Given the ever-increasing toolkit of chemical genetics, such screens represent a powerful and versatile methodology for probing the physiological circuits underlying pattern regulation.
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Affiliation(s)
- Kelly G Sullivan
- Biology Department, and Allen Discovery Center at Tufts University, Medford, Massachusetts 02155
| | - Michael Levin
- Biology Department, and Allen Discovery Center at Tufts University, Medford, Massachusetts 02155
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39
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Levin M, Martyniuk CJ. The bioelectric code: An ancient computational medium for dynamic control of growth and form. Biosystems 2018; 164:76-93. [PMID: 28855098 PMCID: PMC10464596 DOI: 10.1016/j.biosystems.2017.08.009] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/20/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022]
Abstract
What determines large-scale anatomy? DNA does not directly specify geometrical arrangements of tissues and organs, and a process of encoding and decoding for morphogenesis is required. Moreover, many species can regenerate and remodel their structure despite drastic injury. The ability to obtain the correct target morphology from a diversity of initial conditions reveals that the morphogenetic code implements a rich system of pattern-homeostatic processes. Here, we describe an important mechanism by which cellular networks implement pattern regulation and plasticity: bioelectricity. All cells, not only nerves and muscles, produce and sense electrical signals; in vivo, these processes form bioelectric circuits that harness individual cell behaviors toward specific anatomical endpoints. We review emerging progress in reading and re-writing anatomical information encoded in bioelectrical states, and discuss the approaches to this problem from the perspectives of information theory, dynamical systems, and computational neuroscience. Cracking the bioelectric code will enable much-improved control over biological patterning, advancing basic evolutionary developmental biology as well as enabling numerous applications in regenerative medicine and synthetic bioengineering.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Biology Department, Tufts University, 200 Boston Avenue, Suite 4600 Medford, MA 02155, USA.
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
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Pezzulo G, Levin M. Embodying Markov blankets: Comment on "Answering Schrödinger's question: A free-energy formulation" by Maxwell James Désormeau Ramstead et al. Phys Life Rev 2017; 24:32-36. [PMID: 29191410 DOI: 10.1016/j.plrev.2017.11.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 11/23/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Giovanni Pezzulo
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome, Italy.
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, United States
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Fields C, Levin M. Multiscale memory and bioelectric error correction in the cytoplasm-cytoskeleton-membrane system. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 10. [DOI: 10.1002/wsbm.1410] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/19/2017] [Accepted: 10/04/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Chris Fields
- 21 Rue des Lavandiéres, 11160 Caunes Minervois; France
| | - Michael Levin
- Allen Discovery Center at Tufts University; Medford MA USA
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Pezzulo G, Levin M. Top-down models in biology: explanation and control of complex living systems above the molecular level. J R Soc Interface 2017; 13:rsif.2016.0555. [PMID: 27807271 DOI: 10.1098/rsif.2016.0555] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/11/2016] [Indexed: 12/23/2022] Open
Abstract
It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering.
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Affiliation(s)
- Giovanni Pezzulo
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome, Italy
| | - Michael Levin
- Biology Department, Allen Discovery Center at Tufts, Tufts University, Medford, MA 02155, USA
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43
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Moore D, Walker SI, Levin M. Cancer as a disorder of patterning information: computational and biophysical perspectives on the cancer problem. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2017. [DOI: 10.1088/2057-1739/aa8548] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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44
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Galliot B, Crescenzi M, Jacinto A, Tajbakhsh S. Trends in tissue repair and regeneration. Development 2017; 144:357-364. [PMID: 28143842 DOI: 10.1242/dev.144279] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The 6th EMBO conference on the Molecular and Cellular Basis of Regeneration and Tissue Repair took place in Paestum (Italy) on the 17th-21st September, 2016. The 160 scientists who attended discussed the importance of cellular and tissue plasticity, biophysical aspects of regeneration, the diverse roles of injury-induced immune responses, strategies to reactivate regeneration in mammals, links between regeneration and ageing, and the impact of non-mammalian models on regenerative medicine.
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Affiliation(s)
- Brigitte Galliot
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, CH-1211 Geneva 04, Switzerland
| | - Marco Crescenzi
- Department of Cell Biology and Neurosciences, National Institute of Health, I-00161 Roma, Italy
| | - Antonio Jacinto
- CEDOC, NOVA Medical School, NOVA University of Lisbon, Lisboa 1169-056, Portugal
| | - Shahragim Tajbakhsh
- Department of Developmental & Stem Cell Biology, Stem Cells & Development Unit, CNRS UMR 3738, Institut Pasteur, 75015 Paris, France
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45
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Tyler SEB. Nature's Electric Potential: A Systematic Review of the Role of Bioelectricity in Wound Healing and Regenerative Processes in Animals, Humans, and Plants. Front Physiol 2017; 8:627. [PMID: 28928669 PMCID: PMC5591378 DOI: 10.3389/fphys.2017.00627] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 08/11/2017] [Indexed: 12/24/2022] Open
Abstract
Natural endogenous voltage gradients not only predict and correlate with growth and development but also drive wound healing and regeneration processes. This review summarizes the existing literature for the nature, sources, and transmission of information-bearing bioelectric signals involved in controlling wound healing and regeneration in animals, humans, and plants. It emerges that some bioelectric characteristics occur ubiquitously in a range of animal and plant species. However, the limits of similarities are probed to give a realistic assessment of future areas to be explored. Major gaps remain in our knowledge of the mechanistic basis for these processes, on which regenerative therapies ultimately depend. In relation to this, it is concluded that the mapping of voltage patterns and the processes generating them is a promising future research focus, to probe three aspects: the role of wound/regeneration currents in relation to morphology; the role of endogenous flux changes in driving wound healing and regeneration; and the mapping of patterns in organisms of extreme longevity, in contrast with the aberrant voltage patterns underlying impaired healing, to inform interventions aimed at restoring them.
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46
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Ford BJ. Cellular intelligence: Microphenomenology and the realities of being. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 131:273-287. [PMID: 28847611 DOI: 10.1016/j.pbiomolbio.2017.08.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/24/2017] [Indexed: 02/06/2023]
Abstract
Traditions of Eastern thought conceptualised life in a holistic sense, emphasising the processes of maintaining health and conquering sickness as manifestations of an essentially spiritual principle that was of overriding importance in the conduct of living. Western science, which drove the overriding and partial eclipse of Eastern traditions, became founded on a reductionist quest for ultimate realities which, in the modern scientific world, has embraced the notion that every living process can be successfully modelled by a digital computer system. It is argued here that the essential processes of cognition, response and decision-making inherent in living cells transcend conventional modelling, and microscopic studies of organisms like the shell-building amoebae and the rhodophyte alga Antithamnion reveal a level of cellular intelligence that is unrecognized by science and is not amenable to computer analysis.
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Affiliation(s)
- Brian J Ford
- Gonville & Caius College, Trinity Street, Cambridge University, CB2 1TA, United Kingdom.
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47
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Levin M, Pezzulo G, Finkelstein JM. Endogenous Bioelectric Signaling Networks: Exploiting Voltage Gradients for Control of Growth and Form. Annu Rev Biomed Eng 2017; 19:353-387. [PMID: 28633567 PMCID: PMC10478168 DOI: 10.1146/annurev-bioeng-071114-040647] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Living systems exhibit remarkable abilities to self-assemble, regenerate, and remodel complex shapes. How cellular networks construct and repair specific anatomical outcomes is an open question at the heart of the next-generation science of bioengineering. Developmental bioelectricity is an exciting emerging discipline that exploits endogenous bioelectric signaling among many cell types to regulate pattern formation. We provide a brief overview of this field, review recent data in which bioelectricity is used to control patterning in a range of model systems, and describe the molecular tools being used to probe the role of bioelectrics in the dynamic control of complex anatomy. We suggest that quantitative strategies recently developed to infer semantic content and information processing from ionic activity in the brain might provide important clues to cracking the bioelectric code. Gaining control of the mechanisms by which large-scale shape is regulated in vivo will drive transformative advances in bioengineering, regenerative medicine, and synthetic morphology, and could be used to therapeutically address birth defects, traumatic injury, and cancer.
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Affiliation(s)
- Michael Levin
- Biology Department, Tufts University, Medford, Massachusetts 02155-4243;
- Allen Discovery Center, Tufts University, Medford, Massachusetts 02155;
| | - Giovanni Pezzulo
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome 00185, Italy;
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48
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Durant F, Morokuma J, Fields C, Williams K, Adams DS, Levin M. Long-Term, Stochastic Editing of Regenerative Anatomy via Targeting Endogenous Bioelectric Gradients. Biophys J 2017; 112:2231-2243. [PMID: 28538159 PMCID: PMC5443973 DOI: 10.1016/j.bpj.2017.04.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/30/2017] [Accepted: 04/14/2017] [Indexed: 12/22/2022] Open
Abstract
We show that regenerating planarians' normal anterior-posterior pattern can be permanently rewritten by a brief perturbation of endogenous bioelectrical networks. Temporary modulation of regenerative bioelectric dynamics in amputated trunk fragments of planaria stochastically results in a constant ratio of regenerates with two heads to regenerates with normal morphology. Remarkably, this is shown to be due not to partial penetrance of treatment, but a profound yet hidden alteration to the animals' patterning circuitry. Subsequent amputations of the morphologically normal regenerates in water result in the same ratio of double-headed to normal morphology, revealing a cryptic phenotype that is not apparent unless the animals are cut. These animals do not differ from wild-type worms in histology, expression of key polarity genes, or neoblast distribution. Instead, the altered regenerative bodyplan is stored in seemingly normal planaria via global patterns of cellular resting potential. This gradient is functionally instructive, and represents a multistable, epigenetic anatomical switch: experimental reversals of bioelectric state reset subsequent regenerative morphology back to wild-type. Hence, bioelectric properties can stably override genome-default target morphology, and provide a tractable control point for investigating cryptic phenotypes and the stochasticity of large-scale epigenetic controls.
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Affiliation(s)
- Fallon Durant
- Allen Discovery Center at Tufts University, and Department of Biology, Tufts University, Medford, Massachusetts
| | - Junji Morokuma
- Allen Discovery Center at Tufts University, and Department of Biology, Tufts University, Medford, Massachusetts
| | | | - Katherine Williams
- Allen Discovery Center at Tufts University, and Department of Biology, Tufts University, Medford, Massachusetts
| | - Dany Spencer Adams
- Allen Discovery Center at Tufts University, and Department of Biology, Tufts University, Medford, Massachusetts
| | - Michael Levin
- Allen Discovery Center at Tufts University, and Department of Biology, Tufts University, Medford, Massachusetts.
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49
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Mathews J, Levin M. Gap junctional signaling in pattern regulation: Physiological network connectivity instructs growth and form. Dev Neurobiol 2017; 77:643-673. [PMID: 27265625 PMCID: PMC10478170 DOI: 10.1002/dneu.22405] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 12/19/2022]
Abstract
Gap junctions (GJs) are aqueous channels that allow cells to communicate via physiological signals directly. The role of gap junctional connectivity in determining single-cell functions has long been recognized. However, GJs have another important role: the regulation of large-scale anatomical pattern. GJs are not only versatile computational elements that allow cells to control which small molecule signals they receive and emit, but also establish connectivity patterns within large groups of cells. By dynamically regulating the topology of bioelectric networks in vivo, GJs underlie the ability of many tissues to implement complex morphogenesis. Here, a review of recent data on patterning roles of GJs in growth of the zebrafish fin, the establishment of left-right patterning, the developmental dysregulation known as cancer, and the control of large-scale head-tail polarity, and head shape in planarian regeneration has been reported. A perspective in which GJs are not only molecular features functioning in single cells, but also enable global neural-like dynamics in non-neural somatic tissues has been proposed. This view suggests a rich program of future work which capitalizes on the rapid advances in the biophysics of GJs to exploit GJ-mediated global dynamics for applications in birth defects, regenerative medicine, and morphogenetic bioengineering. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 643-673, 2017.
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Affiliation(s)
- Juanita Mathews
- Department of Biology, Tufts Center for Regenerative and Developmental Biology, Tufts University, Medford, MA
| | - Michael Levin
- Department of Biology, Tufts Center for Regenerative and Developmental Biology, Tufts University, Medford, MA
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