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Jaeger J. Assembly Theory: What It Does and What It Does Not Do. J Mol Evol 2024; 92:87-92. [PMID: 38453740 PMCID: PMC10978598 DOI: 10.1007/s00239-024-10163-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024]
Abstract
A recent publication in Nature has generated much heated discussion about evolution, its tendency towards increasing diversity and complexity, and its potential status above and beyond the known laws of fundamental physics. The argument at the heart of this controversy concerns assembly theory, a method to detect and quantify the influence of higher-level emergent causal constraints in computational worlds made of basic objects and their combinations. In this short essay, I briefly review the theory, its basic principles and potential applications. I then go on to critically examine its authors' assertions, concluding that assembly theory has merit but is not nearly as novel or revolutionary as claimed. It certainly does not provide any new explanation of biological evolution or natural selection, or a new grounding of biology in physics. In this regard, the presentation of the paper is starkly distorted by hype, which may explain some of the outrage it created.
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Affiliation(s)
- Johannes Jaeger
- Department of Philosophy, University of Vienna, Universitätsstraße 7, 1010, Vienna, Austria.
- Complexity Science Hub (CSH) Vienna, Josefstädter Straße 39, 1080, Vienna, Austria.
- Ronin Institute, Montclair, USA.
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2
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Hazen RM, Burns PC, Cleaves HJ, Downs RT, Krivovichev SV, Wong ML. Molecular assembly indices of mineral heteropolyanions: some abiotic molecules are as complex as large biomolecules. J R Soc Interface 2024; 21:20230632. [PMID: 38378136 PMCID: PMC10878807 DOI: 10.1098/rsif.2023.0632] [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: 10/30/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024] Open
Abstract
Molecular assembly indices, which measure the number of unique sequential steps theoretically required to construct a three-dimensional molecule from its constituent atomic bonds, have been proposed as potential biosignatures. A central hypothesis of assembly theory is that any molecule with an assembly index ≥15 found in significant local concentrations represents an unambiguous sign of life. We show that abiotic molecule-like heteropolyanions, which assemble in aqueous solution as precursors to some mineral crystals, range in molecular assembly indices from 2 for H2CO3 or Si(OH)4 groups to as large as 21 for the most complex known molecule-like subunits in the rare minerals ewingite and ilmajokite. Therefore, values of molecular assembly indices ≥15 do not represent unambiguous biosignatures.
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Affiliation(s)
- Robert M. Hazen
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA
| | - Peter C. Burns
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - H. James Cleaves
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA
- Earth Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Blue Marble Space Institute for Science, Seattle, WA 98104, USA
- Department of Chemistry, Howard University, Washington, DC 20059, USA
| | - Robert T. Downs
- Geological Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Sergey V. Krivovichev
- Department of Crystallography, Institute of Earth Sciences, St. Petersburg State University, St. Petersburg 199034, Russia
- Nanomaterials Research Centre, Kola Science Centre, Russian Academy of Sciences, Fersmma 14, Apatity 184209, Russia
| | - Michael L. Wong
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA
- Sagan Fellow, NASA Hubble Fellowship Program, Space Telescope Science Institute, Baltimore, MD 21218, USA
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Foote S, Sinhadc P, Mathis C, Walker SI. False Positives and the Challenge of Testing the Alien Hypothesis. ASTROBIOLOGY 2023; 23:1189-1201. [PMID: 37962842 DOI: 10.1089/ast.2023.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The origin of life and the detection of alien life have historically been treated as separate scientific research problems. However, they are not strictly independent. Here, we discuss the need for a better integration of the sciences of life detection and origins of life. Framing these dual problems within the formalism of Bayesian hypothesis testing, we demonstrate via simple examples how high confidence in life detection claims require either (1) a strong prior hypothesis about the existence of life in a particular alien environment, or conversely, (2) signatures of life that are not susceptible to false positives. As a case study, we discuss the role of priors and hypothesis testing in recent results reporting potential detection of life in the venusian atmosphere and in the icy plumes of Enceladus. While many current leading biosignature candidates are subject to false positives because they are not definitive of life, our analyses demonstrate why it is necessary to shift focus to candidate signatures that are definitive. This indicates a necessity to develop methods that lack substantial false positives, by using observables for life that rely on prior hypotheses with strong theoretical and empirical support in identifying defining features of life. Abstract theories developed in pursuit of understanding universal features of life are more likely to be definitive and to apply to life-as-we-don't-know-it. We discuss Molecular Assembly theory as an example of such an observable which is applicable to life detection within the solar system. In the absence of alien examples these are best validated in origin of life experiments, substantiating the need for better integration between origins of life and biosignature science research communities. This leads to a conclusion that extraordinary claims in astrobiology (e.g., definitive detection of alien life) require extraordinary explanations, whereas the evidence itself could be quite ordinary.
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Affiliation(s)
- Searra Foote
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Pritvik Sinhadc
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, Arizona, USA
- Dubai College, Dubai, UAE
| | - Cole Mathis
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, Arizona, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Sara Imari Walker
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, Arizona, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
- Blue Marble Space Institute for Science, Seattle, Washington, USA
- ASU-SFI Center for Biosocial Complex Systems, Arizona State University, Tempe, Arizona, USA
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Sharma A, Czégel D, Lachmann M, Kempes CP, Walker SI, Cronin L. Assembly theory explains and quantifies selection and evolution. Nature 2023; 622:321-328. [PMID: 37794189 PMCID: PMC10567559 DOI: 10.1038/s41586-023-06600-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
Scientists have grappled with reconciling biological evolution1,2 with the immutable laws of the Universe defined by physics. These laws underpin life's origin, evolution and the development of human culture and technology, yet they do not predict the emergence of these phenomena. Evolutionary theory explains why some things exist and others do not through the lens of selection. To comprehend how diverse, open-ended forms can emerge from physics without an inherent design blueprint, a new approach to understanding and quantifying selection is necessary3-5. We present assembly theory (AT) as a framework that does not alter the laws of physics, but redefines the concept of an 'object' on which these laws act. AT conceptualizes objects not as point particles, but as entities defined by their possible formation histories. This allows objects to show evidence of selection, within well-defined boundaries of individuals or selected units. We introduce a measure called assembly (A), capturing the degree of causation required to produce a given ensemble of objects. This approach enables us to incorporate novelty generation and selection into the physics of complex objects. It explains how these objects can be characterized through a forward dynamical process considering their assembly. By reimagining the concept of matter within assembly spaces, AT provides a powerful interface between physics and biology. It discloses a new aspect of physics emerging at the chemical scale, whereby history and causal contingency influence what exists.
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Affiliation(s)
| | - Dániel Czégel
- BEYOND Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, USA
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | | | | | - Sara I Walker
- BEYOND Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, USA.
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA.
| | - Leroy Cronin
- School of Chemistry, University of Glasgow, Glasgow, UK.
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Herter L, Perrin T, Fessard T, Salomé C. Preparation of 3,5-Methanobenzo[ b]azepines: An sp 3-Rich Quinolone Isostere. Org Lett 2023; 25:6161-6166. [PMID: 37573582 DOI: 10.1021/acs.orglett.3c02250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The replacement of the aromatic ring in bioactive compounds with saturated bioisosteres has become a popular tactic to obtain novel structures with improved physicochemical profiles. In this paper, we describe an efficient synthesis of 3,5-methanobenzo[b]azepine analogues and suggest them as isosteres of quinolones. Quinolones are heteroaromatic, flat rings and considered as privileged scaffolds. An isosteric version of this scaffold with more 3D character would offer new options to expand their use.
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Affiliation(s)
- Loïc Herter
- SpiroChem, Rosental area, WRO-1047-3, Mattenstrasse 22, 4058 Basel, Switzerland
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Timothé Perrin
- SpiroChem, Rosental area, WRO-1047-3, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Thomas Fessard
- SpiroChem, Rosental area, WRO-1047-3, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Christophe Salomé
- SpiroChem, Rosental area, WRO-1047-3, Mattenstrasse 22, 4058 Basel, Switzerland
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Srinivasan A, Srinivasan A, Goodman MR, Riceberg JS, Guise KG, Shapiro ML. Hippocampal and Medial Prefrontal Cortex Fractal Spiking Patterns Encode Episodes and Rules. CHAOS, SOLITONS, AND FRACTALS 2023; 171:113508. [PMID: 37251275 PMCID: PMC10217776 DOI: 10.1016/j.chaos.2023.113508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A central question in neuroscience is how the brain represents and processes information to guide behavior. The principles that organize brain computations are not fully known, and could include scale-free, or fractal patterns of neuronal activity. Scale-free brain activity may be a natural consequence of the relatively small subsets of neuronal populations that respond to task features, i.e., sparse coding. The size of the active subsets constrains the possible sequences of inter-spike intervals (ISI), and selecting from this limited set may produce firing patterns across wide-ranging timescales that form fractal spiking patterns. To investigate the extent to which fractal spiking patterns corresponded with task features, we analyzed ISIs in simultaneously recorded populations of CA1 and medial prefrontal cortical (mPFC) neurons in rats performing a spatial memory task that required both structures. CA1 and mPFC ISI sequences formed fractal patterns that predicted memory performance. CA1 pattern duration, but not length or content, varied with learning speed and memory performance whereas mPFC patterns did not. The most common CA1 and mPFC patterns corresponded with each region's cognitive function: CA1 patterns encoded behavioral episodes which linked the start, choice, and goal of paths through the maze whereas mPFC patterns encoded behavioral "rules" which guided goal selection. mPFC patterns predicted changing CA1 spike patterns only as animals learned new rules. Together, the results suggest that CA1 and mPFC population activity may predict choice outcomes by using fractal ISI patterns to compute task features.
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Affiliation(s)
- Aditya Srinivasan
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, 47 New Scotland Ave, Mail Code 126, Albany, NY 12208
| | - Arvind Srinivasan
- College of Health Sciences, California Northstate University, 2910 Prospect Park Drive, Rancho Cordova, CA 95670
| | - Michael R. Goodman
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, 47 New Scotland Ave, Mail Code 126, Albany, NY 12208
| | - Justin S. Riceberg
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, 47 New Scotland Ave, Mail Code 126, Albany, NY 12208
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, 1470 Madison Avenue New York, NY 10029
| | - Kevin G. Guise
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, 1470 Madison Avenue New York, NY 10029
| | - Matthew L. Shapiro
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, 47 New Scotland Ave, Mail Code 126, Albany, NY 12208
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van Duppen P, Daines E, Robinson WE, Huck WTS. Dynamic Environmental Conditions Affect the Composition of a Model Prebiotic Reaction Network. J Am Chem Soc 2023; 145:7559-7568. [PMID: 36961990 PMCID: PMC10080678 DOI: 10.1021/jacs.3c00908] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Prebiotic environments are dynamic, containing a range of periodic and aperiodic variations in reaction conditions. However, the impact of the temporal dynamics of environmental conditions upon prebiotic chemical reaction networks has not been investigated. Here, we demonstrate how the magnitude and rate of temporal fluctuations of the catalysts Ca2+ and hydroxide control the product distributions of the formose reaction. Surprisingly, the product compositions of the formose reaction under dynamic conditions deviate significantly from those under steady state conditions. We attribute these compositional changes to the non-uniform propagation of fluctuations through the network, thereby shaping reaction outcomes. An examination of temporal concentration patterns showed that collections of compounds responded collectively to perturbations, indicating that key gating reactions branching from the Breslow cycle may be important responsive features of the formose reaction. Our findings show how the compositions of prebiotic reaction networks were shaped by sequential environmental events, illustrating the necessity for considering the temporal traits of prebiotic environments that supported the origin of life.
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Affiliation(s)
- Peer van Duppen
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Elena Daines
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - William E Robinson
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Liu Y, Di Z, Gerlee P. Ladderpath Approach: How Tinkering and Reuse Increase Complexity and Information. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1082. [PMID: 36010747 PMCID: PMC9407278 DOI: 10.3390/e24081082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
The notion of information and complexity are important concepts in many scientific fields such as molecular biology, evolutionary theory and exobiology. Many measures of these quantities are either difficult to compute, rely on the statistical notion of information, or can only be applied to strings. Based on assembly theory, we propose the notion of a ladderpath, which describes how an object can be decomposed into hierarchical structures using repetitive elements. From the ladderpath, two measures naturally emerge: the ladderpath-index and the order-index, which represent two axes of complexity. We show how the ladderpath approach can be applied to both strings and spatial patterns and argue that all systems that undergo evolution can be described as ladderpaths. Further, we discuss possible applications to human language and the origin of life. The ladderpath approach provides an alternative characterization of the information that is contained in a single object (or a system) and could aid in our understanding of evolving systems and the origin of life in particular.
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Affiliation(s)
- Yu Liu
- International Academic Center of Complex Systems, Beijing Normal University, Zhuhai 519087, China
| | - Zengru Di
- International Academic Center of Complex Systems, Beijing Normal University, Zhuhai 519087, China
| | - Philip Gerlee
- Department of Mathematical Sciences, Chalmers University of Technology, 405 30 Gothenburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
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Lustosa DM, Milo A. Mechanistic Inference from Statistical Models at Different Data-Size Regimes. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Danilo M. Lustosa
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Anat Milo
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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Sharma S, Arya A, Cruz R, Cleaves II HJ. Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives. Life (Basel) 2021; 11:1140. [PMID: 34833016 PMCID: PMC8624352 DOI: 10.3390/life11111140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
Prebiotic chemistry often involves the study of complex systems of chemical reactions that form large networks with a large number of diverse species. Such complex systems may have given rise to emergent phenomena that ultimately led to the origin of life on Earth. The environmental conditions and processes involved in this emergence may not be fully recapitulable, making it difficult for experimentalists to study prebiotic systems in laboratory simulations. Computational chemistry offers efficient ways to study such chemical systems and identify the ones most likely to display complex properties associated with life. Here, we review tools and techniques for modelling prebiotic chemical reaction networks and outline possible ways to identify self-replicating features that are central to many origin-of-life models.
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Affiliation(s)
- Siddhant Sharma
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA; (S.S.); (A.A.); (R.C.)
- Department of Biochemistry, Deshbandhu College, University of Delhi, New Delhi 110019, India
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Aayush Arya
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA; (S.S.); (A.A.); (R.C.)
- Department of Physics, Lovely Professional University, Jalandhar-Delhi GT Road, Phagwara 144001, India
| | - Romulo Cruz
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA; (S.S.); (A.A.); (R.C.)
- Big Data Laboratory, Information and Communications Technology Center (CTIC), National University of Engineering, Amaru 210, Lima 15333, Peru
| | - Henderson James Cleaves II
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA; (S.S.); (A.A.); (R.C.)
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
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