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Alexander VN. The creativity of cells: aneural irrational cognition. J Physiol 2024; 602:2479-2489. [PMID: 37777982 DOI: 10.1113/jp284417] [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: 06/27/2023] [Accepted: 09/11/2023] [Indexed: 10/03/2023] Open
Abstract
Evidence of cognition in aneural cells is well-establish in the literature. This paper extends the exploration of the mechanisms of cognition by considering whether or not aneural cells may be capable of irrational cognition, making associations based on coincidental similarities and circumstantial factors. If aneural cells do harness such semiosic qualities, as with higher-level creativity, this might be how they are able to overcome old algorithms and invent tools for new situations. I will look at three examples of irrational learning in aneural systems in terms of semiotics: (1) generalisation in the immune system, based on viral molecular mimicry, whereby immune cells attack the self, which seems to be an overgeneralisation of an icon sign based on mere similarity, not identity, (2) the classical conditioning of pea plants to trope toward wind as a sign of light, which seems to be an association of an index sign based on mere temporal proximity, and (3) a pharmaceutical intervention to prevent pregnancy, using a conjugate to encrypt self with non-self, which seems to be an example of symbol use. We identify irrational cognition easily when it leads to 'wrong' outcomes, but, if it occurs, it may also lead to favourable outcomes and 'creative' solutions.
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Miller WB, Baluška F, Reber AS, Slijepčević P. Biology in the 21st century: Natural selection is cognitive selection. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 190:170-184. [PMID: 38740143 DOI: 10.1016/j.pbiomolbio.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Natural selection has a formal definition as the natural process that results in the survival and reproductive success of individuals or groups best adjusted to their environment, leading to the perpetuation of those genetic qualities best suited to that organism's environmental niche. Within conventional Neo-Darwinism, the largest source of those variations that can be selected is presumed to be secondary to random genetic mutations. As these arise, natural selection sustains adaptive traits in the context of a 'struggle for existence'. Consequently, in the 20th century, natural selection was generally portrayed as the primary evolutionary driver. The 21st century offers a comprehensive alternative to Neo-Darwinian dogma within Cognition-Based Evolution. The substantial differences between these respective evolutionary frameworks have been most recently articulated in a revision of Crick's Central Dogma, a former centerpiece of Neo-Darwinism. The argument is now advanced that the concept of natural selection should also be comprehensively reappraised. Cognitive selection is presented as a more precise term better suited to 21st century biology. Since cognition began with life's origin, natural selection represents cognitive selection.
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Affiliation(s)
| | - František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, Germany.
| | - Arthur S Reber
- Department of Psychology, University of British Columbia, Vancouver, BC, Canada.
| | - Predrag Slijepčević
- Department of Life Sciences College of Health, Medicine and Life Sciences, University of Brunel, UK.
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3
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Banerjee M, Srivastava S, Rai SN, States JC. Chronic arsenic exposure induces malignant transformation of human HaCaT cells through both deterministic and stochastic changes in transcriptome expression. Toxicol Appl Pharmacol 2024; 484:116865. [PMID: 38373578 PMCID: PMC10994602 DOI: 10.1016/j.taap.2024.116865] [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: 11/09/2023] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 02/21/2024]
Abstract
Biological processes are inherently stochastic, i.e., are partially driven by hard to predict random probabilistic processes. Carcinogenesis is driven both by stochastic and deterministic (predictable non-random) changes. However, very few studies systematically examine the contribution of stochastic events leading to cancer development. In differential gene expression studies, the established data analysis paradigms incentivize expression changes that are uniformly different across the experimental versus control groups, introducing preferential inclusion of deterministic changes at the expense of stochastic processes that might also play a crucial role in the process of carcinogenesis. In this study, we applied simple computational techniques to quantify: (i) The impact of chronic arsenic (iAs) exposure as well as passaging time on stochastic gene expression and (ii) Which genes were expressed deterministically and which were expressed stochastically at each of the three stages of cancer development. Using biological coefficient of variation as an empirical measure of stochasticity we demonstrate that chronic iAs exposure consistently suppressed passaging related stochastic gene expression at multiple time points tested, selecting for a homogenous cell population that undergo transformation. Employing multiple balanced removal of outlier data, we show that chronic iAs exposure induced deterministic and stochastic changes in the expression of unique set of genes, that populate largely unique biological pathways. Together, our data unequivocally demonstrate that both deterministic and stochastic changes in transcriptome-wide expression are critical in driving biological processes, pathways and networks towards clonal selection, carcinogenesis, and tumor heterogeneity.
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Affiliation(s)
- Mayukh Banerjee
- Department of Pharmacology and Toxicology, University of Louisville, 505, S. Hancock Street, Louisville, KY 40202, USA; Center for Integrative Environmental Health Sciences, University of Louisville, 505, S. Hancock Street, Louisville, KY 40202, USA
| | - Sudhir Srivastava
- Department of Bioinformatics and Biostatistics, University of Louisville, 505, S. Hancock Street, Louisville, KY 40202, USA
| | - Shesh N Rai
- Department of Bioinformatics and Biostatistics, University of Louisville, 505, S. Hancock Street, Louisville, KY 40202, USA; Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville, 505, S. Hancock Street, Louisville, KY 40202, USA; Biostatistics and Informatics Facility Core, Center for Integrative Environmental Health Sciences, University of Louisville, 505, S. Hancock Street, Louisville, KY 40202, USA
| | - J Christopher States
- Department of Pharmacology and Toxicology, University of Louisville, 505, S. Hancock Street, Louisville, KY 40202, USA; Center for Integrative Environmental Health Sciences, University of Louisville, 505, S. Hancock Street, Louisville, KY 40202, USA.
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4
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Johnson MW. Music, cells and the dimensionality of nature. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:57-64. [PMID: 38103652 DOI: 10.1016/j.pbiomolbio.2023.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/15/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023]
Abstract
One of the foundational principles of recent developments in evolutionary biology has been the acknowledgement of homeostasis as an organising principle of cellular development from unicellular origins. Fundamentally, this concerns the balance between the inside of a biological entity and its environment. Given that the organ of balance is the ear, and that the evolutionary provenance of the vestibular system can be traced back to fish, music provides a rich foundation for evolutionary biological inquiry. This paper considers a specific dimensional relationship in sonic experience between noise, signal, redundancy and anticipation. Drawing on the physics of Bohm and more recent developments in Rowlands's nilpotent quantum mechanics, I argue that the relationship between these four parameters is not only that they represent aspects of sonic experience, but that they are dimensionally distinct, where noise can be considered to be scalar, a signal (or a note) is a vector (having magnitude and direction), redundancy is bi-vectorial (involving degrees of repetition of signals over time), and anticipation is tri-vectorial (involving reflexive consideration of different orders of redundancy). In outlining the dimensional distinction between these variables, an analysis is presented which considers the relationship between the Shannon entropy of different dimensions in music. This shows that the entropy of noise has a particular bearing on the entropy of the other dimensions. This dimensional relation is also reflected in biological evidence, where Torday has shown there to be a direct correlation between the effect of gravitational "noise" on cellular communication, and by extension the evolution of consciousness.
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Ellis GFR. Efficient, Formal, Material, and Final Causes in Biology and Technology. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1301. [PMID: 37761600 PMCID: PMC10529506 DOI: 10.3390/e25091301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
This paper considers how a classification of causal effects as comprising efficient, formal, material, and final causation can provide a useful understanding of how emergence takes place in biology and technology, with formal, material, and final causation all including cases of downward causation; they each occur in both synchronic and diachronic forms. Taken together, they underlie why all emergent levels in the hierarchy of emergence have causal powers (which is Noble's principle of biological relativity) and so why causal closure only occurs when the upwards and downwards interactions between all emergent levels are taken into account, contra to claims that some underlying physics level is by itself causality complete. A key feature is that stochasticity at the molecular level plays an important role in enabling agency to emerge, underlying the possibility of final causation occurring in these contexts.
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Affiliation(s)
- George F R Ellis
- Mathematics Department, The New Institute, University of Cape Town, 20354 Hamburg, Germany
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Ilan Y. Constrained disorder principle-based variability is fundamental for biological processes: Beyond biological relativity and physiological regulatory networks. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:37-48. [PMID: 37068713 DOI: 10.1016/j.pbiomolbio.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/26/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
The constrained disorder principle (CDP) defines systems based on their degree of disorder bounded by dynamic boundaries. The principle explains stochasticity in living and non-living systems. Denis Noble described the importance of stochasticity in biology, emphasizing stochastic processes at molecular, cellular, and higher levels in organisms as having a role beyond simple noise. The CDP and Noble's theories (NT) claim that biological systems use stochasticity. This paper presents the CDP and NT, discussing common notions and differences between the two theories. The paper presents the CDP-based concept of taking the disorder beyond its role in nature to correct malfunctions of systems and improve the efficiency of biological systems. The use of CDP-based algorithms embedded in second-generation artificial intelligence platforms is described. In summary, noise is inherent to complex systems and has a functional role. The CDP provides the option of using noise to improve functionality.
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Affiliation(s)
- Yaron Ilan
- Faculty of Medicine, Hebrew University, Department of Medicine, Hadassah Medical Center, Jerusalem, Israel.
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Mistriotis A. Mathematical and physical considerations indicating that the cell genome is a read-write memory. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 178:50-56. [PMID: 36736433 DOI: 10.1016/j.pbiomolbio.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/15/2023] [Accepted: 01/30/2023] [Indexed: 02/03/2023]
Abstract
The molecular mechanisms that govern biological evolution have not been fully elucidated so far. Recent studies indicate that regulatory proteins, acting as decision-making complex devices, can accelerate or retard the evolution of cells. Such biochemically controlled evolution may be considered as an optimization process of logical nature aimed at developing fitter species that can better survive in a specific environment. Therefore, we may assume that new genetic information can be stored in the cell memory (i.e., genome) by a sophisticated biomolecular process that resembles writing in computer memory. Such a hypothesis is theoretically supported by a recent work showing that logic is a necessary component of life, so living systems process information in the same way as computers. The current study summarizes existing evidence showing that cells can intentionally modify their stored data by biochemical processes resembling stochastic algorithms to avoid environmental stress and increase their chances of survival. Furthermore, the mathematical and physical considerations that render a read-write memory a necessary component of biological systems are presented.
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Affiliation(s)
- Antonis Mistriotis
- Agricultural University of Athens, Dept. of Natural Resources and Agricultural Engineering, Iera Odos 75, Athens, Greece.
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Polizzi S, Marzi T, Matteuzzi T, Castellani G, Bazzani A. Random Walk Approximation for Stochastic Processes on Graphs. ENTROPY (BASEL, SWITZERLAND) 2023; 25:394. [PMID: 36981283 PMCID: PMC10047168 DOI: 10.3390/e25030394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/13/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
We introduce the Random Walk Approximation (RWA), a new method to approximate the stationary solution of master equations describing stochastic processes taking place on graphs. Our approximation can be used for all processes governed by non-linear master equations without long-range interactions and with a conserved number of entities, which are typical in biological systems, such as gene regulatory or chemical reaction networks, where no exact solution exists. For linear systems, the RWA becomes the exact result obtained from the maximum entropy principle. The RWA allows having a simple analytical, even though approximated, form of the solution, which is global and easier to deal with than the standard System Size Expansion (SSE). Here, we give some theoretically sufficient conditions for the validity of the RWA and estimate the order of error calculated by the approximation with respect to the number of particles. We compare RWA with SSE for two examples, a toy model and the more realistic dual phosphorylation cycle, governed by the same underlying process. Both approximations are compared with the exact integration of the master equation, showing for the RWA good performances of the same order or better than the SSE, even in regions where sufficient conditions are not met.
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Affiliation(s)
- Stefano Polizzi
- Department of Physics and Astronomy A. Righi, University of Bologna, 40127 Bologna, Italy
| | - Tommaso Marzi
- Department of Physics and Astronomy A. Righi, University of Bologna, 40127 Bologna, Italy
| | - Tommaso Matteuzzi
- Department of Physics and Astronomy, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Armando Bazzani
- Department of Physics and Astronomy A. Righi, University of Bologna, 40127 Bologna, Italy
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Bizzarri M, Fedeli V, Piombarolo A, Angeloni A. Space Biomedicine: A Unique Opportunity to Rethink the Relationships between Physics and Biology. Biomedicines 2022; 10:biomedicines10102633. [PMID: 36289894 PMCID: PMC9599147 DOI: 10.3390/biomedicines10102633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/21/2022] Open
Abstract
Space biomedicine has provided significant technological breakthroughs by developing new medical devices, diagnostic tools, and health-supporting systems. Many of these products are currently in use onboard the International Space Station and have been successfully translated into clinical practice on Earth. However, biomedical research performed in space has disclosed exciting, new perspectives regarding the relationships between physics and medicine, thus fostering the rethinking of the theoretical basis of biology. In particular, these studies have stressed the critical role that biophysical forces play in shaping the function and pattern formation of living structures. The experimental models investigated under microgravity conditions allow us to appreciate the complexity of living organisms through a very different perspective. Indeed, biological entities should be conceived as a unique magnification of physical laws driven by local energy and order states overlaid by selection history and constraints, in which the source of the inheritance, variation, and process of selection has expanded from the classical Darwinian definition. The very specific nature of the field in which living organisms behave and evolve in a space environment can be exploited to decipher the underlying, basic processes and mechanisms that are not apparent on Earth. In turn, these findings can provide novel opportunities for testing pharmacological countermeasures that can be instrumental for managing a wide array of health problems and diseases on Earth.
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Affiliation(s)
- Mariano Bizzarri
- Department of Experimental Medicine, University La Sapienza, 00161 Rome, Italy
- Systems Biology Group Lab, Dip. “P.Valdoni”, University La Sapienza, 00161 Rome, Italy
- Correspondence:
| | - Valeria Fedeli
- Department of Experimental Medicine, University La Sapienza, 00161 Rome, Italy
- Systems Biology Group Lab, Dip. “P.Valdoni”, University La Sapienza, 00161 Rome, Italy
| | - Aurora Piombarolo
- Department of Experimental Medicine, University La Sapienza, 00161 Rome, Italy
- Systems Biology Group Lab, Dip. “P.Valdoni”, University La Sapienza, 00161 Rome, Italy
| | - Antonio Angeloni
- Department of Experimental Medicine, University La Sapienza, 00161 Rome, Italy
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Noble D. Modern physiology vindicates Darwin's Dream. Exp Physiol 2022; 107:1015-1028. [PMID: 35871280 PMCID: PMC9543272 DOI: 10.1113/ep090133] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/11/2022] [Indexed: 11/15/2022]
Abstract
New Findings What is the topic of this review? Revisiting the 2013 article ‘Physiology is rocking the foundations of evolutionary biology’. What advances does it highlight? The discovery that the genome is not isolated from the soma and the environment, and that there is no barrier preventing somatic characteristics being transmitted to the germline, means that Darwin's pangenetic ideas become relevant again.
Abstract Charles Darwin spent the last decade of his life collaborating with physiologists in search of the biological processes of evolution. He viewed physiology as the way forward in answering fundamental questions about inheritance, acquired characteristics, and the mechanisms by which organisms could achieve their ends and survival. He collaborated with 19th century physiologists, notably John Burdon‐Sanderson and George Romanes, in his search for the mechanisms of transgenerational inheritance. The discovery that the genome is not isolated from the soma and the environment, and that there is no barrier preventing somatic characteristics being transmitted to the germline, means that Darwin's pangenetic ideas become relevant again. It is time for 21st century physiology to come to the rescue of evolutionary biology. This article outlines research lines by which this could be achieved.
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Affiliation(s)
- Denis Noble
- Department of Physiology Anatomy & Genetics University of Oxford
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Kull K. Choices by organisms: on the role of freedom in behaviour and evolution. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Neo-Darwinian biology has demonstrated that it is possible to construct a theory of life that excludes the role of organisms’ free choice. In a richer theory, the latter as a possibility needs to be taken into account. For that purpose, it is necessary to introduce the biological concept of choice, analyse its structure and roles, and consider some implications for biological theory. It is argued here that the conditions for free choice emerge together with umwelt—the space of synchronous options. Basically, choice does not require purpose. This leads to the conclusion that freedom is an attribute of life.
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Affiliation(s)
- Kalevi Kull
- Department of Semiotics, University of Tartu , Tartu , Estonia
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12
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Cellular sentience as the primary source of biological order and evolution. Biosystems 2022; 218:104694. [PMID: 35595194 DOI: 10.1016/j.biosystems.2022.104694] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/17/2022]
Abstract
All life is cellular, starting some 4 billion years ago with the emergence of the first cells. In order to survive their early evolution in the face of an extremely challenging environment, the very first cells invented cellular sentience and cognition, allowing them to make relevant decisions to survive through creative adaptations in a continuously running evolutionary narrative. We propose that the success of cellular life has crucially depended on a biological version of Maxwell's demons which permits the extraction of relevant sensory information and energy from the cellular environment, allowing cells to sustain anti-entropic actions. These sensor-effector actions allowed for the creative construction of biological order in the form of diverse organic macromolecules, including crucial polymers such as DNA, RNA, and cytoskeleton. Ordered biopolymers store analogue (structures as templates) and digital (nucleotide sequences of DNA and RNA) information that functioned as a form memory to support the development of organisms and their evolution. Crucially, all cells are formed by the division of previous cells, and their plasma membranes are physically and informationally continuous across evolution since the beginning of cellular life. It is argued that life is supported through life-specific principles which support cellular sentience, distinguishing life from non-life. Biological order, together with cellular cognition and sentience, allow the creative evolution of all living organisms as the authentic authors of evolutionary novelty.
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Recent Progress in Traditional Chinese Medicines and Their Mechanism in the Treatment of Allergic Rhinitis. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:3594210. [PMID: 35444784 PMCID: PMC9015857 DOI: 10.1155/2022/3594210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/17/2022] [Indexed: 02/06/2023]
Abstract
Objective To conduct a systematic review on the mechanism of action and use of traditional Chinese medicines (TCM) in allergic rhinitis treatment. Background Allergic rhinitis (AR) is a type I allergic disease of the immune system induced by immunoglobulin E mediated inflammation and is characterized by sneezing, nasal itching, paroxysmal nasal obstruction, mucosal edema, cough, and rhinorrhea. More than 500 million people have been affected by rhinitis worldwide in the past 20 years, leading to negative effects on health, quality of life, and social relationships. Currently, the trending medicines used in the case of AR include intranasal corticosteroids and oral H1 antihistamines, which are given as combinatorial medicines supplemented with immune therapy. These medications have been found to be very effective in either the short term or long term; however, they have been found to possess some serious side effects. Search Methodology. The information in this article on classical and traditional Chinese medications used to treat AR was derived from original papers and reviews published in Chinese and English language journals. Two Chinese databases (Wanfang and CNKI) and three English databases (Cochrane Library, PubMed, and Embase) were utilized for data gathering. Results Traditional Chinese remedies have been identified to influence the production of cytokines such as IL-5 and IL-6, which are key mediators of eosinophilic inflammation, TNF-α, which stimulates TH2 cells at the site of inflammation, and NF-кB, which is required for cytokine and IgE antibody production. TCM has also been shown to be successful in lowering histamine levels, preserving histological changes by decreasing the thickness of the lamina propria, and downregulating the expression of Orai1, STIM1, and TRYC1, showing low expression of Ca+2 channel proteins. Conclusion In this review, we discussed a series of classical, traditional Chinese medications, including Centipeda minima, Scutellaria baicalensis, licorice root (Glycyrrhiza uralensis), and others, as potential antiallergic agents and investigate their in vivo effect upon the production of cytokines and release of histamines for allergic rhinitis treatment.
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14
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Farnsworth KD. How an information perspective helps overcome the challenge of biology to physics. Biosystems 2022; 217:104683. [PMID: 35460797 DOI: 10.1016/j.biosystems.2022.104683] [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: 11/13/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022]
Abstract
Living systems have long been a puzzle to physics, leading some to claim that new laws of physics are needed to explain them. Separating physical reality into the general (laws) and the particular (location of particles in space and time), it is possible to see that the combination of these amounts to efficient causation, whereby forces are constrained by patterns that constitute embodied information which acts as formal cause. Embodied information can only be produced by correlation with existing patterns, but sets of patterns can be arranged to form reflexive relations in which constraints on force are themselves formed by the pattern that results from action of those same constrained forces. This inevitably produces a higher level of pattern which reflexively reinforces itself. From this, multi-level hierarchies and downward causation by information are seen to be patterns of patterns that constrain forces. Such patterns, when causally cyclical, are closed to efficient causation. But to be autonomous, a system must also have its formative information accumulated by repeated cycles of selection until sufficient is obtained to represent the information content of the whole (which is the essential purpose of information oligomers such as DNA). Living systems are the result of that process and therefore cannot exist unless they are both closed to efficient causation and capable of embodying an independent supply of information sufficient to constitute their causal structure. Understanding this is not beyond the scope of standard physics, but it does recognise the far greater importance of information accumulation in living than in non-living systems and, as a corollary, emphasises the dependence of biological systems on the whole history of life, leading up to the present state of any and all organisms.
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Affiliation(s)
- Keith D Farnsworth
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT95DL, UK.
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16
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DiFrisco J, Jaeger J. Genetic Causation in Complex Regulatory Systems: An Integrative Dynamic Perspective. Bioessays 2021; 42:e1900226. [PMID: 32449193 DOI: 10.1002/bies.201900226] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/01/2020] [Indexed: 12/27/2022]
Abstract
The logic of genetic discovery has changed little over time, but the focus of biology is shifting from simple genotype-phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the traditional reductionist view of individual genes as privileged difference-making causes of phenotypes is re-examined. The scope and nature of genetic effects in complex regulatory systems, in which dynamics are driven by regulatory feedback and hierarchical interactions across levels of organization are considered. This review argues that it is appropriate to treat genes as specific actual difference-makers for the molecular regulation of gene expression. However, they are often neither stable, proportional, nor specific as causes of the overall dynamic behavior of regulatory networks. Dynamical models, properly formulated and validated, provide the tools to probe cause-and-effect relationships in complex biological systems, allowing to go beyond the limitations of genetic reductionism to gain an integrative understanding of the causal processes underlying complex phenotypes.
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Affiliation(s)
| | - Johannes Jaeger
- Complexity Science Hub (CSH) Vienna, Josefstädter Straße 39, Vienna, 1080, Austria.,Department of Molecular Evolution & Development, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
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Braun HA. Stochasticity Versus Determinacy in Neurobiology: From Ion Channels to the Question of the "Free Will". Front Syst Neurosci 2021; 15:629436. [PMID: 34122020 PMCID: PMC8190656 DOI: 10.3389/fnsys.2021.629436] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
If one accepts that decisions are made by the brain and that neuronal mechanisms obey deterministic physical laws, it is hard to deny what some brain researchers postulate, such as "We do not do what we want, but we want what we do" and "We should stop talking about freedom. Our actions are determined by physical laws." This point of view has been substantially supported by spectacular neurophysiological experiments demonstrating action-related brain activity (readiness potentials, blood oxygen level-dependent signals) occurring up to several seconds before an individual becomes aware of his/her decision to perform the action. This report aims to counter the deterministic argument for the absence of free will by using experimental data, supplemented by computer simulations, to demonstrate that biological systems, specifically brain functions, are built on principle randomness, which is introduced already at the lowest level of neuronal information processing, the opening and closing of ion channels. Switching between open and closed states follows physiological laws but also makes use of randomness, which is apparently introduced by Brownian motion - principally unavoidable under all life-compatible conditions. Ion-channel stochasticity, manifested as noise, function is not smoothed out toward higher functional levels but can even be amplified by appropriate adjustment of the system's non-linearities. Examples shall be given to illustrate how stochasticity can propagate from ion channels to single neuron action potentials to neuronal network dynamics to the interactions between different brain nuclei up to the control of autonomic functions. It is proposed that this intrinsic stochasticity helps to keep the brain in a flexible state to explore diverse alternatives as a prerequisite of free decision-making.
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Affiliation(s)
- Hans Albert Braun
- Neurodynamics Group, Institute of Physiology and Pathophysiology, Philipps University of Marburg, Marburg, Germany
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Miller WB, Enguita FJ, Leitão AL. Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution. Cells 2021; 10:1125. [PMID: 34066959 PMCID: PMC8148535 DOI: 10.3390/cells10051125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/27/2021] [Accepted: 05/05/2021] [Indexed: 12/16/2022] Open
Abstract
Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alternative approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a 'harnessing of stochasticity'. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.
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Affiliation(s)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal;
| | - Ana Lúcia Leitão
- MEtRICs, Department of Sciences and Technology of Biomass, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal;
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Marshall P. Biology transcends the limits of computation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 165:88-101. [PMID: 33961842 DOI: 10.1016/j.pbiomolbio.2021.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 11/29/2022]
Abstract
Cognition-sensing and responding to the environment-is the unifying principle behind the genetic code, origin of life, evolution, consciousness, artificial intelligence, and cancer. However, the conventional model of biology seems to mistake cause and effect. According to the reductionist view, the causal chain in biology is chemicals → code → cognition. Despite this prevailing view, there are no examples in the literature to show that the laws of physics and chemistry can produce codes, or that codes produce cognition. Chemicals are just the physical layer of any information system. In contrast, although examples of cognition generating codes and codes controlling chemicals are ubiquitous in biology and technology, cognition remains a mystery. Thus, the central question in biology is: What is the nature and origin of cognition? In order to elucidate this pivotal question, we must cultivate a deeper understanding of information flows. Through this lens, we see that biological cognition is volitional (i.e., deliberate, intentional, or knowing), and while technology is constrained by deductive logic, living things make choices and generate novel information using inductive logic. Information has been called "the hard problem of life' and cannot be fully explained by known physical principles (Walker et al., 2017). The present paper uses information theory (the mathematical foundation of our digital age) and Turing machines (computers) to highlight inaccuracies in prevailing reductionist models of biology, and proposes that the correct causation sequence is cognition → code → chemicals.
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Affiliation(s)
- Perry Marshall
- Evolution 2.0, 805 Lake Street #295 Oak Park, IL, 60301, USA.
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20
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Noble D. The role of stochasticity in biological communication processes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 162:122-128. [DOI: 10.1016/j.pbiomolbio.2020.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 09/01/2020] [Accepted: 09/28/2020] [Indexed: 12/21/2022]
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21
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Ellis GFR. The Causal Closure of Physics in Real World Contexts. FOUNDATIONS OF PHYSICS 2020; 50:1057-1097. [PMID: 32836326 PMCID: PMC7431902 DOI: 10.1007/s10701-020-00366-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/22/2020] [Indexed: 05/11/2023]
Abstract
The causal closure of physics is usually discussed in a context free way. Here I discuss it in the context of engineering systems and biology, where strong emergence takes place due to a combination of upwards emergence and downwards causation (Ellis, Emergence in Solid State Physics and Biology, 2020, arXiv:2004.13591). Firstly, I show that causal closure is strictly limited in terms of spatial interactions because these are cases that are of necessity strongly interacting with the environment. Effective Spatial Closure holds ceteris parabus, and can be violated by Black Swan Events. Secondly, I show that causal closure in the hierarchy of emergence is a strictly interlevel affair, and in the cases of engineering and biology encompasses all levels from the social level to the particle physics level. However Effective Causal Closure can usefully be defined for a restricted set of levels, and one can experimentally determine Effective Theories that hold at each level. This does not however imply those effective theories are causally complete by themselves. In particular, the particle physics level is not causally complete by itself in the contexts of solid state physics (because of interlevel wave-particle duality), digital computers (where algorithms determine outcomes), or biology (because of time dependent constraints). Furthermore Inextricably Intertwined Levels occur in all these contexts.
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Affiliation(s)
- George F. R. Ellis
- Mathematics Department, University of Cape Town, Cape Town, South Africa
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22
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Erenpreisa J, Giuliani A. Resolution of Complex Issues in Genome Regulation and Cancer Requires Non-Linear and Network-Based Thermodynamics. Int J Mol Sci 2019; 21:E240. [PMID: 31905791 PMCID: PMC6981914 DOI: 10.3390/ijms21010240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/22/2019] [Accepted: 12/27/2019] [Indexed: 02/06/2023] Open
Abstract
The apparent lack of success in curing cancer that was evidenced in the last four decades of molecular medicine indicates the need for a global re-thinking both its nature and the biological approaches that we are taking in its solution. The reductionist, one gene/one protein method that has served us well until now, and that still dominates in biomedicine, requires complementation with a more systemic/holistic approach, to address the huge problem of cross-talk between more than 20,000 protein-coding genes, about 100,000 protein types, and the multiple layers of biological organization. In this perspective, the relationship between the chromatin network organization and gene expression regulation plays a fundamental role. The elucidation of such a relationship requires a non-linear thermodynamics approach to these biological systems. This change of perspective is a necessary step for developing successful 'tumour-reversion' therapeutic strategies.
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Affiliation(s)
- Jekaterina Erenpreisa
- Cancer Research Division, Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Alessandro Giuliani
- Environmental and Health Department, Istituto Superiore di Sanità, 00161 Rome, Italy;
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23
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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: 18] [Impact Index Per Article: 3.6] [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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24
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Noble R, Tasaki K, Noble PJ, Noble D. Biological Relativity Requires Circular Causality but Not Symmetry of Causation: So, Where, What and When Are the Boundaries? Front Physiol 2019; 10:827. [PMID: 31379589 PMCID: PMC6656930 DOI: 10.3389/fphys.2019.00827] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/13/2019] [Indexed: 01/23/2023] Open
Abstract
Since the Principle of Biological Relativity was formulated and developed there have been many implementations in a wide range of biological fields. The purpose of this article is to assess the status of the applications of the principle and to clarify some misunderstandings. The principle requires circular causality between levels of organization. But the forms of causality are also necessarily different. They contribute in asymmetric ways. Upward causation can be represented by the differential or similar equations describing the mechanics of lower level processes. Downward causation is then best represented as determining initial and boundary conditions. The questions tackled in this article are: (1) where and when do these boundaries exist? and (2) how do they convey the influences between levels? We show that not all boundary conditions arise from higher-level organization. It is important to distinguish those that do from those that don't. Both forms play functional roles in organisms, particularly in their responses to novel challenges. The forms of causation also change according to the levels concerned. These principles are illustrated with specific examples.
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Affiliation(s)
- Raymond Noble
- Institute for Women’s Health, University College London, London, United Kingdom
| | - Kazuyo Tasaki
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Penelope J. Noble
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Denis Noble
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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Cheong KH, Koh JM, Jones MC. Black Swans of CRISPR: Stochasticity and Complexity of Genetic Regulation. Bioessays 2019; 41:e1900032. [PMID: 31090950 DOI: 10.1002/bies.201900032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 02/21/2019] [Indexed: 12/18/2022]
Abstract
Recent waves of controversies surrounding genetic engineering have spilled into popular science in Twitter battles between reputable scientists and their followers. Here, a cautionary perspective on the possible blind spots and risks of CRISPR and related biotechnologies is presented, focusing in particular on the stochastic nature of cellular control processes.
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Affiliation(s)
- Kang Hao Cheong
- Science and Math Cluster, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Jin Ming Koh
- Science and Math Cluster, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
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26
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Ellis GFR, Kopel J. The Dynamical Emergence of Biology From Physics: Branching Causation via Biomolecules. Front Physiol 2019; 9:1966. [PMID: 30740063 PMCID: PMC6355675 DOI: 10.3389/fphys.2018.01966] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/31/2018] [Indexed: 01/30/2023] Open
Abstract
Biology differs fundamentally from the physics that underlies it. This paper proposes that the essential difference is that while physics at its fundamental level is Hamiltonian, in biology, once life has come into existence, causation of a contextual branching nature occurs at every level of the hierarchy of emergence at each time. The key feature allowing this to happen is the way biomolecules such as voltage-gated ion channels can act to enable branching logic to arise from the underlying physics, despite that physics per se being of a deterministic nature. Much randomness occurs at the molecular level, which enables higher level functions to select lower level outcomes according to higher level needs. Intelligent causation occurs when organisms engage in deduction, enabling prediction and planning. This is possible because ion channels enable action potentials to propagate in axons. The further key feature is that such branching biological behavior acts down to cause the underlying physical interactions to also exhibit a contextual branching behavior.
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Affiliation(s)
- George F. R. Ellis
- Mathematics Department, University of Cape Town, Cape Town, South Africa
| | - Jonathan Kopel
- Texas Tech University Health Sciences Center (TTUHSC), Lubbock, TX, United States
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