Non-living Systems Research Articles

Simultaneous Hypotheses in Cognitive Agents: Commentary on Paxton, Necaise etal., and the Dynamical Hypothesis in Cognitive Science.

The 1998 article by van Gelder proposed a Dynamical Hypothesis (DH) in cognitive science consisting of Nature (cognitive agents are dynamical systems) and Knowledge (cognitive agents should be understood dynamically) hypotheses in contrast to the Computational Hypothesis (CH) that cognitive agents are computers. My commentary focuses on the contributions of Paxton and Necaise etal. in interpersonal motor coordination and radicalization across social media. I do not think that either contribution supports the Nature hypothesis but does conform with the Knowledge hypothesis. I conclude by describing cognitive agents as living systems (or nonliving systems that mimic aspects of living systems) that can be alternately viewed to support the DH or CH or both at the same time.

D’Arcy Thompson and Synthetic Biology—Then and Now

AbstractThough often presented as a recent scientific endeavor, synthetic biology began in the 19th century and was a particularly active field in the years preceding the publication of D’Arcy Thompson’s On Growth and Form. Much synthetic biology of the era was devoted to the construction of nonliving chemical systems that would undergo morphogenesis or dynamic behaviors which had been observed in living organisms. The point was to show that “life-like” structure and behavior could be generated by physicochemical laws and required no vitalist element. D’Arcy Thompson’s careful analysis of physicochemical morphogenetic mechanisms as possible explanations of organic form links closely to this way of thinking. In the modern era, when we can genetically engineer cells to undergo specific behaviors, and program cells to undergo simple morphogenetic behaviors of the kind that Thompson and others felt might underly natural morphogenesis, it is possible to test whether they will in fact produce a predictable multicellular shape. This addresses essentially the same questions about the morphogenetic role of physicochemical forces, such as surface tension, but does so “the other way round”: physicochemical mechanisms are not being used as models for morphogenesis by natural cells but rather as a means to engineer cells to make designed forms.

Engineering Cyborg Pathogens through Intracellular Hydrogelation.

Synthetic biology primarily focuses on two kinds of cell chassis: living cells and nonliving systems. Living cells are autoreplicating systems that have active metabolism. Nonliving systems, including artificial cells and nanoparticles, are nonreplicating systems typically lacking active metabolism. In recent work, Cyborg bacteria that are nonreplicating-but-metabolically active have been engineered through intracellular hydrogelation. Intracellular hydrogelation is conducted by infusing gel monomers and photoactivators into cells, followed by the activation of polymerization of the gel monomers inside the cells. However, the previous work investigated only Escherichia coli cells. Extending the Cyborg-Cell method to pathogenic bacteria could enable the exploitation of their pathogenic properties in biomedical applications. Here, we focus on different strains of Pseudomonas aeruginosa, Staphylococcus aureus, and Klebsiella pneumoniae. To synthesize the Cyborg pathogens, we first reveal the impact of different hydrogel concentrations on the metabolism, replication, and intracellular gelation of Cyborg pathogens. Next, we demonstrate that the Cyborg pathogens are taken up by macrophages in a similar magnitude as wild-type pathogens through confocal microscopy and real-time PCR. Finally, we show that the macrophage that takes up the Cyborg pathogen exhibits a similar phenotypic response to the wild-type pathogen. Our work generalizes the intracellular hydrogelation approach from lab strains of E. coli to bacterial pathogens. The new Cyborg pathogens could be applied in biomedical applications ranging from drug delivery to immunotherapy.

A new perspective on tumor progression: Evolution via selection for function.

Tumorigenesis is commonly attributed to Darwinian processes involving natural selection among cells and groups of cells. However, progressing tumors are those that also achieve an appropriate group phenotypic composition (GPC). Yet, the selective processes acting on tumor GPCs are distinct from that associated with classical Darwinian evolution (i.e. natural selection based on differential reproductive success) as tumors are not genuine evolutionary individuals and do not exhibit heritable variation in fitness. This complex evolutionary scenario is analogous to the recently proposed concept of 'selection for function' invoked for the evolution of both living and non-living systems. Therefore, we argue that it is inaccurate to assert that Darwinian processes alone account for all the aspects characterizing tumorigenesis and cancer progression; rather, by producing the genetic and phenotypic diversity required for creating novel GPCs, these processes fuel the evolutionary success of tumors that is dependent on selection for function at the tumor level.

Design principles as minimal models

In this essay I suggest that we view design principles in systems biology as minimal models, for a design principle usually exhibits universal behaviors that are common to a whole range of heterogeneous (living and nonliving) systems with different underlying mechanisms. A well-known design principle in systems biology, integral feedback control, is discussed, showing that it satisfies all the conditions for a model to be a minimal model. This approach has significant philosophical implications: it not only accounts for how design principles explain, but also helps clarify one dispute over design principles, e.g., whether design principles provide mechanistic explanations or a distinct kind of explanations called design explanations.

Using Methods to Assess the Structure of Water and Water-Containing Systems to Improve the Properties of Living and Non-Living Systems

This paper explores how water and water-based systems change their structure under different conditions, such as pH, temperature, and electric fields. These changes affect the properties and performance of living and non-living systems that use water or water-based systems in various technologies. We can use pH, temperature, and electric fields to measure and control the structural changes in water and water-based systems and improve the outcomes of different technologies in biology and medicine. More research is needed to understand how various factors influence the structure of water and water-based systems and how this affects living and non-living systems.

The Pathologically Evolving Aggregation-State of Cells in Cancerous Tissues as Interpreted by Fractal and Multi-Fractal Dispersion Theory in Saturated Porous Formations.

A recent author's fractal fluid-dynamic dispersion theory in porous media has focused on the derivation of the associated nonergodic (or effective) macrodispersion coefficients by a 3-D stochastic Lagrangian approach. As shown by the present study, the Fickian (i.e., the asymptotic constant) component of a properly normalized version of these coefficients exhibits a clearly detectable minimum in correspondence with the same fractal dimension (d ≅ 1.7) that seems to characterize the diffusion-limited aggregation state of cells in advanced stages of cancerous lesion progression. That circumstance suggests that such a critical fractal dimension, which is also reminiscent of the colloidal state of solutions (and may therefore identify the microscale architecture of both living and non-living two-phase systems in state transition conditions) may actually represent a sort of universal nature imprint. Additionally, it suggests that the closed-form analytical solution that was provided for the effective macrodispersion coefficients in fractal porous media may be a reliable candidate as a physically-based descriptor of blood perfusion dynamics in healthy as well as cancerous tissues. In order to evaluate the biological meaningfulness of this specific fluid-dynamic parameter, a preliminary validation is performed by comparison with the results of imaging-based clinical surveys. Moreover, a multifractal extension of the theory is proposed and discussed in view of a perspective interpretative diagnostic utilization.

Astroecology: bridging the gap between ecology and astrobiology

Abstract Although astrobiology studies how life functions and evolves, ecology is still largely overlooked in astrobiology research. Here we present an argument for astroecology, a merger of ecology and astrobiology, a self-aware scientific endeavour. Ecology is rarely mentioned in influential documents like the NASA Astrobiology Strategy (2015), and terms such as ‘niche’ can end up being used in a less precise fashion. As ecology deals with sequential levels of organization, we suggest astrobiologically-relevant problems for each of these levels. Organismal ecology provides ecological niche modelling, which can aid in evaluating the probability that Earth-like life would survive in extraterrestrial environments. Population ecology provides a gamut of models on the consequences of dispersal, and if lithopanspermia can be validated as a form of space dispersal for life, then metabiospheres and similar astrobiological models could be developed to understand such complex structure and dynamics. From community ecology, the discussion of habitability should include the concept of true vacant habitats (a misnomer, perhaps better called ‘will-dwells’) and contributions from the blossoming field of microbial ecology. Understanding ecosystems by focusing on abiotic properties is also key to extrapolating from analogue environments on Earth to extraterrestrial ones. Energy sources and their distribution are relevant for ecological gradients, such as the biodiversity latitudinal gradient – would tropics be species-rich in other inhabited planets? Finally, biosphere ecology deals with integration and feedback between living and non-living systems, which can generate stabilized near-optimal planetary conditions (Gaia); but would this work for other inhabited planets? Are there ‘strong’ (like Earth) and ‘weak’ (perhaps like Mars) biospheres? We hope to show ecology can contribute relevant ideas to the interdisciplinary field of astrobiology, helping conceptualize further levels of integration. We encourage new partnerships and for astrobiologists to take ecology into account when studying the origin, evolution and distribution of life in the universe.

Using Ecological Stoichimetric Characteristies to Inform Grassland Management in the Karst Desertification Area

C, N and P play an important indicator role in explaining the material cycles and elemental balances of living and non-living systems. In order to control karst rocky desertification, China has established a large number of artificial grasslands for the development of herbivorous animal husbandry, which has played an important role in ecological restoration and economic development. However, the effects of different use patterns on the ecological stoichiometry of the carbon (C), nitrogen (N) and phosphorus (P) of the grassland plant–soil–microorganism are not clear. In this study, the effects of grazing grassland (GG), mowing grassland (MG) and enclosed grassland (EG) on C, N and P and their ecological stoichiometry in the artificial grassland plant–soil–microbe were investigated in the karst desertification control area in Southern China. The results showed that (1) the C content was EG > GG > MG. The N content was GG > EG > MG, while the P content was MG > GG > EG. C:N, C:P and N:P were shown as EG > GG > MG. The plant N:P was more than 20, indicating a P deficiency and limitation, especially in EG. (2) The content of C and P in soil was EG > GG > MG. The N content was GG > EG > MG. The soil C:N showed EG > MG > GG, while C:P and N:P were shown as MG > GG > EG. The soil N:P ratios were all less than 14, indicating that all of them had an obvious N limitation. (3) Soil microbial biomass carbon (MBC) was GG > MG > EG. Soil microbial biomass nitrogen (MBN) was GG > EG > MG. Soil microbial biomass phosphorus (MBP) showed EG > GG > MG. MBC:MBN was MG > EG > GG. MBC:MBP was MG > EG > GG. MBN:MBP was GG > MG > EG. The MBN:MBP in GG and MG was greater than 9.6, which is P-limited, while the MBN:MBP in EG is less than 8.9, which is N-limited. (4) Plant C and N were significantly correlated with soil C and N, but plant P was significantly negatively correlated with soil P, while MBP was significantly positively correlated with soil TP. Soil microorganisms had the tendency to assimilate available P in GG and MG treatments, but the potential of releasing P from mineralized soil organic matter was higher in EG treatment. The results showed that the chemical properties and stoichiometric characteristics of the plant–soil–microorganism were significantly changed by different grassland-use methods, which provided scientific guidance for the management of C, N and P elements and the further optimization of soil microbial environment for artificial grassland in the karst rocky desertification area.

Thermodynamics, organisms and behaviour.

The physical origin of behaviour in biological organisms is distinct from those of non-living systems in one significant way: organisms exhibit intentionality or goal-directed behaviour. How may we understand and explain this important aspect in physical terms, grounded in laws of physics and chemistry? In this article, we discuss recent experimental and theoretical progress in this area and future prospects of this line of thought. The physical basis for our investigation is thermodynamics, though other branches of physics and chemistry have an important role. This article is part of the theme issue 'Thermodynamics 2.0: Bridging the natural and social sciences (Part 1)'.

Reproduction of bacterial chemotaxis by a non-living self-propelled object

Taxic behavior as a response to an external stimulus is a fundamental function of living organisms. Some bacteria successfully implement chemotaxis without directly controlling the direction of movement. They periodically alternate between run and tumble, i.e., straight movement and change in direction, respectively. They tune their running period depending on the concentration gradient of attractants around them. Consequently, they respond to a gentle concentration gradient stochastically, which is called “bacterial chemotaxis.” In this study, such a stochastic response was reproduced by a non-living self-propelled object. We used a phenanthroline disk floating on an aqueous solution of Fe^{2+}. The disk spontaneously alternated between rapid motion and rest, similar to the run-and-tumble motion of bacteria. The movement direction of the disk was isotropic independent of the concentration gradient. However, the existing probability of the self-propelled object was higher at the low-concentration region, where the run length was longer. To explain the mechanism underlying this phenomenon, we proposed a simple mathematical model that considers random walkers whose run length depends on the local concentration and direction of movement against the gradient. Our model adopts deterministic functions to reproduce the both effects, which is instead of stochastic tuning the period of operation used in the previous reports. This allows us to analyze the proposed model mathematically, which indicated that our model reproduces both positive and negative chemotaxis depending on the competition between the local concentration effect and it’s gradient effect. Owing to the newly introduced directional bias, the experimental observations were reproduced numerically and analytically. The results indicate that the directional bias response to the concentration gradient is an essential parameter for determining bacterial chemotaxis. This rule might be universal for the stochastic response of self-propelled particles in living and non-living systems.

Abstract 2348: Mapping the interactome of matrisome targets using extracellular proximity labeling (ePL)

Abstract Classical methods to investigate protein-protein interactions (PPIs) are generally performed in non-living systems, yet in recent years new technologies utilizing proximity labeling (PL) have given researchers the tools to explore PPIs in living systems. PL has distinct advantages over traditional protein interactome studies, such as the ability to identify weak and transient interactions in vitro and in vivo. Most PL studies are performed on targets within or on the cell membrane. We describe a method to investigate PPIs within the extracellular compartment, using both BioID2 and TurboID, that we term extracellular PL (ePL). To demonstrate the utility of this modified technique, we investigate the interactome of the widely expressed matrisome protein Tissue inhibitors of metalloproteinases 2 (TIMP2). Tissue inhibitors of metalloproteinases (TIMPs) are a family of multi-functional proteins that were initially defined by their ability to inhibit the enzymatic activity of matrix metalloproteinases (MMPs), the major mediators of ECM breakdown and turnover. TIMP2 is a unique family member, with a broad expression profile that is expressed in both normal and diseased tissues, even in those with minimal metalloproteinase activity. Understanding the functional transformation of matrisome regulators, like TIMP2, during the evolution of tissue microenvironments associated with disease progression is essential to the development of ECM targeted therapeutics. This knowledge may also garner understanding of therapeutic resistance and the failure of conventional and next-generation cancer therapies. Using carboxyl- and amino-terminal fusion peptides of TIMP2 with BioID2 and TurboID, we describe the TIMP2 interactome in unique tissue compartments. We also illustrate how the TIMP2 interactome changes in the presence of different stimuli, in different cell lines, and with different reaction kinetics (BioID2 vs. TurboID); demonstrating the power of this technique and comparing our findings with classical PPI methods. We propose that the screening of matrisome targets in disease models using ePL will reveal new therapeutic targets for further comprehensive studies. Citation Format: David Peeney, Sadeechya Gurung, Josh Rich, Sasha Coates-Park, Yueqin Liu, William G. Stetler-Stevenson. Mapping the interactome of matrisome targets using extracellular proximity labeling (ePL) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2348.

Is the maximum entropy production just a heuristic principle? Metaphysics on natural determination

The Maximum Entropy Production Principle (MEPP) stands out as an overarching principle that rules life phenomena in Nature. However, its explanatory power beyond heuristics remains controversial. On the one hand, the MEPP has been successfully applied principally to non-living systems far from thermodynamic equilibrium. On the other hand, the underlying assumptions to lay the MEPP’s theoretical foundations and range of applicability increase the possibilities of conflicting interpretations. More interestingly, from a metaphysical stance, the MEPP’s philosophical status is hotly debated: does the MEPP passively translate physical information into macroscopic predictions or actively select the physical solution in multistable systems, granting the connection between scientific models and reality? This paper deals directly with this dilemma by discussing natural determination from three angles: (1) Heuristics help natural philosophers to build an ontology. (2) The MEPP’s ontological status may stem from its selection of new forms of causation beyond physicalism. (3) The MEPP’s ontology ultimately depends on the much-discussed question of the ontology of probabilities in an information-theoretic approach and the ontology of macrostates according to the Boltzmannian definition of entropy.

Light-Activated Assembly of Connexon Nanopores in Synthetic Cells.

During developmental processes and wound healing, activation of living cells occurs with spatiotemporal precision and leads to rapid release of soluble molecular signals, allowing communication and coordination between neighbors. Nonliving systems capable of similar responsive release hold great promise for information transfer in materials and site-specific drug delivery. One nonliving system that offers a tunable platform for programming release is synthetic cells. Encased in a lipid bilayer structure, synthetic cells can be outfitted with molecular conduits that span the bilayer and lead to material exchange. While previous work expressing membrane pore proteins in synthetic cells demonstrated content exchange, user-defined control over release has remained elusive. In mammalian cells, connexon nanopore structures drive content release and have garnered significant interest since they can direct material exchange through intercellular contacts. Here, we focus on connexon nanopores and present activated release of material from synthetic cells in a light-sensitive fashion. To do this, we re-engineer connexon nanopores to assemble after post-translational processing by a protease. By encapsulating proteases in light-sensitive liposomes, we show that assembly of nanopores can be triggered by illumination, resulting in rapid release of molecules encapsulated within synthetic cells. Controlling connexon nanopore activity provides an opportunity for initiating communication with extracellular signals and for transferring molecular agents to the cytoplasm of living cells in a rapid, light-guided manner.

Investigation of the Influence of Taheri Consciousness Fields on the pH of Pure Water in the Vicinity of Air

T-Consciousness Fields (TCFs) have been introduced by Mohammad Ali Taheri and the effects of these fields on living and non-living systems have been studied in various experiments. Taheri’s theory of Mind-of-Matter (Mental Body of Matter) has been discussed in the studies of the behavior of matter under the influence of T-Consciousness Fields. In the present study, changes in pH and temperature of pure water under the influence of three different TCFs have been investigated. Given that the environmental conditions and materials used in this study are the same for the control and the test samples, it is generally expected that all samples behave similarly in terms of pH and temperature of the solution. However, meaningful differences were observed between the behavior of the test samples and that of the control which necessitated performing thermodynamic calculations for better comparison. The results of this experiment, in addition to confirming the distinct effects of the TCFs, showed that: (1) the application of the TCFs has caused states with lower entropy to occur in the systems under the influence of TCFs; (2) The negligibly small difference between the enthalpy of the control and that of the test samples is indicative that there has been no energy transfer in the form of heat. And the energy available for sharing to the system under the influence of TCFs is considerably less than the amount required for conversion to mass. Hence, it seems that the application of TCFs and their interaction with the mind-of-matter have caused matter to transition from one mental state to another, and by assigning a new property appropriate to the new mental state, it has enabled matter to exhibit a new behavior.

Process Metaphysics and Mutative Life: Sketches of Lived Time

Process Metaphysics and Mutative Life: Sketches of Lived Time

The electron as a self-organising entity in physics and biology

A characteristic of living systems is their ability to self-organize. Using appropriate quantum mechanical and mathematical tools, we show that this ability may also be a characteristic of non-living systems, such as the electron, thus establishing an unsuspected relationship between biology and physics, whereby “biology precedes physics”. Planck's constant h is not a pure number but an elementary quantum of action, a “real atom” according to Henri Poincaré. Consequently, Louis de Broglie's equation λ = h/p must be rewritten in the form h = λp or lp. This approach gives a new meaning to quantum physics: the precise equivalence lp = h = Ed combined with the conceptual tools of Laurent Nottale's scale relativity allows the reunification of physics and support the development of promising engineering applications, notably in systems biology and medicine.

Inherency and agency in the origin and evolution of biological functions

AbstractAlthough discussed by 20th century philosophers in terms drawn from the sciences of non-living systems, in recent decades biological function has been considered in relationship to organismal capability and purpose. Bringing two phenomena generally neglected in evolutionary theory (i.e. inherency and agency) to bear on questions of function leads to a rejection of the adaptationist ‘selected effects’ notion of biological function. I review work showing that organisms such as the placozoans can thrive with almost no functional embellishments beyond those of their constituent cells and physical properties of their simple tissues. I also discuss work showing that individual tissue cells and their artificial aggregates exhibit agential behaviours that are unprecedented in the histories of their respective lineages. I review findings on the unique metazoan mechanism of developmental gene expression that has recruited, during evolution, inherent ancestral cellular functionalities into specialized cell types and organs of the different animal groups. I conclude that most essential functions in animal species are inherent to the cells from which they evolved, not selected effects, and that many of the others are optional ‘add-ons’, a status inimical to fitness-based models of evolution positing that traits emerge from stringent cycles of selection to meet external challenges.

Abstract 3836: Mapping the interactome of the endogenous metalloproteinase inhibitor TIMP2 using extracellular proximity labeling (ePL)

Abstract Tissue inhibitors of metalloproteinases (TIMPs) are a family of endogenous proteins that were initially defined by their ability to inhibit the enzymatic activity of matrix metalloproteinases (MMPs), the major mediators of ECM breakdown and turnover. TIMPs are important regulators of ECM structure, function and homeostasis. Since their original discovery, additional MMP-independent functions have been attributed to TIMP family members leading to their designation as multifunctional proteins with discrete functional domains. TIMP2 is a unique family member, with a broad expression profile that is expressed in both normal and diseased tissues, even in those with minimal metalloproteinase activity. Understanding the functional transformation of matrisome regulators, like TIMP-2, during the dynamic evolution of tissue microenvironments associated with disease progression is essential to the development of ECM targeted therapeutics. This knowledge may also garner understanding of therapeutic resistance and the failure of conventional and next-generation cancer therapies. Interactome studies are predominantly performed in non-living systems, and very rarely performed in complex culture systems such as 3D spheroids/co-cultures. To investigate the TIMP-2 interactome in complex biological systems we recently developed carboxyl- and amino-terminal fusion genes of TIMP-2 with the promiscuous biotinylating peptides BioID2 and TurboID. Packaged for retroviral delivery, this system gives us great flexibility in assessing the TIMP-2 interactome in simple versus complex 3D co-culture systems. We show, for the first time, that conditions can be optimized to support proximity labeling reactions in the extracellular milieu, representing an important technical resource for extracellular matrix biologists. Using this method, we identify novel interacting partners for TIMP-2 that provide insight into the tissue-specific actions of this protein in both healthy and diseased tissues. Citation Format: David Peeney, Sadeechya Gurung, Yueqin Liu, Carolyn Lazaroff, Christopher Richie, William G. Stetler-Stevenson. Mapping the interactome of the endogenous metalloproteinase inhibitor TIMP2 using extracellular proximity labeling (ePL) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3836.

How an information perspective helps overcome the challenge of biology to physics

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.