Adaptation as a manifestation of informational connections in living systems

The problem of adaptation of living systems in terms of the concept of informational communications is considered. The informational communication means the qualitative evaluation of information and determines correspondence of living systems to concrete conditions of life during interaction of these living systems to the source of the information. The system of the wholeorganism regulatory chemical communication is the main functional basis for the informational communication. Due to it, the transformation of the information signal in biological systems is performed, which results in their adequate response according to this information. The existence of living systems and their adaptation are determined by peculiarities of functioning of elements of their regulatory systems according to the character of the informational communication.     

Special features of water structure formation in biosystems according to dielkometric data

Experimental data on dielectric function and dielectric loss tangent in living and non-living water-containing systems have been discussed from the viewpoint of our earlier concept on energy transfer in living systems and the role of water in this process. Estimates have been made of a mean length of fractal quasi-crystals, representing the form of biomolecules hydration in the living system; the expected lengths of these quasicrystals are of order of 1000 H₂O molecules. It is concluded that the peaks at the curve of frequency dependence of dielectric loss tangent in living systems is due to water sub-system, but not biomolecular vibrations.     

Meaning-making in the immune system

Meaning-making is the process by which a system responds to an indeterminate signal. This article focuses on meaning-making in living systems. It proposes several guidelines for studying the process of meaning-making in living systems in general, and in the immune system in particular. Drawing on a general framework for studying meaning-making in living systems, I suggest three basic organizing concepts for studying meaning-making-variability of the signal, context markers, and transgradience. Those concepts present a radical alternative to the information-processing approach that governs biological research and may shed new light on biological processes.     

Oxygenic photosynthesis–a photon driven hydrogen generator–the energetic/entropic basis of life

Photosynthesis, as a fundamental element in the life process, is integrated in the evolution of living systems on the basis of hydrogen cycles on various hierarchic levels. Conversion of radiant energy enables the oxidation of water, whereby free oxygen accumulates in the atmosphere. Hydrogen is (reversibly) stored in organic materials formed under reductive CO2-fixation and by the incorporation of the other elements, which are necessary for living systems. All endergonic processes in living cells are finally driven by the energy released through the clean recombination of protons and electrons with oxygen to water. Duration of the stored energy and the complexity of the systems thus produced is correlated negatively with the conversion efficiency of the radiation energy. Entropy is a unifying principle in the evolution of living systems, inclusive human societies.     

Adaptive properties of living beings: proposal for a generic mechanism. (Self-programming machines III)

Living systems are capable to have appropriate responses to unpredictable environment. This kind of self-organization seems to operate as a self-programming machine, i.e. an organization able to modify itself. Until now the models of self-organization of living beings proposed are functions solutions of differential systems or transition functions of automata. These functions are fixed and these models are therefore unable to modify their organization. On the other hand, computer science propose a lot of models having the properties of adaptive systems of living beings, but all these models depend on the comparison between a goal and the results and ingenious choices of parameters by programmers, whereas there are no programmer's intention nor choice in the living systems. From two best known examples of adaptive systems of living beings, nervous system and immune system that have in common that the external signals modify the rewriting of their organization and therefore work as self-organizing machines, we devised machines with a finite set of inputs, based upon a recurrence, are able to rewrite their organization (Self-programming machines or m(sp)) whenever external conditions vary and have striking properties of adaptation. M(sp) have similar properties whatever the operation defining the recurrence maybe. These results bring us to make the following statement: adaptive properties of living systems can be explained by their ability to rewrite their organization whenever external conditions vary under the only assumption that the rewriting mechanism be a deterministic constant recurrence in a finite state set.     

Fundamental taboos of biology

This paper formulates some taboos relating to living systems and cognition of these systems: in nature, there exist no two identical living complex multicellular organisms; there is no way to create an exact copy of a multicellular organism; there is no way to obtain two identical clones of a unicellular organism if they contain a sufficiently large number of cells; based on comparing present-day organisms, it is impossible to restore the structure of the first living cell and the processes that have led to its emergence; it is impossible to create a living cell from its separate simple constituents; the mechanisms determining cell vitality are essentially incognizable.     

Predictive landscapes hidden beneath biological cellular automata

To celebrate Hans Frauenfelder’s achievements, we examine energy(-like) “landscapes” for complex living systems. Energy landscapes summarize all possible dynamics of some physical systems. Energy(-like) landscapes can explain some biomolecular processes, including gene expression and, as Frauenfelder showed, protein folding. But energy-like landscapes and existing frameworks like statistical mechanics seem impractical for describing many living systems. Difficulties stem from living systems being high dimensional, nonlinear, and governed by many, tightly coupled constituents that are noisy. The predominant modeling approach is devising differential equations that are tailored to each living system. This ad hoc approach faces the notorious “parameter problem”: models have numerous nonlinear, mathematical functions with unknown parameter values, even for describing just a few intracellular processes. One cannot measure many intracellular parameters or can only measure them as snapshots in time. Another modeling approach uses cellular automata to represent living systems as discrete dynamical systems with binary variables. Quantitative (Hamiltonian-based) rules can dictate cellular automata (e.g., Cellular Potts Model). But numerous biological features, in current practice, are qualitatively described rather than quantitatively (e.g., gene is (highly) expressed or not (highly) expressed). Cellular automata governed by verbal rules are useful representations for living systems and can mitigate the parameter problem. However, they can yield complex dynamics that are difficult to understand because the automata-governing rules are not quantitative and much of the existing mathematical tools and theorems apply to continuous but not discrete dynamical systems. Recent studies found ways to overcome this challenge. These studies either discovered or suggest an existence of predictive “landscapes” whose shapes are described by Lyapunov functions and yield “equations of motion” for a “pseudo-particle.” The pseudo-particle represents the entire cellular lattice and moves on the landscape, thereby giving a low-dimensional representation of the cellular automata dynamics. We outline this promising modeling strategy.

     

Teaching the origin of the first living systems

The most fundamental of questions in biology, namely that of the origin of living systems, is being lost to teaching and a new technique to rekindle interest in it must be found. This paper presents a novel idea of teaching a scientific concept using a poem, which describes the major perspectives on the origins of living systems, as the medium of instruction. All of the major schools of thought — chemical evolution, DNA vs. RNA, protocell formation, coacervates, panspermia and special creation — are discussed. The aim of the paper is not to be a definitive review on the origin of living systems, but rather to be a focal point on which to hinge further discussion.     

Generation of valuable information and the problem of goal self-setting in living systems

The problem of origination of capacity for goal self-setting is discussed. It was shown that the definition "goal" in living systems differs from the definition "target function" in physical problems concerned with nonliving systems. It was also shown that the main goal of the elements of a system is the storage of information. In biology, this goal is the extension of the principle of struggle for existence. Conditions were determined that the dynamic system describing the goal self-setting process must satisfy. It was shown that living systems meet these conditions. In inorganic nature, such systems may also arise but only as a result of long-term evolution, after which they become living.     

High-throughput screening of cell-free riboswitches by fluorescence-activated droplet sorting

Cell-free systems that display complex functions without using living cells are emerging as new platforms to test our understanding of biological systems as well as for practical applications such as biosensors and biomanufacturing. Those that use cell-free protein synthesis (CFPS) systems to enable genetically programmed protein synthesis have relied on genetic regulatory components found or engineered in living cells. However, biological constraints such as cell permeability, metabolic stability, and toxicity of signaling molecules prevent development of cell-free devices using living cells even if cell-free systems are not subject to such constraints. Efforts to engineer regulatory components directly in CFPS systems thus far have been based on low-throughput experimental approaches, limiting the availability of basic components to build cell-free systems with diverse functions. Here, we report a high-throughput screening method to engineer cell-free riboswitches that respond to small molecules. Droplet-sorting of riboswitch variants in a CFPS system rapidly identified cell-free riboswitches that respond to compounds that are not amenable to bacterial screening methods. Finally, we used a histamine riboswitch to demonstrate chemical communication between cell-sized droplets.     

Ecosphere,biosphere, or Gaia? What to call the global ecosystem

The terms biosphere, ecosphere, and Gaia are used as names for the global ecosystem. However, each has more than one meaning. Biosphere can mean the totality of living things residing on the Earth, the space occupied by living things, or life and life-support systems (atmosphere, hydrosphere, lithosphere, and pedosphere). Ecosphere is used as a synonym of biosphere and as a term for zones in the universe where life as we know it should be sustainable. Gaia is similar to biosphere (in the sense of life and life-support systems) and ecosphere (in the sense of biosphere as life and life-support systems), but, in its most extreme form, refers to the entire planet as a living entity. A case is made for avoiding the term Gaia (at least as a name for the planetary ecosystem), restricting biosphere to the totality of living things, and adopting the ecosphere as the most apt name for the global ecosystem.     

An abstract cell model that describes the self-organization of cell function in living systems

The principal aim of systems biology is to search for general principles that govern living systems. We develop an abstract dynamic model of a cell, rooted in Mesarovi? and Takahara's general systems theory. In this conceptual framework the function of the cell is delineated by the dynamic processes it can realize. We abstract basic cellular processes, i.e., metabolism, signalling, gene expression, into a mapping and consider cell functions, i.e., cell differentiation, proliferation, etc. as processes that determine the basic cellular processes that realize a particular cell function. We then postulate the existence of a 'coordination principle' that determines cell function. These ideas are condensed into a theorem: If basic cellular processes for the control and regulation of cell functions are present, then the coordination of cell functions is realized autonomously from within the system. Inspired by Robert Rosen's notion of closure to efficient causation, introduced as a necessary condition for a natural system to be an organism, we show that for a mathematical model of a self-organizing cell the associated category must be cartesian closed. Although the semantics of our cell model differ from Rosen's (M,R)-systems, the proof of our theorem supports (in parts) Rosen's argument that living cells have non-simulable properties. Whereas models that form cartesian closed categories can capture self-organization (which is a, if not the, fundamental property of living systems), conventional computer simulations of these models (such as virtual cells) cannot. Simulations can mimic living systems, but they are not like living systems.     

A new xanthene‐based two‐photon fluorescent probe for the imaging of 1,4‐dithiothreitol (DTT) in living cells

1,4‐Dithiothreitol (DTT) has wide applications in cell biology and biochemistry. Development of effective methods for monitoring DTT in biological systems is important for the safe handling and study of toxicity to humans. Herein, we describe a two‐photon fluorescence probe (Rh‐DTT) to detect DTT in living systems for the first time. Rh‐DTT showed high selectivity and sensitivity to DTT. Rh‐DTT can be successfully used for the two‐photon imaging of DTT in living cells, and also can detect DTT in living tissues and mice.     

Levels of organization of living systems: Cooperons

All creatures living on Earth are traditionally discussed in the context of structuralmorphological approach, in frame of which there are considered various systems (for instance, organisms and ecosystems) that have different sizes and organization and use different resources for their existence. These characteristics are sometimes added by some particular functional and ecological characteristics, but usually with respect to the structural ones. We believe that such traditional approach, although illustrating, but distracts from the circumstance that any living systems is to be considered an integrated structural-functional complex, the maintenance of existence of this system being impossible without the processes occurring constantly in it and aimed at preserving this complex. This leads us to the concept of cooperons—the self-preserved dynamic structures existing only as a result of various specifically organized cooperative processes (their intensities can vary depending on circumstances). From our point of view, all living systems are cooperons of different hierarchy levels. Some other systems, specifically the symbiotic ones, also are cooperons. In frame of this concept, it is possible to discuss functioning of living systems of different types of organization in a new context closer to physiologists, both for the case of “norm” and for the situation when the cooperative interrelations of parts of the system are impaired (for instance, in systemic diseases).     

关于生命系统熵势函数的建立及应用

依据非平衡非线性系统理论的广义势函数,建立了可描述生命系统的熵势及其表达式．作为应用,分析了生命系统的相变和生命机体内部的熵力．     

Life, Autonomy and Cognition: An Organizational Approach to the Definition of the Universal Properties of Life

This article addresses the issue of defining the universal properties of living systems through an organizational approach, according to which the distinctive properties of life lie in the functional organization which correlates its physicochemical components in living systems, and not in these components taken separately. Drawing on arguments grounded in this approach, this article identifies autonomy, with a set of related organizational properties, as universal properties of life, and includes cognition within this set.     

Bioassay Approach to Prescribe Safe-limits of Exposure to Non Ionizing Radiation in Ecosystems

A biological assay that quantifies hazardous response in living matter to an electromagnetic stimulus, is evolved. Considering the various susceptible aspects of physio-anatomical systems constituting a living subject, a dominance criterion to determine an optimum all-or-none response limit of exposure to electromagnetic pollutions is established. Based on the statistics of proneness and susceptibility of discrete physio-anatomical parts of living systems (biotic components) to polluting radiations (abiotic environment), the stochastic nature of damage involved is considered to formulate a quantal index which specifies a “safe” intensity-level of electromagnetic radiation to which living systems can be exposed without encountering any deleterious effects. The locations of vulnerable parts which are affected by radiation are identified through random mosaic modeling of a test subject. Using this model, a susceptance priority sequence of biotic components is constructed. This sequence is then terminated at a point of weightage proportional to the diversity of victim population. The biotic species falling within this limit of truncation are subsequently studied to assay the tolerance (optimum lethal dose) of the test subject to the radiation in question. The possibility of simulating the entire ecological system under consideration by means of a microprocessor is suggested.     

Principles of self-generation and self-maintenance

Living systems are characterized as self-generating and self-maintaining systems. This type of characterization allows integration of a wide variety of detailed knowledge in biology.The paper clarifies general notions such as processes, systems, and interactions. Basic properties of self-generating systems, i.e. systems which produce their own parts and hence themselves, are discussed and exemplified. This makes possible a clear distinction between living beings and ordinary machines. Stronger conditions are summarized under the concept of self-maintenance as an almost unique character of living systems. Finally, we discuss the far-reaching consequences that the principles of self-generation and self-maintenance have for the organization, structure, function, and evolution of single- and multi-cellular organisms.     

Are attractors 'strange', or is life more complicated than the simple laws of physics?

Interesting and intriguing questions involve complex systems whose properties cannot be explained fully by reductionist approaches. Last century was dominated by physics, and applying the simple laws of physics to biology appeared to be a practical solution to understand living organisms. However, although some attributes of living organisms involve physico-chemical properties, the genetic program and evolutionary history of complex biological systems make them unique and unpredictable. Furthermore, there are and will be 'unobservable' phenomena in biology which have to be accounted for.