Bio Systems

In this work, the morphogenesis mechanisms are considered from the complexity perspective. It is shown that both morphogenesis and the functioning of organs should be unstable in the case of short-range interaction potentials. The repeatability of forms during evolution is a strong argument for its directionality. The formation of organs during evolution can occur only in the presence of a priori information about the structure of such an organ. The focus of the discussion is not merely on constraining potential possibilities but on the concept of directed evolution itself...

The place of living organisms in the natural world is a nearly perennial question in philosophy and the sciences; how can inanimate matter yield animate beings? A dominant answer for several centuries has been to treat organisms as sophisticated machines, studying them with the mechanistic physics and chemistry that have given rise to technology and complex machines. Since the early 20th century, many scholars have sought instead to naturalize biology through thermodynamics, recognizing the precarious far-from-equilibrium state of organisms...

Ervin Bauer (1890-1938) outlined the paradigm of theoretical biology from the perspective of biophysics and bioenergetics. His molecular-based biological theory is centered on the principle of sustainable non-equilibrium, which is continuously produced and maintained by all biological systems throughout their life. Ervin Bauer became the victim of Stalin's Great Terror. Here we present two of the fundamental works of Ervin Bauer in English translation: the paper "The definition of the living being on the basis of its thermodynamic properties and the fundamental biological principles that follow from it" published in Naturwissenschaften (1920)Naturwissenschaften (1920) and the excerpts from his magnum opus "Theoretical Biology" (1935)...

A massive statistical analysis based on the autocorrelation function of the circular code X observed in genes is performed on the (eukaryotic) introns. Surprisingly, a circular code periodicity 0 modulo 3 is identified in 5 groups of introns: birds, ascomycetes, basidiomycetes, green algae and land plants. This circular code periodicity, which is a property of retrieving the reading frame in (protein coding) genes, may suggest that these introns have a coding property. In a well-known way, a periodicity 1 modulo 2 is observed in 6 groups of introns: amphibians, fishes, mammals, other animals, reptiles and apicomplexans...

Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role...

Ervin Bauer (1890-1938) made historical contributions to contemporary biology, provided a new definition of life, defined the contents of theoretical biology. He worked in different countries, perturbed by deep historical events. These historical events necessarily impacted his fate and finally led to the violent loss of his life and the life of his wife. His work and with it his theory of life had a no less complicated history than the history of his personal life. Bauer's main work "Theoretical Biology" was published in 1935 in Russian...

The central problem in transduction is to explain how the energy caught from sunlight by chloroplasts becomes biological work. Or to express it in different terms: how does the energy remain trapped in the biological network and not get lost through thermalization into the environment? The pathway consists of an immensely large number of steps crossing hierarchical levels - some upwards, to larger assemblies, others downwards into energy rich molecules - before fuelling an action potential or a contracting cell...

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Most nutrient uptake problems are modeled by the convection-diffusion equation (CDE) abiding by Fick's law. Because nutrients needed by plants exist in the soil solution as a form of ions and the soil is a typical fractal structure of heterogeneity, it makes the solute transport appear anomalous diffusion in soil. Taking anomalous diffusion as a transport process, we propose time and space fractional nutrient uptake models based on the classic Nye-Tinker-Barber model. There does not appear apparent sub-diffusion of nitrate in the time fractional model until four months and the time fractional models are appropriate for describing long-term dynamics and slow sorption reaction; the space fractional model can capture super-diffusion in short term and it is suitable for describing nonlocal phenomena and daily variations driven by transpiration and metabolism; the anomalous diffusion more apparently appears near the root surface in the modeling simulation...

The coexistence of cladogenesis, i.e., the branching of lineages along an evolutionary tree as observed in the fossil record, and anagenesis, which is the progressive evolution within populations, lacks a clear explanation. In this study, we examine a simple model that simulates the evolutionary changes occurring within populations inhabiting the same environment in sympatry, and driven by ecological competition. Our model characterizes populations through a set of evolving morphological traits represented by mathematical points within a two-dimensional morphospace...

One of the prime reasons of increasing breast cancer mortality is metastasizing cancer cells. Owing to the side effects of clinically available drugs to treat breast cancer metastasis, it is of utmost importance to understand the underlying biogenesis of breast cancer tumorigenesis. In-silico identification of potential RNAs might help in utilizing the miR-27 family as a therapeutic target in breast cancer. The experimentally verified common interacting mRNAs for miR27 family are retrieved from three publicly available databases- TargetScan, miRDB and miRTarBase...

Our previous efforts to probe the complex, rich experiential lives of unicellular species have focused on the origins of consciousness (Reber, 2019) and the biomolecular processes that underlie sentience (Reber et al., 2023). Implied, but unexplored, was the assumption that these cognitive functions and associated unicellular organismal behaviors were linked with and often driven by affect, feelings, sensual experiences. In this essay we dig more deeply into these valenced (We're using the term valence here to cover the aspects of sensory experiences that have evaluative elements, are experienced as positive or negative ─ those where this affective, internal representation is an essential element in how the input is interpreted and responded to...

A non-Kranz C4 photosynthesis of the NAD-ME subtype, specifically in developing wheat grains (14 dpa, days post-anthesis) was originally demonstrated using transcriptome-based RNA-seq. Here we present a re-examination of evidence for C4 photosynthesis in the developing grains of wheat and, more broadly, the Pooideae and an investigation of the evolutionary processes and implications. The expression profiles for the genes associated with C4 photosynthesis (C4 - and C3 -specific) were evaluated using published transcriptome data for the outer pericarp, inner pericarp, and endosperm tissues of the developing wheat grains...

Protein domain repeats are known to arise due to tandem duplications of internal genes. However, the understanding of the underlying mechanisms of this process is incomplete. The goal of this work was to investigate the mechanism of occurrence of repeat expansion based on studying the sequences of 1324 rpsA genes of bacterial S1 ribosomal proteins containing different numbers of S1 structural domains. The rpsA gene encodes ribosomal S1 protein, which is essential for cell viability as it interacts with both mRNA and proteins...

We derive the classic, ubiquitous, but enigmatic Yerkes-Dodson effect of applied stress on real-world performance in a highly natural manner from fundamental assumptions on cognition and its dynamics, as constrained by the asymptotic limit theorems of information and control theories. We greatly extend the basic approach by showing how differences in an underlying probability model can affect the dynamics of decision across a broad range of cognitive enterprise. Most particularly, however, this development may help inform our understanding of the different expressions of human psychopathology...

•The signaling process during mycorrhiza establishment involves intense molecular communication between symbionts. It has been suggested that a group of protein effectors, the so-called MiSSPs, plays a broader function in the symbiosis metabolism, however, many of these remain uncharacterized structurally and functionally. •Herein we used three-dimensional protein structure modeling methods, ligand analysis, and molecular docking to structurally characterize and describe two protein effectors, MiSSP13 and MiSSP16...

Ervin Bauer (1890-1938) was the first to build a general molecular-based biological theory. He defined the basic principles of theoretical biology from a thermodynamic perspective, focusing on the capacity of biological systems to produce and support the state of sustainable non-equilibrium. His central work "Theoretical Biology" (1935) was written long before modern advances in molecular biology, genetics, and information theory. Ervin Bauer and his wife Stefánia were executed in Stalin's Great Terror...

Local interactions between flock members in absence of centralized control generate collective dynamics characterized by coherent large-scale patterns. We investigate whether aggregates of individuals like birds, swarms and fishes behaving in concert with their neighbors may modify the physical properties of the fluid medium in which they are embedded. Using the K-Nearest Neighbours algorithm to simulate collective animal behavior, we showed that the occurrence of collective dynamics can modify the physical parameters of the phase space in which the interacting individuals' trajectories take place...

A primary objective of biology is the development of universal laws that define how organic form develops and how it evolves as a function of size, both ontogenetically and across evolutionary time. Scaling theory has been essential in reaching this goal by giving a complete perspective point, particularly in illuminating the fundamental biological features produced within scaling exponents defining families of equations. Nonetheless, the theoretical basis of the allometric equation within scaling theory are inadequately explained, particularly when it comes to establishing links between micro-level processes at the cellular level and macro-level phenomena...

Ervin Bauer was the only biologist who recognized that the best way to develop theoretical biology on an equal footing with theoretical physics was to follow the method that has ensured the great successes of modern theoretical physics: the general method of science. Following this method, he succeeded to find the universal principle of biology. From this principle he managed to derive all the basic equations of biology, that of metabolism, reproduction, growth, responsiveness and successfully explained all the fundamental phenomena of life...