A quantum model of exaptation: Incorporating potentiality into evolutionary theory

The phenomenon of preadaptation, or exaptation (wherein a trait that originally evolved to solve one problem is co-opted to solve a new problem) presents a formidable challenge to efforts to describe biological phenomena using a classical (Kolmogorovian) mathematical framework. We develop a quantum framework for exaptation with examples from both biological and cultural evolution. The state of a trait is written as a linear superposition of a set of basis states, or possible forms the trait could evolve into, in a complex Hilbert space. These basis states are represented by mutually orthogonal unit vectors, each weighted by an amplitude term. The choice of possible forms (basis states) depends on the adaptive function of interest (e.g., ability to metabolize lactose or thermoregulate), which plays the role of the observable. Observables are represented by self-adjoint operators on the Hilbert space. The possible forms (basis states) corresponding to this adaptive function (observable) are called eigenstates. The framework incorporates key features of exaptation: potentiality, contextuality, nonseparability, and emergence of new features. However, since it requires that one enumerate all possible contexts, its predictive value is limited, consistent with the assertion that there exists no biological equivalent to “laws of motion” by which we can predict the evolution of the biosphere.     

A note on open linear systems

A theorem is given which states a necessary and sufficient condition for the specific activity to be uniform throughout an open compartmental system in the steady state.     

菌心进化论:一种对于动物进化的新理解

达尔文进化论强调了"物竞天择,适者生存"的理念与逻辑,对动物起源与进化提供了重要解释;然而,为什么会有动物、以及为什么会进化出人类等问题,却仍无答案。在我们实验室近年来从事肥胖及相关慢病研究中发现"饥饿源于菌群"并发展出可通过控制肠道菌群向人体传递的饥饿感的生物技术之后,提出科学假说认为,和人类同样具有消化道结构的动物,很有可能也是受到肠道菌群摄食的胁迫压力而进化的,即动物和人体的消化道以"中空"的拓扑学结构为基础,形成可容纳与相应动物种类相适应的肠道菌群微生态系统。这些肠道菌群终生共生于肠道,通过向动物传递饥饿感而迫使动物摄食而生存,同时肠道菌群也通过动物摄食的营养物质繁殖自己的后代,从而提出了以肠道菌群为中心、动物受肠道菌群胁迫而协同进化的"菌心进化论",是对"宿主进化论"的重要补充和完善,有利于我们从新的角度来理解和诠释动物的起源、进化和发展过程,乃至促进我们逐渐理解自然界从动物进化到人类之后,有可能是在实现从菌群主导的以食物为代表的"物质需求"向人类智慧主导的"精神需求"的新跃迁。     

Self-organization in dissipative structures: A thermodynamic theory for the emergence of prebiotic cells and their epigenetic evolution

This paper presents a discussion on self-organization processes in dissipative structures, in order to highlight the general conditions for raising complexity and generate order. In particular, some concepts were introduced from non-equilibrium thermodynamics and from the Molecular Anamorphic Evolution Theory, especially concerning processes of matter randomization.     

A model for renal arterial branching based on graph theory

The kidney is one of the most complicated organs in terms of structure and physiology, in part because it is highly vascularized. The renal vascular development occurs through two mechanisms that sometimes overlap: vasculogenesis and angiogenesis. Here, we consider angiogenesis to model the renal arterial tree with the two processes of vascular angiogenesis: sprouting and splitting. We recognize the vessels are not tubes with ends that get glued but physiological factors are relevant into the vascular development. Our contribution integrates the graph theory and physiological information to derive a quantitative model for the vascular tree in the sense that the vertices and edges represent, respectively, a branching point and a vessel. From such a premise, development of the arterial vascular tree of the kidney is mathematically expressed, including physiological processes as the effect of the vascular endothelial growth factor (VEGF) on the vessel length. A definition of the graph is used to visualize the topology of vascular tree in kidney providing physiological information into the edges. Thus, renal arterial branching is modeled as a graph where edges are labeled and oriented.     

A hierarchical model of the evolution of cooperation in cultural systems

In this paper the following problem is addressed: "Under what conditions can a collection of individual organisms learn to cooperate when cooperation appears to outwardly degrade individual performance at the outset. In order to attempt a theoretical solution to this problem, data from a real world problem in anthropology is used. A distributed simulation model of this system was developed to assess its long term behavior using using an approach suggested by Zeigler (Zeigler, B.P., 1984, Multifaceted Modelling and Discrete Event Simulation (Academic Press, London)). The results of the simulation are used to show that although cooperation degrades the performance potential of each individual, it enhances the persistence of the individual's partial solution to the problem in certain situations."     

A thermodynamic theory of evolution

As a closed thermodynamic system subject to an essentially constant free energy gradient, the biosphere must evolve toward a stationary state of maximum structuring and minimum dissipation with respect to this applied gradient. Since biological evolution occurs opportunistically through chance and selection, rather than as a direct response to the free energy gradient, the conformance of this phase of evolution with thermodynamics requires that natural selection, and the particular adaptive strategies employed by species of organisms, be related to the principles of increasing structuring and decreasing dissipation. In this paper, some general features of this relationship are proposed.     

A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution

Six hundred million years ago, the fossil record displays the sudden appearance of intracellular detail and the 32 phyla. The “Cambrian Explosion” marks the onset of dominant aerobic life. Fossil intracellular structures are so similar to extant organisms that they were likely made with similar membrane lipids and proteins, which together provided for organisation and specialisation. While amino acids could be synthesised over 4 billion years ago, only oxidative metabolism allows for the synthesis of highly unsaturated fatty acids, thus producing novel lipid molecular species for specialised cell membranes.Docosahexaenoic acid (DHA) provided the core for the development of the photoreceptor, and conversion of photons into electricity stimulated the evolution of the nervous system and brain. Since then, DHA has been conserved as the principle acyl component of photoreceptor synaptic and neuronal signalling membranes in the cephalopods, fish, amphibian, reptiles, birds, mammals and humans. This extreme conservation in electrical signalling membranes despite great genomic change suggests it was DHA dictating to DNA rather than the generally accepted other way around.We offer a theoretical explanation based on the quantum mechanical properties of DHA for such extreme conservation. The unique molecular structure of DHA allows for quantum transfer and communication of π-electrons, which explains the precise depolarisation of retinal membranes and the cohesive, organised neural signalling which characterises higher intelligence.     

An epigenetic model for pigment patterning based on mechanical and cellular interactions

Pigment patterning in animals generally occurs during early developmental stages and has ecological, physiological, ethological, and evolutionary significance. Despite the relative simplicity of color patterns, their emergence depends upon multilevel complex processes. Thus, theoretical models have become necessary tools to further understand how such patterns emerge. Recent studies have reevaluated the importance of epigenetic, as well as genetic factors in developmental pattern formation. Yet epigenetic phenomena, specially those related to physical constraints that might be involved in the emergence of color patterns, have not been fully studied. In this article, we propose a model of color patterning in which epigenetic aspects such as cell migration, cell-tissue interactions, and physical and mechanical phenomena are central. This model considers that motile cells embedded in a fibrous, viscoelastic matrix-mesenchyme-can deform it in such a way that tension tracks are formed. We postulate that these tracks act, in turn, as guides for subsequent cell migration and establishment, generating long-range phenomenological interactions. We aim to describe some general aspects of this developmental phenomenon with a rather simple mathematical model. Then we discuss our model in the context of available experimental and morphological evidence for reptiles, amphibians, and fishes, and compare it with other patterning models. We also put forward novel testable predictions derived from our model, regarding, for instance, the localization of the postulated tension tracks, and we propose new experiments. Finally, we discuss how the proposed mechanism could constitute a dynamic patterning module accounting for pattern formation in many animal lineages.     

A synthetic theory of molecular evolution

According to the neo-Darwinian view of evolution evolution rate nu depends solely on the environment variation rate gamma, whereas in the non-Darwinian view evolution rate is determined mainly by the mutation rate mu. We have studied two kinds of population genetics models which exhibit both types of evolution in different parametric regions: one is a dynamical model representing infinite population, and the other is a Markov process model representing a nearly monomorphic finite population. In the infinite population model, after proving general time-derivative and mu-derivative formulas for the population average of quantitative traits, we show that if the mutation rate is adaptively determined, mu must be larger than nu in the stationary state. Loads of evolution are obtained in both regions. A high evolution rate such as nu = 1 per genome per generation is consistent with Haldane's value of tolerable load if and only if the functional constraint is not large and selection is weak, independent of whether the evolution is neo-Darwinian or non-Darwinian. As the selection intensity increases, nu is shown to change discontinuously from nearly mu to gamma at the transition point. In the finite population model, the transition of v is not discontinuous, but is very steep. On the other hand, no steep change of polymorphism takes place at the transition point. The steepness of the transition in our model suggests that real molecular evolution can be divided into either neo-Darwinian or non-Darwinian,and that the intermediate type of evolution is rather rare.     

Lactate is an epigenetic metabolite that drives survival in model systems of glioblastoma

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A dynamical systems perspective on vegetation theory

A dynamical systems perspective is employed to develop a simple conceptual model of vegetation and environment as coupled dynamical systems. The conceptual model characterizes the influence of environment on vegetation, the effect of vegetation on the environment, and the subsequent response of vegetation to the modified environment. Vegetation and environmental dynamics are modeled as trajectories in complementary state spaces, with the trajectories jointly determined by the position of a given site in both spaces. The vegetation and environment state spaces are coupled by the physiological requirements of the component species and the modification of environment by vegetation. From a dynamical systems perspective, current vegetation theory and analyses overemphasize environmental determination of vegetation composition and neglect the effects of vegetation on environment. A dynamical systems perspective is capable of synthesizing previous concepts of vegetation; the continuum and community type concepts are possible consequences of site specific differences in vegetation metabolism and environmental plasticity.I would like to acknowledge the helpful comments and criticisms of Drs G. Cottam, J. D. Aber, T. F. H. Allen, R. P. McIntosh, C. G. Lorimer, and anonymous reviewers.I would like to thank the University of Wisconsin, Madison for a fellowship which supported this research. This paper is dedicated with great respect and gratitude to Professor G. Cottam on the occasion of his retirement from the University of Wisconsin.     

Dynamic measurement of oxidase activity based on oxygen consumption in open systems

Oxidases catalyze the oxidation of a variety of substrates with the concomitant reduction of molecular oxygen as a final electron acceptor. UV‐visible spectrophotometry is a simple and high‐throughput method commonly used to measure oxidase activities. However, drawbacks such as light scattering exist especially concerning the activity assessment of enzymes immobilized on supports. Monitoring of the universal cosubstrate O₂ circumvents these drawbacks. This study aimed at developing a methodology that allows activity measurement of many types of oxidases based on O₂ consumption applicable to various open systems. Dissolved oxygen in the reaction medium was monitored by an O₂ sensor and the reaction rate was deduced from the O₂ mass balance equation correcting for atmospheric diffusion. Common activity units (μM_product min^?1 or U/L) could be subsequently derived using calibration curves. The sensitivity of the method toward temperature, atmospheric pressure, and ionic strength variations was evaluated, and made it possible to define operating windows for the simplification of the proposed methodology.     

An epigenetic perspective on the free radical theory of development

The development of organisms requires concerted changes in gene activity. The free radical theory of development proposes that oxygen serves as a morphogen to educe development by influencing the production of metabolic oxidants such as free radicals and reactive oxygen species. One of the central tenets of this theory is that these metabolic oxidants influence development by altering the antioxidant capacity of cells by changing their production of glutathione (GSH). Here we extend on these principles by linking GSH production and oxygen sensing in the control of gene expression to establish the epigenotype of cells during development. We prescribe this novel role to GSH and oxygen during development because these metabolites influence the activity of enzymes responsible for initiating and perpetuating epigenetic control of gene expression. Increased GSH production influences epigenetic processes including DNA and histone methylation by limiting the availability of S-adenosylmethionine, the cofactor utilized during epigenetic control of gene expression by DNA and histone methyltransferases. Moreover, the recent discovery of histone demethylases that require oxygen as a cofactor directly links epigenetic processes to oxygen gradients during development.