Chemical Ecology and Biomolecular Evolution

The belief in the Darwinian theory of evolution appeared to be shaken when one tried to interpret statements of molecular biology in it. As a consequence there arose a theory of non-Darwinian neutral evolution. The supporters of this theory believe that under natural conditions no factors exist which can distinguish and select organisms on their internal (molecular) structure. In the opinion of these neutralists natural selection cannot in principle control the molecular constitution of organisms. Contrary to the viewpoint of the critics of neutralism it is impossible to admit that nucleic acids, proteins and other biomolecules can evolve without the participation of natural selection. This controversy in contemporary theoretical biology can be solved by integrating the conceptions of molecular ecology with Darwinian theory. Molecular ecology acknowledges the interactions of organisms by means of chemical substances synthesized by them. Such chemical ecological factors play a leading part in the selective stages of biomolecular evolution. These diverse chemical ecological interrelations take place intensively when living beings interact with parasitic microbes.     

Punctualism, non-adaptationism, neutralism and evolution

In its further development the theory of evolution will incorporate molecular biology, synergetics and the theory of information. Using a simple model it is shown that speciation can be similar to phase transition. This is a thermodynamical statement which does not say anything concerning the sharpness and kinetic features of transition. Hence there is no contradiction between punctuated equilibrium and phyletic gradualism. The notion of punctualism can be used in the sense of phase transition. Evolution is directional because of constraints of natural selection due to the structure of organisms already existing and to the possible pathways of development. Correspondingly many characters are non-adaptative. Not only are the structures of proteins important for speciation but also the exact answers to the questions: "how much", "where" and "when"? These answers can be obtained as the results of regulation of genes, particularly of homeiotic regulation. The basis features of the structure of proteins are considered and the sense of the neutral theory is discussed in connection with degeneracy of correlation between the primary structure of a protein, its spatial structure and biological function. Informational aspects of evolution are discussed. Punctualism, non-adaptationism and neutralism form the triad of internally connected features of evolution. The Darwinian theory preserves its fundamental significance.     

Darwinian selection leads to Gaia

The Gaia hypothesis, in its strongest form, states that the Earth's atmosphere, oceans, and biota form a tightly coupled system that maintains environmental conditions close to optimal for life. According to Gaia theory, optimal conditions are intrinsic, immutable properties of living organisms. It is assumed that the role of Darwinian selection is to favor organisms that act to stabilize environmental conditions at these optimal levels. In this paper, an alternative form of Gaia theory based on more traditional Darwinian principles is proposed. In the new approach, environmental regulation is a consequence of population dynamics, not Darwinian selection. The role of selection is to favor organisms that are best adapted to prevailing environmental conditions. However, the environment is not a static backdrop for evolution, but is heavily influenced by the presence of living organisms. The resulting co-evolving dynamical process eventually leads to the convergence of equilibrium and optimal conditions. A simple Daisyworld model is used to illustrate this convergence phenomenon. Sensitivity analysis of the Daisyworld model suggests that in stable ecosystems, the convergence of equilibrium and optimal conditions is inevitable, provided there are no externally driven shocks to the system. The end result may appear to be the product of a cooperative venture, but is in fact the outcome of Darwinian selection acting upon "selfish" organisms.     

Objectivity and Illusion in Evolutionary Ethics: Comments on Waller

In this paper I argue that any adequate evolutionary ethical theory needs to account for moral belief as well as for dispositions to behave altruistically. It also needs to be clear whether it is offering us an account of the motivating reasons behind human behaviour or whether it is giving justifying reasons for a particular set of behaviours or, if both, to distinguish them clearly. I also argue that, unless there are some objective moral truths, the evolutionary ethicist cannot offer justifying reasons for a set of behaviours. I use these points to refute Waller's claims that the illusion of objectivity plays a dispensable role in Ruse's theory, that my critique of Ruse's Darwinian metaethics is built on a false dilemma, that there is nothing to be distressed about if morality is not objective, and that ethical beliefs are subject to a kind of causal explanation that undermines their objectivity in a way that scientific beliefs are not.     

Beyond the DP/DSS controversy

Paul Turke's “Which humans behave adaptively, and why does it matter?” shows, if he we are to take him as being representative of “Darwinian social science” in general, that his school of thought has moved surprisingly close to that of its “Darwinian psychology” critics in accepting the importance if not the primacy of the psychological level of explanation in applying evolutionary theory to human behavior. Disagreements continue over whether the adaptiveness of current behavior should be viewed as an occasionally interesting question because of the light it can shed on evolved psychological mechanisms, or whether, as Turke maintains, it is the central question for human sociobiology. In any event, the “vertically integrated approach,” utterly ignored by Turke, incorporates Darwinian Psychology and is far more powerful than is Turke's approach in explicating the relationship between genes and culture, thereby rendering the current debate pointless.     

再谈“有希望的怪物”

1933年,遗传学家Goldschmidt提出＂有希望的怪物＂假说,以解释宏演化（macroevolution）中有别于＂达尔文式＂的演化机制。近年来,有关内共生和基因倍增等进展表明,＂有希望的怪物＂在自然界中其实非常普遍。这虽然与＂现代综合进化论＂的观点不甚一致,但却能在经典达尔文主义找到契合点：作为自然选择的补充,＂有希望的怪物＂可以为宏演化提供一种潜在的候选机制。这种建立在多元论基础上的进化观是达尔文留给后人最宝贵的遗产。     

Homeostasis and the physiological dimension of niche construction theory in ecology and evolution

Niche construction theory (NCT) has been represented as a new and comprehensive theory of evolution, one that breaks the constraints imposed by the dominant and largely gene-selectionist standard evolutionary model that is presently mischaracterized as “Darwinian.” I will argue that NCT is not so much a new theory, as it is a fruitful readmission of a venerable physiological perspective on adaptation, selection and evolution. This perspective is closer in spirit and philosophy to the original (and richer) Darwinian idea developed by Darwin himself, and that animated much of the rich late nineteenth century debate about evolution, heredity, adaptation and development, a debate that was largely eclipsed by the early twentieth century emergence of the Neodarwinian synthesis. I will argue that a full realization of the promise of NCT turns on a full understanding of another intellectual revolution of the nineteenth century, Claude Bernard’s conception of homeostasis, a profound statement of the nature of life that has, through the twentieth century, come to be widely misunderstood and trivialized.     

A neutral theory of biogenesis

The selective Darwinian theory of chemical evolution is critically reviewed and the tentative conclusion is reached that neither the theoretical analyses nor the experiments with phages can really prove it. An alternative proposal is put forth which considers the possibility that the biogenetic process has been driven by stochastic forces, e.g. it took place in the absence of Darwinian selection which, in turn, started only when the first protocells came into existence. The dynamics of the early self-organization of living structures should be understood in terms of self-assembly. The complexification of living matter is thus not represented as a gradual phenomenon but as a series of abrupt and relatively fast transitions consisting in the aggregation of pre-systems which had evolved by their own. The shift towards new and variegated states proposed by the bifurcation theory are not considered particularly relevant for reasons reported in the text, nor is it believed that dissipation can entirely account for the order observed in living cells.     

Simulation of Left Atrial Function Using a Multi-Scale Model of the Cardiovascular System

During a full cardiac cycle, the left atrium successively behaves as a reservoir, a conduit and a pump. This complex behavior makes it unrealistic to apply the time-varying elastance theory to characterize the left atrium, first, because this theory has known limitations, and second, because it is still uncertain whether the load independence hypothesis holds. In this study, we aim to bypass this uncertainty by relying on another kind of mathematical model of the cardiac chambers. In the present work, we describe both the left atrium and the left ventricle with a multi-scale model. The multi-scale property of this model comes from the fact that pressure inside a cardiac chamber is derived from a model of the sarcomere behavior. Macroscopic model parameters are identified from reference dog hemodynamic data. The multi-scale model of the cardiovascular system including the left atrium is then simulated to show that the physiological roles of the left atrium are correctly reproduced. This include a biphasic pressure wave and an eight-shaped pressure-volume loop. We also test the validity of our model in non basal conditions by reproducing a preload reduction experiment by inferior vena cava occlusion with the model. We compute the variation of eight indices before and after this experiment and obtain the same variation as experimentally observed for seven out of the eight indices. In summary, the multi-scale mathematical model presented in this work is able to correctly account for the three roles of the left atrium and also exhibits a realistic left atrial pressure-volume loop. Furthermore, the model has been previously presented and validated for the left ventricle. This makes it a proper alternative to the time-varying elastance theory if the focus is set on precisely representing the left atrial and left ventricular behaviors.     

Cooperation enhanced by the ‘survival of the fittest’ rule in prisoner's dilemma games on complex networks

Prevalence of cooperation within groups of selfish individuals is puzzling in that it contradicts with the basic premise of natural selection, whereby we introduce a model of strategy evolution taking place on evolving networks based on Darwinian ‘survival of the fittest’ rule. In the present work, players whose payoffs are below a certain threshold will be deleted and the same number of new nodes will be added to the network to maintain the constant system size. Furthermore, the networking effect is also studied via implementing simulations on four typical network structures. Numerical results show that cooperators can obtain the biggest boost if the elimination threshold is fine-tuned. Notably, this coevolutionary rule drives the initial networks to evolve into statistically stationary states with a broad-scale degree distribution. Our results may provide many more insights for understanding the coevolution of strategy and network topology under the mechanism of nature selection whereby superior individuals will prosper and inferior ones be eliminated.     

A complete classification of Darwinian extinction in ecological interactions

The evolution of a population by individual-level natural selection can result in the population's extinction. Selection causes the spread of phenotypes with higher relative fitness, but at the same time, selection can also indirectly produce changes in the physical, biotic, or genotypical environment through population interactions (e.g., environment modification, interspecific interactions, and genomic conflict). Because fitness is environment dependent, this can cause mean fitness to decrease, resulting in extinction. I call this process "Darwinian extinction." Examples of Darwinian extinction include a variety of dynamics and modes of extinction, but the variation is constrained. I determine the complete classification of possible dynamics and modes of Darwinian extinction due to ecological interactions, using bifurcation theory and models with ecological and evolutionary changes occurring on different timescales. This classification is also extended to extinctions due to interactions within the population. The mode of extinction may be either sudden or gradual (requiring additional stochastic processes), and each mode has specific types of dynamics associated with it. Darwinian extinction is a robust and normal phenomenon, and this reasonably complete classification can help us understand more thoroughly its role in nature.     

The individuality of the species: A Darwinian theory? — from Buffon to Ghiselin, and back to Darwin

Since the 1970s, there has been a tremendous amount of literature on Ghiselin's proposal that “species are individuals”. After recalling the origins and stakes of this thesis in contemporary evolutionary theory, I show that it can also be found in the writings of the French naturalist Buffon in the 18th Century. Although Buffon did not have the conception that one species could be derived from another, there is an interesting similarity between the modern argument and that of Buffon regarding the “individuality of species’. The analogy is strong enough to force us to recognize that genuine evolutionary (or Darwinian) questions might be of secondary importance in the discussion. In consequence, the third section of the paper proposes an alternative schema for the “logical structure” of the Darwinian concept of species. Darwin distinguished the problem of the designation of a concrete species, and the problem of its signification of species within his theory of descent? The resulting notion of species involves a logical structure based on the fusion of the logical operations of classification and ordering. The difficulty — and interest — is that this interpretation of species does not entail any precise operational definition of species; it can only tell us what the ultimate signification of classification is within the theory of descent with modification through natural selection.     

Bards,Poets, and Cliques: Frequency-Dependent Selection and the Evolution of Language Genes

The ability of humans to communicate via language is a complex, adapted phenotype, which undoubtedly has a recently evolved genetic component. However, the evolutionary dynamics of language-associated alleles are poorly understood. To improve our knowledge of such systems, a population-genetics model for language-associated genes is developed. (The model is general and applicable to social interactions other than communication.) When an allele arises that potentially improves the ability of individuals to communicate, it will experience positive frequency-dependent selection because its fitness will depend on how many other individuals communicate the same way. Consequently, new and rare alleles are selected against, posing a problem for the evolutionary origin of language. However, the model shows that if individuals form language-based cliques, then novel language-associated alleles can sweep through a population. Thus, the origin of language ability can be sufficiently explained by Darwinian processes operating on genetic diversity in a finite population of human ancestors.     

Preliminary studies of Eutorna phaulocosma (Lepidoptera: Oecophoridae) in New Zealand

Abstract

In 1978 George C. Williams predicted that the last two decades of this century would be a fabulous age, and that evolutionary biology would provide critical insights into the processes of change in the biological world. He suggested that these might come to be described as the “good old days”. I am not so sure that this is likely, but I am very sure that it will be a turbulent time. I think also that those biologists who attended the recent SYSTANZ meeting on evolution must by now be equally convinced. The conference was punctuated by heated debates on major topics such as Darwinian and neo-Darwinian theory, vicariance biogeography, and teleology, to mention but a few.     

Why mental disorders are just mental dysfunctions (and nothing more): some Darwinian arguments

Mental disorders are often thought to be harmful dysfunctions. Jerome Wakefield has argued that such dysfunctions should be understood as failures of naturally selected functions. This suggests, implicitly, that evolutionary biology and other Darwinian disciplines hold important information for anyone working on answering the philosophical question, 'what is a mental disorder?'. In this article, the author argues that Darwinian theory is not only relevant to the understanding of the disrupted functions, but it also sheds light on the disruption itself, as well as on the harm that attends the disruption. The arguments advanced here are partially based on the view that a core feature of Darwinism is that it stresses the environmental relativity of functions and dysfunctions. These arguments show a very close empirical connection between social judgments (values) and dysfunctions (psychopathology), which is of interest for psychiatric theory. Philosophically, they lead to the conclusion that the concept of mental disorder is identical to the concept of mental dysfunction. Consequently, it is both misleading and redundant to conceptualize mental disorders as 'harmful dysfunctions', and not simply as 'mental dysfunctions'.     

Computer simulation of different types of evolutionary process

The computer model of two alternative variants of biological evolution is proposed. The first variant supposes random while the second--directed change of individual features, thus corresponding to the Darwinian and non-Darwinian evolution. The evolution of fish communities in fresh waters serves as a particular example. The model is executed using object-oriented method of programming and mathematical apparatus of fuzzy logics. The investigation of the model showed that process of Darwinian evolution is connected with significantly greater species diversity and variability of evolutionary process trajectories than non-Darwinian one. On the other hand, non-Darwinian type of evolution provides fast achievement of high individual fitness, especially under conditions of constant environment. Non-Darwinian type evolution failed in big evolutionary alteration (for example, transition to predation); while the Darwinian evolution under the same conditions can produce such alterations though it took more time and many extinct species. Phylogenetic tree of Darwinian evolution is always more complex than of non-Darwinian one under the same conditions.     

Control for small-speed lateral flight in a model insect

Controls required for small-speed lateral flight of a model insect were studied using techniques based on the linear theories of stability and control (the stability and control derivatives were computed by the method of computational fluid dynamics). The main results are as follows. (1) Two steady-state lateral motions can exist: one is a horizontal side translation with the body rolling to the same side of the translation by a small angle, and the other is a constant-rate yaw rotation (rotation about the vertical axis). (2) The side translation requires an anti-symmetrical change in the stroke amplitudes of the contralateral wings, and/or an anti-symmetrical change in the angles of attack of the contralateral wings, with the down- and upstroke angles of attack of a wing having equal change. The constant-rate yaw rotation requires an anti-symmetrical change in the angles of attack of the contralateral wings, with the down- and upstroke angles of attack of a wing having differential change. (3) For the control of the horizontal side translation, control input required for the steady-state motion has an opposite sign to that needed for initiating the motion. For example, to have a steady-state left side-translation, the insect needs to increase the stroke amplitude of the left wing and decrease that of the right wing to maintain the steady-state flight, but it needs an opposite change in stroke amplitude (decreasing the stroke amplitude of the left wing and increasing that of the right wing) to enter the flight.     

Patterns and Processes in Cultural Evolution

Darwinian models of cultural change have been motivated, in part, by the desire to provide a framework for the unification of the biological and the human sciences. In this paper, drawing upon a distinction between the evolution of enabling mechanisms for the acquisition and dissemination of knowledge (EEM) and the evolution of epistemic theses as cultural products (EET), we propose a model of how culture emerges as a product of biological evolution on the basis of the concept of reaction norms. The goal of this model is to provide a means for conceptualizing how the biological and the cultural realms are connected, when they start to disconnect, and what the key transitions are. We then assess the viability of a Darwinian approach to cultural change. We conclude that the prospects of producing a Darwinian model of cultural change that unifies the human sciences in a way that mirrors the unification of the biological sciences in the light of Darwin’s theory are rather dim.     

Moral philosophy: A biological approach

In this paper I argue that Darwinian evolutionary theory gives us the key to an adeguate understanding of morality. Althougt in the past the naturalistic fallacy has been thought to be a bar to the application of evolution to ethics I suggest that properly viewed evolutionary ethics can avoid this problems.