Robustness as an evolutionary principle.

We suggest simulating evolution of complex organisms using a model constrained solely by the requirement of robustness in its expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence for dynamical features in the evolved networks is found that can be related to biological observables.     

Winter diatom blooms in a regulated river in South Korea: explanations based on evolutionary computation

1. An ecological model was developed using genetic programming (GP) to predict the time‐series dynamics of the diatom, Stephanodiscus hantzschii for the lower Nakdong River, South Korea. Eight years of weekly data showed the river to be hypertrophic (chl. a, 45.1 ± 4.19 μg L⁻¹, mean ± SE, n = 427), and S. hantzschii annually formed blooms during the winter to spring flow period (late November to March). 2. A simple non‐linear equation was created to produce a 3‐day sequential forecast of the species biovolume, by means of time series optimization genetic programming (TSOGP). Training data were used in conjunction with a GP algorithm utilizing 7 years of limnological variables (1995–2001). The model was validated by comparing its output with measurements for a specific year with severe blooms (1994). The model accurately predicted timing of the blooms although it slightly underestimated biovolume (training r² = 0.70, test r² = 0.78). The model consisted of the following variables: dam discharge and storage, water temperature, Secchi transparency, dissolved oxygen (DO), pH, evaporation and silica concentration. 3. The application of a five‐way cross‐validation test suggested that GP was capable of developing models whose input variables were similar, although the data are randomly used for training. The similarity of input variable selection was approximately 51% between the best model and the top 20 candidate models out of 150 in total (based on both Root Mean Squared Error and the determination coefficients for the test data). 4. Genetic programming was able to determine the ecological importance of different environmental variables affecting the diatoms. A series of sensitivity analyses showed that water temperature was the most sensitive parameter. In addition, the optimal equation was sensitive to DO, Secchi transparency, dam discharge and silica concentration. The analyses thus identified likely causes of the proliferation of diatoms in ‘river‐reservoir hybrids’ (i.e. rivers which have the characteristics of a reservoir during the dry season). This result provides specific information about the bloom of S. hantzschii in river systems, as well as the applicability of inductive methods, such as evolutionary computation to river‐reservoir hybrid systems.     

A teleofunctional account of evolutionary mismatch

When the environment in which an organism lives deviates in some essential way from that to which it is adapted, this is described as “evolutionary mismatch,” or “evolutionary novelty.” The notion of mismatch plays an important role, explicitly or implicitly, in evolution-informed cognitive psychology, clinical psychology, and medicine. The evolutionary novelty of our contemporary environment is thought to have significant implications for our health and well-being. However, scientists have generally been working without a clear definition of mismatch. This paper defines mismatch as deviations in the environment that render biological traits unable, or impaired in their ability, to produce their selected effects (i.e., to perform their proper functions in Neander’s sense). The machinery developed by Millikan in connection with her account of proper function, and with her related teleosemantic account of representation, is used to identify four major types, and several subtypes, of evolutionary mismatch. While the taxonomy offered here does not in itself resolve any scientific debates, the hope is that it can be used to better formulate empirical hypotheses concerning the effects of mismatch. To illustrate, it is used to show that the controversial hypothesis that general intelligence evolved as an adaptation to handle evolutionary novelty can, contra some critics, be formulated in a conceptually coherent way.     

Robustness analysis of EGFR signaling network with a multi-objective evolutionary algorithm

Robustness, the ability to maintain performance in the face of perturbations and uncertainty, is believed to be a necessary property of biological systems. In this paper, we address the issue of robustness in an important signal transduction network--epidermal growth factor receptor (EGFR) network. First, we analyze the robustness in the EGFR signaling network using all rate constants against the Gauss variation which was described as "the reference parameter set" in the previous study [Kholodenko, B.N., Demin, O.V., Moehren, G., Hoek, J.B., 1999. Quantification of short term signaling by the epidermal growth factor receptor. J. Biol. Chem. 274, 30169-30181]. The simulation results show that signal time, signal duration and signal amplitude of the EGRR signaling network are relatively not robust against the simultaneous variation of the reference parameter set. Second, robustness is quantified using some statistical quantities. Finally, a multi-objective evolutionary algorithm (MOEA) is presented to search reaction rate constants which optimize the robustness of network and compared with the NSGA-II, which is a representation of a class of modern multi-objective evolutionary algorithms. Our simulation results demonstrate that signal time, signal duration and signal amplitude of the four key components--the most downstream variable in each of the pathways: R-Sh-G-S, R-PLP, R-G-S and the phosphorylated receptor RP in EGRR signaling network for the optimized parameter sets have better robustness than those for the reference parameter set and the NSGA-II. These results can provide valuable insight into experimental designs and the dynamics of the signal-response relationship between the dimerized and activated EGFR and the activation of downstream proteins.     

The temperature-size rule in ectotherms: simple evolutionary explanations may not be general

In many organisms, individuals in colder environments grow more slowly but are larger as adults. This widespread pattern is embodied by two well-established rules: Bergmann's rule, which describes the association between temperature and body size in natural environments, and the temperature-size rule, which describes reaction norms relating temperature to body size in laboratory experiments. Theory predicts that organisms should grow to be larger in colder environments when growth efficiency decreases with increasing environmental temperature. Using data from 97 laboratory experiments, including 58 species of ectotherms, we found little evidence that growth efficiency is negatively related to environmental temperature within the thermal range that is relevant to the temperature-size rule. Instead, growth efficiency was either positively related or insensitive to environmental temperature in the majority of cases (73 of 89 cases for gross growth efficiency and 18 of 24 cases for net growth efficiency). Two possibilities merit consideration. First, high temperatures may impose constraints on growth that only arise late during ontogeny; this simple and potentially general explanation is supported by the fact that thermal optima for growth efficiency and growth rate decrease as individuals grow. Alternatively, the general explanation for relationships between temperature and body size may not be simple. If the latter view is correct, the best approach might be to generate and test theories that are tailored specifically to organisms with similar behavior and physiology.     

Fatness and fitness: exposing the logic of evolutionary explanations for obesity

To explore the logic of evolutionary explanations of obesity we modelled food consumption in an animal that minimizes mortality (starvation plus predation) by switching between activities that differ in energy gain and predation. We show that if switching does not incur extra predation risk, the animal should have a single threshold level of reserves above which it performs the safe activity and below which it performs the dangerous activity. The value of the threshold is determined by the environmental conditions, implying that animals should have variable ‘set points’. Selection pressure to prevent energy stores exceeding the optimal level is usually weak, suggesting that immediate rewards might easily overcome the controls against becoming overweight. The risk of starvation can have a strong influence on the strategy even when starvation is extremely uncommon, so the incidence of mortality during famine in human history may be unimportant for explanations for obesity. If there is an extra risk of switching between activities, the animal should have two distinct thresholds: one to initiate weight gain and one to initiate weight loss. Contrary to the dual intervention point model, these thresholds will be inter-dependent, such that altering the predation risk alters the location of both thresholds; a result that undermines the evolutionary basis of the drifty genes hypothesis. Our work implies that understanding the causes of obesity can benefit from a better understanding of how evolution shapes the mechanisms that control body weight.     

Explaining how and explaining why: developmental and evolutionary explanations of dominance

There have been two different schools of thought on the evolution of dominance. On the one hand, followers of Wright [Wright S. 1929. Am. Nat. 63: 274–279, Evolution: Selected Papers by Sewall Wright, University of Chicago Press, Chicago; 1934. Am. Nat. 68: 25–53, Evolution: Selected Papers by Sewall Wright, University of Chicago Press, Chicago; Haldane J.B.S. 1930. Am. Nat. 64: 87–90; 1939. J. Genet. 37: 365–374; Kacser H. and Burns J.A. 1981. Genetics 97: 639–666] have defended the view that dominance is a product of non-linearities in gene expression. On the other hand, followers of Fisher [Fisher R.A. 1928a. Am. Nat. 62: 15–126; 1928b. Am. Nat. 62: 571–574; Bürger R. 1983a. Math. Biosci. 67: 125–143; 1983b. J. Math. Biol. 16: 269–280; Wagner G. and Burger R. 1985. J. Theor. Biol. 113: 475–500; Mayo O. and Reinhard B. 1997. Biol. Rev. 72: 97–110] have argued that dominance evolved via selection on modifier genes. Some have called these “physiological” versus “selectionist,” or more recently [Falk R. 2001. Biol. Philos. 16: 285–323], “functional,” versus “structural” explanations of dominance. This paper argues, however, that one need not treat these explanations as exclusive. While one can disagree about the most likely evolutionary explanation of dominance, as Wright and Fisher did, offering a “physiological” or developmental explanation of dominance does not render dominance “epiphenomenal,” nor show that evolutionary considerations are irrelevant to the maintenance of dominance, as some [Kacser H. and Burns J.A. 1981. Genetics 97: 639–666] have argued. Recent work [Gilchrist M.A. and Nijhout H.F. 2001. Genetics 159: 423–432] illustrates how biological explanation is a multi-level task, requiring both a “top-down” approach to understanding how a pattern of inheritance or trait might be maintained in populations, as well as “bottom-up” modeling of the dynamics of gene expression.     

Vicious circles: positive feedback in major evolutionary and ecological transitions

Evolutionary biologists and ecologists often focus on equilibrium states that are subject to forms of negative feedback, such as optima for phenotypic traits or regulation of population sizes. However, recent theoretical and empirical studies show how positive feedback can be instrumental in driving many of the most important and spectacular processes in evolutionary ecology, including the evolution of sex and genetic systems, mating systems, life histories, complex cooperation in insects and humans, ecological specialization, species diversity, species ranges, speciation and extinction. Taken together, this work suggests that positive feedback is more common than is generally appreciated, and that its self-reinforcing dynamics generate the conditions for changes that might otherwise be difficult or impossible for selection or other mechanisms to achieve. Testing for positive feedback requires analysing each causal link in feedback loops, tracking genetic, character and population-dynamic changes across generations, and elucidating the conditions that can result in self-reinforcing change.     

Robustness and evolvability: a paradox resolved

Understanding the relationship between robustness and evolvability is key to understand how living things can withstand mutations, while producing ample variation that leads to evolutionary innovations. Mutational robustness and evolvability, a system's ability to produce heritable variation, harbour a paradoxical tension. On one hand, high robustness implies low production of heritable phenotypic variation. On the other hand, both experimental and computational analyses of neutral networks indicate that robustness enhances evolvability. I here resolve this tension using RNA genotypes and their secondary structure phenotypes as a study system. To resolve the tension, one must distinguish between robustness of a genotype and a phenotype. I confirm that genotype (sequence) robustness and evolvability share an antagonistic relationship. In stark contrast, phenotype (structure) robustness promotes structure evolvability. A consequence is that finite populations of sequences with a robust phenotype can access large amounts of phenotypic variation while spreading through a neutral network. Population-level processes and phenotypes rather than individual sequences are key to understand the relationship between robustness and evolvability. My observations may apply to other genetic systems where many connected genotypes produce the same phenotypes.     

An evolutionary account of status, power, and career in modern societies

We hypothesize that in modern societies the striving for high positions in the hierarchy of organizations is equivalent to the striving for status and power in historical and traditional societies. Analyzing a sample of 4,491 US men and 5,326 US women, we find that holding a supervisory position or being in charge of hiring and firing is positively associated with offspring count in men but not in women. The positive effect in men is attributable mainly to the higher proportion of childlessness among men in non-supervisory positions and those without the power to hire and fire. This effect is in accordance with the positive relationship between other status indicators and reproductive success found in men from traditional, historical, and modern societies. In women, we further find a curvilinear relationship between income percentile and offspring number by analyzing US census data, indicating that women may strive for resources associated with advancement rather than for status per se.     

Robustness mechanisms in primate societies: a perturbation study

Conflict management mechanisms have a direct, critical effect on system robustness because they mitigate conflict intensity and help repair damaged relationships. However, robustness mechanisms can also have indirect effects on system integrity by facilitating interactions among components. We explore the indirect role that conflict management mechanisms play in the maintenance of social system robustness, using a perturbation technique to 'knockout' components responsible for effective conflict management. We explore the effects of knockout on pigtailed macaque (Macaca nemestrina) social organization, using a captive group of 84 individuals. This system is ideal in addressing this question because there is heterogeneity in performance of conflict management. Consequently, conflict managers can be easily removed without disrupting other control structures. We find that powerful conflict managers are essential in maintaining social order for the benefit of all members of society. We show that knockout of components responsible for conflict management results in system destabilization by significantly increasing mean levels of conflict and aggression, decreasing socio-positive interaction and decreasing the operation of repair mechanisms.     

Physical explanations and biological explanations,empirical laws and a priori laws

Philosophers intent upon characterizing the difference between physics and biology often seize upon the purported fact that physical explanations conform more closely to the covering law model than biological explanations. Central to this purported difference is the role of laws of nature in the explanations of these two sciences. However, I argue that, although certain important differences between physics and biology can be highlighted by differences between physical and biological explanations, these differences are not differences in the degree to which those explanations conform to the covering law model, which fits biology about as well as it does physics.     

A mechanism and its metaphysics: An evolutionary account of the social and conceptual development of science

The claim that conceptual systems change is a platitude. That our conceptual systems are theory-laden is no less platitudinous. Given evolutionary theory, biologists are led to divide up the living world into genes, organisms, species, etc. in a particular way. No theory-neutral individuation of individuals or partitioning of these individuals into natural kinds is possible. Parallel observations should hold for philosophical theories about scientific theories. In this paper I summarize a theory of scientific change which I set out in considerable detail in a book that I shall publish in the near future. Just as few scientists were willing to entertain the view that species evolve in the absence of a mechanism capable of explaining this change, so philosophers should be just as reticent about accepting a parallel view of conceptual systems in science evolving in the absence of a mechanism to explain this evolution. In this paper I set out such a mechanism. One reason that this task has seemed so formidable in the past is that we have all construed conceptual systems inappropriately. If we are to understand the evolution of conceptual systems in science, we must interpret them as forming lineages related by descent. In my theory, the notion of a family resemblance is taken literally, not metaphorically. In my book, I set out data to show that the mechanism which I propose is actually operative. In this paper, such data is assumed.I wish to thank both Michael Ruse and Ronald Giere for suggesting improvements in an early draft of this paper. This paper is an abstract of a very long book. The number of people who helped me in developing the ideas set out in this book is extremely large, so large that I decided to defer expressing my gratitude to them until its appearance.     

How-possibly explanations as genuine explanations and helpful heuristics: A comment on Forber

Recently, Forber introduced a distinction between two kinds of how-possibly explanation, global and local how-possibly explanation, and argued that both play genuinely explanatory roles in evolutionary biology. In this paper I examine the nature of these two kinds of how-possibly explanations, focusing on the question whether they indeed constitute genuine explanations. I will conclude that one of Forber's kinds of how-possibly explanation may be thought of as a kind of genuine explanation but not as a kind of how-possibly explanation, while the other kind plays a heuristic role and should not be conceived of as a kind of explanation at all.