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.     

How bright and how nasty: explaining diversity in warning signal strength

The conspicuous displays that warn predators of defenses carried by potential prey have been of interest to evolutionary biologists from the time of Wallace and Darwin to the present day. Although most studies implicitly assume that these "aposematic" warning signals simply indicate the presence of some repellent defense such as a toxin, it has been speculated that the intensity of the signal might reliably indicate the strength of defense so that, for example, the nastiest prey might "shout loudest" about their unprofitability. Recent phylogenetic and empirical studies of Dendrobatid frogs provide contradictory views, in one instance showing a positive correlation between toxin levels and conspicuousness, in another showing a breakdown of this relationship. In this paper we present an optimization model, which can potentially account for these divergent results. Our model locates the optimal values of defensive traits that are influenced by a range of costs and benefits. We show that optimal aposematic conspicuousness can be positively correlated with optimal prey toxicity, especially where population sizes and season lengths vary between species. In other cases, optimal aposematic conspicuousness may be negatively correlated with toxicity; this is especially the case when the marginal costs of aposematic displays vary between members of different populations. Finally, when displays incur no allocation costs there may be no single optimum value for aposematic conspicuousness, rather a large array of alternative forms of a display may have equal fitness.     

Interchromosomal gene conversion as a possible mechanism for explaining divergence patterns of ZFY-related genes

Summary The divergence pattern of mammalian ZFY-related genes from human (ZFY and ZFX) and mouse (Zfy-1 and Zfx) was reexamined on the basis of nucleotide substitutions at the synonymous codon-alternating positions. It is possible to explain the unusual divergence pattern of the mammalian Y-linked ZF genes by interchromosomal gene conversion by X-linked ZF genes. Furthermore, the rates of evolution of mammalian X- and Y-linked ZF genes were shown to agree well with those expected from our model. Offprint requests to: T. Miyata     

Archaeological Inference and Inductive Confirmation

The limitations of the hypothetico-deductive (H-D) method of inductive confirmation are described, and an alternate method, the hypothetico-analog (H-A) method is described in detail. The H-A method can be characterized as a modified and supplemented form of the simple H-D method, and is proposed as being more appropriate for archaeological inference. Aspects of the H-A method that are given particular attention include the establishment of boundary conditions for reference classes, plausibility considerations, multiple working hypotheses, bridging arguments, and criteria for selecting alternative hypotheses . [scientific method, archaeological inference, hypothetico-analog method, inductive confirmation]     

Extending, changing, and explaining the brain

This paper addresses concerns raised recently by Datteri (Biol Philos 24:301–324, 2009) and Craver (Philos Sci 77(5):840–851, 2010) about the use of brain-extending prosthetics in experimental neuroscience. Since the operation of the implant induces plastic changes in neural circuits, it is reasonable to worry that operational knowledge of the hybrid system will not be an accurate basis for generalisation when modelling the unextended brain. I argue, however, that Datteri’s no-plasticity constraint unwittingly rules out numerous experimental paradigms in behavioural and systems neuroscience which also elicit neural plasticity. Furthermore, I propose that Datteri and Craver’s arguments concerning the limitations of prosthetic modelling in basic neuroscience, as opposed to neuroengineering, rests on too narrow a view of the ways models in neuroscience should be evaluated, and that a more pluralist approach is needed. I distinguish organisational validity of models from mechanistic validity. I argue that while prosthetic models may be deficient in the latter of these explanatory virtues because of neuroplasticity, they excel in the former since organisational validity tracks the extent to which a model captures coding principles that are invariant with plasticity. Changing the brain, I conclude, is one viable route towards explaining the brain.     

Measuring and explaining noncompliance in federally managed fisheries

Abstract

This article focuses on measuring and explaining noncompliance in federally managed U.S. fisheries. Novel measurement techniques are used to characterize the extent and patterns of noncompliance in the northeast groundfish fishery. According to the authors’ estimates, noncompliance increased substantially in 1986 and remained high through 1988 in the groundfish fishery. On Georges Bank during 1987, a quarter to a half of all groundfish vessels were identified as frequent violators, committing closed area violations on about one‐third of their trips and using illegal mesh on nearly all trips. Illegal earnings by a typical frequent violator operating in the groundfish fishery on Georges Bank amounted to $225,000 per year in 1987.

A theory of compliance in fisheries is developed and applied to explain the trends and patterns of noncompliance in the northeast groundfish fishery. Biological and economic forces are shown to be dominant causes of the recent deterioration in compliance. Other contributing factors include weak sanctions and insufficient enforcement resources. The article concludes with a prognosis for the fishery and recommendations for improving compliance.     

When and how can homologs overcome errors in the energy estimates and make the 3D structure prediction possible

One still cannot predict the 3D fold of a protein from its amino acid sequence, mainly because of errors in the energy estimates underlying the prediction. However, a recently developed theory [1] shows that having a set of homologs (i.e., the chains with equal, in despite of numerous mutations, 3D folds) one can average the potential of each interaction over the homologs and thus predict the common 3D fold of protein family even when a correct fold prediction for an individual sequence is impossible because the energies are known only approximately. This theoretical conclusion has been verified by simulation of the energy spectra of simplified models of protein chains [2], and the further investigation of these simplified models shows that their true "native" fold can be found by folding of the chain where each interaction potential is averaged over the homologs. In conclusion, the applicability of the "homolog-averaging" approach is tested by recognition of real protein 3D structures. Both the gapless threading of sequences onto the known protein folds [3] and the more practically important gapped threading (which allows to consider not only the known 3D structures, but the more or less similar to them folds as well) shows a significant increase in selectivity of the native chain fold recognition.     

Confirmation of death.

A working party set up to study the problems surrounding the confirmation of death investigated current practice by means of a questionnaire sent to a random sample of accident and emergency departments in district general hospitals. Of the 38 replying, 24 said that bodies were examined in the ambulance, four in the accident and emergency department, and 10 in both. Answers to the other questions also suggest that the present procedures are in general unsatisfactory, and some dissatisfaction was expressed by departments. The individuals and organisations consulted were unanimous that confirmation of death should not be carried out in the ambulance. A change of practice would, however, create practical problems. The working party recommends therefore that the standard practice should be for all bodies to be properly examined by a doctor in the accident and emergency department, and that funds should be made available for any building alterations and increase in staff made necessary by such changes.     

Difference mechanisms: explaining variation with mechanisms

Philosophers of science have developed an account of causal-mechanical explanation that captures regularity, but this account neglects variation. In this article I amend the philosophy of mechanisms to capture variation. The task is to explicate the relationship between regular causal mechanisms responsible for individual development and causes of variation responsible for variation in populations. As it turns out, disputes over this relationship have rested at the heart of the nature–nurture debate. Thus, an explication of the relationship between regular causal mechanisms and causes of variation and between individual development and variation offers both the necessary amendment to the philosophy of mechanisms and the resources to mediate the dispute.     

A conceptual model explaining benthic foraminiferal microhabitats

We present a conceptual model which explains benthic foraminiferal microhabitat preferences in terms of differences in the downward organic flux. We argue that under oligotrophic conditions the microhabitat depth is controlled by the availability of metabolizable food particles in the sediment. Under more eutrophic conditions, the ecosystem is no longer food-controlled, but instead, a critical oxygen level determines down to what depth we find a living fauna. Under food-limited conditions, anaerobic degradation of organic matter may provide an additional food source around the redox front, which could explain deep infaunal maxima reported in the literature. In a sample transect through the Adriatic Sea, both microhabitat controls (food-limited and oxygen-limited) are present. On the shelf and the upper part of the slope, the rather shallow depth of the microhabitat is controlled by a critical oxygen level. In the 1250 m deep southern basin and on the lower part of the slope, on the contrary, the availability of metabolizable organic matter, and not a critical oxygen level, determines down to what depth living foraminifera are found.     

Opinion Dynamics with Confirmation Bias

Background

Confirmation bias is the tendency to acquire or evaluate new information in a way that is consistent with one''s preexisting beliefs. It is omnipresent in psychology, economics, and even scientific practices. Prior theoretical research of this phenomenon has mainly focused on its economic implications possibly missing its potential connections with broader notions of cognitive science.

Methodology/Principal Findings

We formulate a (non-Bayesian) model for revising subjective probabilistic opinion of a confirmationally-biased agent in the light of a persuasive opinion. The revision rule ensures that the agent does not react to persuasion that is either far from his current opinion or coincides with it. We demonstrate that the model accounts for the basic phenomenology of the social judgment theory, and allows to study various phenomena such as cognitive dissonance and boomerang effect. The model also displays the order of presentation effect–when consecutively exposed to two opinions, the preference is given to the last opinion (recency) or the first opinion (primacy) –and relates recency to confirmation bias. Finally, we study the model in the case of repeated persuasion and analyze its convergence properties.

Conclusions

The standard Bayesian approach to probabilistic opinion revision is inadequate for describing the observed phenomenology of persuasion process. The simple non-Bayesian model proposed here does agree with this phenomenology and is capable of reproducing a spectrum of effects observed in psychology: primacy-recency phenomenon, boomerang effect and cognitive dissonance. We point out several limitations of the model that should motivate its future development.     

Proximate and ultimate factors explaining floating behavior in long-lived birds

Avian populations are composed of reproductive individuals coexisting in space and time with young, non-breeding conspecifics or “floaters”. Despite the fact that first breeding can be delayed for years and can exert profound effects on fitness, many aspects of the behavior, ecology and physiology of young floaters remain poorly understood. By means of combining endocrine, behavioral and life history information from a population of black kites (Milvus migrans) monitored long-term, we tested several hypotheses suggesting endocrine function as a determinant of floating status. Sexual function in non-breeding males, estimated through determination of systemic testosterone and progesterone levels, was similar to that in reproductively active conspecifics. Floating females, on the contrary, displayed an endocrine pattern of circulating estrogens and progesterone that was parallel in timing but reduced in magnitude as compared to breeders. Our results suggest that floaters are not physiologically constrained to reproduce, but the cost-benefit balance of attaining complete gonadal function is sexually dependent. While young, unmated males could increase their breeding prospects by attaining sexual maturity regardless of their social environment, natural selection would favor females relying on social cues to mature. Consistent with the sexual roles of socially monogamous species, gonadal recrudescence and testosterone production would allow unmated males to access breeding resources (e.g. through male-male competition and extra-pair fertilizations). Unmated females, on the contrary, would reduce physiological costs by means of delaying ovarian maturation until establishing pair bonds with a male providing access to breeding resources.     

青鳉与食蚊鱼竞争排斥的生态形态学解释

生态形态学理论指出,形态相似的物种生态位相似,是导致种间竞争排斥的关键性因素。在鱼类入侵生态学研究中引入生态形态学理论,对于加深理解入侵种与土著种的种间相互关系有着重要意义。本文利用形态分析方法,对广东怀集燕都国家湿地公园入侵种食蚊鱼对土著种鳍斑青鳉和弓背青鳉的影响机制进行研究。结果表明: 弓背青鳉和鳍斑青鳉在研究区域常同域分布,但两者的空间分布格局差异显著。两者形态高度相似,符合生态形态学“形态相似者竞争排斥”理论。与群落其他鱼类相比,食蚊鱼与2种青鳉鱼类形态更为相似。聚类分析发现,食蚊鱼和青鳉鱼类聚合在同一分枝,且其空间生态位的重叠度极低。种群相对密度调查显示,食蚊鱼与青鳉鱼类种群数量呈显著的负相关关系。食蚊鱼的入侵是导致2种青鳉鱼类种群数量明显下降的关键原因。形态特征的相似性能够初步解释食蚊鱼与青鳉鱼类的竞争排斥关系,尚需从不同角度就食蚊鱼入侵对青鳉鱼类的作用机制进行深入探索。     

Quantitative social dialectology: explaining linguistic variation geographically and socially

In this study we examine linguistic variation and its dependence on both social and geographic factors. We follow dialectometry in applying a quantitative methodology and focusing on dialect distances, and social dialectology in the choice of factors we examine in building a model to predict word pronunciation distances from the standard Dutch language to 424 Dutch dialects. We combine linear mixed-effects regression modeling with generalized additive modeling to predict the pronunciation distance of 559 words. Although geographical position is the dominant predictor, several other factors emerged as significant. The model predicts a greater distance from the standard for smaller communities, for communities with a higher average age, for nouns (as contrasted with verbs and adjectives), for more frequent words, and for words with relatively many vowels. The impact of the demographic variables, however, varied from word to word. For a majority of words, larger, richer and younger communities are moving towards the standard. For a smaller minority of words, larger, richer and younger communities emerge as driving a change away from the standard. Similarly, the strength of the effects of word frequency and word category varied geographically. The peripheral areas of the Netherlands showed a greater distance from the standard for nouns (as opposed to verbs and adjectives) as well as for high-frequency words, compared to the more central areas. Our findings indicate that changes in pronunciation have been spreading (in particular for low-frequency words) from the Hollandic center of economic power to the peripheral areas of the country, meeting resistance that is stronger wherever, for well-documented historical reasons, the political influence of Holland was reduced. Our results are also consistent with the theory of lexical diffusion, in that distances from the Hollandic norm vary systematically and predictably on a word by word basis.