Neutral theory in community ecology

One of the central goals of community ecology is to understand the forces that maintain species diversity within communities. The traditional niche-assembly theory asserts that species live together in a community only when they differ from one another in resource uses. But this theory has some difficulties in explaining the diversity often observed in specie-rich communities such as tropical forests. As an alternative to the niche theory, Hubbell and other ecologists introduced a neutral model. Hubbell argues that the number of species in a community is controlled by species extinction and immigration or speciation of new species. Assuming that all individuals of all species in a trophically similar community are ecologically equivalent, Hubbell’s neutral theory predicts two important statistical distributions. One is the asymptotic log-series distribution for the metacommunities under point mutation speciation, and the other is the zero-sum multinomial distribution for both local communities under dispersal limitation and metacommunities under random fission speciation. Unlike the niche-assembly theory, the neutral theory takes similarity in species and individuals as a starting point for investigating species diversity. Based on the fundamental processes of birth, death, dispersal and speciation, the neutral theory provided the first mechanistic explanation of species abundance distribution commonly observed in natural communities. Since the publication of the neutral theory, there has been much discussion about it, pro and con. In this paper, we summarize recent progress in the assumption, prediction and speciation mode of the neutral theory, including progress in the theory itself, tests about the assumption of the theory, prediction and speciation mode at the metacommunity level. We also suggest that the most important task in the future is to bridge the niche-assembly theory and the neutral theory, and to add species differences to the neutral theory and more stochasticity to the niche theory. __________ Translated from Journal of Plant Ecology, 2006, 30(5): 868–877 [译自:植物生态学报]     

Can the theory of evolution be falsified?

In this paper we discuss the epistemological positions of evolution theories. A sharp distinction is made between the theory that species evolved from common ancestors along specified lines of descent (here called the theory of common descent), and the theories intended as causal explanations of evolution (e.g. Lamarck's and Darwin's theory). The theory of common descent permits a large number of predictions of new results that would be improbable without evolution. For instance, (a) phylogenetic trees have been validated now; (b) the observed order in fossils of new species discovered since Darwin's time could be predicted from the theory of common descent; (c) owing to the theory of common descent, the degrees of similarity and difference in newly discovered properties of more or less related species could be predicted. Such observations can be regarded as attempts to falsify the theory of common descent. We conclude that the theory of common descent is an easily-falsifiable & often-tested & still-not-falsified theory, which is the strongest predicate a theory in an empirical science can obtain. Theories intended as causal explanations of evolution can be falsified essentially, and Lamarck's theory has been falsified actually. Several elements of Darwin's theory have been modified or falsified: new versions of a theory of evolution by natural selection are now the leading scientific theories on evolution. We have argued that the theory of common descent and Darwinism are ordinary, falsifiable scientific theories.     

The Need for a Kinetics for Biological Transport

The traditional theory of transport across capillary membranes via a laminar Poiseuille flow is shown to be invalid. It is demonstrated that the random, diffusive nature of the molecular flow and interactions with the “pore” walls play an important role in the transport process. Neither the continuum Navier-Stokes theory nor the equivalent theory of irreversible thermodynamics is adequate to treat the problem. Combination of near-continuum hydrodynamic theory, noncontinuum kinetic theory, and the theory of fluctuations provides a first step toward modeling both liquid processes in general and membrane transport processes as a specific application.     

Selected effects and causal role functions in the brain: the case for an etiological approach to neuroscience

Despite the voluminous literature on biological functions produced over the last 40 years, few philosophers have studied the concept of function as it is used in neuroscience. Recently, Craver (forthcoming; also see Craver 2001) defended the causal role theory against the selected effects theory as the most appropriate theory of function for neuroscience. The following argues that though neuroscientists do study causal role functions, the scope of that theory is not as universal as claimed. Despite the strong prima facie superiority of the causal role theory, the selected effects theory (when properly developed) can handle many cases from neuroscience with equal facility. It argues this by presenting a new theory of function that generalizes the notion of a ‘selection process’ to include processes such as neural selection, antibody selection, and some forms of learning—that is, to include structures that have been differentially retained as well as those that have been differentially reproduced. This view, called the generalized selected effects theory of function, will be defended from criticism and distinguished from similar views in the literature.     

The Inheritance of Features

Since the discovery of the double helical structure of DNA, the standard account of the inheritance of features has been in terms of DNA-copying and DNA-transmission. This theory is just a version of the old theory according to which the inheritance of features is explained by the transfer at conception of some developmentally privileged material from parents to offspring. This paper does the following things: (1) it explains what the inheritance of features is; (2) it explains how the DNA-centric theory emerged; (3) it clarifies the relation between the DNA-centric theory and the ‘unfolding’ theory of development; (4) it argues that (given what we now know about developmental processes and genetic activity) the DNA-centric theory should be abandoned in favour of a pluralistic (but not holistic) theory of the inheritance of features. According to this pluralistic theory, the reliable reoccurrence of phenotypes must be explained by appealing not only to processes responsible for the reliable reoccurrence of genetic developmental factors but also to processes responsible for the reliable reoccurrence (or persistence) of nongenetic developmental factors.     

The evolution of theory of mind on welfare tradeoff ratios

People seem to attribute beliefs and desires to another person when interacting with them. Such a “theory of mind” capacity is essential for complex and uniquely human behavior such as language, but its evolutionary origin remains elusive. Using the formal tools of evolutionary game theory, we asked what environmental properties are necessary to select for a basic form of theory of mind—the ability to infer the prosociality, quantified by the welfare tradeoff ratio, of another person toward oneself. We found that none of the environments studied in classical or evolutionary game theory give an advantage to this form of theory of mind capacities; theory of mind is advantageous only in a new class of environments with stable opponents and variable payoff structures. In two behavioral experiments (n = 91) we verified that people can, and do use theory of mind in such an environment. These results suggest that some features of early humans’ social environment that were previously neglected in evolutionary game theory may be responsible for the evolution of people’s complex social capacities.     

Methodological problems in evolutionary biology I. Testability and tautologies

The impact of philosophy of science on biology is slight. Evolutionary biology, however, is nowadays an exception. The status of the neo-Darwinian (synthetic) theory of evolution is seriously challenged from a methodological perspective. However, the methodology used in the relevant discussions is plainly defective. A correct application of methodology to evolutionary theory leads to the following conclusions. (a) The theory of natural selection (the core of neo-Darwinism) is unfalsifiable in a strict sense of the term. This, however, does not militate against the theory, because no scientific theory whatever is testable in this way. Under a more liberal testability criterion, the theory is surely testable. None the less, certain (not all) research programs may tend to make the theory untestable in practice. (b) It has often been argued that the tautologous character of the principle of natural selection, allegedly the focus of evolutionary theory, makes the theory untestable through circular reasoning. Actually, the principle is only a tautology if ‘fitness’ is wrongly defined in terms of actual survival. But even then circular reasoning need not ensue. (c) Evolutionary principles do not permit, without additional information, the derivation of statements about evolutionary events concerning particular species or populations. If this were a reason to criticize the theory (as has been argued in the literature), any other scientific theory would be inadequate by the same token.     

Nepotism absent in insect societies — or is it?

Inclusive fitness theory, put forward by English biologist William Hamilton in 1964, is considered by many as the most important addition to the theory of natural selection since Darwin. One prediction of the theory is that animals should often show a tendency to nepotistically favour close relatives. Goodisman et al. (2007 ) test this theory for the first time using molecular methods in a vespine wasp, the eastern yellowjacket, Vespula maculifrons. Somewhat surprisingly, nepotism was found to be absent. This begs the question why nepotism is predicted by theory, yet in a growing list of species is shown to be absent. Is inclusive fitness theory in trouble? As we show, it is not: costs and constraints explain the general absence of queen rearing nepotism, and nepotism in insect societies in fact is well supported in the context of male rearing and manipulation of colony sex ratios.     

Is there a general theory of community ecology?

Community ecology entered the 1970s with the belief that niche theory would supply a general theory of community structure. The lack of wide-spread empirical support for niche theory led to a focus on models specific to classes of communities such as lakes, intertidal communities, and forests. Today, the needs of conservation biology for metrics of “ecological health” that can be applied across types of communities prompts a renewed interest in the possibility of general theory for community ecology. Disputes about the existence of general patterns in community structure trace at least to the 1920s and continue today almost unchanged in concept, although now expressed through mathematical modeling. Yet, a new framework emerged in the 1980s from findings that community composition and structure depend as much on the processes that bring species to the boundaries of a community as by processes internal to a community, such as species interactions and co-evolution. This perspective, termed “supply-side ecology”, argued that community ecology was to be viewed as an “organic earth science” more than as a biological science. The absence of a general theory of the earth would then imply a corresponding absence of any general theory for the communities on the earth, and imply that the logical structure of theoretical community ecology would consist of an atlas of models special to place and geologic time. Nonetheless, a general theory of community ecology is possible similar in form to the general theory for evolution if the processes that bring species to the boundary of a community are analogized to mutation, and the processes that act on the species that arrive at a community are analogized to selection. All communities then share some version of this common narrative, permitting general theorems to be developed pertaining to all ecological communities. Still, the desirability of a general theory of community ecology is debatable because the existence of a general theory suppresses diversity of thought even as it allows generalizations to be derived. The pros and cons of a general theory need further discussion.     

What Conceptions do Greek School Students Form about Biological Evolution?

In Greece, since 2000, the teaching of evolutionary theory is restricted solely to lower (junior) high school and specifically to ninth grade. Even though the theory of evolution is included to the 12th grade biology textbook, it is not taught in Greek upper (senior) high schools. This study presents research conducted on the conceptions of Greek students regarding issues set out in the theory of evolution after the formal completion of the teaching of the theory. The sample comprised 411 10th grade students from 12 different schools. The research results show that the students appear to have a positive view of the idea of evolution, the evolution of man, and the common origin of organisms. However, they have retained many alternative views, or else they are completely in ignorance of basic issues in evolutionary theory regarding: what is considered evolution in biology, the main mechanism of evolutionary changes in what is considered natural selection, what the theory of evolution actually explains, and what the word theory means in science. At least in Greece, these views still prevail because the theory of evolution is marginalized in the teaching of biology in Greek schools, and biology education does not help students formulate overall conceptual structures to enable them to understand the question of biological change.

Asymptotic and explicit formulae for a non-markovian model with linear transition rule

Asymptotic and explicit formulae are obtained for the n-step stochastic kernel of a special class of non-MARKOVIAN models with linear transition rule which occur in learning theory, adaption theory, control theory, and biological research.     

Effective continuing professional development for translating shared decision making in primary care: A study protocol

Background

There is growing interest in the use of cognitive, behavioural, and organisational theories in implementation research. However, the extent of use of theory in implementation research is uncertain.

Methods

We conducted a systematic review of use of theory in 235 rigorous evaluations of guideline dissemination and implementation studies published between 1966 and 1998. Use of theory was classified according to type of use (explicitly theory based, some conceptual basis, and theoretical construct used) and stage of use (choice/design of intervention, process/mediators/moderators, and post hoc/explanation).

Results

Fifty-three of 235 studies (22.5%) were judged to have employed theories, including 14 studies that explicitly used theory. The majority of studies (n = 42) used only one theory; the maximum number of theories employed by any study was three. Twenty-five different theories were used. A small number of theories accounted for the majority of theory use including PRECEDE (Predisposing, Reinforcing, and Enabling Constructs in Educational Diagnosis and Evaluation), diffusion of innovations, information overload and social marketing (academic detailing).

Conclusions

There was poor justification of choice of intervention and use of theory in implementation research in the identified studies until at least 1998. Future research should explicitly identify the justification for the interventions. Greater use of explicit theory to understand barriers, design interventions, and explore mediating pathways and moderators is needed to advance the science of implementation research.     

A Systematic Review Exploring the Social Cognitive Theory of Self-Regulation as a Framework for Chronic Health Condition Interventions

Background

Theory is often recommended as a framework for guiding hypothesized mechanisms of treatment effect. However, there is limited guidance about how to use theory in intervention development.

Methods

We conducted a systematic review to provide an exemplar review evaluating the extent to which use of theory is identified and incorporated within existing interventions. We searched electronic databases PubMed, PsycINFO, CENTRAL, and EMBASE from inception to May 2014. We searched clinicaltrials.gov for registered protocols, reference lists of relevant systematic reviews and included studies, and conducted a citation search in Web of Science. We included peer-reviewed publications of interventions that referenced the social cognitive theory of self-regulation as a framework for interventions to manage chronic health conditions. Two reviewers independently assessed articles for eligibility. We contacted all authors of included studies for information detailing intervention content. We describe how often theory mechanisms were addressed by interventions, and report intervention characteristics used to address theory.

Results

Of 202 articles that reported using the social cognitive theory of self-regulation, 52% failed to incorporate self-monitoring, a main theory component, and were therefore excluded. We included 35 interventions that adequately used the theory framework. Intervention characteristics were often poorly reported in peer-reviewed publications, 21 of 35 interventions incorporated characteristics that addressed each of the main theory components. Each intervention addressed, on average, six of eight self-monitoring mechanisms, two of five self-judgement mechanisms, and one of three self-evaluation mechanisms. The self-monitoring mechanisms ‘Feedback’ and ‘Consistency’ were addressed by all interventions, whereas the self-evaluation mechanisms ‘Self-incentives’ and ‘External rewards’ were addressed by six and four interventions, respectively. The present review establishes that systematic review is a feasible method of identifying use of theory as a conceptual framework for existing interventions. We identified the social cognitive theory of self-regulation as a feasible framework to guide intervention development for chronic health conditions.     

Invasive cancers are not necessarily from preformed in situ tumours — an alternative way of carcinogenesis from misplaced stem cells

Cancers are thought to be the result of accumulated gene mutations in cells. Carcinomas, which are cancers arising from epithelial tissues usually go through several stages of development: atypical hyperplasia, carcinoma in situ and then invasive carcinoma, which might further metastasize. However, we think that the present pathological data are enough to prove that there might be an alternative way of carcinogenesis. We propose that majority of invasive cancers arise in the connective tissue stroma de novo, from the misplaced epithelial stem cells which come to the wrong land of connective tissue stroma by accident. The in situ carcinomas, which are mostly curable, should not be considered genuine cancer, but rather as quasi‐cancer. We design this new theory of carcinogenesis as the stem cell misplacement theory (SCMT). Our SCMT theory chains together other carcinogenesis theories such as the inflammation‐cancer chain, the stem cell theory and the tissue organization field theory. However, we deny the pathway of somatic mutation theory as the major pathway of carcinogenesis.     

How evolutionary biology challenges the classical theory of rational choice

A fundamental philosophical question that arises in connection with evolutionary theory is whether the fittest patterns of behavior are always the most rational. Are fitness and rationality fully compatible? When behavioral rationality is characterized formally as in classical decision theory, the question becomes mathematically meaningful and can be explored systematically by investigating whether the optimally fit behavior predicted by evolutionary process models is decision-theoretically coherent. Upon investigation, it appears that in nontrivial evolutionary models the expected behavior is not always in accord with the norms of the standard theory of decision as ordinarily applied. Many classically irrational acts, e.g. betting on the occurrence of one event in the knowledge that the probabilities favor another, can under certain circumstances constitute adaptive behavior. One interesting interpretation of this clash is that the criterion of rationality offered by classical decision theory is simply incorrect (or at least incomplete) as it stands, and that evolutionary theory should be called upon to provide a more generally applicable theory of rationality. Such a program, should it prove feasible, would amount to the logical reduction of the theory of rational choice to evolutionary theory.     

Elastic,not plastic species: Frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms

Background  

Darwin's evolutionary theory could easily explain the evolution of adaptive traits (organs and behavioral patterns) in asexual but not in sexual organisms. Two models, the selfish gene theory and frozen plasticity theory were suggested to explain evolution of adaptive traits in sexual organisms in past 30 years.     

BLAIR'S "CONDENSER THEORY" OF NERVE EXCITATION

Blair''s recent theory of excitation is analysed with the following conclusions: 1. The theory is inapplicable to currents of long duration; i.e., slowly increasing currents and the opening excitation. 2. The theory is a modification of the condenser theory of excitation but the modification is to be rejected on three grounds: (a) The modification has no obvious physical significance. (b) It does not in fact remedy the divergence between calculation and observation. (c) It leads to certain conclusions of a surprising kind which are contrary to observed fact. 3. The qualitative value of the condenser theory is demonstrated by the fairly close agreement between calculation and observation over a considerable field of enquiry.     

Origin of pre‐islamic architecture in West‐Africa

’Cultural theory’, launched by social anthropologist Mary Douglas, has been highly influential in the inter‐disciplinary field concerned with the study of risk perception and risk communication. The theory derives from the grid‐group analyses that Douglas developed in the 1970s. Cultural theory aims to explain universal ‘cultural bias’ by way of a general typology of group formation and a concomitant cosmology or world view. This article critically examines cultural theory and the study of hazards as culturally construed phenomena.     

Stationary Probabilities and Asymptotic Behaviour of a non-Markovian Model with Linear Transition Rule

Explicit and recursive formulae are obtained for the n-step stochastic kernel, and its stationarity and asymptotic behaviour is examined for a special class of non-Markovian models with a linear transition rule occuring in learning theory, adaption theory, control theory, and biological research.     

Parent–Offspring Conflict in Primates

Parent–offspring conflict (POC) theory (Trivers, 1974) has stimulated controversy in evolutionary biology and behavioral ecology. The theory has been criticized by some primate behavioral researchers on both conceptual and empirical grounds. First, it has been argued that it would be more advantageous to mothers and offspring to agree over the allocation of parental investment and to cooperate rather than to disagree and engage in conflict. Second, some studies have provided data suggesting that primate mothers and offspring engage in behavioral conflict over the scheduling of their activities rather than parental investment. In reality, parent–offspring interactions are likely to involve both cooperation and conflict, and the hypothesis that mothers and infants squabble over the scheduling of their activities is not incompatible with POC theory. Furthermore, the predictions of POC theory are supported by a number of empirical studies of primates. POC theory has enhanced our understanding of the dynamics of parent–offspring relationships in many animal species, and it is very likely that future studies of primates will continue to benefit from using POC theory as an explanatory framework.