Darwin's concept of final cause: neither new nor trivial

Darwin'suse of final cause accords with the Aristotelian idea of finalcauses as explanatory types – as opposed to mechanical causes, which arealways particulars. In Wright's consequence etiology, anadaptation is explained by particular events, namely, its past consequences;hence, that etiology is mechanistic at bottom. This justifies Ghiselin'scharge that such versions of teleology trivialize the subject, But a purelymechanistic explanation of an adaptation allows it to appear coincidental.Patterns of outcome, whether biological or thermodynamic, cannot be explainedbytracing causal chains, even were that possible. They are explicanda of aspecialkind. The form of their explanation, in statistical mechanics or by naturalselection, is not captured by statistical variants of the covering-law model orrelated models of explanation. In them as in classical teleology, types ofoutcome are cited to explain why there are outcomes of those types. But onlywhen types are explanatory by being selected for, as inexplanations of animal and human behavior as well as in Darwin's theory ofnatural selection, but not in statistical mechanics, is the explanationteleological. Darwin's theory is nontrivially teleological.     

Why one model is never enough: a defense of explanatory holism

Traditionally, a scientific model is thought to provide a good scientific explanation to the extent that it satisfies certain scientific goals that are thought to be constitutive of explanation (e.g. generating understanding, identifying mechanisms, making predictions, identifying high-level patterns, allowing us to control and manipulate phenomena). Problems arise when we realize that individual scientific models cannot simultaneously satisfy all the scientific goals typically associated with explanation. A given model’s ability to satisfy some goals must always come at the expense of satisfying others. This has resulted in philosophical disputes regarding which of these goals are in fact necessary for explanation, and as such which types of models can and cannot provide explanations (e.g. dynamical models, optimality models, topological models, etc.). Explanatory monists argue that one goal will be explanatory in all contexts, while explanatory pluralists argue that the goal will vary based on pragmatic considerations. In this paper, I argue that such debates are misguided, and that both monists and pluralists are incorrect. Instead of any goal being given explanatory priority over others in a given context, the different goals are all deeply dependent on one another for their explanatory power. Any model that sacrifices some explanatory goals to attain others will always necessarily undermine its own explanatory power in the process. And so when forced to choose between individual scientific models, there can be no explanatory victors. Given that no model can satisfy all the goals typically associated with explanation, no one model in isolation can provide a good scientific explanation. Instead we must appeal to collections of models. Collections of models provide an explanation when they satisfy the web of interconnected goals that justify the explanatory power of one another.     

Phylogeny,fossils, and model systems in the study of evolutionary developmental biology

The emerging field of evolutionary developmental biology (evo-devo) continues to operate largely under a single paradigm. In this paradigm developmental regulatory genes and processes are compared among a collection of "model organisms" selected primarily on the basis of their historical utility in the study of development. This approach has proven to be extremely informative, revealing an unexpected deep evolutionary conservation among developmental genes and genetic systems. Despite its success, concern has been expressed regarding its limitations. We discuss the "model organism" paradigm in evo-devo research. Based on our interpretation of its limitations, we propose a separate but complementary approach that is centered on "model groups." These groups are selected on the basis of their taxonomic affinity and their relevance to questions of interest to evo-devo biologists. We further discuss the Tetraodontiformes (Teleostei, Pisces) as an example of a "model group" for the evo-devo study of vertebrate skeletal elements.     

Symbolic Healing of Early Psychosis: Psychoeducation and Sociocultural Processes of Recovery

This article analyzes sociocultural processes of recovery in a Danish mental health service providing two years of integrated biopsychosocial treatment following first-episode psychosis. The study is based on ethnographic research in the service and person-centered involvement with 15 clients. The analysis applies Dow's [1986 American Anthropologist 88:56-69] model of universal components of symbolic healing to elucidate sociocultural aspects of therapeutic efficacy that are alternatively disregarded as placebo or nonspecific effects. It is demonstrated how staff engaged with clients to deliver "psychoeducation" that provided scientific and biomedical theories about mental illness, constituting a shared "mythic world" that was accepted as an experiential truth and used to explain clients' illness experiences. The analysis highlights the need to supplement attention in Dow's model to the healing procedure with consideration of variability in the healing process. Depending on individual responses to the intervention, the staff's professional backgrounds and staff-client relationships different recovery models were applied. One suggested "episodic psychosis" and full recovery, and the other suggested "chronic schizophrenia" and the necessity of comprehensive life adjustments to the mental illness. The recovery models influenced clients' perspectives on illness and self as they engaged in identity work, negotiating future plans and individual life projects by including also alternative systems of explanation from the wider cultural repertoire.     

Diffusion-limited predator-prey dynamics in Euclidean environments: an allometric individual-based model

We claim that diffusion-limited rates of reaction can be an explanation for the altered population dynamics predicted by models incorporating local interactions and limited individual mobility. We show that the predictions of a spatially explicit, individual-based model result from reduced rates of predation and reproduction caused by limited individual mobility and patchiness. When these reduced rates are used in a mean-field model, there is better agreement with the predictions of the simulation model incorporating local interactions. We also explain previous findings regarding the effects of dimensionality on population dynamics in light of diffusion-limited reactions and Pólya random walks. In particular, we demonstrate that 3D systems are better "stirred" than 2D systems and consequently have a reduced tendency for diffusion-limited interaction rates.     

Introduction to the symposium "New frontiers from marine snakes to marine ecosystems"

Interest in sea snakes and mythological "sea serpents" dates to ancient times and is represented in the writings of Aristotle, early voyagers, and explorers, and references in the Bible. Since then, awareness of the myriad species of snakes inhabiting the oceans has grown at a gradual pace. Scientific investigations into the biology of marine snakes-especially those in behavior, physiology, and other disciplines requiring living animals or tissues-have been comparatively challenging owing to difficulties in acquiring, transporting, handling, and husbanding these secondarily marine vertebrates. A broadening perspective with increasing interest in these animals peaked during the 1960s and 1970s, and literature from this period contributed to a growing knowledge that marine snakes comprise a very diverse fauna and are a significant part of marine ecosystems. Two persons figured prominently as influential drivers of research on sea snakes during this period, namely William Dunson and Harold Heatwole, and this symposium recognizes the contributions of these two individuals. Following a decline in scientific publications on sea snakes during the 1980s and 1990s, there has been a renaissance of scientific interest in recent years, and a wealth of new research findings has improved the understanding of phylogeny and diversity of marine snakes while simultaneously recognizing threats to marine ecosystems arising from climate change and other anthropogenic causes. The purposes of the symposium are to (1) illustrate the importance and relevance of sea snakes as contributors to better understanding a range of issues in marine biology, (2) establish and promote the use of marine systems as models for investigating conceptual issues related to environment, changing climate, and persistence of biological communities, with focus on marine snakes as novel or useful examples, (3) promote interest in sea snakes as useful organisms for study by scientists in a range of disciplines who might presently work with other organisms or systems, and (4) identify leading-edge topics for which studies of marine snakes might contribute uniquely to the advancement of research.     

生态环境研究中压力-状态-响应模型应用的陷阱与改善

压力-状态-响应(Pressure-State-Response,PSR)模型在国内外生态环境研究领域中应用十分广泛,但有关该模型指标遴选的适宜性和科学性则较少受到重视,导致模型在实际应用中存在指标的套用、误用、混用等现象。通过对国内外100多篇PSR模型应用研究文献的梳理与分析,认为:(1)PSR模型的实质是对人地关系的适应、反应与响应的评估,压力(Pressure)更多源于人类活动对自然资源的利用方式与强度,状态(State)是人类活动压力下生态环境自身的质与量的表现,响应(Response)则是对谋求人地关系和谐所做出的制度安排,PSR模型指标遴选宜与之相契合。(2)目前国内外PSR模型应用主要存在内生性(Endogeneity)、矢量性(Vectority)、指示性(Indexicality)、针对性(Pertinence)等四个方面的缺憾。(3)忽视研究目标的指向性、科学问题的针对性、研究对象的特殊性、人地关系的复杂性以及研究者的主观性等,是造成PSR模型应用陷阱的主要因素。最后,本文提出PSR模型的优化与改善路径,以期为生态环境领域的PSR理论实证和实践应用提供参考。     

Agent-based modelling as scientific method: a case study analysing primate social behaviour

A scientific methodology in general should provide two things: first, a means of explanation and, second, a mechanism for improving that explanation. Agent-based modelling (ABM) is a method that facilitates exploring the collective effects of individual action selection. The explanatory force of the model is the extent to which an observed meta-level phenomenon can be accounted for by the behaviour of its micro-level actors. This article demonstrates that this methodology can be applied to the biological sciences; agent-based models, like any other scientific hypotheses, can be tested, critiqued, generalized or specified. We review the state of the art for ABM as a methodology for biology and then present a case study based on the most widely published agent-based model in the biological sciences: Hemelrijk's DomWorld, a model of primate social behaviour. Our analysis shows some significant discrepancies between this model and the behaviour of the macaques, the genus used for our analysis. We also demonstrate that the model is not fragile: its other results are still valid and can be extended to compensate for these problems. This robustness is a standard advantage of experiment-based artificial intelligence modelling techniques over analytic modelling.     

Modeling games from the 20th century

A scientific framework is described in which scientists are cast as problem-solvers, and problems as solved when data are mapped to models. This endeavor is limited by finite attentional capacity which keeps depth of understanding complementary to breadth of vision; and which distinguishes the process of science from its products, scientists from scholars. All four aspects of explanation described by Aristotle trigger, function, substrate, and model are required for comprehension. Various modeling languages are described, ranging from set theory to calculus of variations, along with exemplary applications in behavior analysis.     

Stimulus-induced bifurcations in discrete-time neural oscillators

Based on theoretical issues and neurobiological evidence, considerable interest has recently focused on dynamic computational elements in neural systems. Such elements respond to stimuli by altering their dynamical behavior rather than by changing a scalar output. In particular, neural oscillators capable of chaotic dynamics represent a potentially very rich substrate for complex spatiotemporal information processing. However, the response properties of such systems must be studied in detail before they can be used as computational elements in neural models. In this paper, we focus on the response of a very simple discrete-time neural oscillator model to a fixed input. We show that the oscillator responds to the stimulus through a fairly complex set of bifurcations, and shows critical switching between attractors. This information can be used to construct very sophisticated dynamic computational elements with well-understood response properties. Examples of such elements are presented in the paper. We end with a brief discussion of simple architectures for networks of dynamical elements, and the relevance of our results to neurobiological models. Received: 7 August 1997 / Accepted in revised form: 22 April 1998     

Finding meaning in first episode psychosis: experience, agency, and the cultural repertoire

The article examines individuals' attempts to generate meaning following their experiences with psychosis. The inquiry is based on a person-centered ethnographic study of a Danish mental health community program for early intervention in schizophrenia and involves longitudinal interviews with 15 of its participants. The article takes an existential anthropological perspective emphasizing agency and cultural phenomenology to investigate how individuals draw on resources from the cultural repertoire to make sense of personally disturbing experiences during their psychosis. It is suggested that the concept of "system of explanation" has advantages over, for example, "illness narrative" and "explanatory model" when demonstrating how some individuals engage in the creative analytic and theory-building work of bricolage, selecting, adding, and combining various systems of explanation. Delusions are equally derived from the cultural repertoire but are constructed as dogmatic explanations that are idiosyncratic to the individual who holds them.     

Addressing water needs of freshwater ecosystems in life cycle impact assessment of water consumption: state of the art and applicability of ecohydrological approaches to ecosystem quality characterization

Purpose

In recent history, human development overbalanced towards economic growth has often been accompanied by the degradation and reduction of freshwater resources at the expense of freshwater dependent ecosystems. For their subsistence and correct functioning, understanding environmental water requirements (EWR) represents an area of great interest for life cycle impact assessment (LCIA) and it has been only marginally explored. The aim of this paper is to investigate how this concept has evolved in ecological and hydrological literature and how it can be better integrated in LCIA, to identify potential options for improvement of LCIA indicators in the short, mid and long term.

Methods

To address the limitations of existing LCIA approaches in modelling EWR, four families of EWR methods have been reviewed, namely hydrological, hydraulic, habitat simulation and holistic methods. Based on existing scientific literature and their broad application, 24 methods have been selected and their suitability to be adopted in LCIA has been evaluated against nine criteria, with regard to data management issues, accuracy, scientific robustness, and potential for future development. A semi-quantitative performance score has been subsequently assigned for each criterion, showing the main strengths and weaknesses of selected methods.

Results and discussion

The underlying rationale of the chosen approaches is markedly different, likewise the input information needed and results applicability. Hydrological methods are well suited for the development of global models and they are the only ones currently considered in LCIA, although their applicability remains limited to water stress indicators. Habitat modelling is identified as an essential step for the development of mechanistic LCIA models and endpoint indicators. In this respect, hydraulic, habitat simulation and holistic methods are fit for the purpose. However, habitat simulation methods represent the best compromise between scientific robustness and applicability in LCIA. For this reason, a conceptual framework for the development of habitat-based characterization factors has been proposed. Among the evaluated habitat simulation methods, ESTIMHAB showed the best performance and was the method retained for the development of an LCIA model that will assess the consequences of water consumption on stream ecosystems.

Conclusions

This study identifies the advantages of specific modelling approaches for the assessment of water requirements for ecosystems. Selected methods could support the development of LCIA models at different levels. In the short-term for improving environmental relevance of water stress indicators, and in the mid/long-term to build up midpoint habitat indicators relating water needs of ecosystems with new endpoint metrics.

     

Modelling and simulation of cell growth dynamics, substrate consumption, and lactic acid production kinetics of Lactococcus lactis

Lactococcus lactis species have been and still are extensively investigated due to their significant commercial importance. Current scientific research focuses on strains utilized in food industry, due to their multiple uses in food and beverages fabrication. Biomass of Lactococcus lactis is of great interest as well as the end products of its metabolism such as lactic acid and nisin. However their production is constantly challenged due to end product inhibition occurring during intensive propagation of the coccus in reactor systems. To successfully predict the behavior of the culture, the approach of combining mathematics with biology, ergo the development of an unstructured mathematical model, was taken. Although Luedeking and Piret is the model that has been extensively used to demonstrate growth in end-product inhibition cultures, its applicability is limited due to its dependance on the specific growth and product coefficients, particularly related to the culturing conditions used. To overcome these hurdles, a combination of the non competitive single product end inhibition Taylor and Hinselwood models was used, with the significance of this model laying in the fact that it offers a feasible alternative to the commonly used model of Luedeking and Piret for describing fermentation kinetics governed by end-product inhibitions. The fitting with the experimental values, in batch mode, was tested in terms of the coefficient of determination (R²), having values 0.97 ～ 0.99 and suggesting a very good fitting with the experimental data. The model was further developed to achieve theoretical predictions of volumetric cell productivity in continuous and fed-batch mode of substrate feed in different culturring systems.     

How thick is blood? The plot thickens . . .: if ethnic actors are primordialists,what remains of the circumstantialist / primordialist controversy?

An investigation of the cognitive models underlying ethnic actors' own ideas concerning the acquisition/transmission of an ethnic status is necessary in order to resolve the outstanding differences between "primordial" and "circumstantial" models of ethnicity. This article presents such data from a multiethnic area in Mongolia that found ethnic actors to be heavily primordialist, and uses these data to stimulate a more cogent model of ethnicity that puts the intuitions of both primordialists and circumstantialists on a more secure foundation. Although many points made by the circumstantialists can be accommodated in this framework, the model argues that ethnic cognition is at core primordialist, and ethnic actors' instrumental considerations - and by implication their behaviours - are conditioned and constrained by this primordialist core. The implications of this model of ethnicity for ethnic processes are examined, and data from other parts of the world are revisited for their relevance to its claims.     

Worldwide Topology of the Scientific Subject Profile: A Macro Approach in the Country Level

Background

Models for the production of knowledge and systems of innovation and science are key elements for characterizing a country in view of its scientific thematic profile. With regard to scientific output and publication in journals of international visibility, the countries of the world may be classified into three main groups according to their thematic bias.

Methodology/Principal Findings

This paper aims to classify the countries of the world in several broad groups, described in terms of behavioural models that attempt to sum up the characteristics of their systems of knowledge and innovation. We perceive three clusters in our analysis: 1) the biomedical cluster, 2) the basic science & engineering cluster, and 3) the agricultural cluster. The countries are conceptually associated with the clusters via Principal Component Analysis (PCA), and a Multidimensional Scaling (MDS) map with all the countries is presented.

Conclusions/Significance

As we have seen, insofar as scientific output and publication in journals of international visibility is concerned, the countries of the world may be classified into three main groups according to their thematic profile. These groups can be described in terms of behavioral models that attempt to sum up the characteristics of their systems of knowledge and innovation.     

The importance of models of infection in the study of disease resistance

Models currently occupy the crucial first step in the research flow for the development of new drugs and vaccines. Some animal models are better at reflecting the host–pathogen interaction in humans than others; this depends on the pathogen and its host specificity. Data gathered from what are often poorly adapted models provide a mosaic of sometimes contradictory information, yet there is little incentive to better delineate the relevance of models or to exploit recent advances to develop improved ones. This review reports on three particularly intractable human pathogens – Mycobacterium, Plasmodium and Schistosoma – and reflects that the extent to which these model systems mimic infection and protection processes in humans might not be sufficiently well defined.     

An easy NMR method to study the formation of parallel β-sheets in peptide aggregates

There is currently great interest in the study of peptide aggregation by -sheet formation because of its relevance in pathological states or in the design of self-assembling systems of technological interest. NMR studies of -sheet aggregates are difficult because of their long correlation times and spectral degeneracy. In this communication we demonstrate the combination of a semiselective TOCSY-NOESY experiment with partial deuterium exchange of labile protons to assign inter-molecular NOE cross peaks and prove the presence of a soluble parallel -sheet in fast exchange with monomeric Ac-ASTTTNYT-NH₂ (Ac-T-NH₂) in solution.