Ecology

2018 ◽  
Author(s):  
John Beatty
Keyword(s):  
Evolutionary Biology ◽  
Comparative Methods ◽  
Related Question ◽  
Historical Contingency ◽  
Causal Connections ◽  
Methodological Problems ◽  
Ecological Hierarchy

Philosophers of science have paid relatively little attention to ecology (compared to other areas of biology like evolution and genetics), but ecology poses many interesting foundational and methodological problems. For example, the problems of clarifying the differences and causal connections between the various levels of the ecological hierarchy (organism, population, community, ecosystem…); the issue of how central evolutionary biology is to ecology; long-standing issues concerning the extent to which the domain of ecology is more law-governed or more a matter of historical contingency, and the related question of whether ecologists should rely more on laboratory/manipulative versus field/comparative methods of investigation.

What Sort of Science Is Evolutionary Biology?

Dialogue ◽  
1991 ◽  
Vol 30 (1-2) ◽  
pp. 129-142
Author(s):  
Mohan Matthen
Keyword(s):  
Population Biology ◽  
Evolutionary Biology ◽  
Evolutionary Epistemology ◽  
Main Theme ◽  
Semantic Account ◽  
Methodological Problems ◽  
Methodological Aspects

Paul Thompson's new book,The Structure of Biological Theories, is about the formalization of evolutionary biology. He is primarily concerned, he says, with the logical, epistemological, and methodological aspects of biological theorizing. The main theme of the book is the opposition between what Thompson calls the syntactic and the semantic conceptions of theories. He wishes to establish that the semantic account is superior to the syntactic in at least three areas: first, it offers a more faithful account of population biology; second, it facilitates a conception of evolutionary biology as a family of interacting theories; finally, it offers us a richer framework for the resolution of methodological problems that have plagued sociobiology and evolutionary epistemology.

Darwin’s molecule

Hemoglobin ◽  
2018 ◽  
pp. 201-232
Author(s):  
Jay F. Storz
Keyword(s):  
Protein Function ◽  
Evolutionary Biology ◽  
Lessons Learned ◽  
Atomic Resolution ◽  
Molecular Adaptation ◽  
Genetic Adaptation ◽  
Biochemical Phenotype ◽  
Causal Connections ◽  
Model Molecule ◽  
Model Protein

Chapter 9 discusses conceptual issues in protein evolution and provides a synthesis of lessons learned from studies of hemoglobin function. Using hemoglobin as a model molecule, we can exploit an unparalleled base of knowledge about structure-function relationships and we can characterize biophysical mechanisms of molecular adaptation at atomic resolution. It is therefore possible to document causal connections between genotype and biochemical phenotype at an unsurpassed level of rigor and detail. Moreover, since the oxygenation properties of hemoglobin provide a direct link between ambient O2 availability and aerobic metabolism, genetically based changes in protein function can be related to ecologically relevant aspects of organismal physiology. We therefore have a solid theoretical framework for making predictions and for interpreting observed associations between biochemical phenotype and fitness-related measures of whole-animal physiological performance. The chapter explores case studies that illustrate how experimental research on functional properties of a well-chosen model protein can be used to address some of the most conceptually expansive questions in evolutionary biology: Is genetic adaptation predictable? Why does evolution follow some pathways rather than others?

scholarly journals Phylogenetic Comparative Methods and the Evolution of Multivariate Phenotypes

2019 ◽  
Vol 50 (1) ◽  
pp. 405-425 ◽  
Author(s):  
Dean C. Adams ◽  
Michael L. Collyer
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary Biology ◽  
Generalized Least Squares ◽  
Comparative Methods ◽  
High Dimensional ◽  
Phenotypic Integration ◽  
Phylogenetic Comparative Methods ◽  
Evolutionary Trends ◽  
Phenotype Space ◽  
Multivariate Phenotypes

Evolutionary biology is multivariate, and advances in phylogenetic comparative methods for multivariate phenotypes have surged to accommodate this fact. Evolutionary trends in multivariate phenotypes are derived from distances and directions between species in a multivariate phenotype space. For these patterns to be interpretable, phenotypes should be characterized by traits in commensurate units and scale. Visualizing such trends, as is achieved with phylomorphospaces, should continue to play a prominent role in macroevolutionary analyses. Evaluating phylogenetic generalized least squares (PGLS) models (e.g., phylogenetic analysis of variance and regression) is valuable, but using parametric procedures is limited to only a few phenotypic variables. In contrast, nonparametric, permutation-based PGLS methods provide a flexible alternative and are thus preferred for high-dimensional multivariate phenotypes. Permutation-based methods for evaluating covariation within multivariate phenotypes are also well established and can test evolutionary trends in phenotypic integration. However, comparing evolutionary rates and modes in multivariate phenotypes remains an important area of future development.

The Social Turn in Moral Psychology

2017 ◽  
Author(s):  
Mark Fedyk
Keyword(s):  
Social Sciences ◽  
Moral Psychology ◽  
Evolutionary Biology ◽  
Ethical Theory ◽  
Scientific Practice ◽  
Human Life ◽  
The Social ◽  
Philosophical Ethics ◽  
Methodological Problems ◽  
The Relationship

In this book, Mark Fedyk offers a novel analysis of the relationship between moral psychology and allied fields in the social sciences. Fedyk shows how the social sciences can be integrated with moral philosophy, argues for the benefits of such an integration, and offers a new ethical theory that can be used to bridge research between the two. Fedyk argues that moral psychology should take a social turn, investigating the psychological processes that motivate patterns of social behavior defined as ethical using normative information extracted from the social sciences. He points out methodological problems in conventional moral psychology, particularly the increasing methodological and conceptual inconsilience with both philosophical ethics and evolutionary biology. Fedyk's "causal theory of ethics" is designed to provide moral psychology with an ethical theory that can be used without creating tension between its scientific practice and the conceptual vocabulary of philosophical ethics. His account aims both to redirect moral psychology toward more socially realistic questions about human life and to introduce philosophers to a new form of ethical naturalism—a way of thinking about how to use different fields of scientific research to answer some of the traditional questions that are at the heart of ethics.

scholarly journals Diachronic change in Indo-European motion event encoding

2014 ◽  
Vol 4 (1) ◽  
pp. 40-83 ◽  
Author(s):  
Annemarie Verkerk
Keyword(s):  
Evolutionary Biology ◽  
Comparative Methods ◽  
Comparative Data ◽  
Historical Change ◽  
Phylogenetic Comparative Methods ◽  
Diachronic Change ◽  
Motion Event ◽  
The World ◽  
Historical Comparative ◽  
Made In

There are many different syntactic constructions that languages can use to encode motion events. In recent decades, great advances have been made in the description and study of these syntactic constructions from languages spoken around the world (Talmy 1985, 1991, Slobin 1996, 2004). However, relatively little attention has been paid to historical change in these systems (exceptions are Vincent 1999, Dufresne, Dupuis & Tremblay 2003, Kopecka 2006 and Peyraube 2006). In this article, diachronic change of motion event encoding systems in Indo-European is investigated using the available historical–comparative data and phylogenetic comparative methods adopted from evolutionary biology. It is argued that Proto-Indo-European was not satellite-framed, as suggested by Talmy (2007) and Acedo Matellán and Mateu (2008), but had a mixed motion event encoding system, as is suggested by the available historical–comparative data.

scholarly journals SOME CONCEPTUAL AND METHODOLOGICAL ISSUES ON HAPPINESS: LESSONS FROM EVOLUTIONARY BIOLOGY

2015 ◽  
Vol 60 (04) ◽  
pp. 1540001 ◽  
Author(s):  
YEW-KWANG NG
Keyword(s):  
Evolutionary Biology ◽  
Well Being ◽  
Scientific Study ◽  
Methodological Issues ◽  
Methodological Problems ◽  
Fitness Maximization ◽  
Happiness Measurement

Despite recent intense interest, happiness studies have been impeded by some conceptual and methodological problems, including viewing happiness (well-being/welfare) as different over different persons, as relative, multi-dimensional, non-cardinally measurable, interpersonally non-comparable and using non-cardinal and interpersonally non-comparable methods of happiness measurement. Using the evolutionary biology of happiness, this paper argues that happiness is absolute, universal, and uni-dimensional and is also cardinally measurable and interpersonally comparable. This is needed to make choices motivated by reward (pleasure) and punishment (pain) consistent with fitness maximization. However, happiness indices obtained by virtually all existing methods of happiness measurement are largely non-cardinal and non-comparable, making the use of averaging in group happiness indices of dubious philosophical validity. A method of measuring happiness to give cardinal and interpersonally comparable indices is discussed. These may contribute towards the more scientific study of happiness that is based on sounder methodological grounds as well as yielding more useful results.

scholarly journals Special care is needed in applying phylogenetic comparative methods to gene trees with speciation and duplication nodes

2019 ◽  
Author(s):  
Tina Begum ◽  
Marc Robinson-Rechavi
Keyword(s):  
Functional Genomics ◽  
Gene Function ◽  
Evolutionary Biology ◽  
Tissue Specificity ◽  
Comparative Methods ◽  
Pairwise Comparisons ◽  
Phylogenetic Comparative Methods ◽  
Gene Trees ◽  
Time Calibration ◽  
Branch Lengths

AbstractHow gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, since genes, like species, are phylogenetically related. Phylogenetic comparative methods should allow to correct for this, but they depend on strong assumptions, including unbiased tree estimates relative to the hypothesis being tested. Such methods have recently been used to test the “ortholog conjecture”, the hypothesis that functional evolution is faster in paralogs than in orthologs. Whereas pairwise comparisons of tissue specificity (τ) provided support for the ortholog conjecture, phylogenetic independent contrasts did not. Our reanalysis on the same gene trees identified problems with the time calibration of duplication nodes. We find that the gene trees used suffer from important biases, due to the inclusion of trees with no duplication nodes, to the relative age of speciations and duplications, to systematic differences in branch lengths, and to non-Brownian motion of tissue-specificity on many trees. We find that incorrect implementation of phylogenetic method in empirical gene trees with duplications can be problematic. Controlling for biases allows to successfully use phylogenetic methods to study the evolution of gene function, and provides some support for the ortholog conjecture using three different phylogenetic approaches.

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