Here we endorse Hull’s replicator/interactor framework as providing the overarching understanding sought by MacCord and Maienschein. We suggest that difficulties in seeing the regeneration of limbs by salamanders and of forest ecosystems after fires as similar evolutionary processes can be overcome in this framework. In generalizing Dawkins’s “selfish gene” perspective, Hull defined natural selection as “a process in which the differential extinction and proliferation of interactors causes the differential perpetuation of the replicators that produced them”. Although genes and bacteria are (...) simultaneously both replicators and interactors, communities and ecosystems are generally only interactors. As reproducers, members of sexual species are intermediate. Within such species, organisms are indeed the interactors whose “differential extinction and proliferation” causes the “differential perpetuation” of replicators. But sexually-reproducing organisms do not individually replicate, persist, or recur as interactors, and in consequence it is only those genes causing an interactor differential that are specifically perpetuated in the long run. Higher-level interactors may seldom if ever reproduce, but their recurrence does enable the “differential perpetuation” of replicators specifically responsible for their “differential extinction and proliferation”. In offering answers to the question “What are the replicators specifically responsible for the differential extinction and proliferation of such higher-level entities?” we hope to unify adaptive regeneration across scales, from organisms to ecosystems. (shrink)

Phenotypic plasticity, or an organism’s capacity to change its phenotype in response to environmental variation, is a pervasive—perhaps even ubiquitous—feature of the biological world. Accordingly, plasticity research suggests serious implications for biological theory, including evolutionary theory. The theoretical implications of plasticity have growing support from empirical literature documenting the range, extent, and adaptiveness of plasticity. However, the empirical evidence for particular instances of plasticity has still not been adequately scrutinized by biologists or philosophers. After reviewing some important conceptual and theoretical (...) background information, this paper synthesizes some past discussions of the methodology of plasticity studies and provides some novel methodological guidance for plasticity researchers. My conclusion is that not all plasticity studies should carry the same weight: there are patterns we can identify in the features of such studies that should contribute to their credibility. In particular, I argue that some types of organisms and some types of plastic phenotypes are more conducive to the empirical study of plasticity than others. (shrink)

Elliott Sober can be understood as advancing two distinct arguments that similarly conclude that evolutionary theory does not say that Scriven’s infamous twins have the same fitness, despite the twins’ identical genotypes and phenotypes. The first argument relies on denying that evolutionary theory can say that the twins are in the same environment, and the second relies on asserting an epistemic access asymmetry between token fitness and trait fitness. Motivated by good reasons, I respond to both of these arguments by (...) showing that the theory of evolution by natural selection has adequate means for determining whether the twins are in the same environment via causal-probabilistic decomposition, and that equivalence in fitness can be asserted even from a partial theory of fitness, regardless of epistemology. Finally, I point out an absurd result regarding genetic drift as indiscriminate sampling that follows if Sober’s conclusion is true. (shrink)

I critically analyze Kevin Elliott’s A Tapestry of Values in order to tease out his views on the nature and status of values or value judgments in the text. I show there is a tension in Elliott’s view that is closely connected to a major lacuna in the philosophical literature on values in science: the need for a better theory of values.

After raising some minor philosophical points about Kevin Elliott’s A Tapestry of Values (2017), I argue that we should expand on the themes raised in the book and that philosophers of science need to pay as much attention to the loom of science (i.e., the institutional structures which guide the pursuit of science) as the tapestry of science. The loom of science includes such institutional aspects as patents, funding sources, and evaluation regimes that shape how science gets pursued, and that (...) attending to these aspects will enable us to provide more robust guidance on the values that infuse the tapestry of science. (shrink)

This response addresses the excellent responses to my book provided by Heather Douglas, Janet Kourany, and Matt Brown. First, I provide some comments and clarifications concerning a few of the highlights from their essays. Second, in response to the worries of my critics, I provide more detail than I was able to provide in my book regarding my three conditions for incorporating values in science. Third, I identify some of the most promising avenues for further research that flow out of (...) this interchange. (shrink)

Kevin Elliott’s A Tapestry of Values is a terrific book, chock full of valuable case studies and incisive analyses. It aims to be useful not only to students of philosophy of science and the other areas of science studies but also to practicing scientists, policymakers, and the public at large—a tall order. And it succeeds admirably for many of these folks. In my comments I suggest what it would need for the rest.

Noting minimal philosophical attention to the shift of the meanings of “genotype” and “phenotype,” and their distinction, as well as to the variety of meanings that have co-existed over the last hundred years, this note invites readers to join in exploring the implications of shifts that have been left unexamined.

Questioning the nature of individuality has a long and a rich history, both in philosophy and in biology. Because they differ in several features from the pervasive vertebrate-human model, plants have been considered as complicating the question. Here, the various plant species on which authors—whether biologists or philosophers—rely to build the picture of plant individuality are examined and tracked for their peculiarities, thus constituting an “herbiary” of plant individuality. The herbiary of plant individuality has as its members species exhibiting a (...) diverse collection of traits and illustrating different questions related to plant individuality. This essay assesses the peculiarity of the features of these plants and the reality of their differences from animals. Because some plant features are supposed to pose a threat to individual genetic homogeneity, higher heterogeneity has been assumed for plants compared to animals. Moreover, individual plants are sometimes identified with communities. How does this supposed heterogeneity appear in particular species? Cultivated plants exhibit distinctive diversity, and their overrepresentation in the study of plant diversity might bias the way plant individuality is understood. Just as there is a vertebrate bias, there may also be a cultivated plant bias. Recent results bring plants much closer to animals in terms of cellular functioning, so plants might not be so different from animals with respect to their diversity, and consequently their individuality. (shrink)

A common view of how-possibly explanations in biology treats them as explanatorily incomplete. In addition to this interpretation of how-possibly explanation, I argue that there is another interpretation, one which features what I term “explanatory strategies.” This strategy-centered interpretation of how-possibly explanation centers on there being a different explanatory context within which how-possibly explanations are offered. I contend that, in conditions where this strategy context is recognized, how-possibly explanations can be understood as complete explanations. I defend this alternative interpretation by (...) analyzing the explanatory value of simple physical models the nineteenth century developmental biologist Wilhelm His constructed for animal development. (shrink)

Simple regression (regression analysis with a single explanatory variable), and multiple regression (regression models with multiple explanatory variables), typically correspond to very different biological questions. The former use regression lines to describe univariate associations. The latter describe the partial, or direct, effects of multiple variables, conditioned on one another. We suspect that the superficial similarity of simple and multiple regression leads to confusion in their interpretation. A clear understanding of these methods is essential, as they underlie a large range of (...) procedures in common use in biology. Beyond simple and multiple regression in their most basic forms, understanding the key principles of these procedures is critical to understanding, and properly applying, many methods, such as mixed models, generalised models, and causal inference using graphs (including path analysis and its extensions). A simple, but careful, look at the distinction between these two analyses is valuable in its own right, and can also be used to clarify widely-held misconceptions about collinearity (correlations among explanatory variables). There is no general sense in which collinearity is a problem. We suspect that the perception of collinearity as a hindrance to analysis stems from misconceptions about interpretation of multiple regression models, and so we pursue discussions about these misconceptions in this light. In particular, collinearity causes multiple regression coefficients to be less precisely estimated than corresponding simple regression coefficients. This should not be interpreted as a problem, as it is perfectly natural that direct effects should be harder to characterise than univariate associations. Purported solutions to the perceived problems of collinearity are detrimental to most biological analyses. (shrink)

We argue that the logical outcome of the cladistics revolution in biological systematics, and the move towards rankless phylogenetic classification of nested monophyletic groups as formalized in the PhyloCode, is to eliminate the species rank along with all the others and simply name clades. We propose that the lowest level of formally named clade be the SNaRC, the Smallest Named and Registered Clade. The SNaRC is an epistemic level in the classification, not an ontic one. Naming stops at that level (...) because there is no currently acceptable evidence for clades within it, not because no smaller clades exist. Later, included clades may be named. They would then become the SNaRCs, while the original SNaRC would keep its original name. We argue that all theoretical tasks of biology, in evolution and ecology, as well as practical tasks such as conservation assessment, are better approached using this rankless phylogenetic approach. (shrink)