Elisabeth Lloyd

The conflation of two fundamentally distinct issues has generated serious confusion in the philosophical and biological literature concerning the units of selection. The questions of how a unit of selection is defined, theoretically, is rarely distinguished from the question of how to determine the empirical accuracy of claims--either specific or general--concerning which unit(s) are undergoing selection processes. In this paper, I begin by refining a definition of the unit of selection, first presented by William Wimsatt, that is grounded in the structure of natural selection models. I then explore the implications of this definition for empirical evaluation of group selection models. I examine an objection to Wimsatt’s definition raised by Elliott Sober, and I conclude by indicating how the proposed refined definition can clarify which sorts of empirical evidence could be brought to bear on group selection controversies.

Feminist philosophers have discussed the prospects for assessing values empirically, particularly given the ongoing threat of sexism and other oppressive values influencing science and society. Some advocates of such tests now champion a “values as evidence” approach, and they criticize Helen Longino’s contextual empiricism for not holding values to the same level of empirical scrutiny as other claims. In this paper, we defend contextual empiricism by arguing that many of these criticisms are based on mischaracterizations of Longino’s position, overstatements of certain claims, and false dichotomies. Her contextual empiricism not only allows for the empirical support and disconfirmation of values, but Longino explicitly discusses when values can be empirically adjudicated and emphasizes the crucial role of the community for standards of evidence. We support contextual empiricism and elaborate a less direct account of “values as heuristics” by reviewing Longino’s theory of evidence and then using a case study from Elisabeth Lloyd on the biology of female orgasm, demonstrating the disconfirmation of androcentric values in evolutionary science. Within Longino’s and Lloyd’s contextual empiricism, values do not get treated as empirical evidence to be directly assessed by individuals, but rather values are heuristic tools to build models whose use can be validated or invalidated by communities based on their empirical fruitfulness in the logic and pragmatics of research questions in specific historical and cultural contexts.

We critically examine Denis Walsh’s latest attack on the causalist view of fitness. Relying on Judea Pearl’s Sure-Thing Principle and geneticist John Gillespie’s model for fitness, Walsh has argued that the causal interpretation of fitness results in a reductio. We show that his conclusion only follows from misuse of the models, that is, (1) the disregard of the real biological bearing of the population-size parameter in Gillespie’s model and (2) the confusion of the distinction between ordinary probability and Pearl’s causal probability. Properly understood, the models used by Walsh do not threaten the causalist view of fitness.

A specific form of research question, for instance, “What is the probability of a certain class of weather events, given global climate change, relative to a world without?” could be answered with the use of FAR or RR (Fraction of Attributable Risk or Risk Ratio) as the most common approaches to discover and ascribe extreme weather events. Kevin Trenberth et al. (2015) and Theodore Shepherd (2016) have expressed doubts in their latest works whether it is the most appropriate explanatory tool or the way of public outreach concerning climate events and extremes. As an alternative, these researchers focus on complementary questions, for example, “How much did climate change affect the severity of a given storm?” advocating a “storyline” approach. New methods and new research questions are neither foreign, nor controversial from the standpoint of history and philosophy of science, especially those, related to public interest. Nevertheless, the new proposal has got a tepid reception from the majority of professionals of the given field. They argued that this approach can cause weakening of standards and neglecting of scientific method. The following paper attempts to find the roots of the supposed controversy. We claim inefficiency of uncompromising approach to D&A in absolute sense and assert that errors of a particular type may have a different level of concern in society, depending on the variety of contexts. Therefore, context defines the risk of over-estimation vs. under-estimation of harm.

Science strives for coherence. For example, the findings from climate science form a highly coherent body of knowledge that is supported by many independent lines of evidence: greenhouse gas emissions from human economic activities are causing the global climate to warm and unless GHG emissions are drastically reduced in the near future, the risks from climate change will continue to grow and major adverse consequences will become unavoidable. People who oppose this scientific body of knowledge because the implications of cutting GHG emissions—such as regulation or increased taxation—threaten their worldview or livelihood cannot provide an alternative view that is coherent by the standards of conventional scientific thinking. Instead, we suggest that people who reject the fact that the Earth’s climate is changing due to greenhouse gas emissions oppose whatever inconvenient finding they are confronting in piece-meal fashion, rather than systematically, and without considering the implications of this rejection to the rest of the relevant scientific theory and findings. Hence, claims that the globe “is cooling” can coexist with claims that the “observed warming is natural” and that “the human influence does not matter because warming is good for us.” Coherence between these mutually contradictory opinions can only be achieved at a highly abstract level, namely that “something must be wrong” with the scientific evidence in order to justify a political position against climate change mitigation. This high-level coherence accompanied by contradictory subordinate propositions is a known attribute of conspiracist ideation, and conspiracism may be implicated when people reject well-established scientific propositions.

Since the fundamental challenge that I laid at the doorstep of the pluralists was to defend, with nonderivative models, a strong notion of genic cause, it is fatal that Waters has failed to meet that challenge. Waters agrees with me that there is only a single cause operating in these models, but he argues for a notion of causal ‘parsing’ to sustain the viability of some form of pluralism. Waters and his colleagues have some very interesting and important ideas about the sciences, involving pluralism and parsing or partitioning causes, but they are ideas in search of an example. He thinks he has found an example in the case of hierarchical and genic selection. I think he has not.

This chapter explores two of the most studied and most damaging aspects of such societal influence on science: racial and gender biases. We discuss two major domains of biological and medical research involving race and gender: cognitive differences research and reproductive health science. In each case, we explore the influence of sexist values like androcentric bias—where researchers focus on men and male bodies as the alleged “norm”—and racist values like white supremacy—where researchers privilege the cultures and attributes of white people as allegedly “superior” to those of people of color. The chapter contends that we must make the culture of research more equitable to make the research itself less biased and more fair for all people.

Modern science’s ability to produce, store, and analyze big datasets is changing the way that scientific research is practiced. Philosophers have only begun to comprehend the changed nature of scientific reasoning in this age of “big data.” We analyze data-focused practices in biology and climate modeling, identifying distinct species of data-centric science: phenomena-laden in biology and phenomena-agnostic in climate modeling, each better suited for its own domain of application, though each entail trade-offs. We argue that data-centric practices in science are not monolithic because the opportunities and challenges presented by big data vary across scientific domains.

In this paper we consider some questions surrounding whether or not regional climate models “add value,” a controversial issue in climate science today. We highlight some objections frequently made about regional climate models both within and outside the community of modelers, including several claims that regional climate models do not “add value.” We show that there are a number of issues involved in the latter claims, the primary ones centering on the fact that different research questions are being pursued by the modelers making the complaints against regional climate models. Further issues focus on historical deficiencies of particular—but not generalizable—failures of individual regional models. We provide tools to sort out these different research questions and particular failures, and to improve communication and understanding surrounding added value in climate modeling and philosophy of climate science.

Natural selection causes adaptation, the fit between an organism and its environment. For example, the white and grey coloration of snowy owls living and breeding around the Arctic Circle provides camouflage from both predators and prey. In this Element, we explore a variety of such outcomes of the evolutionary process, including both adaptations and alternatives to adaptations, such as nonadaptive traits inherited from ancestors. We also explore how the concept of adaptation is used in evolutionary psychology and in animal behavior, and the adequacy of methods used to confirm evolutionary accounts of human traits and behaviors.

As we advance into the twenty-first century, the evidence of climate change is all around us. In the introduction to this volume, we discuss some of the successes of climate science in understanding and attributing the causes of these changes, as well as some of the challenges it faces in addressing questions for which we do not yet have the answers. We focus on the role of climate models and the philosophical and conceptual problems facing climate modelers and climate modeling. We then give the reader an outline of what they will find in each of the 15 Chapters in the volume. The book is divided into three major parts: Part 1 “Confirmation and Evidence”; Part 2 “Uncertainties and Robustness”; and Part 3 “Climate Models as Guides to Policy”.

In this brief chapter, Lloyd sets the stage for the following three papers, most centrally, Santer et al., which discusses whether the satellite data fit with climate models. Its target is a paper by Douglass et al., which claimed that satellite and weather balloon data showed that the climate models were wrong and could not be trusted. The Santer and Wigley “Fact Sheet” gives a nontechnical summary of what is wrong with the Douglass paper, while the full story is in Chap. 5, a reprint of the Santer et al. paper. The context and import of this work is discussed in Lloyd. In this introduction, Lloyd emphasizes the timeliness of this work, as climate deniers testify in Congress presently.

Climate scientists have been engaged in a decades-long debate over the standing of satellite measurements of the temperature trends of the atmosphere above the surface of the earth. This is especially significant because skeptics of global warming and the greenhouse effect have utilized this debate to spread doubt about global climate models used to predict future states of climate. I use this case from an understudied science to illustrate two distinct philosophical approaches to the relations among data, scientist, measurement, models, and theory. I argue that distinguishing between “direct” empiricist and “complex” empiricist approaches helps us understand and analyze this important scientific episode. I introduce a complex empiricist account of testing and evaluation, and contrast it with the basic hypothetico-deductive approach to the climate models used by the direct empiricists. This more developed complex empiricist approach will serve philosophy of science well, as computational models become more widespread in the sciences.

1. Introduction; Elisabeth A. Lloyd and Eric Winsberg.- Section 1: Confirmation and Evidence.- 2. The Scientific Consensus on Climate Change: How Do We Know We’re Not Wrong?; Naomi Oreskes.- 3. Satellite Data and Climate Models Redux.- 3a. Introduction to Chapter 3: Satellite Data and Climate Models; Elisabeth A. Lloyd.- Ch. 3b Fact Sheet to "Consistency of Modelled and Observed Temperature Trends in the Tropical Troposphere"; Benjamin D. Santer et al..- Ch. 3c Reprint of "Consistency of Modelled and Observed Temperature Trends in the Tropical Troposphere"; Benjamin D. Santer et al..- 4. The Role of ’Complex’ Empiricism in the Debates about Satellite Data and Climate Models; Elisabeth A. Lloyd.- 5. Reconciling Climate Model/Data Discrepancies: The Case of the Trees That Didn’t Bark; Michael Mann.- 6. Downscaling of Climate Information; Linda O. Mearns et al..- Section 2: Uncertainties and Robustness.- 7. The Significance of Robust Model Projections; Wendy S. Parker.- 8. Building Trust, Removing Doubt? Robustness Analysis and Climate Modeling; Jay Odenbaugh.- Section 3: Climate Models as Guides to Policy.- 9. Climate Model Confirmation: From Philosophy to Predicting Climate in the Real World; Reto Knutti.- 10. Uncertainty in Climate Science and Climate Policy; Jonathan Rougier and Michel Crucifix.- 11. Communicating Uncertainty to Policy Makers: The Ineliminable Role of Values; Eric Winsberg.- 12. Modeling Climate Policies: A Critical Look at Integrated Assessment Models; Mathias Frisch.- 13. Modelling Mitigation and Adaptation Policies to Predict their Effectiveness: The Limits of Randomized Controlled Trials; Alexandre Marcellesi and Nancy D. Cartwright.

We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, between species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory.

Elisabeth Lloyd is an American philosopher of science whose work is centered in the field of philosophy of biology. The material in this archive documents her work in philosophy of biology. The materials extend over the whole of her career and include manuscript materials, working notes on articles and books in progress, professional correspondence, teaching materials, documents relating to work with professional organizations, talks given to professional audiences, as well as annotated books, manuscripts and preprints. Elisabeth Lloyd's publications include both books and professional articles.

Holobionts, consisting of a host and diverse microbial symbionts, function as distinct biological entities anatomically, metabolically, immunologically, and developmentally. Symbionts can be transmitted from parent to offspring by a variety of vertical and horizontal methods. Holobionts can be considered levels of selection in evolution because they are well-defined interactors, replicators/reproducers, and manifestors of adaptation. An initial mathematical model is presented to help understand how holobionts evolve. The model offered combines the processes of horizontal symbiont transfer, within-host symbiont proliferation, vertical symbiont transmission, and holobiont selection. The model offers equations for the population dynamics and evolution of holobionts whose hologenomes differ in gene copy number, not in allelic or loci identity. The model may readily be extended to include variation among holobionts in the gene identities of both symbionts and host.

Some methodological adaptationists hijacked the term “exaptation,” and took an occasion of Stephen Jay Gould’s misspeaking as confirmation that it possessed an evolutionarily “designed” function and was a version of an adaptation, something it was decidedly not. Others provided a standard of evidence for exaptation that was inappropriate, and based on an adaptationist worldview. This article is intended to serve as both an analysis of and correction to those situations. Gould and Elisabeth Vrba’s terms, “exaptation” and “aptation,” as originally introduced, are very useful, unlike the faded adaptationist echo of “exaptation” devised by the methodological adaptationists, which has made the term incoherent. We will discuss how exaptation relates to function, to aptation, and to adaptation, both primary and secondary. These ideas have been rendered practically useless through their mistaken definitions and misapplications by evolutionary psychologists.

Since the fundamental challenge that I laid at the doorstep of the pluralists was to defend, with nonderivative models, a strong notion of genic cause, it is fatal that Waters has failed to meet that challenge. Waters agrees with me that there is only a single cause operating in these models, but he argues for a notion of causal ‘parsing’ to sustain the viability of some form of pluralism. Waters and his colleagues have some very interesting and important ideas about the sciences, involving pluralism and parsing or partitioning causes, but they are ideas in search of an example. He thinks he has found an example in the case of hierarchical and genic selection. I think he has not.

Most models of generational succession in sexually reproducing populations necessarily move back and forth between genic and genotypic spaces. We show that transitions between and within these spaces are usually hidden by unstated assumptions about processes in these spaces. We also examine a widely endorsed claim regarding the mathematical equivalence of kin-, group-, individual-, and allelic-selection models made by Lee Dugatkin and Kern Reeve. We show that the claimed mathematical equivalence of the models does not hold.

The structure of evolutionary theory has proved difficult to characterize. Most available analyses focus on the existence of evolutionary laws and on the axiomatizability of the theory; such analyses pay insufficient attention to mathematical evolutionary models and their structure, and to the structural complications arising from the variety of evolutionary sub-theories. ;The primary goal of this dissertation is to introduce and develop an analysis of the structure of evolutionary theory that is both precise and useful. The secondary goal is to offer further evidence of the appropriateness and utility of the semantic view of theories, as developed by P. Suppes, B. C. van Fraassen, and F. Suppe, in which the theory is viewed as a family of related mathematical models. ;After reviewing the semantic approach, I provide a formal framework for describing and distinguishing among population genetics models. The interrelations among the models are described through a set of notions developed and made precise through the analysis of several evolutionary sub-theories, including genic selection and species selection. The framework of model specification, combined with the notions describing formal relations among models, are offered as a system capable of describing any part or aspect of the structure of evolutionary theory. ;Finally, I present a view of confirmation that relies on the distinctions present in the above system of theory description. I argue that this view of confirmation has two advantages over a hypothetico-deductive view of confirmation. First, it is possible to establish the reasonableness of viewing a variety of evidence as a form of confirmation. Second, as I show in the analysis of a controversial model, distinctions can be made due to the subtlety of the view that do not appear under the usual approaches. ;I conclude that a semantic approach to the structure of theories offers a natural, precise framework for the characterization of contemporary evolutionary theory. As such, it may provide a means with which progress on outstanding theoretical and philosophical problems can be achieved

This article discusses various dangers that accompany the supposedly benign methods in behavioral evoltutionary biology and evolutionary psychology that fall under the framework of "methodological adaptationism." A "Logic of Research Questions" is proposed that aids in clarifying the reasoning problems that arise due to the framework under critique. The live, and widely practiced, " evolutionary factors" framework is offered as the key comparison and alternative. The article goes beyond the traditional critique of Stephen Jay Gould and Richard C. Lewontin, to present problems such as the disappearance of evidence, the mishandling of the null hypothesis, and failures in scientific reasoning, exemplified by a case from human behavioral ecology. In conclusion the paper shows that "methodological adaptationism" does not deserve its benign reputation.