Alan Love

According to many biologists, explaining the evolution of morphological novelty and behavioral innovation are central endeavors in contemporary evolutionary biology. These endeavors are inherently multidisciplinary but also have involved a high degree of controversy. One key source of controversy is the definitional diversity associated with the concept of evolutionary novelty, which can lead to contradictory claims (a novel trait according to one definition is not a novel trait according to another). We argue that this diversity should be interpreted in light of a different epistemic role played by the concept of evolutionary novelty—the structuring of a problem space or setting of an explanatory agenda—rather than the concept’s capacity to categorize traits as novel. This distinctive role is consistent with the definitional diversity and shows that the concept of novelty benefits ongoing investigation by focusing attention on answering different questions related to comprehending the origins of novelty. A review of recent theoretical and empirical work on evolutionary novelty confirms this interpretation.

John Norton’s argument that all formal theories of induction fail raises substantive questions about the philosophical analysis of scientific reasoning. What are the criteria of adequacy for philosophical theories of induction, explanation, or theory structure? Is more than one adequate theory possible? Using a generalized version of Norton’s argument, I demonstrate that the competition between formal and material theories in philosophy of science results from adhering to different criteria of adequacy. This situation encourages an interpretation of “formal” and “material” as indicators of divergent criteria that accompany different philosophical methodologies. I characterize another criterion of adequacy associated with material theories, the avoidance of imported problems, and conclude that one way to negotiate between conflicting criteria is to adopt a pluralist stance toward philosophical theories of scientific reasoning

Scientific explanation is a perennial topic in philosophy of science, but the literature has fragmented into specialized discussions in different scientific disciplines. An increasing attention to scientific practice by philosophers is (in part) responsible for this fragmentation and has put pressure on criteria of adequacy for philosophical accounts of explanation, usually demanding some form of pluralism. This commentary examines the arguments offered by Fagan and Woody with respect to explanation and understanding in scientific practice. I begin by scrutinizing Fagan's concept of collaborative explanation, highlighting its distinctive advantages and expressing concern about several of its assumptions. Then I analyze Woody's attempt to reorient discussions of scientific explanation around functional considerations, elaborating on the wider implications of this methodological recommendation. I conclude with reflections on synergies and tensions that emerge when the two papers are juxtaposed and how these draw attention to critical issues that confront ongoing philosophical analyses of scientific explanation.

Evolutionary developmental biology (Evo-devo) is a loose conglomeration of research programs in the life sciences with two main axes: (a) the evolution of development, or inquiry into the pattern and processes of how ontogeny varies and changes over time; and, (b) the developmental basis of evolution, or inquiry into the causal impact of ontogenetic processes on evolutionary trajectories—both in terms of constraint and facilitation. Philosophical issues are found along both axes surrounding concepts such as evolvability, novelty, and modularity. The developmental basis of evolution has garnered much attention because it speaks to the possibility of revising a standard construal of evolutionary theory, but the evolution of development harbors its own conceptual questions. This article addresses the heterogeneity of Evo-devo’s conglomerate structure (including disagreements over its individuation), as well as the concepts and controversies of philosophical interest pertaining to the evolution of development and the developmental basis of evolution. Future research will benefit from a shift away from global theorizing toward the scientific practices of Evo-devo.

The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning ‘typological thinking’, essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological thinking can be understood as a scientific tactic that involves representing natural phenomena using idealizations and approximations, which facilitates explanation, investigation, and theorizing via abstraction and generalization. Third, a variety of typologies from different areas of biology are introduced to emphasize the diversity of this representational reasoning. One particular example is used to examine how there can be epistemological conflict between typology and evolutionary analysis. This demonstrates that alternative strategies of typological thinking arise due to the divergent explanatory goals of researchers working in different disciplines with disparate methodologies. I conclude with several research questions that emerge from an epistemological reconfiguration of typology

Comprehending the origin of marine invertebrate larvae remains a key domain of research for evolutionary biologists, including the repeated origin of direct developmental modes in echinoids. In order to address the latter question, we surveyed existing evidence on relationships of homology between the ectoderm territories of two closely related sea urchin species in the genus Heliocidaris that differ in their developmental mode. Additionally, we explored a recently articulated idea about homology called ‘organizational homology’ (Muller 2003. In: Muller GB, Newman SA, editors. Origination of organismal form: beyond the gene in developmental and evolutionary biology. Cambridge, MA: A Bradford Book, The MIT Press. p 51–69. ) in the context of this specific empirical case study. Applying the perspective of organizational homology to our experimental system of congeneric echinoids has led us to a new hypothesis concerning the ectoderm evolution in these species. The extravestibular ectoderm of the direct developer Heliocidaris erythrogramma is a novel developmental territory that arose as a fusion of the oral and aboral ectoderm territories found in indirect developing echinoids such as Heliocidaris tuberculata. This hypothesis instantiates a theoretical principle concerning the origin of developmental modules, ‘integration’, which has been neglected because the opposite theoretical principle, ‘parcellation’, is more readily observable in events such as gene duplication and divergence (Wagner 1996. Am Zool 36:36–43). J. Exp. Zool. (Mol. Dev. Evol.) 306B:18– 34, 2006.

According to Joshua Alexander, philosophers use intuitions routinely as a form of evidence to test philosophical theories but experimental philosophy demonstrates that these intuitions are unreliable and unrepresentative.1 According to Herman Cappelen, philosophers never use intuitions as evidence (despite the vacuous sentential leader ‘intuitively’) and experimental philosophy lacks a rationale for its much-touted existence.2 That two books are diametrically opposed on methodology in philosophy is not noteworthy. But eyebrows might be raised at such contradictory accounts of the phenomenology of philosophical inquiry. What is it that (analytic) philosophers do? Why is it so difficult to achieve consensus on the professional activities in which we engage?

Reductionism encompasses a set of ontological, epistemological, and methodological claims about the relation of different scientific domains. The basic question of reduction is whether the properties, concepts, explanations, or methods from one scientific domain (typically at higher levels of organization) can be deduced from or explained by the properties, concepts, explanations, or methods from another domain of science (typically one about lower levels of organization). Reduction is germane to a variety of issues in philosophy of science, including the structure of scientific theories, the relations between different scientific disciplines, the nature of explanation, the diversity of methodology, and the very idea of theoretical progress, as well as to numerous topics in metaphysics and philosophy of mind, such as emergence, mereology, and supervenience

The origination of novel structures has long been an intriguing topic for biologists. Over the past few decades it has served as a central theme in evolutionary developmental biology. Yet, definitions of evolutionary innovation and novelty are frequently debated and there remains disagreement about what kinds of causal factors best explain the origin of qualitatively new variation in the history of life. Here we examine aspects of these debates, survey three empirical case studies, and reflect on directions for future inquiry that will advance research into the developmental evolution of novel structures.

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

The origin of marine invertebrate larvae has been an area of controversy in developmental evolution for over a century. Here, we address the question of whether a pelagic “larval” or benthic “adult” morphology originated first in metazoan lineages by testing the hypothesis that particular gene co-option patterns will be associated with the origin of feeding, indirect developing larval forms. Empirical evidence bearing on this hypothesis is derivable from gene expression studies of the sea urchin larval gut of two closely related but differently developing congenerics, Heliocidaris tuberculata (feeding indirect-developing larva) and H. erythrogramma (nonfeeding direct developer), given two subsidiary hypotheses. (1) If larval gut gene expression in H. tuberculata was co-opted from an ancestral adult expression pattern, then the gut expression pattern will remain in adult H. erythrogramma despite its direct development. (2) Genes expressed in the larval gut of H. tuberculata will not have a coordinated expression pattern in H. erythrogramma larvae due to loss of a functional gut. Five structural genes expressed in the invaginating archenteron of H. tuberculata during gastrulation exhibit substantially different expression patterns in H. erythrogramma with only one remaining endoderm specific. Expression of these genes in the adult of H. erythrogramma and larval gut of H. tuberculata, but not in H. erythrogramma larval endoderm, supports the hypothesis that they first played roles in the formation of adult structures and were subsequently recruited into larval ontogeny during the origin and evolution of feeding planktotrophic deuterostome larvae.

The theory of punctuated equilibrium holds that long periods of morphological stasis in fossil lineages are interrupted by bursts of geologically rapid evolutionary change. Philip Kitcher’s long and distinguished career is not directly analogous to this pattern, but his philosophy exhibits stasis and change. He has both maintained a position or line of argument consistently and shifted significantly in his views. These evolutionary patterns are on display in the volume co-edited by Mark Couch and Jessica Pfeifer, both of whom were advised by Kitcher though at different institutions. The Philosophy of Philip Kitcher consists of an introduction plus 11 chapters devoted to central themes in Kitcher’s oeuvre. In each chapter, distinguished colleagues offer sustained engagement with one theme followed by a succinct and magnanimous response from Kitcher. The format is illuminating and helps display the complex evolutionary dynamics in the thought of an eminent contemporary philosopher.

“Functional homology” appears regularly in different areas of biological research and yet it is apparently a contradiction in terms—homology concerns identity of structure regardless of form and function. I argue that despite this conceptual tension there is a legitimate conception of ‘homology of function’, which can be recovered by utilizing a distinction from pre-Darwinian physiology (use versus activity) to identify an appropriate meaning of ‘function’. This account is directly applicable to molecular developmental biology and shares a connection to the theme of hierarchy in homology. I situate ‘homology of function’ within existing definitions and criteria for structural assessments of homology, and introduce a criterion of ‘organization’ for judging function homologues, which focuses on hierarchically interconnected interdependencies (similar to relative position and connection for skeletal elements in structural homology). This analysis of biological concepts has at least three broad philosophical consequences: (1) it provides the grounds for the study of behavior and psychological categories as homologues; (2) it demonstrates that philosophers who take selected effect function as primary effectively ignore large portions of comparative, structural, and experimental research, thereby misconstruing biological reasoning and knowledge; and, (3) it underwrites causal generalizations, which illuminates inferences made from model organisms in experimental biology.

Idealization is a reasoning strategy that biologists use to describe, model and explain that purposefully departs from features known to be present in nature. Similar to other strategies of scientific reasoning, idealization combines distinctive strengths alongside of latent weaknesses. The study of ontogeny in model organisms is usually executed by establishing a set of normal stages for embryonic development, which enables researchers in different laboratory contexts to have standardized comparisons of experimental results. Normal stages are a form of idealization because they intentionally ignore known variation in development, including variation associated with phenotypic plasticity (e.g. via strict control of environmental variables). This is a tension between the phenomenon of plasticity and the practice of staging that has consequences for evolutionary developmental investigation because variation is conceptually removed as a part of rendering model organisms experimentally tractable. Two compensatory tactics for mitigating these consequences are discussed: employing a diversity of model organisms and adopting alternative periodizations.

Günter Wagner’s Homology, Genes, and Evolutionary Innovation collects and synthesizes a vast array of empirical data, theoretical models, and conceptual analysis to set out a progressive research program with a central theoretical commitment: the genetic theory of homology. This research program diverges from standard approaches in evolutionary biology, provides sharpened contours to explanations of the origin of novelty, and expands the conceptual repertoire of evolutionary developmental biology. I concentrate on four aspects of the book in this essay review: the genetic theory of homology and character identity networks; the implications for how we explain evolutionary novelties; the expanded set of concepts surrounding homology, and the epistemological conflicts between Wagner’s viewpoint and functionally-oriented evolutionary biology, as well as differences with other Evo–devo researchers. Together these have ramifications for how we interpret different explanatory approaches to evolutionary phenomena and understand relationships between the usefulness of concepts and the reality they represent

Although the role of morphology in evolutionary theory remains a subject of debate, assessing the contributions of morphological investigation to evolutionary developmental biology (Evo-devo) is a more circumscribed issue of direct relevance to ongoing research. Historical studies of morphologically oriented researchers and the formation of the Modern Synthesis in the Anglo-American context identify a recurring theme: the synthetic theory of evolution did not capture multiple levels of biological organization. When this feature is incorporated into a philosophical framework for explaining the origin of evolutionary innovations and novelties (a core domain of inquiry in Evo-devo) two specific roles for morphology can be described: (1) the conceptualization and operational identification of the targets of explanation; and (2) the elucidation of causal interactions at higher levels of organization during ontogeny and through evolutionary time. These roles are critical components of any adequate explanation of innovation and novelty though not exhaustive of the parts played by morphology in evolutionary investigation. They also invite reflection on what counts as an evolutionary cause in contemporary evolutionary biology.