Massimo Pigliucci

Recent debates between proponents of the modern evolutionary synthesis (the standard model in evolutionary biology) and those of a possible extended synthesis are a good example of the fascinating tangle among empirical, theoretical, and conceptual or philosophical matters that is the practice of evolutionary biology. In this essay, we briefly discuss two case studies from this debate, highlighting the relevance of philosophical thinking to evolutionary biologists in the hope of spurring further constructive cross-pollination between the two fields.

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their functionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adaptations, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an opportunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would suggest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to implement novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engineering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engineering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms.

Questions traditionally answered by philosophers are now being tackled by prominent scientists. As the cultural influence of science and technology continues to grow, what room, if any, is left for philosophy? Three philosophers—Dr. Jonathan Kaplan, Dr. Massimo Pigliucci, and Dr. Leonard Finkelman —explore issues related to the philosophy of science, including how philosophy has contributed to scientific progress, why philosophy continues to be important to science, and why there remain questions that only philosophy can answer. The panelists represent four generations of an academic lineage: Dr. Kaplan was Dr. Pigliucci's dissertation advisor, Dr. Pigliucci was Dr. Finkelman's dissertation advisor, and Evan Tracy is a student of Dr. Finkelman.

The term “scientism” is used in a variety of ways with both negative and positive connotations. I suggest that some of these uses are inappropriate, as they aim simply at dismissing without argument an approach that a particular author does not like. However, there are legitimate negative uses of the term, which I explore by way of an analogy with the term “pseudoscience.” I discuss these issues by way of a recent specific example provided by a controversy in the field of bioethics concerning the value, or lack thereof, of homeopathy. I then frame the debate about scientism within the broader context of C.P. Snow’s famous essay on the “two cultures.”

Discussions about the biological bases (or lack thereof) of the concept of race in the human species seem to be never ending. One of the latest rounds is represented by a paper by Neven Sesardic, which attempts to build a strong scientific case for the existence of human races, based on genetic, morphometric and behavioral characteristics, as well as on a thorough critique of opposing positions. In this paper I show that Sesardic’s critique falls far short of the goal, and that his positive case is exceedingly thin. I do this through a combination of analysis of the actual scientific findings invoked by Sesardic and of some philo- sophical unpacking of his conceptual analysis, drawing on a dual professional background as an evolu- tionary biologist and a philosopher of science.

Phenotypic plasticity integrates the insights of ecological genetics, developmental biology, and evolutionary theory. Plasticity research asks foundational questions about how living organisms are capable of variation in their genetic makeup and in their responses to environmental factors. For instance, how do novel adaptive phenotypes originate? How do organisms detect and respond to stressful environments? What is the balance between genetic or natural constraints (such as gravity) and natural selection? The author begins by defining phenotypic plasticity and detailing its history, including important experiments and methods of statistical and graphical analysis. He then provides extended examples of the molecular basis of plasticity, the plasticity of development, the ecology of plastic responses, and the role of costs and constraints in the evolution of plasticity. A brief epilogue looks at how plasticity studies shed light on the nature/nurture debate in the popular media.

In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch’s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened the need for a different conceptual treat- ment of how phenotypes are produced. Old-fashioned metaphors like genetic blueprint and genetic programme are not only woefully inadequate but positively misleading about the nature of G!P, and are being replaced by an algorithmic approach emerging from the study of a variety of actual G!P maps. These include RNA folding, protein function and the study of evolvable soft- ware. Some generalities are emerging from these disparate fields of analysis, and I suggest that the concept of ‘developmental encoding’ (as opposed to the classical one of genetic encoding) provides a promising computational–theoretical underpinning to coherently integrate ideas on evolvability, modularity and robustness and foster a fruitful framing of the G!P mapping problem.

The idea of phenotypic novelty appears throughout the evolutionary literature. Novelties have been defined so broadly as to make the term meaningless and so narrowly as to apply only to a limited number of spectacular structures. Here I examine some of the available definitions of phenotypic novelty and argue that the modern synthesis is ill equipped at explaining novelties. I then discuss three frameworks that may help biologists get a better insight of how novelties arise during evolution but warn that these frameworks should be considered in addition to, and not as potential substitutes of, the modern synthesis. †To contact the author, please write to: Departments of Ecology and Evolution and Philosophy, Stony Brook University, Stony Brook, NY 11794; e‐mail: [email protected].

Stoicism is an ancient Greco-Roman practical philosophy focused on the ethics of everyday living. It is a eudaemonistic (i.e., emphasizing one’s flourishing) approach to life, as well as a type of virtue ethics (i.e., concerned with the practice of virtues as central to one’s existence). This paper summarizes the basic tenets of Stoicism and discusses how it tackles the issues of death and suicide. It presents a number of exercises that modern Stoics practice in order to prepare for death (one’s own, or those of relatives and friends). It argues that modern Stoicism is a viable personal philosophy.

Phenotypic Evolution explicitly recognizes organisms as complex genetic-epigenetic systems developing in response to changing internal and external environments. As a key to a better understanding of how phenotypes evolve, the authors have developed a framework that centers on the concept of the Developmental Reaction Norm. This encompasses their views: (1) that organisms are better considered as integrated units than as disconnected parts (allometry and phenotypic integration); (2) that an understanding of ontogeny is vital for evaluating evolution of adult forms (ontogenetic trajectories, epigenetics, and constraints); and (3) that environmental heterogeneity is ubiquitous and must be acknowledged for its pervasive role in phenotypic expression.

Are science and religion compatible when it comes to understanding cosmology (the origin of the universe), biology (the origin of life and of the human species), ethics, and the human mind (minds, brains, souls, and free will)? Do science and religion occupy non-overlapping magisteria? Is Intelligent Design a scientific theory? How do the various faith traditions view the relationship between science and religion? What, if any, are the limits of scientific explanation? What are the most important open questions, problems, or challenges confronting the relationship between science and religion, and what are the prospects for progress? These and other questions are explored in Science and Religion: 5 Questions--a collection of thirty-three interviews based on 5 questions presented to some of the world's most influential and prominent philosophers, scientists, theologians, apologists, and atheists. Contributions by Simon Blackburn, Susan Blackmore, Sean Carroll, William Lane Craig, William Dembski, Daniel C. Dennett, George F.R. Ellis, Owen Flanagan, Owen Gingerich, Rebecca Newberger Goldstein, John F. Haught, Muzaffar Iqbal, Lawrence Krauss, Colin McGinn, Alister McGrath, Mary Midgley, Seyyed Hossein Nasr, Timothy O'Connor, Massimo Pigliucci, John Polkinghorne, James Randi, Alex Rosenberg, Michael Ruse, Robert John Russell, John Searle, Michael Shermer, Victor J. Stenger, Robert Thurman, Michael Tooley, Charles Townes, Peter van Inwagen, Keith Ward, Rabbi David Wolpe.

The “demarcation problem,” the issue of how to separate science from pseu- doscience, has been around since fall 1919—at least according to Karl Pop- per’s (1957) recollection of when he first started thinking about it. In Popper’s mind, the demarcation problem was intimately linked with one of the most vexing issues in philosophy of science, David Hume’s problem of induction (Vickers 2010) and, in particular, Hume’s contention that induction cannot be logically justified by appealing to the fact that “it works,” as that in itself is an inductive argument, thereby potentially plunging the philosopher straight into the abyss of a viciously circular argument.

The concept of burden of proof is used in a wide range of discourses, from philosophy to law, science, skepticism, and even in everyday reasoning. This paper provides an analysis of the proper deployment of burden of proof, focusing in particular on skeptical discussions of pseudoscience and the paranormal, where burden of proof assignments are most poignant and relatively clear-cut. We argue that burden of proof is often misapplied or used as a mere rhetorical gambit, with little appreciation of the underlying principles. The paper elaborates on an important distinction between evidential and prudential varieties of burdens of proof, which is cashed out in terms of Bayesian probabilities and error management theory. Finally, we explore the relationship between burden of proof and several (alleged) informal logical fallacies. This allows us to get a firmer grip on the concept and its applications in different domains, and also to clear up some confusions with regard to when exactly some fallacies (ad hominem, ad ignorantiam, and petitio principii) may or may not occur

‘‘Theoretical biology’’ is a surprisingly heter- ogeneous field, partly because it encompasses ‘‘doing the- ory’’ across disciplines as diverse as molecular biology, systematics, ecology, and evolutionary biology. Moreover, it is done in a stunning variety of different ways, using anything from formal analytical models to computer sim- ulations, from graphic representations to verbal arguments. In this essay I survey a number of aspects of what it means to do theoretical biology, and how they compare with the allegedly much more restricted sense of theory in the physical sciences. I also tackle a recent trend toward the presentation of all-encompassing theories in the biological sciences, from general theories of ecology to a recent attempt to provide a conceptual framework for the entire set of biological disciplines. Finally, I discuss the roles played by philosophers of science in criticizing and shap- ing biological theorizing.