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Volume 9 (2017) Current Volume

Four Pillars of Statisticalism

Denis M. Walsh, André Ariew, Mohan Matthen

Over the past fifteen years there has been a considerable amount of debate concerning what theoretical population dynamic models tell us about the nature of natural selection and drift. On the causal interpretation, these models describe the causes of population change. On the statistical interpretation, the models of population dynamics models specify statistical parameters that explain, predict, and quantify changes in population structure, without identifying the causes of those changes. Selection and drift are part of a statistical description of population change; they are not discrete, apportionable causes. Our objective here is to provide a definitive statement of the statistical position, so as to allay some confusions in the current literature. We outline four commitments that are central to statisticalism. They are: 1. Natural Selection is a higher order effect; 2. Trait fitness is primitive; 3. Modern Synthesis (MS)-models are substrate neutral; 4. MS-selection and drift are model-relative.

Two Dogmas of Biology

Leonore Fleming

The problem with reductionism in biology is not the reduction, but the implicit attitude of determinism that usually accompanies it. Methodological reductionism is supported by deterministic beliefs, but making such a connection is problematic when it is based on an idea of determinism as fixed predictability. Conflating determinism with predictability gives rise to inaccurate models that overlook the dynamic complexity of our world, as well as ignore our epistemic limitations when we try to model it. Furthermore, the assumption of a strictly deterministic framework is unnecessarily hindering to biology. By removing the dogma of determinism, biological methods, including reductive methods, can be expanded to include stochastic models and probabilistic interpretations. Thus, the dogma of reductionism can be saved once its ties with determinism are severed. In this paper, I analyze two problems that have faced molecular biology for the last 50 years—protein folding and cancer. Both cases demonstrate the long influence of reductionism and determinism on molecular biology, as well as how abandoning determinism has opened the door to more probabilistic and unconstrained reductive methods in biology.

Evolution of Individuality: A Case Study in the Volvocine Green Algae

Erik R. Hanschen, Dinah R. Davison, Zachariah I. Grochau-Wright, Richard E. Michod

While numerous criteria have been proposed in definitions of biological individuality, it is not clear whether these criteria reflect the evolutionary processes that underlie transitions in individuality. We consider the evolution of individuality during the transition from unicellular to multicellular life. We assume that “individuality” (however it is defined) has changed in the volvocine green algae lineage during the transition from single cells, to simple multicellular colonies with four to one hundred cells, to more complex multicellular organisms with thousands of differentiated cells. We map traits associated with the various proposed individuality criteria onto volvocine algae species thought to be similar to ancestral forms arising during this transition in individuality. We find that the fulfillment of some criteria, such as genetic homogeneity and genetic uniqueness, do not change across species, while traits underpinning other aspects of individuality, including degrees of integration, group-level fitness and adaptation, and group indivisibility, change dramatically. We observe that different kinds of individuals likely exist at different levels of organization (cell and group) in the same species of algae. Future research should focus on the causes and consequences of variation in individuality.

Ontologies of Living Beings: IntroductionSPECIAL ISSUE

A. M. Ferner, Thomas Pradeu

Identity and Self-KnowledgeSPECIAL ISSUE

John Perry

Self, person, and identity are among the concepts most central to the way humans think about themselves and others. It is often natural in biology to use such concepts; it seems sensible to say, for example, that the job of the immune system is to attack the non-self, but sometimes it attacks the self. But does it make sense to borrow these concepts? Don’t they only pertain to persons, beings with sophisticated minds, and perhaps even souls? I argue that if we focus on the every-day concepts of self and identity, and set aside loftier concepts found in religion, philosophy, and psychology that are applicable, at most, to humans, we can see that self and identity can be sensibly applied widely in biology.

Stem Cell Lineages: Between Cell and OrganismSPECIAL ISSUE

Melinda Bonnie Fagan

Ontologies of living things are increasingly grounded on the concepts and practices of current life science. Biological development is a process, undergone by living things, which begins with a single cell and (in an important class of cases) ends with formation of a multicellular organism. The process of development is thus prima facie central for ideas about biological individuality and organismality. However, recent accounts of these concepts do not engage developmental biology. This paper aims to fill the gap, proposing the lineage view of stem cells as an ontological framework for conceptualizing organismal development. This account is grounded on experimental practices of stem cell research, with emphasis on new techniques for generating biological organization in vitro. On the lineage view, a stem cell is the starting point of a cell lineage with a specific organismal source, time-interval of existence, and ‘tree topology’ of branch-points linking the stem to developmental termini. The concept of ‘enkapsis’ accommodates the cell-organism relation within the lineage view; this hierarchical notion is further explicated by considering the methods and results of stem cell experiments. Results of this examination include a (partial) characterization of stem cells’ developmental versatility, and the context-dependence of developmental processes involving stem cells.

What Organisms Once Were and Might Yet BeSPECIAL ISSUE

Christopher Shields

Organisms receded from view in much of twentieth-century biology, only to undergo a sort of renaissance at the start of the twenty-first. The story of why this should be so is complicated and fascinating, but belongs primarily to the history of biology. On the other hand, to the extent that it is so, a question naturally arises: what, after all, are organisms? This question has a long and complicated history of its own, both within and without of biology; an investigation of this history yields some guidance as to how organisms might yet be conceived today. One suggestion borne of these investigations is this: organisms are, for better or worse, normatively delineated unities.

Reengineering Metaphysics: Modularity, Parthood, and Evolvability in Metabolic EngineeringSPECIAL ISSUE

Catherine Kendig, Todd T. Eckdahl

The premise of biological modularity is an ontological claim that appears to come out of practice. We understand that the biological world is modular because we can manipulate different parts of organisms in ways that would only work if there were discrete parts that were interchangeable. This is the foundation of the BioBrick assembly method widely used in synthetic biology. It is one of a number of methods that allows practitioners to construct and reconstruct biological pathways and devices using DNA libraries of standardized parts with known functions. In this paper, we investigate how the practice of synthetic biology reconfigures biological understanding of the key concepts of modularity and evolvability. We illustrate how this practice approach takes engineering knowledge and uses it to try to understand biological organization by showing how the construction of functional parts and processes can be used in synthetic experimental evolution. We introduce a new approach within synthetic biology that uses the premise of a parts-based ontology together with that of organismal self-organization to optimize orthogonal metabolic pathways in E. coli. We then use this and other examples to help characterize semisynthetic categories of modularity, parthood, and evolvability within the discipline.

Animal Self-AwarenessSPECIAL ISSUE

Rory Madden

Part of the philosophical interest of the topic of organic individuals is that it promises to shed light on a basic and perennial question of philosophical self-understanding, the question what are we? The class of organic individuals seems to be a good place to look for candidates to be the things that we are. However there are, in principle, different ways of locating ourselves within the class of organic individuals; organic individuals occur at both higher and lower mereological levels than the stereotypical bounded and physiologically unified vertebrate organism. The view that we are organic individuals smaller than the physiological organism is one that has recently been endorsed by Derek Parfit. This paper attempts to resolve a dispute between Parfit’s ‘embodied part’ view and a contrary ‘animalist’ view according to which we are whole organisms. It is explained why a problem of multiple thinkers presents a serious obstacle to a straightforward resolution of this dispute. Parfit’s own strategy for dealing with this obstacle is found to be problematic. However his strategy has a certain general shape, which can be instantiated in a different, and better, specific way. I close in the final section, not with a definite resolution of the dispute, but with illustration of how progress on the question of about which organic individuals we are requires engagement with questions about the nature and function of self-awareness.

The Sum of the Parts: Large-Scale Modeling in Systems BiologySPECIAL ISSUE

Fridolin Gross, Sara Green

Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed studies of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts.

Individuality and AggregativitySPECIAL ISSUE

Stéphane Chauvier

Why is there a specific problem with biological individuality? Because the living realm contains a wide range of exotic particular concrete entities that do not easily match our ordinary concept of an individual. Slime moulds, dandelions, siphonophores are among the Odd Entities that excite the ontological zeal of the philosophers of biology. Most of these philosophers, however, seem to believe that these Odd Cases oblige us to refine or revise our common concept of an individual. They think, explicitly or tacitly, that to be a living, evolutionary entity is to be a living individual. In this paper, we explore an alternative proposal: the variety and oddity of the forms of the living realm might be ontologically regimented through an increase in the categorial complexity of the living realm, by admitting, beside living individuals, living non-individuals or by acknowledging, more generally, that the evolutionary development of the living forms is not necessarily a process of building individuals, that life is not necessarily individuals-oriented. We claim that, from an ontological point of view, the spectacle of the living realm obliges us to take aggregativity seriously.

Are Clusters Races? A Discussion of the Rhetorical Appropriation of Rosenberg et al.'s “Genetic Structure of Human Populations”

Melissa Wills

Noah Rosenberg et al.'s 2002 article “Genetic Structure of Human Populations” reported that multivariate genomic analysis of a large cell line panel yielded reproducible groupings (clusters) suggestive of individuals' geographical origins. The paper has been repeatedly cited as evidence that traditional notions of race have a biological basis, a claim its authors do not make. Critics of this misinterpretation have often suggested that it follows from interpreters' personal biases skewing the reception of an objective piece of scientific writing. I contend, however, that the article itself to some degree facilitates this misrepresentation. I analyze in detail several verbal and visual features of the original article that may predispose aspects of its racial interpretation; and, tracing the arguments of one philosopher and one popular science writer, I show how these features are absorbed, transformed into arguments for a biological basis of race, and re-attributed to the original. The essay demonstrates how even slight ambiguities can enable the misappropriation of scientific writing, unintentionally undermining the authors' stated circumspection on the relationship between cluster and race.

Cultural Attractor Theory and Explanation

Andrew Buskell

Cultural attractor theory (CAT) is a highly visible and audacious approach to studying human cultural evolution. However, the explanatory aims and some central explanatory concepts of CAT remain unclear. Here I remedy these problems. I provide a reconstruction of CAT that recasts it as a theory of forces. I then demonstrate how this reinterpretation of CAT has the resources to generate both cultural distribution and evolvability explanations. I conclude by examining the potential benefits and drawbacks of this reconstruction.

Organisms as Persisters

Subrena E. Smith

This paper addresses the question of what organisms are and therefore what kinds of biological entities qualify as organisms. For some time now, the concept of organismality has been eclipsed by the notion of individuality. Biological individuals are those systems that are units of selection. I develop a conception of organismality that does not rely on evolutionary considerations, but instead draws on development and ecology. On this account, organismality and individuality can come apart. Organisms, in my view, are as Godfrey-Smith puts it “essentially persisters.” I argue that persistence is underpinned by differentiation, integration, development, and the constitutive embeddedness of organisms in their worlds. I examine two marginal cases, the Portuguese Man O’ War and the honey bee colony, and show that both count as organisms in light of my analysis. Next, I examine the case of holobionts, hosts plus their microsymbionts, and argue that they can be counted as organisms even though they may not be biological individuals. Finally, I consider the question of whether other, less tightly integrated biological systems might also be treated as organisms.