Maureen A. O’Malley

Do simple models lead to generality in ecology

Modellers of biological, ecological, and environmental systems cannot take for granted the maxim simple means general means good. We argue here that viewing simple models as the main way to achieve generality may be an obstacle to the progress of ecological research. We show how complex models can be both desirable and general, and how simple and complex models can be linked together to produce broad-scale and predictive understanding of biological systems.

The roles of integration in molecular systems biology

A common way to think about scientific practice involves classifying it as hypothesis- or data-driven. We argue that although such distinctions might illuminate scientific practice very generally, they are not sufficient to understand the day-to-day dynamics of scientific activity and the development of programmes of research. One aspect of everyday scientific practice that is beginning to gain more attention is integration. This paper outlines what is meant by this term and how it has been discussed from scientific and philosophical points of view. We focus on methodological, data and explanatory integration, and show how they are connected. Then, using some examples from molecular systems biology, we will show how integration works in a range of inquiries to generate surprising insights and even new fields of research. From these examples we try to gain a broader perspective on integration in relation to the contexts of inquiry in which it is implemented. In todays environment of data-intensive large-scale science, integration has become both a practical and normative requirement with corresponding implications for meta-methodological accounts of scientific practice. We conclude with a discussion of why an understanding of integration and its dynamics is useful for philosophy of science and scientific practice in general.

When integration fails: Prokaryote phylogeny and the tree of life.

Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because todays literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history (often called universal phylogeny). Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a meta-heuristic in the normative commitments guiding scientific practice.

Endosymbiosis and its implications for evolutionary theory

Historically, conceptualizations of symbiosis and endosymbiosis have been pitted against Darwinian or neo-Darwinian evolutionary theory. In more recent times, Lynn Margulis has argued vigorously along these lines. However, there are only shallow grounds for finding Darwinian concepts or population genetic theory incompatible with endosymbiosis. But is population genetics sufficiently explanatory of endosymbiosis and its role in evolution? Population genetics “follows” genes, is replication-centric, and is concerned with vertically consistent genetic lineages. It may also have explanatory limitations with regard to macroevolution. Even so, asking whether population genetics explains endosymbiosis may have the question the wrong way around. We should instead be asking how explanatory of evolution endosymbiosis is, and exactly which features of evolution it might be explaining. This paper will discuss how metabolic innovations associated with endosymbioses can drive evolution and thus provide an explanatory account of important episodes in the history of life. Metabolic explanations are both proximate and ultimate, in the same way genetic explanations are. Endosymbioses, therefore, point evolutionary biology toward an important dimension of evolutionary explanation.

Data availability and model complexity, generality, and utility: a reply to Lonergan

Comment on Do simple models lead to generality in ecology? [Trends Ecol Evol. 2013]Do simple models lead to generality in ecology? Evans MR, Grimm V, Johst K, Knuuttila T, de Langhe R, Lessells CM, Merz M, OMalley MA, Orzack SH, Weisberg M, et al. Trends Ecol Evol. 2013 Oct; 28(10):578-83. Epub 2013 Jul 1. Data availability constrains model complexity, generality, and utility: a response to Evans et al. [Trends Ecol Evol. 2014]

Evolutionary Systems Biology: Historical and Philosophical Perspectives on an Emerging Synthesis

Systems biology (SB) is at least a decade old now and maturing rapidly. A more recent field, evolutionary systems biology (ESB), is in the process of further developing system-level approaches through the expansion of their explanatory and potentially predictive scope. This chapter will outline the varieties of ESB existing today by tracing the diverse roots and fusions that make up this integrative project. My approach is philosophical and historical. As well as examining the recent origins of ESB, I will reflect on its central features and the different clusters of research it comprises. In its broadest interpretation, ESB consists of five overlapping approaches: comparative and correlational ESB; network architecture ESB; network property ESB; population genetics ESB; and finally, standard evolutionary questions answered with SB methods. After outlining each approach with examples, I will examine some strong general claims about ESB, particularly that it can be viewed as the next step toward a fuller modern synthesis of evolutionary biology (EB), and that it is also the way forward for evolutionary and systems medicine. I will conclude with a discussion of whether the emerging field of ESB has the capacity to combine an even broader scope of research aims and efforts than it presently does.

Small Things, Big Consequences: Microbiological Perspectives on Biology

Microbiology is a broad-ranging area of research that has developed out of 400 years of observation, analysis and theorizing about microscopic life forms. The study of microbes has not yet received a great deal of attention from philosophy of biology, but there are many reasons why it should. In this chapter, we outline the value of thinking philosophically about microbes and microbiology via a discussion of concepts of life, biological individuals and levels of selection. These discussions will show how taking a philosophical perspective on microbiological studies can enrich not only microbiology but also biology in general and its philosophy. We conclude by drawing out some of the implications of philosophical perspectives on microbiology for educational strategies in the teaching of biology.

A cautionary note for claims about the microbiome’s impact on the “self”

In their essay, “How the microbiome challenges our concept of self,” Rees and colleagues [1] argue that recent discoveries about the microbiome have far-reaching effects on our understanding of self and what it means to be human. They claim these effects are so profound that they require a new mode of operation for the arts and humanities: “a breakdown of the anachronistic barriers between the natural and the human sciences.” While we strongly support interdisciplinary collaboration between the arts and sciences, the authors overinflate the microbiome’s influence in ways that are conceptually and empirically problematic. The empirical problems come from statements about the microbiome’s causal power as a unitary entity, which we think need to be more carefully phrased. The conceptual problems turn upon the unsystematic way the authors talk about the “self.” Throughout the article, the meaning of “self” oscillates between three specific biological understandings defined by the authors and far less precise usage (e.g., in claims like “interactions with microorganisms define the individual human self,” “profound implications. . .for our philosophical comprehension of the human self,” or in the essay’s title, “How the microbiome challenges our concept of self”). The context in which these looser attributions of “self” are deployed suggests at least three additional understandings that are more commonly the subject of humanistic or psychological inquiry. By conflating these various interpretations of self, Rees and colleagues create the impression that the microbiome’s impact on one specific biological notion automatically entails a similar impact on all notions of self (or perhaps on some unified notion). But these entailments are neither obvious nor argued for.

Methodological Strategies in Microbiome Research and their Explanatory Implications

Early microbiome research found numerous associations between microbial community patterns and host physiological states. These findings hinted at community-level explanations. “Top-down” experiments, working with whole communities, strengthened these explanatory expectations. Now, “bottom-up” mechanism-seeking approaches are dissecting communities to focus on specific microbes carrying out particular biochemical activities (e.g., choline metabolism pathways, Clostridium difficile suppression). To understand the interplay between methodological and explanatory scales, we examine claims of “dysbiosis,” when host illness is proposed as the consequence of a community state. Our analysis concludes with general observations about how methodologies relate to explanations, and the implications for microbiome research.

THOMAS PRADEU The Limits of the Self: Immunology and Biological Identity

Let us start with the cover. The jacket of the hardback edition is adorned with an image of an ancient ceramic depicting a chimera. In this case, it is an awkward but classic fusion of a lion, a goat with excessively long horns, and possibly a snake (serving as the creature’s tail). The hybrid entity looks conflicted, with the lion prancing forward and the antelope gazing backwards despairingly. The sex of the chimera is possibly also mixed: the body has lactating nipples, but the lion has a male’s mane. Chimeras are one part of Pradeu’s story, not in this Homeric form but in the form of the more generic notion of the ‘heterogeneous organism’. The other part of the story is immunological. Having led us through more than a century of immunological research and theory, Pradeu argues that the best current immunological knowledge, in the form of ‘continuity theory’, requires the heterogeneous concept of the organism. His book is structured so that he proceeds—after an introduction telling us what he’s going to do—from an account of why continuity theory is best toward its inherent concept of the individual. I will review the book backwards for two reasons. One is that, as Pradeu admits (p. 220), it is the discussion of biological individuality that will be of most immediate philosophical relevance; the other is that it will be interesting to see whether his thesis works in both directions. Starting with the organism (as a subset of different types of biological individual) rather than the evolutionary individual, Pradeu seeks an appropriately strict physiological theory that will specify what organisms are. Immunology supplies this physiological theory and ‘functional integration’,