Biology & Philosophy

Measurement in biology is methodized by theory Abstract We characterize access to empirical objects in biology from a theoretical perspective. Unlike objects in current physical theories, biological objects are the result of a history and their variations continue to generate a history. This property is the starting point of our concept of measurement. We argue that biological measurement is relative to a natural history which is shared by the different objects subjected to the measurement and is more or less constrained by biologists. We call symmetrization the theoretical and often concrete operation which leads to considering biological objects as equivalent in a measurement. Last, we use our notion of measurement to analyze research strategies. Some strategies aim to bring biology closer to the epistemology of physical theories, by studying objects as similar as possible, while others build on biological diversity.

Teleosemantics, selection and novel contents Abstract Mainstream teleosemantics is the view that mental representation should be understood in terms of biological functions, which, in turn, should be understood in terms of selection processes. One of the traditional criticisms of teleosemantics is the problem of novel contents: how can teleosemantics explain our ability to represent properties that are evolutionarily novel? In response, some have argued that by generalizing the notion of a selection process to include phenomena such as operant conditioning, and the neural selection that underlies it, we can resolve this problem. Here, we do four things: we develop this suggestion in a rigorous way through a simple example, we draw on recent neurobiological research to support its empirical plausibility, we defend the move from a host of objections in the literature, and we sketch how the picture can be extended to help us think about more complex "conceptual" representations and not just perceptual ones.

Evolution of multicellularity: cheating done right Abstract For decades Darwinian processes were framed in the form of the Lewontin conditions: reproduction, variation and differential reproductive success were taken to be sufficient and necessary. Since Buss (The evolution of individuality, Princeton University Press, Princeton, 1987) and the work of Maynard Smith and Szathmary (The major transitions in evolution, Oxford University Press, Oxford, 1995) biologists were eager to explain the major transitions from individuals to groups forming new individuals subject to Darwinian mechanisms themselves. Explanations that seek to explain the emergence of a new level of selection, however, cannot employ properties that would already have to exist on that level for selection to take place. Recently, Hammerschmidt et al. (Nature 515:75–79, 2014) provided a 'bottom-up' experiment corroborating much of the theoretical work Paul Rainey has done since 2003 on how cheats can play an important role in the emergence of new Darwinian individuals on a multicellular level. The aims of this paper are twofold. First, I argue for a conceptual shift in perspective from seeing cheats as (1) a 'problem' that needs to be solved for multi-cellularity to evolve to (2) the very 'key' for the evolution of multicellularity. Secondly, I illustrate the consequences of this shift for both theoretical and experimental work, arguing for a more prominent role of ecology and the multi-level selection framework within the debate then they currently occupy.

The Social Amplification View of facial expression Abstract I offer a novel view of the mechanisms underlying the spontaneous facial expression of emotion. According to my Social Amplification View (SAV), facial expressions result from the interplay of two processes: an emotional process that activates specific facial muscles, though not always to the point of visible contraction, followed by a social cognitive process that amplifies these activations so that they may function more effectively as social signals. I argue that SAV outperforms both the Neurocultural View and the Behavioral Ecology View, as well as previously proposed syntheses of these views, in accounting for various empirical findings.

Race and reference Abstract The biological race debate is at an impasse. Issues surrounding hereditarianism aside, there is little empirical disagreement left between race naturalists and anti-realists about biological race. The disagreement is now primarily semantic. This would seem to uniquely qualify philosophers to contribute to the biological race debate. However, philosophers of race are reluctant to focus on semantics, largely because of their worries about the 'flight to reference'. In this paper, I show how philosophers can contribute to the debate without taking the flight to reference. Drawing on the theory of reference literature and the history of meaning change in science, I develop some criteria for dealing with cases where there is uncertainty about reference. I then apply these criteria to the biological race debate. All of the criteria I develop for eliminating putative kinds are met in the case of 'race' as understood by twentieth century geneticist Theodosius Dobzhansky and his contemporary proponents, suggesting that we should eliminate it from our biological ontology.

Overcoming the underdetermination of specimens Abstract Philosophers of science are well aware that theories are underdetermined by data. But what about the data? Scientific data are selected and processed representations or pieces of nature. What is useless context and what is valuable specimen, as well as how specimens are processed for study, are not obvious or predetermined givens. Instead, they are decisions made by scientists and other research workers, such as technicians, that produce different outcomes for the data. Vertebrate fossils provide a revealing case of this data-processing, because they are embedded in rock that often matches the fossils' color and texture, requiring an expert eye to judge where the fossil/context interface is. Fossil preparators then permanently define this interface by chiseling away the material they identify as rock. As a result, fossil specimens can emerge in multiple possible forms depending on the preparator's judgment, skill, and chosen tools. A prepared fossil then is not yet data but potential data, following Leonelli's (Philos Sci 82:810–821, 2015. https://doi.org/10.1086/684083) relational framework in which data are defined as evidence that scientists have used to support a proposed theory. This paper draws on ethnographic evidence to assess how scientists overcome this underdetermination of specimens, as potential data, in addition to the underdetermination of theories and of data, to successfully construct specimen-based knowledge. Among other strategies, paleontology maintains a division of labor between data-makers and theory-makers. This distinction serves to justify the omission of preparators' nonstandard, individualized techniques from scientific publications. This separation has benefits for both scientists and technicians; however, it restricts knowledge production by preventing scientists from understanding how the pieces of nature they study were processed into researchable specimens.

Contingency's causality and structural diversity Abstract What is the relationship between evolutionary contingency and diversity? The evolutionary contingency thesis emphasizes dependency relations and chance as the hallmarks of evolution. While contingency can be destructive of, for example, the fragile and complex dynamics in an ecosystem, I will mainly focus on the productive or causal aspect of contingency for a particular sort of diversity. There are many sorts of diversities: Gould is most famous for his diversity-to-decimation model, which includes disparate body plans distinguishing different phyla. However, structural diversity construed more broadly spans scales, such as organization in and among cells, structural arrangements and biomechanics on various scales, and even the profile of ancestor-descendent relationships or community structure of interactions within ecosystems. By focusing on stochastic processes in contingent evolution, I argue that contingency causes structural diversity. Specifically, I focus on the plurality of structural types of cells, genetic codes, and phyla diversity as case studies.

Let me tell you 'bout the birds and the bee-mimicking flies and Bambiraptor Abstract Scientists have been arguing for more than 25 years about whether it is a good idea to collect voucher specimens from particularly vulnerable biological populations. Some think that, obviously, scientists should not be harvesting (read: killing) organisms from, for instance, critically endangered species. Others think that, obviously, it is the special job of scientists to collect precisely such information before any chance of retrieving it is forever lost. The character, extent, longevity, and span of the ongoing disagreement indicates that this is likely to be a hard problem to solve. Nonetheless, the aim of this paper is to help field biologists figure out what do to when collecting a voucher specimen risks extinction. Here I present and assess varying practices of specimen collection for both extant (i.e., neontological) and extinct (i.e., paleontological) species in order to compare and contrast cases where extinction risk both is and is not a problem. When it comes to taking vouchers from extant species at some risk of extinction, I determine that those advocating for conservative approaches to collection as well as those advocating for liberal information-gathering practices have good reasons to assess things in the way they each do. This means that there is unlikely to be a decisive, one-size-fits-all response to this problem. Still, progress can be made. We can acknowledge the risks of proceeding in either manner, as well as the uncertainty about how best to proceed (which will be deep in some cases). We can proceed as thoughtfully as possible, and be ready to articulate a rationale for whichever procedure is used in any particular case.

Evidential reasoning in historical sciences: applying Toulmin schemes to the case of Archezoa Abstract This article is a study of the role and use of evidence in the evaluation of claims in the historical sciences. In order to do this, I develop a "snapshot" approach to Toulmin schemas. This framework is applied to the case of Archezoa, an initially supported then eventually rejected hypothesis in evolutionary biology. From this case study, I criticize Cleland's "smoking gun" account of the methodology of the historical sciences. I argue that Toulmin schemas are conceptually precise tools that allow for the building of enriched reconstructions of evidential reasoning. From the application of this framework, I discuss three ways in which the construction and use of facts in the historical sciences are theory-laden. Despite its inherent limits, TS are heuristically useful tools to identify epistemic moves that could be further investigated. It also sheds light on the positive roles of speculation in the historical sciences. Finally, I argue that it provides a context-specific and individuated understanding of hypothesis evaluation in the historical sciences. Overall, I think the application of Toulmin schemas to cases of evidential reasoning in the historical sciences is a promising descriptive and heuristic tool for philosophers of science.

Ancient genetics to ancient genomics: celebrity and credibility in data-driven practice Abstract "Ancient DNA Research" is the practice of extracting, sequencing, and analyzing degraded DNA from dead organisms that are hundreds to thousands of years old. Today, many researchers are interested in adapting state-of-the-art molecular biological techniques and high-throughput sequencing technologies to optimize the recovery of DNA from fossils, then use it for studying evolutionary history. However, the recovery of DNA from fossils has also fueled the idea of resurrecting extinct species, especially as its emergence corresponded with the book and movie Jurassic Park in the 1990s. In this paper, I use historical material, interviews with scientists, and philosophical literature to argue that the search for DNA from fossils can be characterized as a data-driven and celebrity-driven practice. Philosophers have recently argued the need to seriously consider the role of data-driven inquiry in the sciences, and likewise, this history highlights the need to seriously consider the role of celebrity in shaping the kind of research that gets pursued, funded, and ultimately completed. On this point, this history highlights that the traditional philosophical and scientific distinctions between data-driven and hypothesis-driven research are not always useful for understanding the process and practice of science. Consequently, I argue that the celebrity status of a particular research practice can be considered as a "serious epistemic strategy" that researchers, as well as editors and funders, employ when making choices about their research and publication processes. This interplay between celebrity and methodology matters for the epistemology of science.