Do biologists infer to the best explanation?

The modern debate about scientific realism is to a large extent a debate about the reliability of inference to the best explanation (IBE). Proponents of anti-realism argue that IBE is inherently problematic. We cannot expect it to lead us to true theories, since it only picks the best of the available hypotheses, leaving us susceptible to unconceived alternatives. Newtonian physics was certainly a powerful explanation — until a patent clerk in Bern conceived a superior alternative, special relativity. Realists in turn defend IBE, arguing, for example, that IBE has become more powerful over time because the scientific community has grown; or that those parts of theories that fuel their explanatory success have actually proved stable over time; or that explanatory theories are strongly confirmed only if they made novel predictions.

In a forthcoming paper co-authored with Aaron Novick, we approach this debate in a different way. We concede that IBE is a dangerous method, just as anti-realists have argued. But biologists already recognize its dangers and insist on more stringent methodological standards before they accept hypotheses as established. Explanatory power is not enough. We propose that biologists instead adhere to versions of the vera causa standard. It requires that causes be shown to exist, to be competent to produce the kinds of effects ascribed to them, and to be responsible for particular instances of those effects. Until this standard has been met, the biological community accepts causal claims only provisionally, regardless of how powerfully they explain. We support this thesis by studying debates about the physical basis of heredity from the late 19th century (when multiple ingenious hypotheses failed) to the early 20th century (when Mendelian genes were localized to chromosomes) and finally to the middle of the 20th century (when DNA was shown to transmit at least some heritable traits). While explanatory power certainly served as a guide to the “pursuitworthiness” of hypotheses, it played little or no role in their acceptance. We thus de-emphasize the importance of explanatory power and emphasize instead the importance of detection and intervention, and of inferring causal competence by various experimental and observational methods. On this basis, we develop a new case for scientific realism about many (not all) claims in biology.

One distinction is crucial in this debate. We do not deny that scientific activity is often bound up with explanation. Once scientists have inferred the truth or likely truth of a hypothesis, they use that hypothesis in order to explain things. But IBE postulates something more: that we infer the truth or likely truth of hypotheses because they explain. This is where we disagree: Biologists seem to ask much more of their hypotheses.

The paper is titled “Presume it not: True causes in the search for the basis of heredity”. It is forthcoming in the British Journal for the Philosophy of Science, and a preprint is now available on the PhilSci archive. I like how this one turned out.

Difficulties and Intricacies of Creating and Using Historical Case Studies

Joseph Pitt has written a review for Metascience of our Boston Studies volume on The Philosophy of Historical Case Studies. We appreciate his generally positive tone. I think he is correct that our title overpromises: it would have been more accurate, as he suggests, to title the volume Difficulties and Intricacies of Creating and Using Historical Case Studies. But there must be some concessions to catchiness.

My contribution with Tim Räz gets a few kind words:

What is rewarding in the approach Scholi and Räz develop is its nuanced appreciation of the intricate dance that history and philosophy engage in as they support and confront each other.

That’s not how I usually spell my name, but you take the bitter with the better.

“Words, words, words, I’m so sick of words!”

Many scientists seem to agree with a favorite adage of the best film directors: “show, don’t tell”. A look at the latest articles in Nature will often reveal that half of the available space is devoted to pictures and diagrams rather than text. Supplemental materials may even consist exclusively or almost exclusively of diagrams.

While historians of science have long paid attention to visual representations, philosophers have by and large ignored them. But this is slowly beginning to change. In the last decade or so there have been recurrent bubbles of philosophical interest in diagrams, including a project directed by William Bechtel and Adele Abrahamsen at UCSD under the lovely acronym Worgods (Working Group on Diagrams in Science). While I was at the Pittsburgh Center with the two of them, I quickly recognized not only how important diagrams are in scientific practice, but also that they had figured prominently in much of my previous research. I had just never stopped to consider them as objects of inquiry in their own right.

Take this diagram as an example:

Spot the difference figures
A figure from Fire et al. in Nature, 1998, volume 391, p. 808.

The figure appeared in a 1998 paper in Nature by Fire et al. It shows fluorescence micrographs of green fluorescent protein (GFP) in C. elegans. In a and b, GFP is expressed in a larva and in an adult, respectively. In d and e, the expression is suppressed. In g and h, the expression is suppressed in the nucleus, but not in mitochondria. What is the point of figures like this one?In a forthcoming paper, I give a pretty straightforward answer. Many of the diagrams in your routine scientific publication depict what I call “causal contrasts”. They show what happens to a particular outcome variable if a specific intervention is performed, comparing this to a control in which the intervention is not performed. In the diagram above, the point is to show that an intervention with double-stranded RNA can suppress the expression of sequence-homologous genes (compare a and d, b and e). What is more, the diagram shows the specificity of this effect: if the double-stranded RNA is targeted only against the nuclear GFP gene, then the expression of mitochondrial GFP remains unaffected (compare a and g, b and h). For their demonstration of this extremely effective technique for gene suppression, the authors received the 2006 Nobel Prize in physiology or medicine.

I argue in the paper that many diagrams show causal contrasts, even though they differ significantly on the surface. Causal contrasts appear in many guises, some more obvious than others. They also appear in many scientific contexts, from the experimental to the observational to the purely theoretical.

Causal contrast diagrams are philosophically significant. They are a window into one of the key practices of scientific epistemology: causal inference. I suggest that this goes far in explaining why scientists, when reading a paper, turn to the diagrams first. A study’s key results can often be found there. Intriguingly, diagrams are often much more than merely a preferred representational tool for causal inferences. Diagrams themselves often constitute evidence: think of the ubiquitous photographs of electrophoresis gels in molecular biology, or the fluorescence micrograph shown above.

I call the paper “Spot the difference: Causal contrasts in scientific diagrams”. A preprint is available on the PhilSci archive, and the finished paper is about to come out in Studies in History and Philosophy of Biological and Biomedical Sciences.

The philosophy of historical case studies

Cover: The Philosophy of Historical Case StudiesThe Philosophy of Historical Case Studies is now available as a volume of the Boston Studies in the Philosophy and History of Science. I co-edited the book with Tilman Sauer.

The title is bit of grammatical play: one can read the genitive “of” in two different ways. On the one hand, our interest is in the philosophy involved in studying historical cases — how to minimize bias in choosing cases, how to draw robust conclusions from them, how to adjudicate between different interpretations of the same case, and so on. On the other hand, however, we are also talking about the philosophy that emerges from historical case studies: many worthwhile questions in the philosophy of science are best answered (and perhaps only answerable) by looking closely and carefully at the past and present of actual science.

So the volume is part manifesto, part user’s manual, and part affirmation of a research program – we hope that many different kinds of readers will get something out of it.

The table of contents is available on the Springer website. A preprint of my own contribution (with Tim Räz) is available on the PhilSci archive.

Towards a methodology for integrated history and philosophy of science

It has been claimed that the integration of history and philosophy of science is nothing but a marriage of convenience. I think this is wrong — it is really a passionate romance, and I argue why in a recent co-written paper. Beyond a discussion of what is to be gained by integrated HPS in principle, we focus particularly on the methodology of integration in practice: how should we relate philosophical concepts to historical cases, and vice versa? Our penultimate draft is now on the PhilSci Archive.

The paper is forthcoming in a collected volume titled The Philosophy of Historical Case Studies, which was co-edited by Tilman Sauer and myself and will appear in the Boston Studies in the Philosophy and History of Science.