Philosophy of science 101 for ecologists: recommended readings (UPDATED)

Recently, Meg emailed Brian and I the following question:

Hi Brian and Jeremy,

You’ve both written about philosophy of science, and those posts always make me realize that I have not read nearly enough of that. I’ve read Platt and Chamberlin, but not Lakatos and Mayo who you both favor.

I’m wondering if:
1. you have general recommendations on Readings in the Philosophy of Science 101, and
2. if there might be interest in a blog post along these lines, since I’m sure lots of other folks are clueless about this, too.

Brian and I replied at sufficient length that we decided that we could just publish edited versions of our replies as a blog post.*

Our replies take for granted that you want to read some philosophy of science. If you’re not convinced of that, you should read this old post first.

Jeremy’s reply:

Ooh, good question! But one which, embarrassingly, I’m not sure I’m a good person to answer, because my own reading has been quite haphazard. I’ve found what little I’ve read to be useful. But I’m not sure if the stuff I happen to have read and found useful would necessarily be a great starting point for anyone else.

If I was going to pick one philosophy paper that I’d recommend to any scientist, it’d be Wimsatt 1987, “False models as means to truer theories”. It’s a book chapter in Neutral Models in Biology. I’ve linked to it and summarized it in an old post on how false models are useful because they’re false. I read it as a grad student and it really opened my eyes. And it’s totally non-technical and accessible, any scientist can read it easily. Wimsatt also has a book called Re-Engineering Philosophy for Limited Beings that lays out his overall point of view. But it’s aimed more at philosophers than scientists.

That classic Richard Levins piece on “the strategy of model building in population biology” is something everyone should read. And philosophers like Steve Orzack, Elliott Sober, and Michael Weisberg have written papers commenting on the philosophy of science implicit in Levins’ piece (see here and here for instance).

I’d like to read some Karl Popper. It’s embarrassing that I still only know him n-th hand. I think reading him is kind of the philosophy of science equivalent of reading Darwin’s Origin. From what I hear, he’s different (and more sophisticated) than the sort of garbled cartoon version scientists know.

I’ll let Brian talk about Lakatos since he’s read him and I haven’t.

I guess besides Wimsatt’s piece, I’d probably suggest philosophers who are writing about some bit of science that interests you and that you know a bit about. I find that sort of stuff both more interesting and easier to follow than “general” philosophy of science that’s either example-free, or that focuses on examples about which I know nothing and on issues that I as a scientist have no reason to care about. So I’ve read a decent amount of philosophy of evolutionary biology. Folks like Elliott Sober, Samir Okasha, and Peter Godfrey-Smith on issues like the levels of selection. Sober’s 1993 book The Nature of Selection is a classic that set the agenda for that whole subfield of philosophy of science. I like that stuff a lot, because it’s an area where there are very tight links (or maybe very fuzzy boundaries) between philosophical and scientific issues. But if you’re not into the levels of selection or whether selection is a “force” or whatever, it might not grab you.

Philosophers of science haven’t paid much attention to ecology, unfortunately, in large part because to outsiders ecology seems like a mess with no conceptual core. But Chris Eliot, who’s commented on the blog, is a philosopher of science who writes about ecology. He’s published several philosophy papers about community ecology. I read Cooper’s The Science of the Struggle for Existence, which is all about ecology, but had mixed feelings. But apparently philosophers liked the book better.

Bob Holt suggested Deborah Mayo’s error statistics book to me in grad school. I loved it and it had a big influence on me, but I’m not sure it’s for everyone. It’s a long book and repetitive at times. And she spends a lot of time attacking a philosophy of statistics (subjective Bayesianism) that’s never gotten much traction among either professional scientists or practicing statisticians as far as I know. But if you wanted something on philosophy of statistics, that’d be my suggestion. (UPDATE: Deborah Mayo herself has been kind of enough to comment and make clear something I should’ve made clearer here, namely that her attacks on subjective Bayesianism are only a part of her much larger project to develop a philosophy of statistics and experimentation. That broader project, not just the bits about subjective Bayesianism, is what influenced me and why I recommend the book. See this old post where I had a go at summarizing and extolling the virtues of Deborah Mayo’s work.) And the link above goes to her website, where you can also find papers presenting condensed versions of her ideas (which lose something compared to her book, I think). Or you could have a look at a couple of volumes she’s edited or written chapters for, one of which was edited by ecologists: Error and Inference, and The Nature of Scientific Evidence.

You could also try reading scientists who write about their own philosophy of science, like the Levins piece. But I have to say that, having read some philosophy by proper philosophers, I find the philosophy of science that scientists write to be a pretty mixed bag (and that includes my own tentative attempts at philosophy on the blog). Robert Peters’ A Critique for Ecology is poor philosophy, I think–it’s worth reading, but more as a provocation. There are various ecosystem ecologists who’ve written philosophical things that I just haven’t found very compelling for whatever reason, but I know other ecologists like that stuff. There are several chapters in Resetarits & Bernardo’s Experimental Ecology in which ecologists like Earl Werner and Peter Morin talk about the philosophy behind their research programs. I don’t know that that counts as “philosophy of science”, exactly, but it’s close. As I’ve mentioned on the blog, Dennis Chitty’s Do Lemmings Commit Suicide? is a really interesting read. It’s Chitty’s memoir of his career studying small mammal population cycles. Any population ecologist would be totally into it. And Chitty’s pretty clear about his philosophy of science and how it shaped his work–and also about how he failed to answer the questions he spent his career trying to answer. It’s interesting to think about whether he’d have done different work and maybe made more progress if he’d had a different philosophy of science.

Brian’s reply:

Here’s the link I give my stat students for reading Lakatos: You can actually listen to him lecture if you prefer (although the lectures are also transcribed). The “Science and Pseudoscience” lecture which was for the general public is an especially good introduction. Essential features of Lakatos are: 1) all theories are falsified sometimes (direct slam on his PhD adviser, Popper). 2) To propose a theory you individually have to have a core idea that you assume to be true. 3) So what distinguishes successful theories are that they make novel, risky predictions that pan out. 4) Over time, other scientists will vote with their feet and choose research programs that are sucessfully making new predictions instead of post hoc explaining away inconsistencies (so there is a strong social element, much like Kuhn but more realistic in my opinion).

Quinn & Dunham (1983 AmNat On Hypothesis Testing in Ecology and Evolution ), is an interesting critique of Platt and whether it can apply to ecology.

The Golem  is a very quick read popular book that picks apart the idea that science has a special formula and highlights just how messy science is and reinterprets many classic stories used by philosophers of science to show how things were fudged, misrepresented,etc. I once guest lectured for several weeks in a “Methods of Science” for high school teachers class that used this as a text. Even though its goal is subversive, it teaches a lot of core ideas by explaining them before trashing them.

It is hard to go too far and escape Kuhn’s very short readable book on The Structure of Scientific Revolutions.

Bacon’s Novum Organum (online lots of places) is a pretty short and interesting read. It is the backlash to the idea that science was 100% deduction that lasted for ~2000 years after Euclid (go look at Newton’s Principia sometime – everything is theorem, proof, theorem, proof). Seriously. Newton barely mentions fitting empirical reality. Even though Lakatos will cite him 300 years later for making a bold prediction in predicting the existence of Neptune to explain deviations between empirical reality and theory.

What passes for philosophy of science in philosophy departments is pretty far removed from what practicing scientists care or think about. So most “introduction to philosophy of science” is going to be dry and irrelevant. Two exceptions:
Theory and Reality an Introduction to the Philosophy of Science (haven’t read it but after a quick scan of Amazon this is what I would buy – indeed I”m tempted to buy it – although the reviews say it gives a harsh treatment of Lakatos). The Philosophy of Science Encyclopedia ($500 nobody is going to order this but lots of libraries have it in their reference section – I have used this fairly often although obviously its a reference and not an introduction)

Meg’s thoughts:

Lots of great thoughts from the two of you, as I expected! I think I read Do Lemmings Commit Suicide as a grad student, but don’t remember it very well, which suggests I should reread it. Thinking about this more prompted me to go take the binder where I have all my notes from the Quantitative Methods in Ecology and Evolution course (taught by my advisor, Alan Tessier) off my book shelf. Alan devoted the second lecture to the philosophical framework for doing ecology and evolution. Looking back through my notes, the paper we read for this class was Quinn and Dunham’s On hypothesis testing in ecology and evolution. I’d forgotten about that paper, but, based on a quick skim, I really ought to reread it! Alan contrasted this with Loehle’s Hypothesis testing in ecology: Psychological aspects and the importance of theory maturation. That also looks well worth reading.

So, I’m back to feeling like I need to set aside more time to read! We’ve compiled quite a reading list here! I’d love to hear suggestions from readers, too.

UPDATE: The comment thread has a bunch of great suggestions, from both scientists and philosophers of science. As with many of our posts, you’re really missing out if you don’t read the comments.

*We are nothing if not lazy efficient.

39 thoughts on “Philosophy of science 101 for ecologists: recommended readings (UPDATED)

  1. Everything by Robert Brandon, especially “Adaptation and Environment”, but also “Concepts and Methods in Evolutionary Biology”, “Genes, Organisms, Populations: Controversies Over the Units of Selection” (with Richard Burian), “Biology’s First Law: The Tendency for Diversity and Complexity to Increase in Evolutionary Systems” (with Dan McShea) and “Integrating Evolution and Development: From Theory to Practice” (with Roger Sansom).

    • Good suggestions. Brandon’s another philosopher who’s very familiar with and grounded in the everyday practice of the scientific fields he writes about. If memory serves (which it may not…), I think he did his PhD with Joel Kingsolver, who’s a top evolutionary biologist.

      I read Adaptation and Environment a long time ago and don’t recall it except that I liked it.

      I read Biology’s First Law when it came out and confess I found it puzzling. The point seemed obvious to me and I wasn’t clear why Brandon and McShea found it so profound or important. But perhaps I should give it another look at some point.

  2. Reiners & Lockwood’s Philosophical Foundations for the Practice of Ecology is worth a look. An introduction to philosophy of science that’s written by and aimed at ecologists who’ve read a wider range of (and more recent) philosophy of science than just Popper and Kuhn.

    There’s also Keller & Golley (eds.) The Philosophy of Ecology, which is a collection of readings, mostly from ecologists but with a few philosophers thrown in. I confess I find it a quite mixed bag, both in terms of the individual pieces, and in terms of the idiosyncratic (to my eyes) choice of pieces, many of which are “philosophical” only in the broadest and loosest sense. And many of the pieces are quite old and arguably of only historical interest–stuff from folks like Clements and Tansley.

  3. Another suggestion that might interest readers: David Hull. Very influential philosopher of evolutionary biology, and of science more generally. His magnum opus is Science as a Process, which argues that science progresses because it’s analogous to evolution by natural selection. I read it a long time ago and want to reread it. Tries to account for why science as it’s actually done by real scientists works, as opposed to arguing for some idealization of science that not only can’t be realized in practice but can’t even be usefully aimed at. It uses the phenetics vs. cladistics wars as a case study, which I’m not sure was the best choice because I think that fight was atypical of science in some ways.

  4. If your library has a subscription, the online Stanford Encyclopedia of Philosophy also is a useful reference, though I think it helps to have read a bit of philosophy from other sources first.

    • You don’t need a library subscription to read SEP. I second the recommendation, though! Sahotra Sarkar and Dan Faith, among others, have written some great articles on ecology-related topics.

  5. When I was in college, I read and truly enjoyed “For and against the method” (here the introduction), which contains a series of very accessible lectures by Lakatos as well as the correspondence between Lakatos and Feyerabend. Plus, the mugshots on the cover of the book are well worth the price!

    • I should probably read a bit of Feyerabend, he’s a big name. I confess that my n-th hand knowledge of his philosophy makes him sound too odd to be worth my time (I vaguely recall (?) some line of his about how scientific laws should be decided by democratic vote, just like any other laws in a democracy…). But since you found some of his views worth reading maybe I should take the plunge.

      • Feyerabend says a lot of things to be deliberately provocative. It’s quite a challenge – albeit an amusing one – to tease out which of his statements are meant to be taken seriously, and which are at least a little bit tongue-in-cheek.

      • My notes from Alan’s Quantitative Methods course include: “read Feyerabend 1978 if want fun”.

      • @Meg:
        Ah, that’d be Science in a Free Society: The Stanford Encyclopedia of Philosophy entry certainly does hint at an entertainingly polemical read:

        “The critical reaction to Against Method seems to have taken Feyerabend by surprise. He was shocked to be accused of being aggressive and nasty, so he replied by accusing his accusers of the very same thing. He felt it necessary to respond to most of the book’s major reviews in print, and later assembled these replies into a section of his next book, Science in a Free Society, entitled “Conversations with Illiterates”. Here he berated the unfortunate reviewers for having misread Against Method, as well as for being constitutionally incapable of distinguishing between irony, playfulness, argument by reductio ad absurdum, and the (apparently rather few) things he had really committed himself to in AM. The spectacle of Feyerabend levelling these accusations at others is not itself without irony.”

  6. Popper can go on a bit, but Chapter 1 of Conjectures and Refutations is a pretty succinct statement of the main ideas. It’s always nice to feel you read the man himself rather than some disco remix.

  7. I’d be curious if anyone has read Ecological Paradigms Lost (eds. Cuddington & Beisner) book listed on Chris Eliot’s list above. I flipped through it once after spotting it in an ecologist’s office – like Kuhn, the book seemed to blend a lot of history and philosophy, which I like, but I couldn’t tell much more than that.

    (Not to be confused with The Ecology of Paradise Lost:

  8. As a first year zoology undergraduate at Leeds in 1974 we had a course called Philosophy of Science taught by the late Edward Broadhead and the set text was Karl Popper – at the time we all hated it!

  9. Suggestions as to readings in the Philosophy of Science would not be complete without Steven Weinberg’s DREAMS OF A FINAL THEORY (1993), particularly his chapter “AGAINST PHILOSOPHY’, where he asks why PoS has contributed so little to the advancement of physics. And he should know, being one of the greatest physicists of the 20th century.

    • Which raises the question of whether there are certain fields of science, or certain people within any given field, that would get something out reading some philosophy of science, and others that wouldn’t.

      Tentatively, I’d suggest that in a young field like ecology, where it’s not always obvious what questions to ask or what would even count as an answer, that some philosophy of science is likely to be helpful.

  10. Bachelard’s “The new scientific spirit” was very formative for me. Bachelard was a physicist (and a poet), and his book is about (I grossly oversimplify) the need for a solid mathematical foundation, why the search for patterns with no hypotheses is vain, and why models should work hand in hand with experiments (all very valid points in ecology). It also has many interesting discussions about the importance of methodology and technics for research. It’s a brilliant book.

    Feyerabend’s “the tiranny of science” was also one with a profound effect. It’s provocative but really interesting.

    Oh, and Descartes. Especially the unfinished “rules”. It’s boring and dogmatic and sometimes misguided but an important read nonetheless, especially on the role of evidence, certainty, and doubt.

    • Thanks for the tip on Bachelard, that sounds very interesting. I’m particularly intrigued by the futility of searching for patterns without hypotheses.

      “Oh, and Descartes.”

      Dynamic Ecology: the only ecology blog where commenters recommend Descartes. 🙂

  11. Hello! I’m a philosopher of biology, myself, and Secretary of ISHPSSB, which you should come and join! Also known as “Ishkabibble”, The International Society for the History, Philosophy and Social Studies of Biology welcomes scientists, historians, and philosophers! There are many talks on the history, teaching, and current practice of ecology at our upcoming meeting in Montreal: Join us!!
    Philosophy of ecology has actually had a renaissance of late; there are many young philosophers dipping into this field. I recommend the following authors, in addition to the ones listed above (I think well especially of Wimsatt, Sober, Godfrey-Smith, Okasha, and Weisberg): Jay Odenbaugh, Mark Colyvan, Sahotra Sarkar, James (Jack) Justus, Marc Ereshefsky, Philippe Hunneman, Roberta Millstein, Yrjo Haila, Carlos Santana, Alkistis Elliott-Graves, and Stefan Lindquist. See also this website with links to current publications in philosophy: The best journals are: Philosophy of Science, British Journal for Philosophy of Science, Biology and Philosophy, and Studies in History and Philosophy of the Biological and Biomedical Sciences. There are also quite a few philosophers writing about science policy and science in society, as well as science and the law, though this is a rather crowded field! I recommend: Philip Kitcher, Carl Cranor, Wendy Parker, Nancy Cartwright, Julian Riess, Daniel Steel, Heather Douglas, and Sandy Mitchell.

    • Thanks for this Anya, I’m familiar with some of these other names but not most of them. I’m actually embarrassed not to have mentioned Jay Odenbaugh in the post, as I know his work and in fact he got his PhD here at Calgary. And of course my Calgary colleague Marc Ereshefsky is a leader in thinking about philosophical issues raised by different species concepts.

  12. I’d recommend Samir Okasha’s ‘Philosophy of Science: a Very Short Introduction’ ( as a very good introductory book. Cheap, very readable and informative.

    Also James Ladyman’s ‘Understanding philosophy of science’ ( for a more comprehensive and in-depth treatment, but still easy to follow.

    And finally ‘Philosophy of pseudoscience’ (, more technical but providing an up-to-date, fascinating discussion of current ideas about what science really is, and the problem of demarcating sound science from pseudoscience – a big philosophical problem with many societal repercussions.

  13. My 1996 book is largely involved in developing a general error statistical philosophy of science and solving problems: underdetermination, Duhem’s problem, induction; the criticism of subjective Bayesians is a very small part. As for the remark: ” And she spends a lot of time attacking a philosophy of statistics (subjective Bayesianism) that’s never gotten much traction among either professional scientists or practicing statisticians as far as I know.” you may notice that Howson announced he was quitting doing philosophy of statistics after my EGEK won the Lakatos prize (moving over to pure probability logic), and the general rise of attempts at “non-subjective” or conventional Bayesian soon followed in both philo and practice. Confirmation theory folded soon after. Formal epistemology is just that: using probability ideas to phrase positions in analytic epistemology.

    That said, I think the main contribution of my work is toward philosophy of experiment. Now it’s taught mainstream.

    Admittedly, philosophy of methodology and statistics has dissipated–to the great regret of those who realize just how badly it’s needed by those now drowning in the swamp of replication crises (as in some conferences I just came from).

    I’m afraid Sober gives a highly confused and distorted view of basic statistical tests and actually claims N-P statistics occurred before Fisher.

    I’d recommend Popper, Salmon, Peirce.

    • Thanks as always for your comments Deborah. Your remarks about your larger project and its place in philosophy of statistics and philosophy of experiment are very interesting. Apologies that my passing remark gives a mistaken impression of EGEK; I should’ve made clearer that your critiques of subjective Bayesianism were only part of a much larger project.

      Which of Peirce’s writings, or writings about Peirce, would you recommend to a scientist curious about his philosophies of statistics and science? Peirce is high on my own to-read list, but I’m daunted by where to start. Or maybe an intellectual biography of Peirce might be a better choice for a scientist like me than reading Peirce himself?

      • I wouldn’t have noticed it except that someone sent it to me, saying: “We wonder why there’s so much confusion about statistical foundations in practice.” Definitely read Peirce (“Pragmaticism”) and not a book about Peirce. Referencing him is odd because of the way his work has been compiled and recompiled, references to the Harvard volumes may be found in Chapter 12 “Error Statistics and Peircean Error Correction”.
        It occurs to me that the Taper and Lele book is a good collection for (and by) ecologists. Through somewhat of an accident (or so Royall says) many ecologists are likelihoodists, and as Royall emphasizes, that means evidence is distinct from error probabilities (which are regarded–by them– as relevant for long-run error control only). Much of the hand-wringing about non-replication these days concerns biased selection effects (e.g., cherry-picking, P-hacking, barn hunting)–all of which disappear under the likelihood approach.
        Then again, that might not be relevant for ecologists in the course under consideration. For general philosophy of science, let me add to others mentioned: Glymour, Alan Chalmers, Kent Staley. By the way, Mayo (1996) is intended to be read piece-meal–just like my philosophy. My “Error and Inference” includes exchanges among/between me, Glymour, Chalmers, Achinstein, Laudan, Musgrave, Worrall, Cox, Spanos and has a list of topics and specific questions at the start. I’ll soon have a new book: “How to Tell What’s True About Statistical Inference”. Then I’ll return to philosophy of experiment. Or something.

  14. I am a philosopher of science who has written a lot on philosophical issues in ecology. Some of my work has been historical mostly on Robert H. MacArthur and Richard Levins respectively. Additionally, I have written on mathematical modeling in ecology, what are ecosystems and communities, and mostly recently on controversies concerning neutral versus niche theories, and individual-based modeling. Conservation biology and the roles of values and advocacy has been an interest as well. My webpage has a list of my papers and I happy to send them to those who are interested if you can’t find them otherwise. The overviews of philosophy of science mentioned above are great and Chris Eliot’s bibliography is a rich resource if you just want to dive into the philosophy of ecology.

  15. Sort of like Simon, I took a mandatory course in my MSc called “Research Methods” which was an evening class (6-9pm), and which most of couldn’t abide. Chamberlain, Platt, and Popper were featured prominently, and I still have my class notes (Class 1: “Could someone please come up to the board and draw science?”)

    It’s not been mentioned yet, so I’ll plug Gauch’s “Scientific Method in Practice” ( as an easily accessible (at least for this neophyte) introduction starting at the basics.

    • I should add that had I taken the class mid-way through my PhD I would have enjoyed it much more, and probably gotten more out of it (rather than semester 1 of my MSc), though by then is it too late? I don’t think so.

    • Interesting, I never had a research methods course, but they’re common of course. Now I’m curious how many of them include some philosophy of science, specifically Chamberlin, Platt, and Popper.

      • It really was a philosophy of science course that was called “Research Methods”, the idea being that the philosophy of science underpinned how research is done across biology & forestry (in our case)

  16. Pingback: Pollinators and highway rights-of-way: the flipside. | Brianne Du Clos

  17. Cosmopolis: The Hidden Agenda of Modernity, by Stephen Toulmin presents an investigation of the history of how the development of Western science is related to social history. He concludes that modern science has moved beyond the “Hidden Agenda of Modernity,” but I found it interesting to think how my my views of science and research explicitly and implicitly reflect this historic “baggage.”

  18. Pingback: Personal case study on the usefulness of philosophy to biology | Theory, Evolution, and Games Group

  19. Pingback: Book review: The Knowledge Machine by Michael Strevens | Dynamic Ecology

Leave a Comment

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.