Evolving Thoughts

This three-part series is a talk I gave a while back to some ecologists and molecular biologists. It is a brief overview of the aims and relationship between science and philosophy of science, with a special reference to the classification wars in systematics, and the interface of science and the broader community. I will present my own overview of the elements of science – as a dynamic evolving entity of knowledge gathering rather than as a timeless methodology or as a purely social movement.

[Part 2, Part 3]

It isn’t often that an ornithologist gets to talk to birds. It’s even less frequent that they have an interest in the ornithologist’s point of view. Most rare of all is that the birds can talk back. And as for them being interested… But this is the position I find myself in today, so I hope you’ll forgive my nervousness.

What I’m going to do is to give an overview of the philosophy of science – necessarily a personal view of it – before I cover some of the topics we usually discuss. Then, I will describe a view of science as a dynamic historical evolutionary process which I think is the most realistic and fruitful view. Towards the end, I’ll suggest some ways in which philosophy, unlike ornithology, can assist its subjects, and then we’ll look at a couple of issues to see how this plays out.

One might ask what value philosophy has for science, and I’ve heard a number of scientists suggest, more or less tactfully, that philosophy is less than useful in the real world. In fact, some of my scientist friends are very untactful in making that suggestion.

But this is undercut to a degree by the fact that scientists themselves do philosophy. I once heard a theologian say that all Christians do theology, and the difference is whether they do it well or badly. Likewise, everybody does philosophy. The question is whether they do it well, and reduce confusion in their thinking, or do it badly, and increase it. Scientists like Stephen Hawking, Ernst Mayr, Stephen Jay Gould, Richard Dawkins, and so forth, all advance philosophical agendas and arguments in the course of interpreting their science. It’s only fair that philosophers get a look-in from time to time to see whether they do it well or not.

So we should start with the question of what the philosophy of science is, and how it came to be a distinct discipline, distinct, but not separate, from general philosophy.

What is philosophy of science?

Traditionally, philosophy has always dealt with the logic and methods of science, as far back as the scientific revolution and John Locke, who famously said that philosophy cleared the undergrowth to permit science to grow. In the wake of the massive developments in science in the nineteenth century, philosophy started to separate into distinct disciplines, one of which was scientific philosophy, which became, around the middle of the last century or a bit earlier, philosophy of science.

At first, the philosophy of science focussed on physics and astronomy as the “standard” notion of what a science was, and so much discussion centred on what made a physical theory a good one. A lot of it relied upon there being “laws” in scientific explanation. Once the focus shifted, around the 1960s with the rise of molecular genetics, to biology, it was immediately claimed that biology, lacking laws, was either not a science or some other kind of science. Of course, then people also began to argue that biology does have laws, and so an ongoing debate began.

Some of this debate dealt with an issue in the philosophy of science generally with went by the title of “reductionism”. This is the question of when one theory or domain of science can be explained by reducing it to another theory or domain. Hence, in biology, Mendelian genetics was said to be reducible to molecular genetics, in that all the entities and processes of Mendelian or population genetics could be accounted for by the entities of molecular genetics. Those who opposed this called themselves “holists”, based on the ideas of several prior philosophers and popular writers like Arthur Koestler. It has been said by G. C. Williams, the evolutionary biologist, that what distinguishes holists from reductionists in biology is the size of their glassware.

Recently philosophy of science has differentiated into several subdisciplines – there’s the philosophy of mathematics, which in recent years has dealt with, among other things, the use of Bayesian reasoning to make inferences and test hypotheses. In particular, the field known as “confirmation theory” has developed on from the old Popperian view that all science does is falsify hypotheses, not confirm or generate them in any systematic manner.

Then there’s the old standby, philosophy of physics, which these days can include time-travel and cosmology. But now, and most relevant to this audience, is the philosophy of biology. Philosophy of Biology started up in the period between 1959, when Morton Beckner published his The biological way of thought, and 1974, when David Hull published his Philosophy of Biological Science. It has generally covered mostly the philosophical implications of genetics and evolution. Genetics raises issues of what causes organisms, and in particular humans, to be what they are. It has affected discussions of race, ethics, medical research and public policy, because it deals with the animal that everybody knows, us. Evolution raises a range of different issues, ranging from whether we are selfishly determined to serve our own interests or those of our genes, to whether life is predetermined in how it unfolds. And it is interesting in its own right, of course.

But evolution and genetics are not the whole of biology. More recently a field of the philosophy of ecology has developed, and we also look at the area that is closest to my heart, that of biological classification, which is squarely in the old philosophical issues of logic.

So let’s look at what the issues are in the philosophy of science.

First and higher order questions about science

Philosophy of science asks questions about science. Some of these are zeroth order questions like, “Is hypothesis X a good one?”, which any scientists can and should ask. But we also ask first order questions like, “What makes hypothesis X a better hypothesis than hypothesis Y?” This leads philosophers to either say that the matter is without an answer, which is rare (nearly all philosophers of science agree that science does find things out and explain them better than before), or to offer an account of comparing and choosing between competing hypotheses. These are first order questions. This then raises second and higher order questions that abstract away from scientific practices and ideas – why should a given account of why science succeeds be accepted over another? and so forth.

First order questions can also include analyses of some of the core concepts that are used in science – like “species” or “cause” or “correlation” or “gene”. Sometimes this takes the course of agreeing with one or another scientist. A great many philosophers, for example, believe that a species is what Ernst Mayr said species – the category – are; that they are reproductively isolated groups of organisms. Other philosophers will accept some other option; it might be the ecological concept of species, or the so-called species nominalism which treats species as matters of convenience, as Darwin is supposed to have done (but didn’t) and John Maynard Smith and JBS Haldane did.

Then a philosopher might seek to synthesise several concepts to form a new one, or may even try to situate the various conceptions together in a single framework. These are second and higher order questions that one only does when one is doing philosophy.

There’s a very indeterminate line between science and philosophy. Theoretical biology, for example, often deals with these higher order questions as part of the business of forming new hypotheses. For example, in the development of methodological techniques in, say, phylogenetics, researchers will appeal to a criterion of a good inferential technique like Bayesian inference, or of good science, like verisimilitude (or “truthiness” to use a political term) or falsifiability. Often these disputes are indeed philosophical. This is unsurprising, because until fairly recently in historical terms, the enterprises of philosophy and science were considered the same.

Motivation: That’s where the cognitive action is

Why do philosophers flock around science like ants at a picnic? It’s the same reason – that’s where the sugar is. Philosophy is in large part concerned with knowledge, and the most active knowledge gathering is, and has been for four centuries or so, science. Nothing else has come close through human history. Four hundred years ago we thought water was watery form imposed on a neutral substance; now we are manipulating the basic building blocks of matter and converting elements into other elements. We can take genes from one “kingdom”, say insects, and place them in another to make luminous plants. While there are other forms of knowledge gathering, such as economics and literature, none of them can tag active genes or make a polymer that never existed before.

So it is something to know, how we know. And why it works. And if it will work in the future, and so on. That’s the next post.


  1. #1 coturnix
    June 5, 2007

    Is anyone doing philosophy of cell biology? Or of physiology or behavioral biology?

  2. #2 John Wilkins
    June 5, 2007

    Cell biology? Not that I know. Physiology not since Claude Bernard in the 19th century. Behavioral biology? Yes, but it mostly goes by the name of ethology or evolutionary psychology, depending.

  3. #3 ChemJerk
    June 6, 2007

    Why no love for the philosophy of chemistry? Once again chemistry gets treated like the neglected middle child.

    Still, great stuff for this amateur philosopher of science – looking forward to the other installments.

  4. #4 John Wilkins
    June 6, 2007

    Well, I am a philosopher of biology addressing biologists. But I really haven’t seen a lot of philosophy of chemistry, apart from some inane ramblings about the patriarchal nature of molecular bonds…

  5. #5 CaptainBooshi
    June 9, 2007

    Just to clarify, versimilitude and truthiness are nothing alike. Truthiness is a term that was coined by Stephen Colbert to specifically indicate believing in something because you know it is true no matter what the evidence or reality says (which is unfortunately the way government officials act today). Not quite what you meant, I’m pretty sure.

  6. #6 John Wilkins
    June 9, 2007

    I know, and when I gave the talk Colbert had just given his talk in front of Bush. It was a way od making light of the subject…

  7. #7 Clifford Dubery
    December 8, 2007

    I have just bought Cosmos 18, DEC 07/JAN 08 page 44 Dissecting Science. If you need a copy of the article let me know via e-mail and I will send a pdf version to you?

    Will comment later

  8. #8 Rob Lockett
    February 24, 2008

    Isn’t philosophical coherence itself the foundation of science? I mention it because many people argue that philosophical coherence is not the ambition of science so much as empirical testing. And that is confusing since the whole validity of testing is found in the assumption that matching two or more entities into a coherent pattern results in a third element of harmony and confirmation.

    So in order for science to be valid, our thinking and assumptions of logic must first be valid. Before material coherence and empiricism can be valid, philosophical coherence (the empirical testing of ideas) must be valid. Since both match when systemic coherence is obtained, we can test our internal ideas against the external world.

    C.S. Lewis pointed this out in a book that truly enlightened me. He said, “…Unless human reasoning is valid, no science can be true.

    It follows that no account of the universe can be true unless that account leaves it possible for our thinking to be a real insight. A theory which explained everything else in the whole universe but which made it impossible to believe our thinking was valid, would be utterly out of court. For that theory itself would have been arrived at by thinking, and if thinking is not valid that theory would, of course, be itself demolished. It would have destroyed its own credentials. It would be an argument which proved no argument was sound -a proof that there are no such things as proofs- which is nonsense.” (C.S. Lewis / Miracles / Chap 3 The cardinal Difficulty of Naturalism / pgs 21, 22)

    I say all of this because it seems to me that only the truly empirical sciences can be valid. There is a lot of theory today that appears more and more to me, to be utterly unempirical be it in the material or philosophical sense.

    It appears that the presumed questions and conflicts between ‘science’ and ‘religion’ are not really over the existence of God (or the question of God’s existence being relevant). That is because ‘God’ and ‘reality’ are synonymous conceptually. Both science and religion believe in an absolute, ultimate, and sovereign reality, therefore both believe in God so to speak. I think the question is really one of God’s (or reality’s) nature. Is reality a personal living spirit, or an impersonal as yet unknown material force? Whatever or whoever reality is, reality is God by definition.

    Also striking is the fact that the triune nature of ‘empiricism’ as a philosophy, assumes an order that is also consistent with the idea of the Biblical triune God. I heard one Christian philosopher (Ravi Zacharius) put it this way: ‘We seek unity in diversity, and the only way to have unity and diversity in the effect (creation) is to have unity and diversity in the first cause (creator)’.

    Our current convention of science (Methodological Naturalism) asserts and exalts a philosophical position that cannot be tested empirically (in the material sense), and cannot be stated with philosophical coherence. It says that only material explanations are scientific, even though that assertion itself is a philosophical case. It is self defeating as Lewis demonstrated for us.

    In fact, with the advent of the quantum, and the recognition that energy and gravity cannot be understood in material terms, it appears that we have in fact proven the existence of some form of super nature that can only be understood philosophically, hence the theoretical physicists. As Paul Davies reminds us, ‘it is absolutely ‘theo’.

    So I ask you, is reality a ‘what’ or a ‘who’?

    If energy can only be defined materially as the ‘capacity to do work’; then, is it worth taking the philosophical coherence as scientific, when two thousand years ago a Jewish carpenter who claimed to be the creator said, “My Father is always at his work to this very day, and I, too, am working.” John 5:17

    “The reason my Father loves me is that I lay down my life–only to take it up again. No one takes it from me, but I lay it down of my own accord. I have authority to lay it down and authority to take it up again. This command I received from my Father.” John 10:17-18

    Science is nothing but philosophical coherence applied to the natural world. The most coherent pattern match between the two (our internal philosophy and the external world) must be taken to be the inference to the best explanation if we are to remain scientific.

    Logic (order) must be assumed to be God no matter what our philosophy, and that is very telling since without it all things become unintelligible philosophically, and fall to pieces materially.

    ‘What’ or ‘who’ is this logic?

    Is it not the way, the truth and the life, whereby no man comes to the Father but by Him?

    He is before all things, and in him all things hold together. Colossians 1:17