General Science

There are a number of other metaphors used by the media and explainers when communicating about genes. Some of them have an acceptable interpretation, but may mislead; others only mislead. Before we consider the genes-as-information issue (next post), let’s look at some of these:

Genes as the essence of an organism

A while back I was contacted by a philosopher who specialises in metaphysics, which is the study of what ideas are necessary to make sense of the world. He asked me (as a philosopher of biology) whether, if a coat was made of my own DNA, I would become “bigger” than without that coat on. The idea that he seemed to have was that in modern biology, DNA was my “essence”, what made me who and what I am.

This is a fundamental mistake. DNA does contribute to some of my traits, and it may even contribute to how I develop my personality over time. But it is not my “essence”. The reason I quote mark “essence” is that it is a vague and largely meaningless term. In philosophy it means the properties that make some individual thing what it is: humans, for example, were held to be rational animals, which meant that they had an essential nature that was rational, along with the essential natures of animals (sensitivity to the environment, ability to move), along with the essential natures of all living things (ability to eat and grow, ability to reproduce).

But while DNA is implicated in how all organisms (of which we know) develop and mature, it is not their “essence”. DNA in a test tube will slowly denature (lose its structure and breakdown into its components, called monomers). DNA in an organism that lacks the right conditions (egg, maternal environment, atmosphere) will not enable that organism to continue. A newborn animal placed in a hard vacuum will do little apart from drying out. In short, the relationship between genes and the organism and its environment is summed up with the standard mnemonic:

G & E -> O

or, Genes plus Environment gives you the Organism.

What counts as the environment, however, is a complicated issue. Not only does the environment (for genes) include the ecosystem, as well as the maternal resources (egg yolk, placenta), it also includes the cell mechanisms of the fertilised egg as well; this means the mitochondria, the nuclear membrane, transport mechanisms like the actin cytoskeleton, and a host of other thing, not least ribosomes and cell membrane (or wall in plants). As well as this, it also includes the non-genetic structures that are needed to “express” genes – the polymerases and spliceosomes that are used in the process of making proteins. Finally, the environment for genes includes the machinery that replicates the genes themselves when cells divide – helicases and proteins that initiate replication.

Without all this machinery, genes would do nothing much. So, they are not, on their own, the “essence” of the organism.

Genes “for” a trait

The media often uses the phrase “the gene for” this or that trait, such as language, homosexuality, religion, rape, and so on. This is always misleading, and should never be said, by teachers or the media.

For a start, no gene does anything in isolation from other genes, so finding out that a gene like FOXP2 is implicated in the development and evolution of language is like finding out that 3/4 inch bolts are used in bridge building. They are crucial to the integrity of the bridge, but the bridge is a lot more than those bolts.

Second almost every gene has some other role in the body. Non-biologists will often talk about “the” function of a gene or other body part, but in fact parts of organisms, including genes, will always have many different roles in the normal function of an organism, and claims that “the” function is X are usually based upon what happens when a gene goes wrong. Delete or impair that gene, and language won’t develop. These are called “knockout studies”, because geneticists often remove the gene (knock them out of the organism being studied) to see what effects this has on the physiology of the organism.

Rather than saying FOXP2 is a “gene for language” it would be better to say it is a gene “involved in the development and evolution of language”. It takes longer to say, but it is at least accurate.

Genetic reductionism: it’s all about the genes

In 1976, Richard Dawkins published a book entitled The Selfish Gene. In this book, Dawkins argued that modern evolutionary theory considered that it was the gene, not the organism, that evolved. Critics pointed out some difficulties with this view, and today the consensus is that evolution occurs at all levels from genes to colonies or populations. But one outcome of Dawkins’ book was the introduction of what has come to be called genetic reductionism. Most people think this is a bad idea.

To reduce one level of talk about the world to another used to be considered progress in science. For example, we reduced talk about chemistry to physics when we developed quantum mechanics. Now we know that the reason why molecules for in reactions is that the molecules are made of smaller particles which attract each other and have certain energies that are reduced when a reaction takes place (roughly).

Dawkins seemed to be reducing talk about organisms, and their behaviour, to talk about the interests of genes (which were like selfish economists, trying to maximise their return on investment). However, many people objected to this, because it suggested that only genes were the beneficiaries in evolution, and that all that happened in evolution was adaptation by natural selection.

A philosopher once noted that in philosophy, “there’s the bit where you say it, and the bit where you take it back”. Dawkins expanded his view in subsequent books until he did not differ much from other evolutionary thinkers, but he remained convinced that natural selection was the main engine of evolution. Most evolutionary biologists will argue that much that happens to genes in evolution is anything but adaptive, and that much of what is important in evolution is anything but genetic. This leads us to the next metaphor:

Genetic determinism: biology is destiny

One thing genetic reductionism is thought to imply is genetic determinism. Sometimes summarised as “biology is destiny”, this is the idea that everything you do is directly determined by your genes. Dawkins wrote something like this in the Selfish Gene:

Was there to be any end to the gradual improvement in the techniques and artifices used by the replicators to ensure their own continuation in the world? There would be plenty of time for improvement. What weird engines of self-preservation would the millennia bring forth? Four thousand million years on, what was to be the fate of the ancient replicators?

They did not die out, for they are past masters of the survival arts. But do not look for them floating loose in the sea; they gave up that cavalier freedom long ago. Now they swarm in huge colonies, safe inside gigantic lumbering robots, sealed off from the outside world, communicating with it by tortuous indirect routes, manipulating it by remote control.

They are in you and in me; they created us, body and mind; and their preservation is the ultimate rationale for our existence. They have come a long way, those replicators. Now they go by the name of genes, and we are their survival machines.

The implication is that “we” (as bodies) are just what genes “program” us to do and be, and the genes determine our fate.

This idea is much older than genetics. Plato [in The Republic] thought we were all born with gold, iron or bronze souls, and our fates were determined at birth. Likewise, in the middle ages people thought that one’s “blood” determined one’s social rank (as an aristocrat or a peasant).

In the late nineteenth century this became the foundation for “eugenics”, which sought to breed humans the way a farmer breeds cattle or horses. This was then turned to justifying the extermination of millions by the Nazis, who followed the United States and Canada and Australia in its eugenics program.

Genes don’t “hardwire” people to behave in particular ways. Studies of psychopaths show that many of them live perfectly normal and law-abiding lives, because the negative side of their genetic dispositions was never triggered as they grew (see above, genes-as-essence). Just as people with a metabolic genetic disease can develop normally by avoiding the triggers (phenylketonuria can be prevented by avoiding phenylalanines in their food), pathological behavioural traits don’t always cause particular behaviours. But they can bias how a person responds to the environment as they develop.

In short, biology is not destiny, but it is an influence. Genetic conditions do not force behaviours, but they make some behaviours more likely to develop,

Common genes: what we share with chimps and mice (and bananas)

You will often see “similar DNA” numbers like this: Humans share 99.5% of their genes with chimps, 90% with cats, 82% with dogs, 80% with cows, 75% with mice, 60% with flies, and so on, and supposedly 50% with bananas.

While these percentages scale roughly with the amount of time since we shared a last common ancestor with them, the numbers are often wildly varying. Why?

It all hinges upon the notion of “similar”. There are three main kinds and several minor kinds of ways in which the DNA of one species can be similar to another’s.

One is “base pair similarity”. If each species has a gene X with around 10000 base pairs (“letters” A, T, C and G), and 400 differ, then they are (in that gene alone) 96% similar. However, gene X may be “the same” in its place in the genome and functions despite these differences, and so it can be 100% similar between the two species. Then you have the overall structure of the genome, which is arranged in chromosomes.

If each species has the same chromosome structure, then it can be 100% similar even if many genes are different between the species. But differences can arise when multiple copies of genes are made between species. If Gene X has three copies in species A but only one copy in species B, that can change the “similarity” measure.

Finally, chromosomes can be duplicated even in one species (this is called polyploidy): a species can have 1, 2, 3 or more copies of each chromosome. Obviously whether these count as differences or not depends on whether you are counting the genes, the base pairs, or the chromosome numbers.

So take care. A banana can have a whole host of genes that humans and other eukaryotes (roughly, plants, animals and fungi) have because they are basic genes for organisms to survive. But it will be very unlikely to have the same genes at a finer level of detail (base pair sequence, position, chromosomal arrangement).

I have done quite a lot of blogging under this heading lately so I thought it might be useful to get all the posts used in order:

On beliefs

On religion
On the arguments
On science and religion

Concluding posts

Many other posts from this blog have been used in the book manuscript, and this is not the order in which they will appear, but you can find your way around from here.

If science and religion do conflict, what are the points of conflict that have occurred? These tend to have arisen in historical contexts as the science evolved. I shall consider five sciences and how religion has responded to them: astronomy, or cosmology, geology, evolutionary biology and biology in general, medicine, and psychology. There are many other fields in which sciences have made claims that some religious traditions have found objectionable, though, so this is not an exhaustive list by any means.

For example, many human sciences have caused religious objections, such as archeology (especially archeology that deals with the Ancient Near East, but also archeological work done on Indian and American pasts, which Hindus and Mormons have found contrary to their sacred texts), history (which is arguably a science) and sociology (which often applies theoretical explanations to religious institutions that contradict the narratives of the religions themselves). However, the human sciences tend to involve both proponents and critics of theoretical views giving differing interpretations of events and even of the gathering of data, so in the interests of clarity, we will leave these aside.

Astronomy and religion

Once upon a time, as the fairytales begin, we believed that the world was flat, and then along came the scientists who showed that it was round. Religion, especially in the Bible, told us the world was flat, and sometime around the beginnings of modern science we learned that religion was wrong. Or so the fairytale goes. But it is, actually, a fairytale.

There is no doubt that ancient near eastern traditions of around 1000 BCE casually described the world as flat, and that these expressions found their way into the biblical sources. But in cosmopolitan societies, this was not what the educated thought. The world was known to be round by the Greeks, one of whom even calculated the circumference to a high degree of accuracy. Through Aristotle, the Arabs and the Europeans knew of the sphericity of the earth, and no sensible religious authority challenged this, apart from Lactantius (tutor to Constantine’s children) around the fourth century CE, Bishop Isidore of Seville, in the late sixth and early seventh century, and Indicopleustes, a monk in the seventh century, and they had little to no influence on later thinkers.

The really influential thinkers were the sphericists, as we might call them. Following Eudoxus, a student of Plato’s, another of Plato’s intellectual progeny, Aristotle wrote of a “two sphere” universe: where the earth was placed in the centre of a space enclosed by the outer sphere that the stars were placed upon. A second century Greek writer in Egypt, Ptolemy, developed a complicated model (a mathematical one, used for calculating the positions of the planets, sun and moon in the sky) which reign supreme in the western world until the sixteenth century, when it was challenged by Copernicus.

Although Aristotle’s model and Ptolemy’s were inconsistent, throughout this period few made much of the lack of consistency between it and Aristotle’s “four element” theory of physics – fire and air, which naturally moved up, and earth and water which naturally moved down, relative to the centre of the universe. The heavens were made of different stuff, which came to be known as the quintessence (fifth element, sometimes called the aither or ether), which was eternal and unchanging, and tended to move in the only motion which could be eternal and unchanging, in circles.

Ptolemy suggested that instead of circular motion around the centre of the universe, as Aristotle required, there had to be circles moving in circles in the heavens. He needed these to explain why planets moved the way they did (which we now know to be caused by irregular elliptical orbits). Ptolemy’s mathematics was widely accepted even as Aristotle’s physics were also, even though the two were not entirely compatible. Ptolemy was treated as a “computational technique” rather than a physical explanation, right up until the beginnings of the renaissance.

Aristotle’s physics was, for its time, relatively well elaborated and made sense of observational data. Its fourfold structure was extended to medicine (the four humours), to alchemy, and to conceptual schemes for recording and recalling information. It became, as it were, the groundwork on which all other science was done.

However, in the twelfth century, some thinkers (theologians like Oresme and Occam) started to challenge Aristotle’s physics. According to Aristotle, nothing moved except in “natural” ways (up and down) unless it was forced to by something acting on it. This raised the problem of the arrow. Arrows move up and down, and horizontally (in what was called “rectilinear motion”). According to Aristotle’s physics, to move up when they should move down, and to move horizontally, there had to be a moving force, and there was none. Aristotle explained this by the air moving behind the arrow to fill up the space left (because vacuums are impossible, according to Aristotle) imparted a force that kept it moving.

This was rather a forced explanation, and few were happy with it. Oresme and Occam (who is famous for his Razor) noted that barges would continue to move in water after being pushed, and came up with the idea of a conserved force they called “impetus” instead. Here is a case of religion and science in conflict. As theologians, Oresme and Occam (and other theologians of the time) felt it was their duty to revise and correct ideas about the natural world, especially those that came from pagan sources. And yet, their correction was more correct than Aristotle’s ideas were; in short, they advanced science.

Later, another theologian and priest, Nicholas Copernicus, proposed the idea that the earth revolved (in our terms, orbited; “rotation” applies to the earth’s daily rotation around the polar axis, while “revolution” applies to the movement of one heavenly body around another) around the sun (heliocentrism). Again, this is a case of a theological conflict with the science. Philosophically, Copernicus was somewhat influenced by neo-Platonic ideas in which physical things reflected a transcendental order, and the sun, being the source of light, must therefore represent the light of knowledge (Kuhn 1959). It is unclear how influenced Copernicus was (Rosen 1983), but that there was some influence is, I think, likely.

So we come to Galileo. The idea of a sun-centred universe is often called, following Kuhn, the “Copernican Revolution” (this being a historian’s double entendre), but as revolutions go, it was as slow as that of Saturn. Copernicus published in 1543, and Galileo in 1632, and by his death in 1642, 99 years after Copernicus’ own death, many but not all astronomers had adopted heliocentrism. Political revolutions that take so long are called reform movements; I suggest we should think that this is also a reform movement in astronomy.

As I noted, Galileo’s error lay in not realising that the usual Catholic theological tradition of reinterpreting scripture to cope with science was something he could not employ. Instead he had to get the Church to employ that. He made the mistake of telling theologians how to interpret scripture. Let me make one thing clear, though; he was not censured because he said the earth went around the sun. He was censured because he taught that the Church was wrong about how to read scripture, at a time when that was the bone of contention between the Church and the Protestants. In short, Galileo fell afoul of internal Church politics in a theological dispute about what the magisterium of the Church was.

However, the heliocentric theory was widely adopted and extended in Catholic as well as Protestant countries, and within another century had taken over, with little to no criticism by the Church.* However, some bemoaned the loss of the old certainties, such as John Donne in his poem “An Anatomy of the World” in 1611:

And new philosophy calls all in doubt,
The element of fire is quite put out,
The sun is lost, and th’earth, and no man’s wit
Can well direct him where to look for it.
And freely men confess that this world’s spent,
When in the planets and the firmament
They seek so many new; they see that this
Is crumbled out again to his atomies.
’Tis all in pieces, all coherence gone,
All just supply, and all relation; [lines 205-214]

All coherence was gone now, with this new science (“philosophy”) that dissected phenomena. This has more to do with the aesthetics of intellectual systems than religion as such. In any case, the conflict between religion (the Church) and science (astronomers) was not greatly effective in halting science here, nor would a lack of opposition made much difference in the advancement of heliocentrism, in my opinion.

Newton, another well-known religious enthusiast, although he was a unitarian or Arian rather than an orthodox Trinitarian, cemented the heliocentric theory – and extended it way beyond what either Copernicus or Galileo might have expected – and established a new physics that would completely replace the old four-elements two-sphere universe of Aristotle. Coherence was achieved again. But notice that it was achieved in 1687, a full 144 years after Copernicus’s death and publication. In each step, and I have left out a good many which can be found in such histories as Koestler’s (1964) or Toulmin and Goodfield’s (1962), religion was not always or even often a scientific inhibitor or barrier.

In subsequent developments, Napoleon famously asked his old teacher, Laplace, where God was in his book on astronomy, to which Laplace famously replied “I have no need of that hypothesis, sire”. The context changes it slightly from the usual interpretation, however. Newton could not explain why the solar system was stable, and he imposed God’s action, possibly via angels, to make sure the system did not collapse over time. Napoleon, who had studied physics and astronomy with Pierre Laplace, knew this, and when Laplace worked out that such a system could be stable without intervention, he dropped God’s intervention. It was this that Napoleon picked up on. Laplace was not rejecting God, so much as pointing out that God was a hypothesis of last resort.

In each of these episodes we see that the issue is not really religion against science, but either religion against other religion or old science against new science. Religions, unlike sciences, however, have a strong conservative aspect, and so once a view has been given a red light by a religious tradition, it can take a very long time for the religion to adapt to the new science it once objected to.

The religious views of the scientists involved do not seem to have had much if any real impact on the science itself. Newton did not present an Arian view of the solar system; Galileo did not contrast his religious beliefs with Protestant astronomy. In fact, quite the opposite: religious differences played almost no role in these debates unless they were religious issues being debated. Science, it seems, has always been secular even in the most contentious periods of religion in the west.


Koestler, A. (1964). The sleepwalkers: a history of man’s changing vision of the universe. Harmondsworth, Penguin by arrangement with Hutchinson.

Kuhn, T. S. (1959). The Copernican revolution: planetary astronomy in the development of Western thought. New York, Vintage Books.

Rosen, E. (1983). “Was Copernicus A Neoplatonist?” Journal of the History of Ideas 44(4): 667-669.

Toulmin, S. and J. Goodfield (1962). The Fabric of the Heavens: the development of astronomy and dynamics. Chicago, University of Chicago Press.

* The Church issued prohibitions until 1664, but by 1758 had dropped heliocentrism from the Index. Rabbinic opposition took about the same delay to abate.

[As I write the first draft of my accommodationism book, I will post chapters here under the Category “Accommodationism”. Here is the latest – which comes before Undefining Religion]

The religion-versus-science debate took a special turn in the West because of the existence not only of doctrinal religion but of a monopolistic doctrinal religion that made the crucial mistake of meddling in statements of fact, providing us with a long list of particularly precise, official and officially compelling statements about the cosmos and biology, supposedly guaranteed by Revelation, that we now know to be false. In every instance where the Church has tried to offer its own description of what happens in the world and there was some scientific alternative on the very same topic, the latter has proved better. Every battle has been lost and conclusively so. (Boyer 2001, 320)

In 2009, a blog war erupted among those who saw themselves as defending science, and in particular evolution, from attacks by religious activists in the public sphere, especially in education. There is an excellent, if underfunded, nonprofit organisation in San Francisco, the National Center for Science Education, which for several decades now has been providing information about and to the defenders of science education in schools. One of the main targets until recently has been the unending tide of bills in state legislatures, quite contrary to the United States Constitution separation of church and state, to enforce the teaching of creationism or its stalking horse intelligent design in state schools. The NCSE has provided comparative evidence about the motivation of these bills, which is always based upon a religious (or in the case of intelligent design, quasi religious) foundation.

The then-director of the NCSE, Dr Eugenie Scott (“Genie” to her friends, who are numerous) has always insisted that the task of the NCSE is not to attack religion, but to promote science education and knowledge in the broader community. In fact, the NCSE has, as part of its mission statement, the following passage:

What is NCSE’s religious position?

None. The National Center for Science Education is not affiliated with any religious organization or belief. We and our members enthusiastically support the right of every individual to hold, practice, and advocate their beliefs, religious or non-religious. Our members range from devout practitioners of several religions to atheists, with many shades of belief in between. What unites them is a conviction that science and the scientific method, and not any particular religious belief, should determine science curriculum.[1]

This innocuous statement is inclusive. In short, it doesn’t matter what religious affiliation an NCSE supporter has, so long as they are advocates for good science education and policy. It would seem a fairly agreeable view to take. But some find this highly objectionable. Professor Jerry Coyne, a well known evolutionary biologist who specialises in speciation, took the NCSE to task. He wrote on his blog:

Among professional organizations that defend the teaching of evolution, perhaps the biggest offender in endorsing the harmony of science and faith is The National Center for Science Education.  Although one of their officers told me that their official position on faith was only that “we will not criticize religions,” a perusal of their website shows that this is untrue.  Not only does the NCSE not criticize religion, but it cuddles up to it, kisses it, and tells it that everything will be all right.

In the rest of this post I’d like to explore the ways that, I think, the NCSE has made accommodationism not only its philosophy, but its official philosophy. This, along with their endorsement and affiliation with supernaturalist scientists, philosophers, and theologians, inevitably corrupts their mission.[2]

Coyne argues the following:

… my main beef is this: the NCSE touts, shelters, or gives its imprimatur to intellectuals and scientists who are either “supernaturalists” (the word that A. C. Grayling uses for those who see supernatural incursions into the universe) or who have what Dan Dennett calls “belief in belief”—the idea that while religion may be based on false beliefs, those beliefs are themselves good for society. (Among the former are Kenneth Miller and John Haught, the latter Michael Ruse and Francisco Ayala).  Both of these attitudes draw the NCSE away from its primary mission of promoting evolutionary biology, and push it into the hinterlands of philosophy and theology.

If we’re to defend evolutionary biology, we must defend it as a science: a nonteleological theory in which the panoply of life results from the action of natural selection and genetic drift acting on random mutations.

According to Coyne, evolutionary biology is nonteleological: it offers no support for the idea there is purpose in the world. This, however, is not how many (not the majority by any means) philosophers of science and biologists see things. They interpret evolution by natural selection as a purpose maker. In a view called teleosemantics (Macdonald and Papineau 2006), purpose is what you get when something is the result of selection for a trait or property (Sober 1984). Hence, one outcome of evolution, they say, is that natural selection (henceforth just “selection”) gives things purpose. Could this offer a hook on which to hang God? The answer to that varies according to who gives one. Theologically inclined writers think it does. Others, known in the philosophical trade as naturalists, say that it merely gives the illusion of purpose. But it is far from clear that selection, and evolution itself, in nonteleological. We will return to this later. For now, let’s ask this question: does evolution preclude belief in a providential deity? On this one example, among many such scientific challenges to religious belief, hangs a deep issue, about knowledge, belief, rationality, and social policy. It’s not an abstract philosophical issue, but one which has wide ramifications and urgency in the modern world. In what follows, I will attempt to get at the heart of this issue.

Science is one of the best and probably most enduring of all human activities, if not the best. Where once we widely believed that the world was made of an undifferentiated “substance” to which “form” was applied, now we are dealing with the most fundamental aspects of reality, creating physical conditions in our laboratories and supercolliders that haven’t been seen since the Big Bang. We can explain why physical bits of stuff behave the way they do to a very high degree of accuracy and precision. We explain why stars form, why planets orbit stars, and why some bits of stuff on the surface of at least one of those planets reproduces and evolves. We know more now than we ever have, and perhaps more than will be known anywhere else in the universe. That ain’t hay.

And there is no apparent contender to the pre-eminence of science. If there is a way to correct or revise the ideas that science has produced, it is only by science that we can do this. Science, or something that is very like it, is the sole way to know about the universe. The role of religion, often in the past and in pre-scientific cultures, has been deprecated to being an observer of knowledge creation, rather than a source of it. I won’t go into the history of this. There are many very good introductions to it from a historical and philosophical perspective, and we do not need it for what follows. All I will say here is that if we know something about the world, we do so through science.

So the religious are left with a quandary: either religious traditions are not sources of knowledge, or they conflict with the knowledge we get from scientific investigation. So they either have to say that religion doesn’t actually help you understand how the world is, and reduce their scope of authority, or they must challenge the belief that science does help you understand how the world is. Both strategies have been employed, sometimes simultaneously. I take it that we have no better metric of knowledge than that something has been properly investigated scientifically. I will not challenge the role of science in this book, but take it as a provisional given.[3] Of course, there are deeper philosophical questions about whether that is true, or warranted. Some of these will come up later. But we will start, as Coyne does, with the view that science is how we know things about the world, and that if we teach our children and advise our policy makers, we must do so based on that knowledge, and not some other claimant to know.

Thus far, we agree with Coyne and those who he makes common cause with. But they take it a step farther. Only science is relevant when we know the world. Since religion has beliefs that are either contrary to science or unnecessary for doing it (science is a verb as well as a noun), we must eliminate these from consideration in formulating education and policy. This is a much more restricted claim.

The term “accomodationism” has been used to label the idea that science and religion are compatible, although there are some wrinkles we’ll get to shortly.[4] The contrary view is sometimes called “anti-accommodationism”, which is cumbersome and defines a position solely in terms of it not being what another view is. I will therefore divide these views up in another fashion.

The argument goes roughly like this (for instance, as given in the Boyer epigram at the head of this post):

  • Science acquires knowledge through observation and experiment, and is subject to revision in the light of new evidence.
  • Religion acquires its beliefs through the process of supposed revelation, and is not revisable except through further revelation.
  • Science believes in testable entities and processes.
  • Religion believes in things that are either not testable, or have been tested and found not to exist.
  • Therefore religion is not compatible with science.

Now many religious beliefs are not based upon revelation – for example, the Protestant doctrine of sola scripture is not to be found in the Bible or any personal revelations,[5] but then neither is it revisable in the light of experience and evidence. So incompatibilist critiques of religion often focus on the implications of these beliefs. For instance, if the Bible teaches that mental illness is due to demons (Luke 8: 26-39), and we have learned scientifically that mental illness always has a physiological basis, then belief in the Bible must be abandoned. However, not only do religions not abandon those beliefs, they often double down and assert that science is false, or incomplete (which amounts to the same thing; an idea cannot be only a bit true. It is either true or false[6]).

The accommodationism debate, however, has several aspects. One is whether or not religion can be made compatible with science. It can. All that has to happen is to change the religious beliefs. That this is not a popular choice among the religious is obvious. What it does not imply, however, is that we could reach a rapprochement by changing the science. Many so-called compatibilists try to do this, and we’ll look at that later. The problem with doing it, though, is clear: by what criteria would religion evaluate the knowledge claims of science? If they are religious criteria alone, then they deny that science is, in fact, our best way of knowing the world, and deny the facts one way or another. Nobody seriously considering this issue can accept that. If they are experiential, by which I mean based on observation and experiment, then those criteria are properly scientific anyway. It is just possible that a religion encodes in its doctrines the outcomes of some protoscientific investigations that science has not yet studied or attempted independently, in which case that religion would be contributing to science, but the historical evidence is against it. I suppose William James’ Varieties of Religious Experience (James 1902) comes close, but James was a scientist and religion merely the subject of his psychological investigations.

The harder problem here is whether the changes that need to be made to religion to accommodate science could be made without destroying the basic core tenets of that religion. There is no real answer to this. For a start, the core beliefs of religions change over time anyway as they adapt to differing social, economic, and political circumstances. At one point, the God of the Tanakh, El[7], was one among many gods who “owned” as it were the tribes of Israel (see Psalm 82 for an example). Later, Judaism evolved after the Israelites were exiled in Babylon and they encountered Zoroastrian dualism, and when they returned to Palestine, their deity was the only one in existence, although there was a demigod, Satan, who gave him a run for his money. The very core belief of modern “Abrahamic” religions was once a revision to the religion itself (Smith 2001). What core beliefs change and how they do so is not something one can speak of in general terms. It really is up to the believers of a religion to decide what they can revise without damage, not anyone else.

Another issue, often mixed in uncritically with the former question, is how to promote peaceful coexistence of religion with science. The so-called “warfare hypothesis” first promoted by Draper (1875) and White (1896) in the nineteenth century, that science and religion are and always have been at war with each other, was constructed in the context of debates over the secularisation of education (Brooke 1991), and is widely regarded as at best overstated and at worst, quite false. And yet, there are enough cases of actual conflict to raise the issue for us. Critics on both sides take from history what they need: accommodationists find cases of affable cooperation and scientists who were devout, and anti-accommodationists find cases of religion impeding or even blocking entirely avenues of scientific work.

A counter argument presented by many religious believers and some scholars (see the overblown case made by Stark 2005) is that religion caused science. Usually this is the more specific claim that Christianity caused science. There is both truth and falsity in that claim. It is true that the religion in which science developed, and the cultural tools of which were used to do so, was Christianity. Most if not all scientists in the western tradition prior to, say, 1900 were Christians of one kind or another (but as we shall see in the next chapter, it pays to attend to the kind of believers they were). Some go so far as to say that Christianity is a rational religion and so it is a prerequisite for science to develop, or even (as we shall see later) to do science at all!

This borders on the inane. The tools used to develop science were the tools developed by the ancient Greeks and Romans, along with a large dose of Islamic philosophy mediated to the Christian West around the 12th century. Science had to develop somewhere if it did at all; it happened to develop in a quickly industrialising and capitalising society, and that was the Christian west, but prior to that science was being done by Greek “pagans” and philosophers of all kinds, Romans, Muslims, Chinese, Indians and so on. What happened in the west was largely a socio-political change: science was being done in the open, publicly, due to trade links between competing societies.

Christians can be proud of their heritage, however. When all is said and done, it was scholars within the Christian tradition who discovered or established heliocentrism, chemistry (out of another Christian tradition – alchemy), taxonomy, anatomy, physics (by that mystic unitarian, Newton), and so on. But there is a curious pattern in each case. While Christians were the ones who, on the whole, did the work, the religious institutions were often cautious or even hostile to these novelties. Copernicus’ views were represented contrary to his own position as a hypothetical method for computation of the positions of the planets by his Lutheran “editor” Osiander. Galileo was banned from teaching his version of heliocentrism as fact by the Catholic Church authorities who tried him. Chemistry and anatomy were constantly resisted by various church figures. The record is not unequivocal.

The Warfare Thesis has some bite then. Again and again it depends upon who you count as “religious”.

A history of accommodationism

The view known as “accommodationism” has a past history of some note, and we had better get that out of the way before we consider the modern debate.

The word accommodationism has two prior meanings, tangential to this question. One is: the accommodation of religious practices and beliefs within a secular society. This is a legal use, and refers to states either permitting or assisting the religious in carrying out things that are either regulated or prohibited for the non-religious (Brady 1999).

The other, which is more relevant, has to do with how to read the Bible. In the Christian period before the modern age, science was often discovering facts that contradicted the literal meaning of the Bible. This goes right back to the beginnings of Christianity; it isn’t new. As science fluttered into existence during the late medieval period, this posed a problem for theologians and Christian scientists,[8] who adopted what they called the “accommodatory language” view. God spoke the truth, but in terms that people of the day could understand, and so He used words that implied falsehoods in strict scientific terms. Thus, the words that have the earth fixed, with pillars rest in the waters, and a fixed and hard heavens, used in various places in the Bible, were of no more account than the vernacular use of “the Sun rises in the East” means that we think the Sun, not the earth, revolves.

Notice that this latter meaning is relevant to our topic. When facts (science) contradict the Biblical passages, then our interpretation of the language used in the Bible must give way to them. This approach was adopted by Galileo, Copernicus and others all the way back to Augustine (Moran 2003). In fact, the default view of the Catholic tradition has always been to do this. A parallel tradition that took a hard literalist approach, known as the Antiochan tradition, never got that much traction in the broader Christian tradition, and those who took scripture to be literally true, like Lactantius (third century) or Cosmas Indicopleustes (sixth century) and so asserted a flat earth, were few and generally ignored by educated Christians, who had read their Aristotle or their Plutarch (Toulmin and Goodfield 1962). But when Christian theologians began to engage with the best science of their day, they did not trim science to suit doctrine, but reinterpreted doctrine to not conflict with science. And the means by which they did this was called allegory: finding the hidden meaning in the stories told in the Bible that led to a theological or deeper truth. However, the default view was also that if there are no reasons not to take the scripture as literally true, especially in claims of the events and people described, like Noah or Moses, then you must do. It reminds one of the passage from T. H. White’s Once and Future King, where the Wart is transformed into an ant, and as he enters the nest sees a sign “Everything not forbidden is compulsory”.[9]

As science began to infringe upon some of the more treasured core doctrines of religion, however, the tensions began to rack up. When Galileo, naively thinking that he was well within the usual practice of the Church, wrote his Dialogues, he expected that the Church authorities would reinterpret doctrine once again. His timing was awful. The Church was in the midst of dealing with the Lutheran schism as they saw it, and Galileo unfortunately tried to lecture the Church on how to interpret scripture, which was their and only their domain of expertise in Christendom at the time (which of course the Lutherans challenged). He got roundly slapped down. It took the Church over 500 years to “apologise”, although how good an apology is to a man 500 years dead is disputable.

Tensions continued as the pace of scientific discovery increased. One of the more significant challenges to doctrine was the discovery of chemical elements. According to the key issue, apart from the authority of the pope, that separated the Catholic Church from the Lutherans, the doctrine of transubstantiation, the physical aspect of the Host (the consecrated bread and wine) was replaced when the bell was rung in the consecration with the physical substance of Jesus’ body and blood. This relied upon the Aristotelian distinction between substance and form: the outward properties of a thing were given by its form, and the substance was a propertyless gunk that only bore the form. In Catholic doctrine, the outward form, called the “accidents” or “species”, of the bread and wine remained at consecration, but the gunk was now fully Jesus.

When Dalton proposed his atomic elemental theory of chemistry in 1802, the properties of things were now the result of the inherent properties of the elemental particles and how they were arranged. So the doctrine of transubstantiation no longer made any sense. Change the elemental particles, and instead of bread-like stuff, you would now have something that literally looked like it had been carved off a living organism. The wine would taste of blood. It was no longer possible to be scientific and Catholic. For a little while, that was. In the 1870s, when Catholics began an attempt to become relevant in intellectual life, they quietly redefined “substance” and “accident” so that the former was some kind of metaphysical stuff, and the accidents now included the physical stuff bread and wine were made of (Artigas, Glick et al. 2006). Ironically, Catholic doctrine did not settle on a response to Darwin for some time later.


Stephen Jay Gould was a pluralist in many things. He was a palaeontologist who wrote wonderfully literate and humanistic essays in Natural History, the magazine of the American Museum of Natural History in New York. Shortly before his death, he gathered some of these together and published and Leonardo’s Mountain of Clams and the Diet of Worms (1998) and then Rock of Ages (1999) in which he argued that science and religion each had what he called “non-overlapping magisteria” (abbreviated by him as NOMA). A magisterium is a domain of appropriate authority in which one may speak as a specialist or teach. While he did not deny that science and religion did fall into conflict, historically, he characterised this as “bump[ing] right up against each other, interdigitating in wondrously complex ways along their joint border” (Gould 1998). In short, they were politely passing each other on a crowded sidewalk. This view, he thought, resolved the question of the compatibility of science and religion. So long as each cobbler stuck to his last, there was no professional dispute to be had.

Now this view was widely applauded by many religious thinkers, but it was not at all liked by incompatibilists. Religion has forbad science to investigate some things, and instructed scientists in what to teach or think. Buffon, who did the first empirical experiments on the age of the earth, was forced to recant by the theologians of the Sorbonne. Richard Owen, sadly remembered today only for being anti-Darwin, in fact proposed a kind of evolutionary theory before Darwin (there were many pre-Darwinian evolutionary theories) only to be severely chastised by Adam Sidgwick, a devout Christian and geologist, and his patrons at Cambridge University for heterodoxy bordering on heresy (Rupke 1994 chapter 4). Ironically, when the Origin came out, he anonymously reviewed it, saying that it was wrong, and anyway he had come up with the theory first (he hadn’t, not really).

The idea of magisteria is a kind of epistemic division of labor. It assumes that we do not all have the time, inclination or capacity to investigate each and every domain by ourselves. We have instead specialists who do the work on our behalf (and who we fund, some of the time, from the common purse), and whose results we rely upon when they are needed. This applies to science in spades. Specialists can be so narrow as to spend their lives cataloguing, describing and studying a single group of organisms, or even just the one. Or they can be specialists at a higher level of abstraction than even most scientists would be willing to consider. We alway must appeal to some specialists when we are doing or learning science.

This is sometimes cast as a religious decision: you have your authorities and I have mine. However it is more like the idealised notion of an economic market in which there are butchers, bakers and candlestick makers, and each sticks to their own task and makes their products available for sale. We have to trust each specialist that they will make a good product, since we cannot make all the things we need ourselves. Likewise, specialists in science produce what we expect will be good science. Sometimes it isn’t, either because of fraud or because there is a broad problem with the techniques used. As an example, the very nature of statistics in science is presently the subject of much criticism, especially in the biomedical sciences (Cumming, Fidler et al. 2007). But there is still nothing that we can replace the specialists’ work with that is any better.

The notion of magisteria gets murkier when we move outside science. It is obvious that a theologian of some sophistication and note is a better source of religious ideas than a tent preacher, if by that we think there is some specialty they better express. However, the notion that the theologian has his domain and it does not intersect with the domain of the scientific community is at best wishful thinking and question begging, and at worst ignorant and contrary to the historical record. Many of the key issues in science (how did this get here? What is its importance?) are also key issues in theological debate, and it is inevitable that in these cases when both sides offer solutions, they will come into conflict.

Another issue is when the scientists make claims that the philosophers and theologians properly consider to be their domain. For example, Victor Stenger, a physicist, has published a number of books in which he claims that the “God hypothesis” has failed and science has shown this (2007; 2009; 2009). However, he does this by evaluating the “God Hypothesis” as a scientific hypothesis. That this is question begging is obvious, although it is true that a number of theological writers do treat religion as a kind of scientific hypothesis. Another example is Sam Harris’ Moral Landscape, in which he makes the case that morality is just human flourishing, a view that goes back to Aristotle, and that science can determine what that means. Philosophers rightly object that showing that something contributes to human flourishing is quite distinct from establishing that it is good or moral. As a final example, consider the physicist Lawrence Krauss (2012), who argues against philosophy being necessary on the grounds that science tells us how something comes from nothing (where “nothing” means quantum fields, which is not nothing to a philosopher). Similarly Hawking and Mlodinow (2010) claim that philosophy is dead because science has answered all the philosophical questions. Philosophers consider this arrogance borne of ignorance of their field. Theologians often make the same point about scientists who criticise theology. We will return to this later.

Trimming science

One oft-made claim is that accommodationism requires trimming science to fit religion, not the other way around. And if you read some of the popular books on how science confirms this or that religion (often eastern style religion) that is a fair claim to make. Ranging from “physics confirms Buddhism” to “science is fine except for evolution”, religious thinkers (rarely scientists themselves) have argued that religious belief sets a limit on science and what it may assert. This is not so much an accommodationist thesis as it is religious exceptionalism. If that is how religious believers have to go in order to deal with science, that’s their business, but it has no weight whatsoever to those who are not within the theological tradition and community concerned. It is, in other words, special pleading.

The problem with this was pithily dealt with in another context (morality) by Bishop Joseph Butler (Butler 1749 Sermon VII):

Things and actions are what they are, and consequences of them will be what they will be: why then should we desire to be deceived?

If Christians or any other believer must deny what things are in order to believe, then they have a real problem, and one we do not need to attend to unless we are also of the same mind. Few if any accommodationists in the present debate would allow religion the right to deny facts or our best theories in order to include religious believers among the pro-science group, for in doing so, this deprecates the very idea of science. And to that we now turn.

What is “science”?

As much as religion is a confusing and heterogeneous category, so too is science. It has numerous meanings and supposed shared properties and methods. Much of the accommodationism debate relies upon these ambiguities and different interpretations.

Often one will read, in a textbook or popular treatment, that science has a “method”, usually capitalised to show its importance: The Scientific Method. However, when you start to look at the flowcharts, decision diagrams, and other such representations, it becomes very clear that there is no single pathway to doing science accepted by everyone who calls themselves “scientific”. This is a widely discussed topic in the philosophy of science.

If science were done by recipe, that is if there were a Scientific Method, then there would be an easy test whether a claim was scientific or not. But science, it turns out, is not so easily demarcated from nonscience; this is called the Demarcation Problem (see the introduction to Pigliucci and Boudry 2013 for a summary of the issues). A commonly appealed to Demarcation Criterion was proposed by Karl Popper, who said that something is science if it is open to empirical falsification (Popper 1965). The trouble with this was immediately noted by other philosophers and scientists. As the nineteenth century physicist Pierre Duhem (1954[1991]) had already noted, when you test a hypothesis, and get a negative result, you are onto just testing the hypothesis by itself but all the other hypotheses used in the test: how the equipment works, other theoretical assumptions, and any methodological assumptions (like the use of statistical inference) that are employed in the research. You know that something must be wrong, but what it is, is not immediately clear.

Popper applied his Criterion to psychoanalysis and Marxian economics, and saw it as a simple way to show these were false. He wanted to isolate science from the boundary “sciences” popular in the 1930s when he came up with it. Since then, many scientists have exhibited a kind of multiple personality disorder: when they do science, they do not behave the way they criticise nonscience. Popper, for example, argued that science is not inductive: that it did not do lots of observations and then draw general rules or laws from the observations (I include the making of formal models as induction here). Instead it came up with hypotheses (any old how) and tried to falsify them, that is to show they are false by counterexamples. This is referred to as falsificationism in the philosophical literature.

Now when those who adopted a sociohistorical approach to actual “science” considered Popper’s view, they discovered that this Criterion was in fact not often, if at all, applied, even within physics, which Popper took to be the very exemplar of scientific investigation. Instead, as Paul Feyerabend, an Austrian philosopher who moved to America after the second world war and saw himself as a gadfly among the philosophers, wrote, if there is a Method in science, it can only be the rule that “anything goes” (Feyerabend 1975). Of course, Feyerabend qualified this claim with the more nuanced view that in fact there were scientific methods, but that they formed a cluster of approaches, and not a single Method. Moreover, he rejected the idea that these methods were subject to any central ruling principle. The science historian Thomas Kuhn (1962) went even further: what rules the rules is a worldview, which he called a “paradigm” (one of the most abused of all philosophical terms ever). A paradigm set what counted as evidence, what counted as confirmation or disconfirmation of a theory, and even what the very terms used in a theory meant.

Duhem’s point was taken up by the American philosopher Willard Van Ormand Quine (Van to his friends), who generalised it to the point that we test entire sets of beliefs when we test a hypothesis, not the one hypothesis (Quine 1953). Consequently, science was like a genetic complement being subjected to natural selection, tested as a whole and rejected when it failed to work out. He explicitly drew the parallel with natural selection (not original to him, though. Thomas Henry Huxley had made exactly the same point shortly after Darwin had published). Science evolves, not through revolutions as Kuhn had asserted, but by gradual adaptation of the entire set of beliefs and techniques.

What this meant was that there is no point at which a proponent of a theory can be said to have become irrational or unscientific, even though there are clear cases, like phlogiston, phrenology and land bridges in geology, where they have clearly ceased to be good science. Like pornography, we can’t define bad science or nonscience, but we know it when we see it.

This is significant in the case of science versus religion, because all the positions taken by, say, the Catholic Church, in such disputes were previously accepted as good science. What was at issue was a host of hard-to-define issues like whether a novel approach solved more problems than it raised, and the promise of the new theory being fruitful in future research, a set of issues that are very much alive within science itself. There were also questions of doctrinal or philosophical concern, but often, the “religious” were also well educated in the science of the day, and saw themselves carrying out a scientific debate, only with the authority and power of the ruling elite.

When opponents of accommodationism criticise the religious for their failure to accept science, there are therefore many things to keep in mind. What exactly counts as science in this case? Is it the best theories of today (as determined by whom)? Is it what experts put into textbooks (and who are the experts)? Is it something like a consensus of those who work in the particular field? When does an idea cease to be acceptable within the science?

Generally, curricula for schools are determined by specialists in the field being taught. In the United States, however, this is reviewed by elected nonspecialists, often with no scientific training at all (or if they have a “science” degree, it is likely to be in medicine or dentistry or some other vocational field that claims scientific foundation). This unique system is not shared by any other western democracy of which I am aware, and it causes massive downstream effects in those other nations, since the current curriculum publishing business model tends to begin with American sources and modify them to suit local needs. Often textbooks are given a light editing by a local specialist and published as the “Australian” edition or the like. The School Board system if the United States thus influences, subtly or overtly, how science is taught elsewhere in the world. For this reason, the battles over what is included in the textbooks approved in Texas or California are of global importance.

Scientists also have their regional differences in emphasis or subject matter. Since scientists are typically educated into their specialty in one nation, they are very likely to adopt as a given whatever ruling views are adopted by authoritative scientists in their country. So for a long time, French biologists tended to downplay Darwinian evolution in favour of their countryman Lamarck’s notion of evolution (Burian, Gayon et al. 1988), until the molecular biologists Jacques Monod (1972) and François Jacob (1973) promoted the Darwinian synthesis extensively.

Given all this, what is the “science” that the religious believer must accommodate to? It is not so clear when a scientific field is in a state of flux, either because the progress of discovery in that field is rapid, or because there are within the scientific field itself multiple interpretations and theories in play. Especially in highly abstract general theories like modern quantum physics, it is not clear what must be taught at schools, or what the import of a theory is for religious believers. But the real conflict lies at a much lower level, usually. This is why it is not quantum mechanics that causes real problems for believers, but theories of psychology, biology and environment, which are areas that affect everyone. Do we have free will? Is there a purpose in the living world? Is our environment going to remain stable or change? How old is the world? Such questions raise problems for believers in a way that quantum foam and entanglement, as fun as they may be to think about when one is a teenager (or the equivalent in later life), do not.

If we cannot identify “the science” that must be accommodated, can we at least identify the issues that are controversial to a believer? That will be the subject of later posts.


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[1] accessed 16 February 2014.

[3] Science is, in the end, a human activity, and so it has fashions, failures and fictions. However, given that it is our best source of knowledge, there is no other standard we can apply to claim of knowledge about the world. Hence we should rationally accept science, in a provisional fashion, as being true. If there were some other standard source of knowledge, we might be able to assess science by that. But this is not to say we think all our science is correct or true, nor that we need to take it on, one might say, faith.

[4] The term was introduced, as far as I can tell, by Professor Lawrence Moran, a biochemist at the University of Toronto, on his blog Sandwalk <>. He informs me that he chose it to replace the term “Chamberlainists” introduced by Richard Dawkins in his God Delusion, which he felt was unfair on Neville Chamberlain. Thanks to Josh Rosenau for help tracking this down.

[5] Claims to the contrary, based, for instance upon 2 Timothy 3:16: “All scripture is inspired by God and profitable for teaching, for reproof, for correction, and for training in righteousness” which cannot refer to itself, are based on a prior belief in the inspiration of the canon chosen at the Synod of Hippo Regius in the fourth century, which was ratified in subsequent councils with variation. Early Christians used the “Hebrew Bible (the Tanakh) as “scripture, along with a choice of gospels and letters.

[6] Of course, philosophers spend a lot of ink on that very question. A belief can be held with a degree of confidence, or to cover a part of a statistical sample, or perhaps the Law of the Excluded Middle in logic, which says that either the sentence A is true or A is false, is itself wrong, and there can be sentences that are neither true nor false. Have fun with that. It doesn’t affect us here.

[7] There were a number of gods who were folded into the final God of the Bible (I use Tanakh to denote what Christians call the Old Testament, since the Jewish view is that it is not old or superseded). El was the generic term for “god”, and was usually given a place or tribal name such as “El Yeshrun” or “El Yisrael”, or some power, such as “El Shaddai” (the mighty god) or “El Tsaddik” (the righteous god). In the west semitic religions in which the Bible writers wrote, El Elyon was the “most high god”, the supreme deity of the pantheon. YHWH was the southern tribal deity. These and the plural form of El, Elohim (the gods), were collapsed into a single entity after the Exile. Female gods like Ishtar or Asheroth were dropped or reinterpreted as “wisdom”. See Smith 2001 for a summary of these developments.

[8] Although they were not then called “scientists”, as that term wasn’t invented until 1834. The two fields of what we would now call science were then natural philosophy, which broadly covered physics and astronomy, and natural history, which broadly covered biology, geology and geography. Sometimes the former were referred to as “mathematicians”, although that could also mean “astrologer”.

[9] Even as a kid I knew that ants recognise nest mates by their smell, so the Wart should have immediately been torn apart by the soldier caste guarding the nest. But if you are going to accept that a human can be made into an ant and retain all his cognitive abilities, why not that Merlin could simulate the pheromones of that particular nest?

Recent posts and stuff online has led me to suspect it would be worthwhile my writing a book on this topic, as short posts often lead to misunderstandings and trolls. I’ve started sketching out the contents, and putting in various posts from here to use as a skeleton, but I thought it would be worthwhile crowdsourcing some of the material from my readers. So have at it in the comments: what would you like me to discuss, both issues and events? Or are you aware of any interesting literature? Or anything else.

I’m thinking of this as a semipopular book (aimed at making me a fortune some money). Any suggestions on publishers, forums, etc will be paid for gratefully acknowledged. If you have a literary agent you could connect me with would be even better. That will get you a beer.

Nature of classification

It occurs to me that I haven’t plugged my own book here. What a failure on my part! It was published in December, so it is really time I did so.

In this book, Malte Ebach and I discuss a topic not often discussed in the philosophy of science: the classification of nature in the absence of a theory that delineates natural kinds. Since when we begin the investigation of a new field, there is no theory of that domain yet, by definition, how do we begin? The standard answer has been that we take the kinds posited by a closely related theory and refine the theory to include that domain. But this doesn’t account for the domains that have no closely related theories that could potentially cover them. For example, classifications of living things began, and were relatively sophisticated, well in advance of anything resembling a theory of life. Instead, researchers refined the folk taxonomies in existence, and approached the domain in a naive empirical fashion. In short, they looked for patterns in the data.

The Standard View is that what we observe is determined by our theories – we literally cannot see what we do not expect. This, the theory-dependence of observation hypothesis, presumes rather bluntly that the observational salience of phenomena is first constructed and then observed. This may be true in cases where there already exists an elaborated theory that is relatively relevant to this new domain. And it is almost dogma that we do not have what Michela Massimi has called “ready-made phenomena”. It is this we take some guarded exception to. There is the following conundrum: if we cannot see until we have a theory, and yet we can learn to see phenomena as children, then “theory” must include not only the formal explanatory models of science, but indeed any disposition to see some things and not others, which makes theory everything we are biased to observe. This is, I think, to attenuate the notion of “theory” so far that it becomes a meaningless term. We see much of what we see because we evolved to see it, so our evolutionary past becomes theory. A concept like that cannot be useful in science. It is much better to separate our dispositions inherited from biology and culture out from the technical apparatus of theory in science, so we capitalise the latter: Theory.

Our brains are wired to find patterns in data, in large part because they are neural networks, and that is what neural networks are good at. We are classifier systems. A classifier system finds regularities in large data sets (including, but not just, measurements using instruments like a pan balance or a thermometer), and once they are found, they call for an explanation. Now, I realise that induction is supposed to be a problem in philosophy, as no finite number of observations of this kind can determine a unique general solution or generalisation, and yet, that is what every child who learns a language or not to touch hot things does. There simply are some ready-made phenomena, even if we cannot justify the regularities deductively. I think we might do so abductively, though, just as Peirce thought.

So, we formulate our classifications and find patterns to explain. We give examples of this in meteorology, pedology (soil science), chemistry, psychiatry, and several other cases. But of course the other kind of natural kinds occur too. It actually is the case that some kinds are formulated by our theories. How do we relate the two? The answer lies, we argue, in the dynamic nature of science. Science is not just a theory-driven enterprise, but when we have theory, we test it and refine it on empirical foundations. If a theory asserts the existence of some kind, and we find that it does so with precision and accuracy, then we have confidence that the kind is real. But if we find the kind is not matching the patterns we identify from direct observation, whether experimental or field observations, then there is something wrong with the theory (i mean here, all the theories used in the investigation of the domain; some theoretical foundations include distal theories as components).

We argue that theory-naive (or just “naive”) classifications are formed by a process of trial and error, to determine the marks that make the classification stable and useful. We call these marks, following the biological practice, homologies, and the marks that are not good discriminata, analogies. In brief, homologies allow projection of our inductive conclusions, while analogies offer no more information than is used in their construction. To give an example, all homologically related organisms in a classification will tend to share the same sets of marks (“characters”), so if most or all of that group have been found to have a mark, any newly discovered kind of organism will very likely have it too, even if that has not been observed. Homological classifications are, as Goodman termed it, projectible.

This isn’t a general solution to the grue problem Goodman formulated, but then classification isn’t about induction. It is about recognising patterns and using those patterns to refine our beliefs. We have to do this in order to survive, as Quine noted a long time ago, but at best a classification is something that is highly defeasible, and the relation of classification to Theory is itself dynamic. A classification is at its best, the beginnings of knowledge. It is a call for Theory to explain what we see.

In one chapter – Monster and misclassifications – we discuss how unnatural classifications are formed and what they tell us. I would summarise it this way: a natural classification formed on homologies, which are usually causal regularities or etiological classifications, tells us two things. It tells us what we, the observers, find salient (as does any statement about the world, for there are an infinite number of things we might say), but it also tells us about the structure of the domain being observed. It is a two-place system, us and it. But a monstrous classification (which includes paraphyletic classifications in biology, for example) tells us only about our salience dispositions. While there are observations being made of the world, the selection of the marks themselves is all about us, and so a monstrous classification is a statement about us and our dispositions only.

Finally, in order to evade the political aspects of classification, we propose a neutral, functional, set of terms to discuss what scientists mean by classificatory terms. Science is done by people, and people, among other things, play political games (in the Wittgensteinian sense of “game”) in order to mark in-group from out-group loyalties. This, while it may seem to be less than admirable from a purely formal perspective, is an irreducible aspect of human science, and indeed it may tend to drive science by motivating, as David Hull called it, the “I’m gonna get that son of a bitch” responses to claims, thus acting as a selective pressure against groupthink. Since all scientists do or ought to take empirical evidence as their starting point, if an opponent can show that a model is not empirically adequate enough, even abstract ideas like “monophyly” in biology can be revised.

I commend our book to my readers. It seems like a silly thing to write about, but I believe the classification of nature has for too long been seen as a merely conventional practice in science. Nobody would deny that there is a conventional aspect to science, just as there is any other human social activity, but it is time to abandon the idea that this is all there is to it.

One final note. This book was written, at the editor’s instructions, to be accessible to both philosophers and scientists, so the language may seem a little untechnical. The result is surely that the scientists will find it too difficult to read, and the philosophers not difficult enough. I beg of my readers not to think that because of this it is either useless or shallow.