Dear Msrs. Johnson, Behe, Dembski, Calvert, et al.:
As leaders of the movement to bring intelligent design into science education, you believe that science, properly construed, can get us to God. You claim that science as it’s usually presented presumes naturalism as a philosophical starting point, and so rules out intelligent design (ID) on grounds that ID is supernatural. If only science and scientists would rid themselves of this naturalistic bias, then the design hypothesis could compete with Darwinian accounts on an equal footing, thus lending scientific support for the existence of divine intervention in human affairs. You say that as long as science persists in this discriminatory philosophical assumption, it violates the constitutional prohibition on government establishing or favoring a particular religious or philosophical viewpoint. Therefore, in order to restore philosophical balance into science, states should challenge its presumption of naturalism by requiring that science teachers present ID as a viable scientific hypothesis. 
But, does science as it’s currently practiced really presume naturalism? Does science invoke a metaphysical assumption about causes being strictly natural in order to conduct it’s inquiry? Do scientists start out by declaring their allegiance to naturalism and their rejection of the supernatural? It would seem not. The vast majority of scientific texts, papers, experiments, hypotheses, conjectures, and napkin scribblings make no mention of the natural/supernatural distinction. Scientists rarely, if ever, pronounce up front an allegiance to naturalism as a guiding philosophy when laying out their methodological presuppositions (if indeed that is their guiding philosophy, since many scientists are religious). Science operates without any a priori ontological commitment as to what sorts of entities exist. It need not make such claims in advance, and indeed to make them might very well bias inquiry. Science is, and should be, open to the existence of any entity which gains sufficient empirical, theoretical support in the course of scientific investigation and explanation.
But although science does not presume naturalism, scientific inquiry tends by its very nature to unify our understanding of the world, and such unity is indeed the heart of naturalism. The basic characteristics of scientific explanation  are such that phenomena are connected within theories across vastly different levels (from molecules to galaxies) and types (from neurons to consciousness to culture). The success of science lies exactly in demonstrating that empirically grounded fundamental laws, constants, and particles (whether conceived as matter or energy) are the universal building blocks from which all other phenomena in its purview are constructed. The world described by science is of a piece, and necessarily so, since scientific explanations are just those which show how phenomenon X arises as a function of phenomena Y and Z. Whatever becomes the object of scientific investigation will, if the investigation is successful, be incorporated within the single, unified understanding that is the goal of science. Although scientific theories have and will continue to change in response to new objects of inquiry, the goal of science does not.
Monistic naturalism is, therefore, simply the result of sticking with science as one’s preferred route to knowledge about the ultimate constituents of the world. God, traditionally conceived of as a non-physical, spiritual being set apart or above nature in some respect,  is logically barred from being incorporated into a scientific understanding of the world. Science as it’s practiced can’t get us to God, since God is exactly that which escapes being pinned down as one of many facts or entities within a unified understanding of existence. Put another way, if science as its currently practiced were successful in proving the existence of God, that god could no longer have the supernatural characteristics traditionally attributed to it.  In its pursuit of comprehensive explanations, science tends toward ontological unification, not dualism.
Perhaps, you might say, scientific methods of explanation, although they don’t explicitly presume naturalism or make mention of the natural/supernatural distinction, are nevertheless biased by virtue of this unifying tendency, a tendency which rules out categorically supernatural entities from being included in science. Why should science be monistic and not dualistic in its aims and methods? Doesn’t this constitute a motivational and methodological prejudice that infects the heart of empirical inquiry?
The answer is that scientific inquiry is driven by the urge for explanatory unification, so that in questioning that urge, you question science itself. Scientific empiricism is a human, motivated enterprise that speaks to a defining human characteristic: the desire to understand, predict, and control. From a wider standpoint (which I strongly encourage everyone to adopt), such a desire is just one among many human motives, and so science isn’t the only game in town, by any stretch. But, you can’t fault science for its drive for unity, since that’s just an expression of a widely shared human motive, a motive as valid as the desire for food, companionship, and discovering meaning in life. 
Those of us that stick with science in deciding knowledge claims about what fundamentally exists aren’t compelling anyone else to do so. You are free to justify what you believe is true by any and all means that suit you, e.g., appeals to faith, tradition, commonsense, intuition, revelation – whatever it may be. But equally, you can’t compel science to lead where, by it’s very nature, it cannot. Such an effort can only end in the manifest contradiction of using methods which generate ontological unity while trying to safeguard the categorically different nature of a deity, designer, or supreme intelligence. It can’t be done anymore than you can draw a round square.
A monistic naturalism – which is implied by but not presumed by science – may have implications for our self-concept, for how we conceive of human purposes, meaning, morality, freedom, merit, responsibility, punishment, and other issues. I have explored some of these at Naturalism.Org, as have many other philosophers, scientists, and thinkers in schools and universities around the world, and we have found the consequences of naturalism not at all daunting, quite the reverse in fact. Given that you won’t take so sanguine a view, I don't think you are entitled to impugn science just because of where ontological unification might lead. Science is too central a human endeavor, too rooted in the human desire for comprehension and understanding, too useful a tool, and simply too fascinating to give up in order to protect traditions, intuitions, and commonsense notions that are, after all, legitimately open to question and improvement.
Again, you are free to champion and use non-scientific justifications for knowledge claims about the supernatural, and free to defend your traditions in the intellectual and cultural marketplace we so fortunately share. But unless I am seriously mistaken about the nature of scientific inquiry, I think that you waste your time trying to turn science to the ends of dualism.
Tom Clark, March 24 2002
1. See, for instance, Phillip Johnson’s work, or the letter by John Calvert mailed to Kansas school board members. For the impact of this line of thought on proposed legislation, see Ohio bill HB 481, which ostensibly "seeks to promote effective science education." In its statement of intent, this bill says: "Presently national science organizations and others use an irrebuttable assumption that phenomena in nature result only from a combination of chance and natural law - the laws of chemistry and physics - and that design conceptions of nature are invalid in scientific inquiry. This is essentially a philosophical assumption and not a scientific conclusion based on a scientific investigation and analysis per the scientific method. The assumption is technically called methodological naturalism. It is also known as "scientific materialism."....Good science and effective science education requires that origins science be conducted objectively and without an irrebuttable naturalistic assumption, or, for that matter, any other religious or philosophic assumption." My claim here is that this statement badly misdescribes science as it's practiced, in that it makes no irrebuttable or philosophical assumption about naturalism.
2. For some examples of such characteristics, and why the intelligent design hypothesis doesn’t exemplify them, see "Why Intelligent Design Isn’t Science".
3. For a discussion of the supernatural/natural distinction, see "Spirituality Without Faith," the section on naturalism.
4. For an excellent discussion of the antipathy between science and dualism in the context of consciousness studies, see Maurice K.D. Schouten, "Theism, Dualism, and the Scientific Image of Humanity," Zygon, V36 #4, December 2001, pp. 679-708. See also Dembski, naturalist? about the naturalization of God that would likely ensue were he scientifically demonstrated to exist.
5. Meaning in life is quite discoverable within a naturalistic view of the world, see the Spirituality page.