In the 1600s, the enterprise now called natural science got fully underway. How to define it and determine its limits are controversial questions. Science cannot be limited to experiments (Galileo dropping spheres from the Leaning Tower of Pisa) because experiments do not stand alone, and scientists do other things: they measure, discover, observe, classify, and build models, for example. But even if we bracket the question, “What is science?” we should acknowledge that it has generated remarkable truths. The heart circulates the blood, germs cause disease, human beings evolved from other primates, and our values originated as adaptive traits of a primate species. These are not truths “for science” or “within the scientific framework”: they are true.
But if all truths were scientific truths, we would be in deep trouble. We would then reject any claims that science cannot support. For example, do all human beings have equal value or worth? Either that makes no scientific sense (because objective or intrinsic value is not a scientific idea), or it is manifestly false, because science translates “value” into something like capacity or functioning, and then it is obvious that not all humans are equal. A hospice patient has nothing like as much capacity, potential, flourishing, or significance as, say, Mitt Romney.
Human equality is just one example of a truth that we would have to jettison if all truths were scientific. All other moral assertions would also have to go. There would not even be any point to practicing science. As an individual, I might have good reason to take advantage of pertinent scientific findings–for example, to take drugs that attack germs causing me harm. But I would have no reason to contribute to science or to acknowledge scientific findings that were inconvenient to me. I will only respect and support science if public service, the pursuit of truth, or integrity are values, but they are not discoveries of science. So the value of science is not a scientific truth.
Fortunately, we are already used to a pluralist world in which there are truths generated by science and also other truths. Mathematics, logic, and basic epistemological and ontological truths are not findings of science. Some are separate from science, and some are preconditions of science. That does not mean that science is relative (i.e., only valid if one adopts certain preconditions), because the preconditions may be truths as well. But they are not generated by science; they stand separately.
Along with science, we have another very richly elaborated way of thinking about human beings and the world. This moral or “agential” perspective does not regard people as complex biological machines in a causal network with all the other objects in the universe. We are indeed such machines, but as agents, we are also reasoning creatures guided by principles and objectives and responsible for the goodness and rightness of our actions. All the work of moral philosophers, novelists, and historians has enriched and complicated our understanding of human beings as moral agents.
So we have a choice: Science is the only source of truth, the agential perspective is the only source of truth, neither view is true, or both are true. The answer is not given by science, and science does not imply or presume that it is the only source of truth. Science just rolls along generating the kinds of truths that it generates, saying nothing about ontology, morality, or the role of science in a good life. Those questions are philosophical.
The way to think about this is to assess the benefits and limits of science from the outside. What perspective is available outside of science is a controversial question, but I would use an ethical/pragmatic stance, basically asking what contributes to a fully good human life. The answer, it seems to me, includes a very strong respect for science, because science provides knowledge that we need in order to act effectively and also because pursuing empirical truth is a virtue. But the answer also includes a strong critique of science, because science is amoral and can give us Zyklon B as well as penicillin, anomie as well as the “CUDOS norms,”and despair as well as hope.
[Disclaimer: This is basically a naive post because I have not read the vast and impressive literature on naturalism. I've been pondering these issues since hearing a good presentation by Mario De Caro, but one 30-minute talk, no matter how skillful, does not replace an entire literature review. Probably the best way to describe the above is as my default view--what I would need a good argument to be talked out of.]