Chris Mooney points out that 'Intelligent Design' people, and other anti-evolutionists, are working from an incorrect assumption, that evolutionists are necessarily atheistic. This is a major error and it will alienate potential allies:
In Kansas, criticisms of evolutionary theory have been accompanied by a direct philosophical assault upon the nature of science itself.
Kansas’s previously proposed science standards had appropriately defined science as "the human activity of seeking natural explanations for what we observe in the world around us." Anti-evolutionists want to change this language to the following: "Science is a systematic method of continuing investigation, that uses observation, hypothesis testing, measurement, experimentation, logical argument and theory building, to lead to more adequate explanations of natural phenomena."
This may seem harmless at first glance. But the change carefully removes any reference to science's search for natural explanations in favor of “more adequate” explanations, creating a opening for creationists to insert the supernatural. Such a change reflects the fact that the new generation of anti-evolutionists has launched an attack on modern science itself, claiming that it amounts, essentially, to institutionalized atheism. Science, they say, has a prejudice against supernatural causation (by which they generally mean “the actions of God”). Instead, the new anti-evolutionists claim that if scientists would simply open their minds to the possible action of forces acting beyond the purview of natural laws, they would suddenly perceive the weaknesses of evolutionary theory.
...scientists since the Enlightenment have seen fit to distinguish between supernatural beliefs based on faith or metaphysics and scientific findings based on observed evidence and inferences about natural causation. Such inquiry is technically termed "methodological naturalism," more commonly known as the "scientific method." It has quite a successful track record over the years, from medicine to nuclear science.
But methodological naturalism deeply offends today's anti-evolutionists. Because the theory of evolution is perceived to have contributed to the undermining of religious belief, the intelligent design movement has taken to arguing that the theory itself betrays a deep philosophical prejudice against God and the supernatural. Hence, they seek to overturn not just evolution but methodological naturalism itself.
...The Boston Globe's Nina Easton effectively refuted the argument equating evolution with atheism with a single article: A profile of Kansas scientist Keith Miller, an evangelical Christian who says he was "called by God to be a geologist" and who has been a leading critic of the new attacks on evolution, including in his book Perspectives on an Evolving Creation (a collection by Christian evolutionists). "Science does not affirm or deny the existence of a creator," Miller told Easton. "It is simply silent on the existence or action of God."
As Miller's words suggest, while evolution may well suggest atheism for some people, it does not suggest it to all. The atheistic conclusion is itself philosophical, not scientific -- as is the theistic conclusion, for that matter. That's crucial to bear in mind, because attacking science as atheism isn't just wrongheaded; it's dangerous. Going down this road will only generate still more strife between the scientific community and the overlapping community of people of faith -- two groups we should be bringing closer together rather than driving further apart.
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