By mandating methodological naturalism evolutionists place themselves into a no-win scenario. Like Star Trek's Captain Kirk who reprogrammed the computer in order to defeat the Kobayashi Maru scenario training exercise, evolutionists can only cheat their way out of their methodological naturalism mandate. If they give a straight answer they undermine their own claims about evolution. The problem here is not methodological naturalism itself, which is a perfectly reasonable way to do science. The problem is that, in the hands of evolutionists, it becomes dogma rather than guidance. And the problem is not merely a philosophical fine point--in mandating methodological naturalism evolutionists reveal the absurdity of their ideas and simultaneously do substantial harm to science.
Evolutionists mandate methodological naturalism but they don't explain exactly what this means. The reason why we do science is because we don't have all the answers. If we had all the answers then there would be no reason for science. Methodological naturalism places a constraint on the answers which we do not yet have. In so doing, something is lost.
We either lose objectivity by assuming that all of reality conforms to our constraint, or we lose any guarantee of completeness by limiting science to those phenomena within our constraint, or we lose any guarantee of realism by forcing a constraint which excludes explanations which could be true.
Of course we could get lucky. It could be that reality conforms to our constraint and that we have not excluded any true answers. In this case, if all of reality is strictly naturalistic then methodological naturalism is a good mandate. But we don't know that right now. So the question for evolutionists who mandate methodological naturalism is: what do we forfeit, objectivity, a guarantee of completeness, or a guarantee of realism?
Why methodological naturalism is a no-win scenario
These are the alternatives and evolutionists cannot accept any of them. If they explain that they believe nature and its origins are completely naturalistic then this would reveal a non scientific presupposition. They would lose scientific objectivity.
If they explain that science should be limited to naturalistic phenomena then they would be admitting that we have no guarantee that evolution can explain all things. They would also be giving sanction to the problem of identifying natural versus supernatural phenomena, an activity which they insist is non scientific.
On the other hand they could explain that if science ever encounters a problem outside the bounds of naturalism then its answers are fictional. In this case science is not limited, but it comes at the cost of opening the door to fictional explanations, and so losing the guarantee of realism. This too is unacceptable. Evolutionists insist their idea is an accurate description of nature and a fact.
Justifications and what they reveal
So how do evolutionists explain their methodological naturalism mandate? Not surprisingly they rarely if ever provide a logical answer. This question was well understood four centuries ago when thinkers seriously engaged such questions about how science should work. Bacon and Descartes worked through these issues and explained their positions. But we cannot expect such reasoning from evolutionists today. Instead evolutionists respond with a battery of fallacies which are, frankly, embarrassing.
As is typical, many of their responses are attacks on the questioner. For instance, they say that the questioner is attacking methodological naturalism, or that he is smuggling in supernatural assumptions. But asking evolutionists for clarification is not attacking methodological naturalism. And the only assumption being made is that nature and its history might not be completely naturalistic. In other words, science might stumble upon a problem that doesn't fit methodological naturalism. If anything it is the evolutionists who are making heroic assumptions by mandating methodological naturalism.
SETI and ID
Another response that evolutionists give is that methodological naturalism is simply the way science works, period. But in fact the way science works is a complicated question. From Leibniz to Linnaeus the history of science is littered with examples of the blackballing and embracing of ideas that today's methodological naturalism would find confusing.
And if you think times have changed think again. More recent scientific ideas such as quantum mechanics and the Big Bang seem to push the envelope. Particles are waves (sometimes), observers influence outcomes, and the universe and its natural laws began in a one-time explosion. And the evolutionist's appeal to a multiverse hardly falls neatly within methodological naturalism.
And what about all the metaphysical claims upon which evolutionary thought is motivated and justified? Why is it OK to mandate naturalism with theological claims but not OK to allow for design based on empirical science?
Another recent confounding example is the SETI (Search for Extra Terrestrial Intelligence) project which looks for intelligent radio signals from distant planets. SETI and ID share the same relationship with methodological naturalism, and yet evolutionists give a pass to the former while rejecting the latter.
This is contradictory. If you attempt to dismiss ID as not in accord with methodological naturalism, then you also dismiss SETI. On the other hand, if you say SETI passes the methodological naturalism test, then you also give ID a pass. You cannot blackball one without blackballing the other. You cannot let one in without letting the other in.
The evolutionist's methodological naturalism mandate also makes their claim that evolution is a fact appear suspicious. How curious it is that not only is evolution's naturalism-only story mandated by science, but it also turns out to be true. Do evolutionists ever realize how lucky they are? Or do evolutionists ever think twice about their serendipity?
Meanwhile skeptics wonder if the game has been fixed. Is it really such a coincidence that the paradigm that is mandated is also the one that is declared to be a fact?
This brings us to what is perhaps the greatest problem with the methodological naturalism mandate: the damage it causes to scientific progress. The most common response evolutionists give, when asked about their methodological naturalism mandate, is that science has shown naturalism to be true. We once thought that everything from lightning and earthquakes to love and consciousness were supernatural phenomena, but we now have scientific explanations for all these things. If there were evidence that any phenomenon is not completely natural then we would think twice, but given the complete lack of such evidence, methodological naturalism is the obvious choice.
The problem here is that the methodological naturalism mandate drives the evaluation of the scientific theories. Once it is mandated that all phenomena must be described naturalistically, it is only a short step to assuming that all phenomena can be described naturalistically, and indeed have been described naturalistically. From a scientific perspective it would be absurd to think we have a plausible explanation for the DNA code, histone IV, biosonar or consciousness. What we have is speculation driven by the demand for natural explanations. It is not that the data reveal such explanations, it is that we require such explanations.
Naturalism is now unscientific according to the evolutionist's own criterion of testability. This is because naturalistic explanations are the only explanations that are allowed. They therefore cannot be tested because they are true by definition. The only testing that can be done is between different sub-hypotheses of naturalism.
The mandating of methodological naturalism is bad for the philosophy of science and, not surprisingly, bad for science itself. It places evolutionists in a no-win situation, like Star Trek's Kobayashi Maru scenario training exercise. The difference is that rather than solving the problem like Captain Kirk, evolutionists make matters worse for themselves by continuing to mandate methodological naturalism. Religion drives science and it matters.