"Methodological naturalism" is a euphemism for "philosophical naturalism."

No it isn't. Rest of screed ignored.

Philosophical naturalism has its roots in Western civilization in the ancient Greek philosophers (or that's the "standard" account), and of course, their philosophies as transmitted and filtered down through the ages to us, mostly through the hands of Christian (and Muslim) theologians and philosophers.

(That must seem bizarre and unthinkable to persons deriving their knowledge of science and philospphy from the latest posts on the "InternetInfidels" and "Answers in Genesis" websites.)

Via that process of transmission and filtration, modern philosophical naturalism has evolved out of theological naturalism, which is also truly ancient, but comes to us directly via scholastic controversies (particularly over the impetus theory) from the Twelfth Century Renaissance. There is nothing new in philosophy. And just like everything else in Western civilization it has been substantively and subtly influenced by religiously inspired thinkers. That includes science.

Recall that what we would consider "scientists" weren't even commonly called scientists until near the end of the 19th century (due to Whewell?"”a religiously inspired "scientist" and philosopher of science). Scientists were called natural philosophers, and by that was meant that they believed and practiced the "experimental philosophy." (The "scientific method," And everyone does, don't they?)

Around the end of the 19th century the scientific community itself made that demarcation between science and philosophy by self-consciously referring to themselves as scientists and no longer as natural philosophers. (And the transition from "philosophers" and mathematicians to "natural philosophers" occurs earlier. In the century between Copernicus and Newton.)

If "methodological naturalism" is just the methods of science (And I've seen nothing in the various definitions proffered that indicates otherwise.), and if the program of philosophical naturalism is, as many philosophers say, to render philosophy wholly and consistently scientific, then it must be true that philosophers of naturalism practice "methodological naturalism," in which case they aren't philosophers at all but scientists!
So there neither is a such a thing as "methodological naturalism" or "philosophical naturalism," there is just science! (Philosophers have science-envy just as biologists have been accused of having physics-envy. No doubt! Scientific achievements are to be "envied." And just like Cool-Mo-Dee has his "posse" of hangerson, enviers and other "parasites," so science has its erstwhile "posse," the "philosophical naturalists.")

But it ain't science we're arguing about"”its philosophy! And we are arguing about it because philosophers of naturalism (or philosophers of "methodological naturalism") have not rendered their philosophy wholly and consistently scientific. They can't. Because they are philosophers not scientists.

I like to believe I have sensitive propaganda sensors and, while I don't think evolutionary theory is inherently atheistic, this notion comes from both sides of the big ditch.

Actually it's not evolution you should be worried about. Gravity is the scientific theory that is the most atheistic. Or is it quantum mechanics? Gaaah, I've forgotton again. Where did I put my 'scale of atheism in science'? I should know this stuff.

Hang on just a second though. I'm sure I've heard someone say somewhere (not far from this very blog) recently that evolution is an ideology and requires belief. Wouldn't that make evolution theistic? i.e. the exact opposite of atheistic?

Now I'm really confused.

God doesn't have to intervene in the universe in a scientifically detectable manner in order for his will to be done.

It doesn't follow that he is restricted from doing that and why would a theistic evolutionist insist on it or care whether it was detectable or not? Just asking.

Don't buy the propoganda that evolutionary theory is inherently atheistic;

I like to believe I have sensitive propaganda sensors and, while I don't think evolutionary theory is inherently atheistic, this notion comes from both sides of the big ditch.

If they can't, does that make it false? Is scientific research the only way to discover truth or is there truth beyond the reach of science?

No, that doesn't make it false, and scientific research isn't the only way to discover truth. Its the IDists at the DI who insist that IDism is scientific, and the truth of IDism can be discovered through scientific research. Theistic evolutionists, of whom there are many, believe in God, they just recognize that evolutionary theory is the best explanation of the evidence, and God doesn't have to intervene in the universe in a scientifically detectable manner in order for his will to be done. Don't buy the propoganda that evolutionary theory is inherently atheistic; its no more atheistic than meteorology, which can't scientifically falsify or validate Pat Robertson's hypothesis that Katrina was God's judgment on New Orleans.

There really isn't much wiggle room for hard core defenders of MN here.

There is plenty because the whole thing is one big strawman argument based on a series of logical fallacies.

For example:

non-naturalistic concepts "“ purpose, design, creation, supernatural agency - are excluded by fiat

Only one of these is a non-naturalistic concept and that is the supernatural. All of the others are demonstable in the natural world and therefore amenable to scientific investigation.

So Johnson and Ratzsch start by basing their argument on a fallacy, and a pretty big one at that.

one imposes a priori human constraints on the range of legitimate theories

The only constaint is empirical evidence. If you have empirical evidence then you can scientifically test something. The supernatural is generally considered to be outside of science because there is no empirical evidence for science to work with.

If there is a supernatural being whose purposes, decisions, and actions are involved in the existence, governance or structure of physical reality

You wouldn't be talking about (gasp!) God would you? And here I was reading all the propaganda from the DI that ID is not about religion…

It's very telling that Behe admits that the plausibility of ID as a (cough, hack) 'scientific theory' depends on your beliefs in a higher power. If you believe in a god or gods then ID seems more plausible. If you don't then it isn't plausible at all. I can't think of any real scientific theory that suffers from this problem.

I disagree, but you the miss point entirely, if NeoDarwinists were unable to detect that I added designed features to a genome, their typical default assumption would be that the features were not designed, instead of being rightfully agnostic on the question. In short, they would be WRONG. And they would have no choice but to be wrong, because of their own ideological box.

There is no default assumption that features are not designed. There is no ideological box either. Until very recently there was never any need to suspect design in a genome, because there was no known designer with the capabilities to alter a genome. Nowadays there is one. Humans.

And finding a functioning human insulin gene in a bacterium would indeed lead any scientist to suspect design - human design. Asking around, they could then find the lab and the researchers that put it there. But that's a pretty obvious change. If all you did was introduce a couple of point mutations, then that would be indistinguishable from the normal mechanisms of random mutation, and would therefore be undetectable as 'design'.

If I introduced a mutation in a bacterium by creating a new copy of an existing bacterial gene next to the original copy, would you be able to detect that I'd done it? I suspect not, because that kind of mutation happens all the time without the intervention of a human designer.

When we are talking about something like a bacterial flagellum however, the situation is entirely different. We are talking of something that appeared long before the only known category of potential genome designer we know about appeared on the scene. So who's your candidate for designing a flagellum? There is no evidence for one. None. So while the flagellum looks vaguely like something that might have been designed, without a candidate for the designer that is as far as we can go. Was the flagellum designed? Not as far as we can tell, no.

if NeoDarwinists were unable to detect that I added designed features to a genome, their typical default assumption would be that the features were not designed, instead of being rightfully agnostic on the question. In short, they would be WRONG. And they would have no choice but to be wrong, because of their own ideological box.

Good point. Consider the way Philosopher of Science Del Ratzsch puts it in his article Design Theory and Its Critics: Monologues Passing in the Night. Commenting on an essay by Phillip Johnson, Ratzsch writes

The allegation [by Johnson]
is that naturalism is the stipulated metaphysic of contemporary mainstream science,
meaning that non-naturalistic concepts "“ purpose, design, creation, supernatural agency
"“ are excluded by fiat and that purely naturalistic theories are the only ones even eligible
for a hearing. (That is, as Johnson sees it, particularly true with Darwinian versions of
evolutionary theory.) Consequently, even if naturalism is false, and even if some
implicitly supernaturalist theory is true, the (or a) competing "“ and ex hypothesi
mistaken "“ naturalistic scientific theory will triumph within the scientific community,
and since any force that the available evidence might have had in a non-naturalistic
direction will be denied as a matter of policy, the naturalistic theory will be advanced as
scientifically established by objective evidence. At that point, of course, evangelical
atheists within the scientific community (e.g., Dawkins) will publicly proclaim that
science has established their naturalistic worldview. In simplest terms, the idea is that if
one imposes a priori human constraints on the range of legitimate theories, then if
reality itself happens to fall outside those human stipulated constraints, human science
is at serious risk of generating an irreparably skewed scientific picture of reality. Surely,
as Johnson sees it, the rational thing to do, the objective thing to do, indeed the scientific
thing to do is to let data "“ and not human edict "“ establish the relevant boundaries.

A bit later on Ratzsch writes:

…there is one thing, it seems to me, that [Phillip] Johnson has gotten exactly right. If there is
a supernatural being whose purposes, decisions, and actions are involved in the
existence, governance or structure of physical reality, then any stipulated blanket
prohibitions against non-naturalistic explanatory resources runs the serious risk of
producing an inescapably skewed picture of physical reality. That is not, of course, to say
that if the supernatural does play a role, that if we dropped any naturalistic restrictions
that we would automatically be able to construct the correct theory. But the alternative
route (under the conditions postulated) would guarantee that we would not.

There really isn't much wiggle room for hard core defenders of MN here. Either accept a skewed picture of reality and pretend it is fact or toss the stipulation of MN into the Mississippi River.

So far it doesn't seem like IDists have had much interest in engaging in speculation about how design could have occurred.

I'm not sure what you mean here? Do you mean did a designer "poof" something into existience? I'm open to that. I'm led to believe that the universe was formed in a big poof.

It would be interesting to see them come up with some ideas which could be researched.

If they can't, does that make it false? Is scientific research the only way to discover truth or is there truth beyond the reach of science? I have posted a quote here from a "founding father" saying ID needs a theory in order to direct research and I have heard others express doubt as to its qualification as science so the criticism you raise has not escaped them. I'm always curious as to why many who say there is no confilict between religion and science seem so desperate to kill ID in the cradle.

Forget natural or supernatural. What I'm interested in as an agnostic is whether a given biological mechanism is designed or not. Simple as that.

Without a viable candidate for a designer - i.e. one with evidence for their existance - then there is no reason to conclude design.

I disagree, but you the miss point entirely, which is if NeoDarwinists were unable to detect that I added designed features to a genome, their typical default assumption would be that the features were not designed, instead of being rightfully agnostic on the question. In short, they would be WRONG. And they would have no choice but to be wrong, because of their own ideological box.

Whenever you have opinions rendered on a matter when there is no clear evidence, it is a manifestation of ideology. "I don't know" is the proper scientific answer in such cases. Darwinists should employ it much more than they do.

(Whether or not anyone could identify me personally as the designer is a side issue of no importance whatsoever to the question of detecting my design.)