We can see this through two people, one at the beginning of modern thought and the other a contemporary modern thinker. The first is Descartes, who it may be argued was the foundational thinker of modern thought by establishing the insistence on method as an intellectual first principle. The other is Daniel Dennett, a champion of method in contemporary thought and the supposed scourge of Cartesianism in the philosophy of mind. But as I argue in this post, Dennett is mistaken in seeing dualism as a foundational principle of Cartesianism; it is method that is the foundational principle and it is the insistence on method that has the consequence of dualism. This is why the contemporary philosophy of mind is so haunted by Cartesianism and why thinkers like Dennett, the more they struggle to free themselves of Descartes through method, only find themselves more tightly bound to him.
The problem with insisting on method as primary in thought is that it isn't. It isn't personally, as we all explore and come to know the world as youth without an a priori method in hand. It isn't historically, as there was an undeniable body of knowledge accrued through cultural accumulation over millenia. Nor was it even true of the seventeenth century philosophers who began to insist on the primacy of method. Descartes begins his Discourse on Method not with a method, but with an extended justification of his insistence on method in terms of his historical views and personal experience. He dismisses the philosophical tradition with this comment:
I will say nothing of philosophy except that it has been studied for many centuries by the most outstanding minds without having produced anything which is not in dispute and consequently doubtful and uncertain. (Discourse on Method, First Part)
He then goes on in the Second Part to describe the rules of his method and later, in the Fourth Part, summarizes the method thusly:
... I thought that I should take a course precisely contrary, and reject as absolutely false anything of which I could have the least doubt, in order to see whether anything would be left after this procedure which could be called wholly certain.
When he began implementing his method, Descartes doubted many things, but not everything. He certainly didn't doubt his original historical assessment of philosophy as doubtful and uncertain, his main justification for method in the first place. If he had, he might have considered points like this: If the mere fact of disputation is sufficient to condemn something as uncertain, then uncertainty is a self-fulfilling prophecy, for we can render something uncertain merely by disputing it. And this, in a just historical irony, is exactly what later happened to Descartes and his method.
The point is that Descartes did not doubt everything because he couldn't. However skeptical he wished to become, Descartes remained a man nonetheless, an embodied knower forced to found his thinking in common sense and nowhere else. There is an entire worldview of thought and history buried in the first part of Descartes's Discourse; his insistence on method has the effect of protecting that worldview from criticism (dialectical criticism) or even acknowledgement that it exists. This is why the insistence on primary method can be considered a debased form of dialectic. All it does is hide the non-methodical assumptions from view and protect them from dialectical criticism. It doesn't transcend dialectic or protect itself from the pathologies of a degenerate dialectic, but only provides the illusion of transcending dialectic by assuming dialectical conclusions without argument.
We can see why philosophy has gotten such a bad reputation in the modern world. The reason is that modern philosophers, beholden to method, find it nearly impossible to engage on the issues that really separate them. For those issues involve the pre-methodical views of the world they must have and that inform their selection and establishment of method. In that earlier post I mention John Searle, who in his books on the mind states flatly his assumption that the fundamental particles described by physics are also the metaphysical fundamentals of reality, and that anyone who disagrees with this should be summarily dismissed. Searle, like Descartes, makes an a priori insistence on method in thought, only Searle's method is the method of science rather than the method of universal doubt of Descartes. But in any case, science is a product of the mind, and to insist a priori on the non-negotiability of the metaphysical significance of science is to already cast in concrete certain conclusions about the mind, e.g. that the mind is such that its methodical conclusions are more certain than any other conclusions it might make. Naturally, the view of the mind baked into Searle's assumptions about the metaphysical meaning of science is not indisputable, but disputing it is very difficult, because Searle has made his scientistic assumptions a barrier to entry to conversation (if you don't accept them, you are not worth talking to). Searle is not unusual but typical in this regard. And since not every thinker will make the same pre-methodical assumptions, discussions between modern thinkers have the flavor of circling the real issue in dispute without ever quite getting to it; for the disputants assume that "real thought" can only begin with their preferred approach, and when it becomes clear that the disputant does not share the same pre-methodical assumptions, bad faith or naivete is concluded.
In the dialog in response to the post on Feser's blog, my disputant insisted that I propose a method before we could discuss the metaphysical ordering of final causes. Without that, he asserted, we could be the victims of wishful thinking, psychological bias, and have no way to know whether we were tracking the truth. Now if I were to accept his demand, I would be implicitly agreeing to his views on wishful thinking, psychological bias and the rest as pre-methodical established facts, for those facts would stand in judgment of any method I might propose. But my insistence is that final causes and their ordering are primary facts about nature that stand in judgment of method rather than vice versa. For instance, why are we concerned with wishful thinking at all? Wishful thinking is a form of error, that is, failure to fulfill the final cause of the intellect to know the truth. Methods are to be judged in light of the extent to which they fulfill the final cause of the mind to know truth. But if the final cause of the mind is doubtful, what objective reason is there to prefer truth to error? Moreover, to allow facts like wishful thinking to implicitly stand in judgment of facts like the final cause of the mind is to already concede the case against final causes; for if final causes are not basic facts of nature at least as transparent as facts about wishful thinking, then they are nothing at all, or at best the illusions modern thinkers think they are.
The point is not that the brief analysis I just gave is a knockout argument in favor of final causes, but that the real point of disagreement between us is at a level that can only be resolved dialectically rather than by an a priori assertion of method. Were I to give into his demands for method, I would be conceding the case against final causes at the outset. The discussion would then be a playing out of that logic to its inevitable conclusion against final causes, or dawn in the eventual realization that the real argument is to be found in the category of pre-methodical facts of nature rather than post-methodical conclusions, at which point the original concession would have to be rescinded (perhaps generating an accusation of bad faith).
I brought up Daniel Dennett in the conversation, and he is a good example of how pre-methodical facts are unconsciously assumed in the development of method that is then used to bludgeon all rivals. In Consciousness Explained, Dennett develops a method for exploring consciousness called "heterophenomology." Like Descartes, prior to explaining and deploying his method, he gives reasons for its development. For Descartes, the villain was the endless disputes of philosophers; for Dennett it is "introspection:"
Or perhaps we are fooling ourselves about the high reliability of introspection, our personal powers of self-observation of our own conscious minds. Ever since Descartes and his "cogito ergo sum," this capacity of ours has been seen as somehow immune to error; we have privileged access to our own thoughts and feelings, an access guaranteed to be better than the access of any outsider...
But perhaps this doctrine of infallibility is just a mistake, however well entrenched. Perhaps even if we are all basically alike in our phenomenology, some observers just get it all wrong when they try to describe it, but since they are so sure they are right, they are relatively invulnerable to correction. (Consciousness Explained, p. 67)
The qualification "some" Dennett puts in front of "observers" may seem inconsequential, but it is crucial to the further development of his project. But more on this in a moment. The idea is that Dennett plans to put the subjective experience of consciousness under suspicion. Rather than accepting at face value what subjects say about their consciousness, Dennett will take a step back and only commit to saying that, when a subject describes his consciousness, we can only strictly conclude that what they are describing is how their consciousness seems to them, not necessarily how their consciousness really is. It may be that how their consciousness really is may coincide with how it seems to them, but then again it may not. Dennett uses the example of anthropologists encountering a primitive tribe. The natives speak of a being called Feenoman, whom the anthropologists gradually figure out is a kind of forest god. The "heterophenomenological fact" here is the fact that the natives are truly and sincerely speaking of Feenoman. But that Feenoman is fictional rather than real is something known to the anthropologists and not the natives; in other words, the anthropologists are able to discern how the native's world seems to them (Feenoman is just as real as anything else) compared to how it really is (Feenoman is fictional). More deeply, the cause of the natives belief in Feenoman is not the existence of the real Feenoman (as the natives think), but some other complex of causes unrelated to an actual Feenoman (since their isn't one).
Dennett's plan is to extend this procedure beyond native beliefs in forest gods to the contents of consciousness in general. His ultimate target is the experience of the unitary "I" itself, which Dennett calls the "Cartesian theater", and he claims in good heterophenomenological fashion to only seem to be real rather than really be real. The procedure is to interview subjects about their experiences of consciousness, and remain objectively neutral as regards their veridical nature until a complete account has been given. The interviewer is happy to grant the subject the authority to define how his conscious experience seems to him, but certainly not how his subjective experiences ultimately relate to reality. This is done later in an analogous manner to the anthropologist described above. And if he finds, like the anthropologist, that there are no objective reasons to believe in the reality of some element of the subject's conscious experience, and he can provide an alternative causal explanation for the subject's seeming to experience it, then the element in question can be reasonably dismissed as illusion. At the end of process, you end up with what is really true about consciousness, results the interview subject should then accept as a generous gift, but usually rebels against because his cherished beliefs in things like the self and gods are shown to be illusions.
Now I mentioned that it is critical that Dennett used the phrase "some observers" in the paragraph quoted above. This is because of the problem of the Prime Interviewer, a problem latent in the heterophenomenological procedure but not acknowledged by Dennett. With respect to subjects who do not meekly submit to heterophenomenological conclusions but have the temerity to question its authority to debunk consciousness, Dennett has this to say:
If you want us to believe everything you say about your phenomenology, you are asking not just to be taken seriously but to be granted papal infallibility, and this asking too much. You are not authoritative about what is happening in you, but only about what seems to be happening in you, and we are giving you total, dictatorial authority over the account of how it seems to you, about what it is like to be you. (p. 96, emphasis in original.)
Well, who has the authority to pronounce on how things really are, and not just how they seem? The interviewer, naturally. But the interviewer is just a man like the subject, and so presumably subject to the same cognitive suspicion as everyone else. He is only authoritative about what things seem like to him, not how things really are. If he is to legitimately serve as a heterophenomenological authority, it stands to reason that he must have already gone through a prior heterophenomenological vetting so that he could know what is real and what is illusion with respect to his own consciousness. No doubt you can see the infinite regress coming, and at some point there must be a Prime Interviewer, an individual whose consciousness is itself not under suspicion so it can serve as the methodical anchor for all other consciousnesses. In the paragraph quoted above, if Dennett had written that "Perhaps even if we are all basically alike in our phenomenology, all observers just get it all wrong when they try to describe it.." rather than just "some" observers, the problem of the Prime Interviewer would have been made explicit. If all observers get it wrong, how can the method get going? No points for guessing who gets the mantle of implicit Prime Interviewer in Consciousness Explained.
The method Dennett describes in Consciousness Explained is really just a way of privileging certain pre-scientific, pre-methodical scientistic assumptions by baking them into the cake of his method, then demanding that all other accounts of consciousness submit to the strictures of his method, which of course means that his pre-methodical account of things must triumph. Dialectic has not been transcended through method; it has merely been avoided through pre-methodical assumptions, and will inevitably reemerge when those assumptions are disputed. Which is why Dennett must order his reader to accept his results.
There are of course cases in which it is appropriate to establish a method and remain suspicious of conclusions not arrived at methodically. But the establishment of method cannot substitute for a dialectical justification of the method itself. And, finally, method cannot be the first thing in thought, for method is not self-evident, otherwise everyone would have it and there would not be disputes about methods. This is one of the many ironies of the modern age. The Enlightenment insistence on method was supposed to put an end to the endless dialectical wranglings of philosophers; instead it just substituted endless wrangling about method, a wrangling that is worse than dialectical because the dialectics were assumed and then forgotten in assumptions about method.