As Thomas Kuhn wrote, a concept of history can be considered decisive to philosophy of science. I don't find it convincing to speculate on the face value authority of scientific knowledge. I would instead attempt to draw a rough background, to what science is which is to a large extent an orthodox construct (what we call an institution or "community") of modern humans, and judge progress in simpler terms of science.
I think it would not be far fetched to say that modern science began around the time of Galileo, whose story I take it, is well enough known, and emblematic for establishing some grounds for the basis of an empirical (experiment based) methodology.
The myth and perpetuated dialogue about a need for continual liberation of "free thinking" from the belfries of dogmatic human institutions, is overbroad, and partial human attitude that tends to reveal itself. After all, isn't this human institution - isn't God - Dead? This kind of discussion is about a rival institution securing itself, in face of a dogmatic institution, yet in this it has become more about that, than naturalism. In any case, philosophers of science say that science may come up against its own structure today, rather than convenient oppositions.
It was Renes Descartes, who around the same time as Galileo, who really proposed the rationale for a "method of doubt", in technical terms, the epistemelogical background for science. We greet Descartes epistemology as basic to the world, constantly being broached in terms of a "subject and object". (Discourse on Method). Descartes' method of arriving at "certain foundations for knowledge" through a method of doubt is roughly the assumed way that we practically and in a human way conceive that our conjectures naturally, and in their only possibility seek objectivity. Objectivity is posed in opposition to subjectivity, or what we refer to as what does not reach an appropriate consensus. Objectivity is the implied basis of things as they can only be, both in reality and in conjecture. To put it one way, anything subjective that is "real" is actually objective. We follow these realist metaphysics and epistemology today, even as we apportion the whole domain of metaphysics (what is foundational to Descartes's theory - "I think therefore I am") to subjectivity.
But aside from realism, what else is hardly appreciated, is that "science" wasn't institutionalized, or actually conceived in the sense we today refer to it as "science" until the 19th century. Before that, what we call science, was referred to as natural philosophy.
To put it in specific terms of this change, natural philosophy is the study of physis in its capacity as nature. Today naturalism is posed in terms of oppositions, a technical and essentialistic notion of falsification (derived from a cultural attitude to empiricism) which suggests that what is, is mainly understood by what is not, and binds what is to this opposition. This is where our conjectures both in a technical sense, and in a larger culture are to be found in terms of.
The development of a simple point of reference to sciencia, - meaning literally and somewhat obliquely "knowledge" - as well as a human institution of "science", coincided when in the scope of our knowledge, the way we gathered knowledge (methodology) was taken for granted to simply reflect the natural world (cosmology) like a mirror. William Whewell coined the term science in 1833, to be precise.
In the 19th century it was generally thought that the standing of sciences as they are, from reductive physics to chemistry, to biology, to the human social sciences, were all found within the formality of constraints established, so that science itself was completely straight forward, and simple point of reference, to an idea of filling in the details and gathering data for the existing textbooks or departments in the university. At that particular time, when we were so simply gathering "knowledge" it was thought that philosophy, the ways philosophers reflect on the world, could be dispensed with.
Yet that was a relatively short period of time. Come to the twentieth century and you find that in spite of the techtonic shifting of human knowledge, a human insitution holds on to the philosophy of "objectivity", "empiricality", "science". This institution is the reality of science. As the ground of grounds - not merely a subject among other - but physis or nature itself completely changed, it has become obvious that the way we gather knoweledge no longer reflects knowledge. It is pragmatic. Science has actually been mostly undermined through history rather than ever established, and has continued further and further into this "trend".
The institutional sciences should look to a consistent empirical method, which is one, as Hume suggested, that does not make a priori perscriptions. This has to be considered a subtle point, sciences need also look to look to nature or physis itself. The technical equipment used to observe, or the technicality of conjectures, is really what characterizes science to modern people. Science consists in an endorsement of technicality of discipline to the laity, which is necessary, but the institution has cleaved too much to this for its basis. Science, and their conjectures should be meeting philosophers of science, because that is where the human economy of securing grants and funding lies.
Philosophers will say what they will, and modernity will go on riding on the outdated sense of institutional authority, and the laurels of technological production. Naturalism is dead, and meaningless, and all we take it to mean is the technically projected idea of what is, rather than what isn't. The idea that a totalizing or holistic conception of nature has even been touched on for a long time, and won't be, until institutional authority is loosened up.
Short answer, is it may seem like methodology reflects cosmology/nature, but it only does, so far as it satisfies a pretty marginal human utility.
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