No. Science is methodologically naturalistic, not ontologically naturalistic. So while it's confined by its methodology to the natural world, it does not and cannot count out the supernatural.
Yet science has a prior assumption that only physical stuff exists which counts out the supernatural. This takes science beyond method and into metaphysics.
It’s because of those assumptions that science restricts its methods to only finding and allowing certain types of causes which are physical/material such as matter, particles etc and that the supernatural doesnt exist or cannot be included.
There are a wide range of ontological, epistemic, and ethical presuppositions weaved into any given scientific paradigm (for some examples of this, see Sect. 4b).
Science and Philosophy: A Love–Hate Relationship - Foundations of Science
6Methodological naturalism is an epistemological principle that governs how science is practiced. The naturalistic view is espoused by science as its fundamental assumption.
Methodological naturalism is an epistemological principle that governs how science is practiced. It prohibits the use of supernatural explanations in science.
“Science acts as if the supernatural did not exist.”17
Usually this view amounts to a kind of materialism and therefore it denies the existence of non-material beings such as God.
Naturalism and Science - Metanexus
Therefore as this paper states its but a short step to make claims about how science measures nature/reality to what nature/reality is.
At first glance, this would seem to be adequate since it gives the scope of science and meets the other goals set for naturalism. But science does seek to tell us something about reality; and metaphysics, defined as thought or explanation about reality in the deepest sense, is not easily marginalized. In fact science does sometimes deliver new reality to us: we now know about elementary particles, genes, quasars, black holes, and dark matter because of science.
Partly because of this, it is but a short step from claiming that science must be based on naturalism or naturalistic statements, to saying that only naturalistic phenomena exist. So if science cannot explain or describe something, it does not exist. This is metaphysical naturalism, because it draws conclusions about reality, about what exists. Metaphysical naturalism goes far beyond methodological naturalism and states that only “natural” things exist. (As does ontological naturalism my emphasis).
As usually interpreted, it states in effect that the “supernatural” does not exist, and that all explanations of phenomena can be made by means of explanations that fall under the category of methodological naturalism.
This metaphysical assertion cannot be a result of science; it is a distinctly philosophical position which must be justified on non-scientific grounds. It is, in fact, a radical form of reductionism; the doctrine that all phenomena and the underlying reality can be reduced to whatever it is that particle physics studies.
Unfortunately metaphysical naturalism is often proffered as a scientific conclusion or an inference from science, without explicit acknowledgment of its philosophical—not scientific—status and pedigree.
It is a philosophical task—one which is often carried out by physicists—to clarify the concepts of space, time, matter, energy, information, causality, etc. that figure in a given theory. This analysis makes explicit the implicit assumptions in the uses of these concepts: assumptions that scientific theories do not themselves normally state. Hence it moves beyond the point where the concepts appear as irreducible elements in the postulates of a theory.
Science and Philosophy: A Love–Hate Relationship - Foundations of Science
By restricting its methodology to only physical stuff the supernatural will never have a chance to be discovered because even indirect effects of the supernatural will be deemed to be caused by the physical.
Even if supernaturalism is real it will be given a different physical cause even if that physical cause is not supported at that time. It wil be a case that there has to be some physical cause but we just don't know it yet. Or that a new physical cause will be introduced even if that is not verified just to fit with the materialistic view.
The example if prayer claimed a miracle there will be some naturalistic explanation and considering that science has a great track record people will tend to side with the naturalistic cause even if there is no support for it. Dark matter and energy also comes to mind. Though it has never been verified directly it is still a well-accepted idea to account for and align with the current physical theories already in place.
This is why so many scientists are theists. There's no conflict between science and faith and never has been.
The problem is as mentioned above is the inherent assumption that everything is caused by the physical. This attaches an ontological position to mainstream science.
Theistic scientists may believe that what we see is Gods handy work and that science is just measuring that. But secular scientists take another ontological position. It is because science is practiced, accepted and proved successful under a secular view that we have seen it being used to claim what nature and reality is. That there are only physical effects and causes and there is no supernatural.
That’s why when we hear of anyone trying to claim that there are supernatural or even non-physical ideas like consciousness that mainstream science calls this WOO and will deny any papers along these lines within mainstream science i.e.
“[These] well-meaning defenders of Enlightenment-style rationalism ... clearly regard themselves, and current mainstream science itself, as reliably marshalling the intellectual virtues of reason and objectivity against retreating forces of irrational authority and superstition. For them the truth of the [physicalist view] has been demonstrated beyond reasonable doubt, and to think anything different is necessarily to abandon centuries of scientific progress, release the black flood of occultism, and revert to primitive supernaturalist beliefs characteristic of bygone times.”[17]
Consciousness: Why Materialism Fails - Campaign for Open Science
Kuhn also claims that all science is based on an approved agenda of unprovable assumptions about the character of the universe, rather than merely on empirical facts. These assumptions—a paradigm—comprise a collection of beliefs, values and techniques that are held by a given scientific community, which legitimize their systems and set the limitations to their investigation.[33] For naturalists, nature is the only reality, the "correct" paradigm, and there is no such thing as supernatural, i.e. anything above, beyond, or outside of nature. The scientific method is to be used to investigate all reality, including the human spirit.[34]
Naturalism (philosophy) - Wikipedia
This is true. Evolution is just one way God does things in this world. He uses nature for most things He does here. Why wouldn't he? It's what He made it for.
Yes I agree but when it comes to a world view science is being used as a vehicle to promote the idea that nature is physical and the causes of those physical effects are also within the physical parameters. In other words no Gods allowed. This was highlighted by the Copernicus and Darwinian revolutions that took God out of the picture as to what created nature and life.
Darwin's greatest contribution to science is that he completed the Copernican Revolution by drawing out for biology the notion of nature as a system of matter in motion governed by natural laws. With Darwin's discovery of natural selection, the origin and adaptations of organisms were brought into the realm of science. The adaptive features of organisms could now be explained, like the phenomena of the inanimate world, as the result of natural processes, without recourse to an Intelligent Designer. The Copernican and the Darwinian Revolutions may be seen as the two stages of the one Scientific Revolution. They jointly ushered in the beginning of science in the modern sense of the word: explanation through natural laws.
Darwin's greatest discovery: Design without designer
