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One of the most important mythologies that are widespread among so many thinkers, for example Alvin Plantinga as one of the most influential philosophers, is that the science is being supported by some metaphysical presuppositions as the same way that religious thinking is. However, it seems to me that this viewpoint will collapse just by a more exact exploration of the science metaphysical presuppositions.
The structure of science metaphysical presuppositions
The firs and I think the most important feature behind the metaphysical backgrounds in our scientific structure is their changeability and deformability. There is no metaphysical background in the structure of science that has not been changed. For example in the structure of medieval ages the pair "up-down" way one of the most important metaphysical presuppositions. On the basis of this presupposition there was an essentially preferable direction that it was "up" and down was towards the centre or the surface of the earth. By the light of Newtonian physics this presumption was replaced by the idea of isomorphic and isotropic space. Just for another example in the structure of medieval ages' physics the motion couldn't be produced without any force, but by the light of Galileo and after that Newtonian physics we know that the motion is completely unrelated to the force exerting to the body. A body can be in motion without feeling any force. In this way the motion and stability are just relative notions; the very notions those were imagined to be absolute ones. Nowadays by the light of Einstein we know that "space" and "time" and even especially the notion of "simultaneity" are not absolute notions. The bar, for example, that is one meter for you in a coordination system can be just 1cm for another person in another coordinator system. Two events which are simultaneous for you in a coordination system can happen by an hour delay for another person in another specio-temporal situation. In brief you cannot find any metaphysical presupposition in the structure of science that it has not changed or it cannot be changed; i.e., no body can give you a complete proof to show you that there is one metaphysical presupposition in the structure of science that it cannot be changed, and also there is no scientist who is trying to prove these kinds of propositions.
Now I want to explore some metaphysical presuppositions in the structure of contemporary physical science.
Isotropic space: this metaphysical presupposition just says us that in the process of solving a physical problem that is not important that where are setting on you coordination system. By a closer view it is just a result of the structure of our mathematics. In mathematics we know that it is not important where are setting on your coordination system. Then if we want our physical world to be expressible by our mathematical rules and laws then we should accept this presupposition. The denial of this metaphysical presupposition is in contrast to our determination to use our mathematical laws and rules in our physical science. Another problem that we will encounter to if we deny this presupposition is that we will lose the continuity of the space and time. This continuity is the structure of our physical comprehension. Nowadays even though by the light of Kuhn and Feyerabend we know that the duty of science is not just to express our common comprehensions by some physical language, it is also acceptable that one of our physical sciences duty is to express our common feelings in the structure of the scientific language. The only question that can raise here is that "why our physical world is expressible by our mathematical rules and laws?" this is the question that I will discuss about in what follows. The same goes for the presupposition of "Isomorphic spacio-temporal" structure of our contemporary physical science.
Why our physical world is expressible by our mathematical rules and laws?
Even though this question is very important, I think it is suffering from some kind of faults in its formalism. This is not our world that is expressible by our mathematical rules and laws; these are us who have decided about. We know that in the process of physical research we have so many problems; there are so many notions that they cannot be expressed in a measurable structure, in thee situation we change the notions so that they are fitted to our needs. So many times we find that there are some contradictions between different notions that we have then we try to solve this contradiction. You cannot find any contradiction in the structure of science that nobody is working on it as her/his research program. So many times we find that there are some problems in the structure of some metaphysical presuppositions those prevent us to convert qualitative notions to quantitative ones. We should change them too. This is not nor our world that is expressible in mathematical form; we have decided to do this job then we find some ways to do that.
In the structure of scientific research we are obliged just to make an intersubjective structure. Every structure that has not this property it is not scientific. It is also clear that every intersubjective system is not a scientific one, but every scientific system is intersubjective. This is the most important difference between the structures of science and religion. You cannot find two religious thinkers that they are agreeing about "God", but you cannot find two students of physics that they are nit agreeing on the interpretation of a photo of "Wilson cloud-room". The language of science is independent of the structure of the cultured of individuals, but that is not right for the structure of religion.
By the light of all these realities science and religion has not anything in common, but maybe there is some similarities in the structure of psychological motives that enforces individuals and acts on them. However, the most important discrimination between science and religion is that the first is obliged to solve contradictions but the latter is not. Just for an example let study the Catholic encyclopedia about polytheism and monotheism:
In the unity of the Godhead there are three Persons, the Father, the Son, and the Holy Spirit, these Three Persons being truly distinct one from another. Thus, in the words of the Athanasian Creed: 'the Father is God, the Son is God, and the Holy Spirit is God, and yet there are not three Gods but one God.
Is not it just a very ridicules contradiction which no religious personals not only do not want to solve but tries to save it? You cannot find these kinds of joking in the structure of science. The only way to solve the religious contradiction is to make intrsubjective religious notions. However, the problem is that when you try to do that then you will lose religious notions. All your notion will be converted to scientific ones.