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According to ontological naturalism, the existence of an incorporeal cause for the world is in conflict with science, and basically the world does not need such a cause. According to methodological naturalism, too, scientific method is the most successful method for understanding the structure of the world and the causal relationships governing it. Looking at the issue from the perspective of theoretical philosophy, which does not belong to anything other than the outer world, we find that science has a limited share in the explanation of nature in terms of its method, and if the empirical findings arising from it are not in interaction with the metaphysical foundations of science, then it cannot have decisive theories in the explanation of the world and has nothing to say in the ontological issues. It seems that by considering the link between science and metaphysics, one can use philosophical theology in order to defend the belief in God as a complementary element in the explanation of the world of existence, and the use of science in the realm of ontology is considered unscientific and fallacious. Regarding essentialism in science, Ellis believes realistically that instead of lacking properties, creatures have powers and capacities that make up their essence and inherent properties and make their nature active and full of properties. It can be concluded that naturalism is valuable as a way of understanding material nature, without being in conflict with the transcendental and incorporeal cause. Methodological naturalism does not necessarily correlate with ontological naturalism, and what brings these two closer together is the metaphysical foundations of science, which alone is efficient in theology and the ontological explanation of nature. In sum, new essentialism establishes a connection between the inherent properties and the existence of things, and builds an objective and real foundation on the proof of the metaphysical foundations of science, from which theology can open a way to prove the belief in God.

After Darwin's theory, the teleological argument from design faced numerous challenges and transformations to the extent that it could no longer explain order according to modern science, as the final cause was unable to account for Darwin's theory. In fact, there was a need for an argument from nature that could, in line with the transformation of Aristotelian natural philosophy, explain the existence of order and its connection to the creator of order within empirical sciences. This is because the teleological intent in Aquinas's argument from design, based on the final cause, suggested the will of an intelligent agent behind the world. But it seemed, the theory of evolution - understanding nature through the "efficient cause" – has rendered this transcendental intelligence unnecessary. Thus, the teleological argument from design failed to align with modern science and gradually, its application to the existence of God was deemed unscientific and unnecessary. Therefore, it is necessary to articulate order in such a manner and utilize it differently in theology and in the defense of theism, so that the empirical order of the world continues to necessitate the existence of God. In reality, it can be shown that the efficient naturalistic order is the only common point between monotheism and atheism that cannot be effective in attributing to the existence or non-existence of God. It is necessary to refine and complete this natural order in defense of theism. Based on this, the teleological argument from design remains significant in its own right.

William Craig has sought to defend theism by participating in numerous debates. In a debate with the American philosopher Sinnott Armstrong, which is also published in a book entitled "God", Craig in his first reason tries to prove the existence of God by denying "real infinity" and relying on the concept of beginning and "the need of every beginning for a cause" and on the other hand, he takes Big Bang as a witness to his claim. While Armstrong rejects Craig's argument by referring to the existence of real infinity in the outside world and the existence of scientific evidence to negate the implication of the Big Bang on the beginning of the world. Based on this, when it is not possible to properly use experimental evidence as a proof of theological reasoning, such methods can put the belief in God in crisis. Therefore, lack of establishing the correct interaction between theology and science can be considered one of the most important weaknesses of Craig's argument on the existence of God. Finally, by introducing a scientific model, it is possible to provide a solution to establish a correlation between science and theology in such a way that theological evidence matches with experimental evidence and external truth, and no contradiction threatens the belief in God.

One significant skepticism surrounding God’s existence and attributes arises from the presence of evils, a challenge not only faced by atheists but also by theists. Upon analysis, it becomes apparent that evils in the material world do not reflect any flaws in the divine essence. In fact, there are several reasons behind the human perception of evils. Thus, since evils existentially manifest, they possess inherent goodness, with any perceived flaw being merely a product of human perspective. Evils are perceived in various ways—stemming from conflicts within the material world, as a result of human choices, or due to certain outcomes not aligning with human desires. It is essential to recognize that the overall balance of the universe is not dictated solely by human will and desires; instead, causal necessity governs the events of the world. Humans, through their choices, contribute to this evolutionary course. While evils may not be desirable from a human standpoint, the causal system of the world indicates the permanent agency and power of God, alongside the influence of human free will as a natural entity within this system. Creatures' effects cannot be eliminated from this causal system; thus, evils can be addressed by rectifying one’s individual practices. Moreover, evils are inherent to the material world and are part of divine power within the causal system.

Because of his philosophical method in studying nature and his attempt to intellectually prove natural propositions, Aristotle always sought to obtain perpetual and metaphysical results from the relationships in the universe. For this reason, natural philosophy lacked features such as falsifiability. With the scientific developments in Europe, this philosophical attitude, which was no longer considered as refelecting the reality of the world, changed and philosophers tried to introduce the method of observation, hypothesis, and induction as an efficient method in studying nature because they holded that this experimental method could describe the truth of the world. Thus, the philosophical and metaphysical view of nature gave way to the empirical and falsifiable view of experimental sciences. In addition to the distinctions created in the evolution of nature study, the method and goal of natural philosophy also changed to the new method and goal of experimental sciences. This major distinction in investigating the nature has had many consequences. In this article, we discuss these differences and developments.