The Mind (God) who supposedly made All can indeed be refuted, even a Deity, by the only way possible for that of invisibles, that of self-contradiction, for this Guy who does planning and creation is still a system, and thus not fundamental at all, since something had to come before Him, which He would therefore be dependent on for His existence. If the notion of Him being fundamental and making everything is removed, then all one has is a smart life form (alien), not a God.
All this still holds for a Theity, plus that there then can be yet another disproof, for He is supposed to be everywhere, but is found nowhere. Only the natural is found, all operating just the same as if there was nothing super, extra, or beyond.
In other cases where evidence is supplied, such as that of the Bible, there can then be a triple refutation, for the Bible has been shown to be wrong but for some ancient traditions of tribes.
There are also claims for Gods-who-are-not-minds, such as QM and its pair production basis or the superposition state, math, a zero-balance equation, or just plain old stuff having been around forever. These mindless states are not God.
Some believers have appropriated quantum mechanics to claim a more holistic picture of nature. However, the standard model of particles and fields developed in the 1970s is fully reductionist. This model has agreed with all the data. Reductionism isn't defeated just by the fact that it can't derive everything that happens, such as predicting the stock market.