The cardinal difficulty with naturalism, in the opinion of Lewis, is that if it is true that everything or events should be explained with due regard to the Total System, then it is hard for it to expect other things to start happening under the system. These, in this case, are the miracles that Lewis says can not live on their own since they are dependent on the whole system. The explanation of this phenomenon of all these things which exist would determine their existing knowledge scientifically explained with due regard to the total system. This kind of explanation should express their qualities to be part of nature as a whole and not to exist on their own.
The other problem which portrays a major difficulty with naturalism is that older scientists believed that small particles of matter moved according to strict laws and regulations, meaning that their movement was interlocked within the total system of nature. This is the basic understanding of naturalism which does not allow any other thing to break ties with its dependency on the main thing in the Total System. This has since then been proved wrong by modern scientists who think that units of matter move in a random manner, each “on its own” way and “on its own accord.” the movement of the bodies is because of millions of smallest invisible units thus each of them has its own idiosyncrasies of unit behavior.
The union movement is found to be incalculable but can only be predicted the way one can predict when tossing a coin. It is also found that these small particles move at a very high speed. The truth of this theory brings in something else which turns out not to be based on naturalism because, according to naturalism, all events and things can not move “on their own” nor move at their own accord. Substances and particles are interlocked into the whole system. Now that the movement in this theory is on its own, then it would be a great shock to describe naturalists as “super” naturalists. Lewis proposes to call the naturalists sub-naturalists, although nature has no doors at the same time. To sub-naturals, all bodies are as they were fed, and it could as well have many other doors, and such could be openings to the supernaturals, and events might be fed into it through the doors.