True Science is about using the scientific method to assess mechanisms within the universe.
This is a good definition of the scientific method from the Department of Physics and Astronomy, University of Rochester (USA):
I. The scientific method has four steps
1. Observation and description of a phenomenon or group of phenomena.
2. Formulation of an hypothesis to explain the phenomena. In physics, the hypothesis often takes the form of a causal mechanism or a mathematical relation.
3. Use of the hypothesis to predict the existence of other phenomena, or to predict quantitatively the results of new observations.
4. Performance of experimental tests of the predictions by several independent experimenters and properly performed experiments.
If the experiments bear out the hypothesis it may come to be regarded as a theory or law of nature (more on the concepts of hypothesis, model, theory and law below). If the experiments do not bear out the hypothesis, it must be rejected or modified. What is key in the description of the scientific method just given is the predictive power (the ability to get more out of the theory than you put in; see Barrow, 1991) of the hypothesis or theory, as tested by experiment. It is often said in science that theories can never be proved, only disproved. There is always the possibility that a new observation or a new experiment will conflict with a long-standing theory.
Note that item (2) is that an hypothesis is required. This is a first assumption. It is by definition unprovable itself. In accordance with (3) and (4), this unprovable hypothesis is checked against observations and experiments.
Note that a new hypothesis completely different to a previous one may fit the data from (3) and (4) better. The new hypothesis will then be regarded as more likley to be true than the previous one. (This has of course happened many many times in different areas of science over the years).
It should be noted that the new hypothesis can not be proven to be absolutely true any more than the previous one could.
So science cannot absolutely prove anything natural let alone supernatural!
Of course many areas of what is called 'science' today cannot strictly follow the scientific method. You cannot for instance observe or do repeat experiments on the start of the universe or on the evolution of fish to amphibians to reptiles etc. etc.
These forms of 'science' might be more accurately termed 'philosophical science' rather than true science.
Many of these 'theories' (as you cannot really `do items (3) and (4) there is even less proof here) start from a naturalistic assumption in (2). In other words the hypothesis is that there is no supernatural and everything must come about by 'natural' means. Most theories of macro evolution and the 'Big Bang' etc. would fit into this category.
As the non existence of any supernatural is taken as the (unproven) hypothesis in (2), the end result must be that there is no supernatural or else the theory would be self contradicting. This is merely circular reasoning however and can prove nothing.
You can of course take as your unproven hypothesis (2) for instance that there is a supernatural, such as 'God'. You can ascribe attributes to this 'God' and then do your tests (3) and (4) to the degree that they are possible. This of course would not prove that 'God' existed anymore than the previous 'naturalistic version would prove there was no supernatural.
If you reviewed the evidence objectively and found however that the 'God' hypothesis fitted the evidence better than the 'naturalistic' hypothesis then 'scientifically' you should adopt the 'God' hypothesis in preference. This is of course a bit difficult if you are (philosophically) an atheist! So really the problem of reconciling 'science' and religion' in our modern era is not really that at all, it is reconciling Atheism with Theism. The former can be achieved, (and although a minority today, there are still many theistic scientists). The latter is of course logically impossible.
The comment that a machine will produce 'supernatural' results is of course a totally absurd one. Machines will only produce whatever they are told to produce by whatever (human) input into them. As I have explained in a previous contribution, all machines are essentially dumb. The hardware of a computer really has no more intrinsic knowledge than that of a vacuum cleaner or a cooking stove!
kind regards to all,
Gordon.