The word “theory is often misused when referring to the scientific sense of the term.
All kinds of knowledge are based on assumptions, including Torah knowledge.
A scientific theory is never proven. It is an explanation that accounts for the facts observed. A theory may be disproven, when scientific observations demonstrate that it cannot be. In general, theories are modified as more scientific information is acquired. No scientific theory is expected to be final, as we will always be increasing our levels of accuracy of measurement, as well as designing new methods of measurement. When measured observations contradict a theory, it is the theory that must be modified to fit the observations, not vice-versa.
Of course, conflicting theories about a given topic may exist. The conflict can remain until a set of experiments can be devised that disproves one or the other. Other than that, usually the one that has the preponderance of evidence supporting it will prevail.
I am not sure why Joseph is posting EDITED about scientific theory. Is he trying to show that scientific knowledge is acquired in a different manner than is Torah knowledge? We all know that.