Science allows questions within narrow rules. For instance question evolution and you get what we have going on now. There are fossils that seem to indicate reptiles evolving into humans but since there is no real evidence of this being true evolution is taught as a disprovable theoretical fact. The fossils looked on as transitional could in fact be animals that "adapted" and then went extinct because the "adaption" was in fact fatal. In other words evolution interprets what it sees through a preconceived idea of what it wants to see.
Another example of "questioning" science that makes many scientists go ballistic is to question the consistency of the speed of light. Any science that removes all variables in any equation by defining them as constants and then defining the value of the constant is not looking for truth.
Now take your orange analogy. We can develop new strains of oranges. Many of the fruits and vegetables we eat today are in fact hybrids of what are found in nature. We have improved them by design. Have you ever seen a wild rose, if you have compare it to a grandiflora or a hybrid tea.
Although science should be cold and unemotional, when science wants to so control the hearts and minds of men that emotion is left by the roadside society in general suffers.
To me Darwinian evolution is illogical as it depends on chance bringing together so many necessary componants of life that if valid should still be happening today. And the truth is evolution on the grand scale of the Cambrian explosion only happened once.