Cause and Effect and the Scientific Method

Experiments and studies are often conducted to identfy causes for observed effects.  'Why does this symptom appear?' or 'Why are oranges orange?'  The problem is, it's easy to innocently create causes that are not really there.  Sometimes the identified 'cause' may be something that is present, but doesn't have anything to do with the effect you are studying. "Oranges are orange because they have lots of vitamin C.'  Well, lots of other things have lots of vitamin C but are not orange.  Look at Kiwi.
 
There are so many potential causes for so many occurrances, that assignment of cause is often difficult.  You need to look for differences.  'How are the ingredients of an orange differentent than those of a Kiwi?' or similarities 'How are the ingredients of an orange like other orange things?'

Then there's post hoc ergo propter hoc': After this, therefore because of this.  In the middle ages, scientists thought that fruit flies spontaneously generated from garbage.  How did they know this? They put fruit in a jar and closed the lid. Lo and behold, fruit flies appeared!  Proof?  The actual cause was discovered in later years.  The fruit flies had laid eggs in the fruit prior to it being placed in the jar.  Post hoc ergo proter hoc.