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Is it more correct to form a sentence such as
John went to academic conference by the bus
using by as the preposition indicating what he took to the conference, or is using on the correct way? Better yet, could both of them stand for the same meaning?
The only thing wrong with your assumption is that anyone but a non-native speaker would say "by the bus." As the others have pointed out, the construction would be "by bus" or "by train" or whatever.
Nevertheless, it is certainly possible to say
John went to the academic conference on the bus.
Here is a movie poster that illustrates what I'm talking about:
Some may object that this might seem ambiguous, that it might seem as if the conference were being held on the bus itself, but in normal informal speech it would be easily understood. More likely the sentence would be reordered in this case, such as
John went on the bus to the academic conference.
In English, using "by" + "form of transportation" is the way to say it. However, no indefinite (or definite) article is needed. Thus...
"By bus" and not "By the bus"
"By bike" and not "By the bike"
It looks like you're mixing two possible ways of expressing what you want to say:
In the second example, you'd be drawing more attention to the specific bus John took, (Perhaps you mentioned the type or bus route previously, for example.) whereas the first sentence merely highlights the mode of transport he chose to use and the academic conference takes the focus.
