How to place 'not' reasonably in a clause?

Question

Is it true that we often use 'not' with a verb or auxiliary verb i.e. 'not to do', 'do not need to do'? 'not' does not have this limitation when it forms a fixed collocation with other words, such as 'not...but...', 'not only... but also...'

1. The second fact is that many linguists work not just on languages other than English but on languages which have been little studied or not studied at all.
2. If this project fails, it will affect not only our department, but also the whole organization.

But I came across this sentence today.

a. In the discussion of (3) above, we observed that, although we analyse clauses and sentences individually for convenience, in real language they do not occur in isolation but as part of longer texts.

In my view, it should be

b. In the discussion of (3) above, we observed that, although we analyse clauses and sentences individually for convenience, in real language they occur not in isolation but as part of longer texts.

What's the difference between a and b? Is a formal?

Answer 1

Your re-written version is missing some punctuation:

in real language they occur, not in isolation, but as part of longer texts.

Now that you're talking about something occurring (as opposed to 'not occurring') you have a created a contrasting element that needs to be offset from your main statement about what does occur.

Yes, they are two ways of saying the same thing, but grammatically different. The original version is effectively "not this, but that", and your version is saying "this (and, parenthetically, not that"). The way you suggest is not exactly more "formal", but lends itself better to the written word than the spoken. When speaking extemporaneously, we tend to tag exceptions and contrasting elements to the end of a statement.