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That being said, it is generally best to place javascript in an external file instead of having it in the actual page itself, because what can happen is that, by using javascript, you end up pushing the content that the engines can read further down the page. This can have the effect of reducing it's relevance in the eyes of the engines.
So, to answer your question, directly...no...but it can indirectly effect a pages ranking by pushing your indexable content further down the page.
That being said, it is generally best to place javascript in an external file instead of having it in the actual page itself, because what can happen is that, by using javascript, you end up pushing the content that the engines can read further down the page. This can have the effect of reducing it's relevance in the eyes of the engines.
Not sure that I agree.
On general principles, I would assume that the search engines all begin by parsing their input (just like a compiler would). Comments are almost certainly discarded at this stage, and I would assume that constructs that the SE ignores, like SCRIPT, are also discarded.
If my assumptions are correct the script should not push the HTML down in the actual text that the analysis module of the SE sees.
I make no claim to knowing how SEs really work, just seems to me to be the way I would design it.
This issue comes up quite often (most commonly about comments), would love to hear what others think.