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Yes, but why is it harmful? I don't think there is any
documented evidence that it is harmful.
I don't think anyone has advocated teaching that a=F/m has[snip]
any advantages over F=ma, so this is a red herring. What has
been said is that a=F/m is more understandable, and
establishes a relationship that students can begin to make
sense of. There have also been comments that it seems to work better.
Now what is the advantage of a=F/m? It basically makes the
relationship more concrete, so it is a very good way of
introducing the law. Indeed when one models the law you
measure the a and vary either the F or the m. Then you find
that a is proportional to F and inversely proportional to m
hence a=F/m. This makes it an experimental problem which
students can readily model in the lab. Notice that the
independent variables are F and m. Now most students will
not tend to think of m as being a cause, but they will most
certainly think of F as being a cause.
So in the end, I propose that insisting on introducing F=ma
as NTN2 is not optimal. Whether of not you say that force
causes acceleration, it is implied in the minds of many
students. If you try to deny this idea, the lower students
will probably never have a good handle on NTN2, and will in
the end memorize it as a piece of random mathematics.