I'm not completely sure what you mean. Darius's response seems relevant (in particular, you may want to look at the difference between a general non-deterministic Turing machine and an alternating Turing machine). However, there seems to be possibly another issue here: When mathematicians and computer scientists discuss polynomial time, they are talking about polynomials of the length of the input, not polynomials of the input (similarly, for exponential time and other classes). Thus, for example, to say that PRIMES is in P we mean that there's an algorithm that answers whether a given integer is prime that is time bounded by a polynomial of log_2 p (assuming p is written in base 2).