[jiggawatts]

There is no difference between comparing A versus B or B1 versus B2. The data collection process and and the mathematical methods are (typically) identical or subject to the same issues.

E.g.: profiling an existing application and tuning its performance is comparing two products, it just so happens that they’re different versions of the same series. If you compared it to a competing vendor’s product you should use the same mathematical analysis process.

[gwd]

I was kind of scratching my head at what GP was getting at as well; I suspect that "better" has a different metric in the second case: i.e., the scientist is asking which chemical A or B has the stronger desired medical effect; the engineer is assuming we're going with chemical B, and trying to drive down cost of producing the chemical or improve lifespan of the pills or decrease discomfort administering or increase absorption speed or tweak the absorption curve or something like that. Those metrics are often much easier to measure than the effectiveness of the chemical itself, and much less scientifically interesting.