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.