The epistemological scientific method is commonly presented as in an abbreviated sense being employed when a person formulates a hypothesis, an untested guess about what might come about if a given thing is to happen, then conducts an experiment to observe the results and compare them with the hypothesis, and then alters their hypothesis as needed to fit what they found with their senses, which in turn could lead to additional experiments and revision. There is something very important about the nature of a hypothesis that is relevant to core rationalistic truths: it is not just that a person is not in error for thinking of a hypothesis without next carrying out an experiment, but also that a hypothesis is not on its own any sort of assumption. It could be recognized by a person as potentially true, whether or not there is any particular evidence suggesting it already, without the person believing it is true.
No one, from a "layperson" to a professional scientist, has to make assumptions when dwelling on what, if anything, they expect the outcome of a scientific event to be. To assume is always irrational in itself, moreover, concerning science or anything else. If something is not provable by logical self-necessity (the veracity of axioms or one's own conscious existence) or because it follows by necessity from something logically verifiable which either is or is not self-evident, with scientific ideas such as the existence of a proton being empirically supportable rather than logically verifiable, it might be true--as long as it does not contradict any logically necessary fact. That is, a logically necessary fact cannot be false. However, it is always unjustifiable and outright, inherently irrational to assume that something is true when it is not necessarily so, even if that thing is logically possible or evidentially probable. It is a leap in the philosophical dark based upon whim, and so even believing in something that can be proven when one only does so on the basis of assumptions is still inflexibly irrational.
If a new species is discovered and its reproductive system turns out to be unique, for instance, a researcher would have to see its method of reproduction firsthand, as opposed to relying on hearsay, to come as close to knowledge as possible. All of the epistemological limitations of the senses would of course have to apply [1], so this is not knowledge of anything more than fallible perceptions of things that are seemingly true but still wholly lesser than logical necessities either way. Still, it would not be irrational to expect the reproductive system of this novel creature to be a certain way, if it is indeed logically possible and suggested by probabilistic empirical evidence--in this case, that might be the appearance of its outward body as relevant to sexual reproduction. It would also not be irrational to think of various genuine possibilities beforehand, all while never assuming that possibility makes them true.
All assumptions can be avoided, so there is nothing special about the nature of any pre-experiment hypothesis that has to be believed. Yes, after the experiment, a hypothesis can be revised to more closely match the observations, perhaps before more empirical testing that could lead to additional revision, but this does not mean anyone actually believes the hypothesis beforehand. No one has to. Even if they are a very confident scientist, a person would be an utter irrationalistic fool to do such a thing, or to assume more foundationally that observations logically necessitate that the external world is really as it appears. There is nothing irrational about the scientific method although it is epistemologically inferior in all ways to the inherent, universally accessible, all-encompassing truth of logical axioms and what follows from them [2], the same superiority being metaphysically true of reason over whatever material world is out there beyond the mind and its senses. Only a conscious being can err, not reason.
[2]. A person can recognize logical possibilities and necessities about what could or would be true of a scientific matter if a given notion is true, such as that electrons flow through conductors, though the lack of logical necessity in such a premise being true means the only way to obtain fallible evidence for it is sensory observation. However, this is an epistemological limitation of non-omniscient beings, not a flaw of the intrinsic truths of reason.
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