Perfect science begins with no assumptions; but that isn’t what we have.
We have incrementally developed knowledge of facts that are shaped and developed within a certain “way” of searching for knowledge.
There is the assumption that this way is the best, but the search for knowledge is not monolithic, and thus not just one way.
Take Einstein, for example, who despaired of making headway by building up knowledge from basic facts — the way of science as practiced today — and instead did it differently by analyzing everyday experience and deriving general principles from that. His theory has stood the test of time, while so many constructive theories have fallen away.
There is the assumption that each incremental step may bring us greater accuracy of knowledge, but science advances by often going backwards and reexamining things already assumed to be accurate, but which are found to not be so.
And jumping ahead, so as not to get bogged down in the myriad of assumptions at play within scientific practice, there is the assumption that reality is structured a certain way and this forces the exclusion of conflicting evidence and reduces the range of possible knowledge. Thus the practice of science limits itself and excludes anything that falls outside of those limits. Technically, Einstein’s greatest work is only “scientific” because it isn’t “religious.” Those two being the walls of the narrow alleyway we allow ourselves to travel in our search for knowledge.