Yes, I agree. I think the reason is not because there is no rational basis in one or the other part of the communication participants, but there are combinations of people whose communication habits simply do not fit together and this then produces major misunderstandings and leads to death ends. I guess there are many things implicit in our lines of reasoning that we should try to make explicit when communicating about scienctific “facts and fictions” for the goal of clarifying how we came to our statements.
In my own essay I tried to push the reader to the fact that we often confuse beliefs with knowledge. An interesting question would be whether or not this also works the other way round cognitively: confusing knowledge with belief, means doubting things that are considered secured scientific knowledge. This surely would necessitate to make auxiliary, yet unproven assumptions about reality, what is not per se forbidden by the scientfic method. I write this because I read your very interesting comment on the essay site “the geometry of counterfactual science” and as you wrote, the question is indeed how far one should go with such auxiliary assumptions, especially when they are not provable experimentally in principle. Or stated differently: where should we establish the line between facts and fiction?
By thinking a little bit about that question, it seems to me that at least a – yet to be discovered? - fundamental theory of “all there is” is doomed being unable to logically derive its fundamental base assumptions unambigously. Here your essay's approach gets most interesting for me, since for that case (maybe in the future, who knows) we are then faced again with the epistemological question about whether or not these fundamental assumptions are merely auxiliary assumptions – because by their very nature they will not be provable or disprovable by any means!
Now let's suppose we cannot find such a theory of everything (due to arbitrary reasons). Then the question still remains, and more pressing, where we should draw the line between facts and fiction. Moreover, one instant of that question is surely whether or not such a theory of everything is at all implicit and hence allowed by what we call reality. The only answer I have found to that conundrum is to always differentiate between temporary, secured knowledge and mere beliefs. I cannot imagine how it could be other than that for human beings trapped in a world that only allows the frog's eye perspective. I think a way out of that problem could indeed be to rediscover the “God of the gaps” as it occasionally was termed by some people. Without applying a certain religion to that assumption, I would call for re-examining this old-fashioned idea again on the basis of the human conditions and its lack for a true bird's eye perspective. And especially on the basis of the above mentioned epistemological gaps, gaps that obviously are an inherent part of the reality we live in.
Now comes my main point: in my opinion, I we want to make progress on all these issues, we at first must intuitively find a consistent scheme about whether or not reality allows for a transcendent realm of existence. A realm where those gaps do not exist. This is surely a religious, philosophical, or better termed, a metaphysical task, but I think not doomed right from the start. I think it critically hinges only on whether or not one is willing to accept that logics can transcend itself such that it logically infers that reality cannot have been emerged out of some illogical assumptions, like for example “absolute nothing”, “chaos”, “randomness”, “miracles”. The latter, namely “miracles” is what some people think is what led to reality. Either it existed forever, or it emerged from some reduced “reality”. It is clear that there are no other, more “rational” options if one wants to explain “it all”. But there seems to me to be one exception: for explaining all these miracles we can also assume an intentional creator who is superior to causality and to any logical systems (at least to all humanly knowable systems). That's what my essay is about. I would like and be happy if you could comment on what I wrote there – since I am interested in your feedback!