Marcus,
Thanks for commenting on my essay.
However, you have a mistaken view about what it is to observe something. You suppose that to observe something we merely have to observe the thing *indirectly* by virtue of its effects. That is absurd. If some crackpot claims that unicorns exist because he has seen an imprint of a hoof in the woods, do you believe him? Of course not. Yet when the top brass in physics claims that the Higgs bosons exist because they have seen traces of it, everybody is in shock and awe. But the emperor has no clothes on. The conclusion "X exists" cannot be drawn from the premises "if X exists, then trace T will be observed" and "trace T has been observed". It's a fallacy when a crackpot does it, it's a fallacy when a sophomore student does it, and it's a fallacy when the top brass in physics does it. Period.
N.B. Another fallacy is circular reasoning. You don't get so say: these are traces of a Higgs boson, so therefore the Higgs boson exists. Then you are assuming what has to be proven!
Futhermore, if by underdetermination of theory we have theories T, T' and T" that are consistent with experiment, then you simply don't get to say that T is more likely than T' or T". You gave two ridiculous examples of T' and T", but if you have this situation in reality (so three well-defined theories T, T' and T" in agreement with experiment) then theory choice depends largely on social factors. If you then believe in the theory T, then you will simply have to live with the situation that others will believe in another theory T' or T", while there is no instrument - at that moment! - to decide between the theories. In my PhD thesis I mentioned a transition from modern physics to postmodernism in physics: that is precisely this situation.
Last but not least, you seem to confuse the notions "discovery" and "explanation". Suppose that from theory T we can deduce the premise "if X exists, then trace T will be observed", and suppose that from experimental results we can deduce the premise "trace T has been observed". Then you don't get to claim that you have discovered X, that is, that you have proven that X exists. However, you do get to claim that theory T is an explanation of the results; and if there is no other theory T' that makes the same quantitative prediction then you even get to say that T is the best explanation avalable. Don't get me wrong: this is the situation at hand with the Higgs boson. Of course this is an additional justification for believing in the Standard Model and the Higgs boson. So you can say that you believe in P (you used the word "assume" but "believe" fits better in the language of philosophy of science) if Q has been observed and P --> Q follows from theory. But note that this also holds for the crackpot and his unicorn. The point here is that the statement "the Higgs boson is the best explanation available" and the statement "the Higgs boson has been discovered" are two distinct conclusions. Saying that it is the same is not how science works: only by a degradation of the traditional standard of scientific quality we can say that it lies within the realm of scientific discourse to identity these statements with another. I consider it malpractice.
By the way, as I remarked in an earlier post, the member of the CMS collaboration who reviewed my criticism for publication in Physics Letters B said that the criticism is correct but that physicists need no reminder of that. I doubt that: I think physicists do need a reminder. Hence my essay.
Best regards,
Marcoen