Dear Philip,
Thanks for submitting your well-written, and well-thought-out essay. I especially appreciated your list of biases. Have you ever considered coding any of these biases or other logical fallacies into RDF/OWL? My hope is that such a system would detect articles with excessive bias and logical error (and save me the trouble of reading them). The Semantic Web will help enhance our thinking (and reduce our biases) in other areas (e.g. law, medicine), not just scientific discovery, is one of the Three Crucial Technologies ) that I mention in my essay (feel free to critique it).
I do wonder if the "IKEA effect" has more to it than just bias. As Richard Feynman said, "What I cannot create, I do not understand." OK, IKEA uses low-strength particle board instead of wood, but their design engineering and supply chain methods are fantastic.
You say that we are illogical because of bias, but then you don't ask the next question. What is the evolutionary advantage of bias in thought? Maybe I should leave it as an exercise for the reader, but the short answer is, "Because for a large enough percentage of the time, it works." Those of our ancestors who did not employ bias in their reason died before they could become our ancestors.
I understand that the current publishing system could use some improvement, and I appreciate your hard work in establishing a more open publishing venue. But, not being an academic (and most of the world are not academics) I'm not sure that it really matters. People who reify scientific ideas into products (like Steve Jobs), or people who incentivize (or disincentivize) socially beneficial work (like the governments who make the laws of a democratic capitalist country) matter a lot more than we do. And while it is humbling for us scientists and engineers, it turns out that most discoveries usually pop up in more than once place near the same time. We really don't matter that much. :-(
You mentioned the importance and desirability of "carefully considered logic." Well, yes, and I do call for it in my essay, but we must remember that logic has it's limits (as proven by Godel, and recognized by anyone who has done any work with Descriptive Logics that do inferences over Semantic Web data. The upshot is that knowledge is not enough. Even wisdom may not be enough, if you don't have the advanced nanotechnology needed to feed the hungry (and heal the obese) without overloading our ecosystem. And even advanced nanotechnology can't save us from large K/T asteroids, nuclear war, and the like--for that we need a space-faring civilization.
Fixing the peer review of today's journal publishing system would be a good thing, but it won't save the world.