Assumptions and Illusions
As a scientist, I've always been told by my professors, supervisors and colleagues to clearly state the assumptions that I've made during the elaboration of my experiments and my models. Of course, they are referring to the assumptions that specific to my situation and not the underlying assumptions that are embedded in the field of ecology and biology. For example, you'll see very few theoretical biologists highlight and attempt to justify the use of differential equations to model complex systems when declaring the assumptions of their mathematical model, as it just assumed that complex systems can be modelled in such a way.
These sort of underlying basic assumptions or "basic statements" (following Popper and others) are taken as a given not only in biology, but in all "hard" and "soft" sciences, though which basic statements are taken for granted change from field to field (for example, a basic assumption regarding the lethality or danger of chemical substances is different for chemists who look at single dose lethality versus environmental scientists who look at repeated and prolonged exposure to chemicals in the environment at low levels). The problem of determining which basic statements to use is very difficult, with most solutions involving some sort of conventionalism (we all agree at the beginning to use the same basic assumptions in building the field). However, while such a system would be useful in theory, most scientists do not share the same basic statements despite a large amount of indoctrination in traditional science curriculum, creating large misconceptions and poor communication between scientific schools and fields.
These problems are not only limited to science, but are commonplace in society at large. For example, political ideologies rarely share similar basic assumptions, as realists believe in a very negative perception of humanity (Hobbesian brutes, Machiavellian deceivers who would engage in an all out battle against each other if not for social contracts that enforce order on the chaos) while liberals have a rosier picture of humanity (born mostly good, and through education can become enlightened individuals, of the Mill and Locke mold). Other such differences in basic assumptions emerge between neo-liberals, neo-conservatives, neo-realists, neo-socialists, postmodernists, religious fundamentalists and other political ideologies. These discrepancies in the foundational construction of our realities results in different interpretations of the same events (this view is espouse quite forcefully in the works of Feyerabend, which is normally called the theory-laden view of reality).
For example, to those who believe God punishes the wicked for their sins and that God's will shall not be opposed will vehemently denounce the HPV vaccine as it allows sinners to go unpunished. To someone who believes that God does not punish but loves his flawed creatures and does not wish to cause them undue suffering will believe they do God's will in giving out the HPV vaccine. Now, let us say that both of these groups of people refer to themselves as Christian and both "find" these messages in their holy books. Which group is right? Which group is truly representing the Christian faith? Well, both are. They are both right as Christianity, as the collected works of the New and Old Testament, is a self-contradictory system. Within it, one can logically justify any behaviour as the belief system is inconsistent and cannot lead a unique solution to a problem such as this.
However, human beings dislike such moral ambiguity (hence the derision of self-professed postmodernists and "relativists", though even they make fundamental assumptions as they proclaim not to) and will quickly cherry-pick whatever data satisfies their initial leanings (they could be hidden assumptions or known assumptions), ignore and reject others and will proceed to declare their solution to be the one, true way (the unique solution). Hence, there will be moral absolutism within this framework, even though this certainly does not mean that this new belief system is not rife with real contradictions and inconsistencies, but they are simply not perceived by the followers or they will be addressed with ad hoc explanations that are completely foreign to the governing framework.
With all these assumptions in tow, one arrives at the illusion of an objective reality, where one who follows the belief system is "right" while those who don't are "wrong". These illusions are fundamental in creating an environment in order to get things done, but this doesn't make them any more true.
I'll continue with these thoughts later...