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Can a lack of knowledge or understanding invalidate a positive claim?

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Consider the example of causal determinism. It can be phrased in many ways, all with identical meaning:
- The idea that "every event, including human cognition and behavior, decision and action, is causally determined by an unbroken chain of prior occurrences” (Van Inwagen, 1983).
- The world is governed by (or is under the sway of) determinism if and only if, given a specified way things are at a time t, the way things go thereafter is fixed as a matter of natural law. (SEP)
- Everything has a cause.

My question is in reference to people who hold that the lack of complete understanding in a particular field can invalidate a positive claim. Continuing with the example of determinism, one of the most oft-used counter-arguments is the Heisenberg uncertainty principle. This is the principle that claims "precise inequalities that constrain certain pairs of physical properties, such as measuring the present position while determining future momentum of a particle. Both cannot be simultaneously done to arbitrarily high precision. In other words, the more precisely one property is measured, the less precisely the other can be controlled, determined, or known." Everyone knows that the principle cannot give free will, but some suggest that it invalidates determinism. How?

In the same regard, the fundamental nature of quantum mechanics is said to be indeterminate, that is, the measurements of an observable at the quantum level is said to have an indeterminate value. Stated more simply, the value is not determinable via our current methods of observation. This is another "lack of knowledge" position, just as the first one is.

Do these kind of "lack of knowledge" positions invalidate or otherwise lessen the strength of determinism as a theory? I'm having difficultly conceiving why there is any conflict. A lack of knowledge or understanding simply means we need to find out more before we know for sure. Some of the greatest minds of quantum theory asserted this (Einstein, Rosen, Podolsky). In fact, they wrote a paper where they went on to say that there must be "hidden variables" which haven't been accounted for which allow for strict determinacy. That was in 1935. 76 years later (as of this post), some physicists have seemed to have ruled out "local hidden variables", but global hidden variables and other explanations are still very much on the table. Again, we just don't know enough yet. It doesn't seem to follow that uncertainty about certainty can disprove certainty.

I have one further example that might help clarify: As you know, given the nature of science we may very well never be 100% absolutely, objectively "certain" about anything; but that doesn't mean all our theories are invalid. For example: I am uncertain that my aunt's apple pies are made with handpicked apples. I don't see how my uncertainty about the nature of the apple pies has any effect whatsoever on the actual possibility of the composition of the pies. Either the apple pies are made from handpicked apples, or they aren't. My uncertainty about it does not make either possibility more or less probable.

Keep in mind my question is about the general ability to use a "lack of knowledge" claim to invalidate a positive claim. Determinism/apple pies are just examples. Feel free to use whatever thought experiment or intuition pump that serves you best.

Note I wanted to avoid using the term "negative claim" because it's thrown around a lot and doesn't quite capture the essence of what I mean by a "lack of knowledge" claim; at least insofar as I see it being used today. E.G., some people think "There is no flamingo on my desk" is a negative claim, merely because it posits the non-existence of something. To me, anything which asserts a knowledge of the existence or non-existence of something is a positive claim. A "lack of knowledge" claim, on the other hand, is one which acknowledges an uncertainty or "non-knowledge" (if you will) of something. I will consider revising my question and simply stating my definitions at the top if people think it will aid in clarity.

Here is some background info with regard to my first example:
http://en.wikipedia.org/wiki/Quantum_indeterminacy
http://en.wikipedia.org/wiki/Uncertainty_principle
http://en.wikipedia.org/wiki/Hidden_variable_%28physics%29
http://en.wikipedia.org/wiki/Indeterminism#Quantum_mechanics
Einstein, A.; Podolsky, B.; Rosen, N. (1935). "Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?". Phys. Rev. 47 (10): 777–780.


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