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W. W. Bartley III criticised presupposititionalism in his book "The Retreat to Commitment". Bartley pointed out that knowledge doesn't need to be justified, i.e. - there is no need to show that it is true or probable. Rather, rationality has to do with holding all of your positions open to criticism. We don't need justification because theories can be criticised without justifying anything. If I make an experimental observation that clashes with a theory then there is a problem to be solved independently of whether the observation is right or wrong. The problem is solved not by justifying anything but by proposing explanations for the observation and then trying to criticise them with respect to whether they solve problems, whether they are compatible with other explanations and so on. A theist who held his views open to criticism would have to ditch his belief in God because the theory that God exists solves no problems.
See also the first two sections of chapter 1 of Karl Popper's book "Realism and the Aim of Science", "The Fabric of Reality" by David Deutsch and the following links
http://www.criticalrationalism.net/2010/02/15/explanation-versus-justification/ http://www.criticalrationalism.net/2010/04/17/criticism-of-salmon-on-popper/.