For me the questions come in the mechanism of change and the intermediate steps, which Pearl has alluded to. Without direct evidence of all of the intermediate steps it does require a leap of faith of some sort to get from one to the other, or at least a bunch of assumption.
It's like we are counting to 1,000,000 with no prior knowledge of numbers at all, starting from a point of being able to see clearly the #1 and the #1,000,000. We have uncovered say 1000 random numbers in between, yet we really cannot see clearly how they tie in. Those numbers fit in like Pi, and 1,218.2345, and 3/5, and the square root of 386,000. We can see that they are numbers, and that they share some things in common, but there is no clear connection directly from one to the other.
A fish bladder is kind of like a lung, so we assume, or go on faith, that the bladder simply became a lung at some point. Can someone show the mechanism of how that happened, and the intermediate steps to get from bladder to lung? That is the biggest part of Berninski's questions that got me thinking, when he talked about modeling, and that there just haven't been any successful models of biological evolution. Either we do not understand the mechanism well enough to build a predictive model, or we do not understand the starting and end points well enough (maybe it wasn't a fish bladder that became a lung, maybe it was something else entirely), or maybe the simply don't fit together. But, just like religion, without the "proof", without the burning bush or visitation from heavenly beings, or in this case without the clearly defined intermediate steps that led from invertebrates to vertebrates then it is still an act of faith, informed by what evidence we can see, but still an act of faith nonetheless, to believe that an organism with a nervous system just became a shark, then became something else. Without the full picture in its entirety, you are still trusting in something you have not seen, and believing that is the way it works. Well, just like with religion, without that complete picture, no matter how many believers you find, some just won't buy into it.
And just like lots of arguments about religion, just because you get a large number of people who believe it does not make it true.