DarkStar,
I'm not sure what all these quotes necessarily have to do with evolution, common ancestry, or empirical evidential inquiry. I gather that the quotes are meant to suggest that science's methodology is so well established that it's impossible to get scientists to be objective. Certainly I can agree that short-sightedness and vested interests are just as present in science as they are in other areas of our society. However, that's not to say that firmly-entrenched ideas aren't that way for a reason.
In trying to understand this sort of position, I start by asking whether heliocentrism is a valid scientific theory. After all, for millennia people assumed the Sun orbited the Earth. Common sense and observable reality supported geocentrism, which could accurately predict solar and lunar motion. The problem was planetary motion: the apparently retrograde paths that planets took in their orbits around Earth could never be explained through the geocentric model. The heliocentric theory put planetary motion into an explanatory framework that yielded testable predictions.
Empirical evidential inquiry doesn't depend on just observations: the vast majority of the time, all the planets are not observable from Earth. Does this constitute a leap of faith on the part of scientists? Are astronomers allowed to infer based on limited observations? The answer is yes.
The evolution of species is seen at a high level in the fossil record, which records the progression of life-forms from ancient to modern. Even without assumptions of ancestry, the changes in the biosphere are real and verifiable. The evolution of viruses like HIV provide a real-time verification of the mutation-selection engine proposed by Darwin as the foundation for all biological diversity. But do these views really see the same thing?
The genes are the link between the two views. If all life shares ancestry, there should be genetic links among diverse organisms that can help retrace their paths of evolution. Scientists have looked at several molecules (such as hemoglobin) to gauge the degree of divergence among various organisms. These molecular phylogenies have a degree of correlation with the family trees constructed using only morphology that is far too high to be considered coincidental (
thanks, mark24). They have also found non-coding areas in the genomes of separate organisms where identical mutations appear in a sequence that is otherwise identical to a functioning gene in a third organism. This type of phenomenon so strongly supports common ancestry that it can't be attributed to mere wishful thinking. It may as well be claimed that using DNA in establishing paternity presupposes a commitment to naturalism or some other such imagined bias.
So is everything in the biological history of Earth understood in detail? Not by a long shot. However, the evolutionary framework has been indispensible in clarifying so many former mysteries (and in the process illuminating just how much we have left to learn) that science's reliance on the theory is understandable. When a better theory comes along, which explains everything Darwin's theory did and more, we will have the same shift in perspective as when geocentrism was abandoned. However, in the absence of any better scientific lens through which to view biology, it's unfair to accuse scientists of being jaundiced or biased for sticking with what works.
regards,
Esteban Hambre