On April 17, 2009 Herman van Barneveld included this question in a comment on Tony's article:
"Is it within the realm of science to speak authoritatively on historical matters? (especially when it contradicts the Word through which God "...makes Himself more clearly and fully known as far as neccessary ......to His glory (Belgic Confession Art. 2)) Science can try to speak on history, but it can't do so without saying 'maybe' or 'we think' and make numerous assumptions."
Thank you, Herman, for your question. You do not explain what you mean by history. I shall take you to ask whether science can speak authoritatively on the history of nature because that is what science deals with. I know that some natural scientists include religion and morality under their conception of nature. This would make the history of religion and morality part of the natural sciences - a very controversial move indeed. For now I shall answer the former question.
First, three areas of the natural sciences that deal with history are the history of the cosmos in astronomy, the history of the earth in geology, and the history of life in biology. All can speak on history. Since I am a biologist, I will give you a biological example. Perhaps someone else can contribute one from astronomy.
One of the implications of continental drift is that South America, the Antarctic and Australia were once connected. Fossil studies show that pouched mammals (Marsupials) lived in both Australia and S. America before these three continents broke up. The prediction was made that there should be fossils of pouched mammals in the Antarctic. They were found in 1982. For the original publication, see
http://www.sciencemag.org/cgi/content/abstract/218/4569/284 . For a recent confirmation, see http://www.springerlink.com/content/h5r16469kqr06560/ . For a popular rendition, see http://www.naturalworlds.org/thylacine/introducing/about_marsupials_5.htm . This shows that in biology theories about historical events (continental drift, biogeographical distribution) can be used to make predictions which can be tested and accepted or rejected. For an animation of continental drift showing the distribution of fossils see http://www.exploratorium.edu/origins/antarctica/ideas/gondwana2.html .
A second example concerns cladograms (binary phylogenetic trees). The procedure of making a cladogram works exclusively with extant animals or plants. Specific DNA sequences are compared say between living fish, amphibians, reptiles, birds and mammals, and the number of differences in nucleotides counted. The more differences the longer the organisms concerned have been separately accumulating mutations. That is, the longer ago it is that they had a common ancestor. This information is used to construct a cladogram which shows the theoretical sequence in which the various groups compared separated from the ancestral line. In other words, this cladogram is a hypothesis which is then used to predict the sequence in which fossil representatives should be found. Again this shows that a theory (the tree) leads to predictions which can be empirically tested and rejected or accepted. For more background see http://en.wikipedia.org/wiki/Cladistic .
Assumptions are made as you say. The assumptions of scientific knowledge do not set it apart because all human knowledge makes assumptions. This compels us to be humble about knowledge claims.