There are critics of string theory, and it may be that there is some other explanation that will account for the differences - or that we will never figure it out. The point is that we continue to make better and better sense of the world we see around us. Since I am not trying to make a religion of science - I don't need science to be true in some sort of ultimate sense - I am looking for it to be an accurate tool for understanding the natural world.
The reason that I continue to return to certain central themes is because the "science is provisional" argument is regularly employed to imply that
I see the concerted efforts of conservative Christians to mislead their constituents into believing that science is lying to them, misleading their constituents into believing that there is now (or is every likely to be) evidence that the earth is young, evolution did not happen, or that we are NOT all descended from common ancestors is a direct threat to the health and well-being of the human race. It threatens to return us to superstition and ignorance, at a time when we face unprecedented challenges that require us to think about the world in clear-eyed and accurate ways.
The difficulty with the objections to the provisional nature of science is that they also apply to whatever it is that the objectors believe. We have no access to ultimate truth, except by faith. You can’t know that your confidence in a revelation, scripture or the inner workings of your own mind are getting you any closer to ultimate truth than does science. So whatever fault you find with methodological naturalism (or philosophical naturalism) is just as true of whatever you replace it with. The one advantage that science has over faith is that science can demonstrate its conclusions. As a result, in the limited arena in which science operates, we can actually have broader agreement that it reflects truth than any faith - because faith is a subjective experience, and varies widely from time-to-time and culture-to-culture.
For example, compare the Genesis 1 account of creation with the Pythagorean Theorem. Rabbis, early church leaders and various modern-day theologians have a wide variety of approaches to what Genesis 1 means. On the other hand, the Pythagorean Theorem remains clear, unambiguous and universally affirmed to this day. None of the discoveries of science threaten it, and there is no reason to expect anything different in the future, the provisional nature of science not withstanding. Do you (or anyone else) know the Ultimate Truth with respect to Genesis 1? Maybe. But we have no way of verifying who that group or individual might be. Can you independently verify the Pythagorean Theorem? Yes.
So faith and science are very different, and in its realm, science is a reliable guide to knowledge about the world.