Rebuttals to arguments I have heard too many times:

scientific

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Something is not scientific simply because it makes use of scientific tools.

When I use a lowpass filter on my holiday snapshots I am using a scientifically devised tool to remove noise. I am not engaging in science.

theory

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A Theory is the greatest truth in science, as science doesn't deal in absolutes. Rather than claiming a perfect understanding of a process, it acknowledges that there are always unknowns. (A law, by the way, is hardly ever true, in a strict sense. They are usually correlations between variables, which yield mathematical truths, and can be used to approximate real world correlations). In science, something is not called a Theory, unless there are countless pieces of evidence in its favour.

Evolution, for example, has never been falsified by a fossil appearing out of context, in a layer of rock it shouldn't be in. Never have we found a dinosaur in a recent layer, nor have we found a sparrow in the time of the dinosaurs. If evolution was without merit, and dinosaurs and modern sparrows lived together, surely we should have found such fossils by now.

first cause

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All concepts of creation face the same problem: what caused it. Creationists sidestep this problem by calling on god, Intelligent Design advocates ignore it, say they make no claim about the specific characteristics of the designer, and should therefor not have to answer this question. But the problem remains: if everything requires a cause, who caused god and/or 'the designer' to come into existance? It is unfair to try to discredit the Big Bang Theory by suggesting that this is a gap in our understanding of it.

gaps

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Evolution has some gaps, yes. But it has no inconsistencies. Gaps merely mean we do not fully understand it. They do not mean we are probably wrong. And obviously, even if, somehow, evolution were ever proven to be wrong, it would lend no credence to religious concepts.

There are no specific gaps that have withstood scrutiny. But many completely disproven arguments seem to persist, as urban myths. The Talk.Origins Archive lists many such arguments, and a rebuttal.

naturalism

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Science assumes a naturalistic world. In that sense it is a philosophy of sorts. Instead of an unknowable force (or forces) it assumes that the universe is governed by a knowable force (or forces). Technically, it's obviously possible that there is actually a great unknowable force behind it all. No-one is denying that, even if not all people believe in such a force. But since he/she/it/they has been kind enough to fit our world with a semblance of natural rules (assuming he/she/it/they exists), science is useful.

When a farmer wants to know what the weather is going to be like, he will consult a meteorologist, not a cleric. And the meteorologist will be able to help him. That is (part of) the value of science. Science obviously has value. We use scientifically derived tools, materials and knowledge every day.

Science does not seek to disprove the existance of a deity, and indeed could never do so. But it does assume, for the sake of argument, that natural laws govern the natural world (most of the time). Under that assumption, science works. And gives us polyester.

Just as science could never disprove the existance of an unknowable force, it can never truly PROVE anything. We can touch a brick, taste it, smell it, spectrographically analyse it, toss it though something and hear its effects. But science knows it can never prove that the brick is not a complicated illusion (How could it?) Science knows there is always the great unknown: that there may be an unknown factor. And that is why a Theory is called a Theory.

That is the only reason. Science can never be sure it has all the answers, and does not propose it does. But, for all intents and purposes, Theories are proven facts, and have been tested for validity thousands of times, and by hundreds of people. Each of whom has a vested interest in proving it wrong: they would probably get a Nobel prize if they could disprove the Theory.

Next time you answer your cellphone, thank science, and remember that the technology is based on the Theory of Electromagnetism, Acoustic Theory and Antenna Theory, to name but a few.

falsifiability

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Something is falsifiable when conceivably, physical evidence could disprove it. Falsifiability is a basic tenet of science, because without it, everything could be explained as an 'act of God', and thus, nothing would be explained. A single example of physical evidence that goes contrary to a Theory would disprove a Theory, or force the Theory to be modified to fit the new data.

The Theory of Thermodynamics might be falsified by finding a source of physical energy that needs no fuel, such as an ever burning candle.
The Theory of Evolution might be falsified by finding that cells can function and reproduce without DNA. Or by finding that genes are uniquely created for each creature, as opposed to a combination of genes from the parents or progenitor.
The geologic time scale, as determined through dating and fossil finds might be falsified by finding two animals, which supposedly existed in entirely different times, fossilised together in a layer of rock, such as a fossilised domesticated animal or of a lion next to the fossil of a dinosaur. It might also be falsified by finding that re-testing a rock provides an ever changing age depending on the mood of the researcher.
Intelligent Design cannot be falsified. Its basic premise is: "Maybe, someone or something did it, somehow." No amount of physical evidence could ever prove that to be false. Whether it is believable is a personal matter, and a topic of philosophy.