They are natural in that you have them by virtue of existing; if you were alone on a deserted island you would be able to exercise them. The traditional interpretation in the US is that they come from God: "We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness."
Of the five main drafters of the Declaration, Thomas Jefferson was the only slaveowner. Jefferson was definitely a huge hypocrite on this question, but he at least had the decency to feel guilty about it. In fact, Jefferson's initial draft of the document included a paragraph condemning slavery and blaming the British crown for it—though unfortunately, this passage was excised from the final version.
