Why don't we use a computer to select the national lottery numbers? Why do we think that they are random when they come out of machine that stirs the balls around?
If you have a sufficiently complex system - regardless of it being deterministic, then it will generate a random sample. This is why we have the balls in the lottery. So we get randomness from a non-random process!
For sampling there are lots of problems with collecting data and trying to make sure that your behaviour is not affecting the sample. We usually collect the easy data first but the easy data might not be a true reflection of the true sample space.
For example for genomes there are none done from algae because they are hard work and not commercially significant. So out genome samples are biased towards medically or commercially important organisms. If this is the case then you have to be careful about how you use the data and what questions you ask.