Gene, as such traits are passed down through genes
That would refer to naked seeds :)
The scientific method is a process of steps in order to get a conclusion. First, a scientist will observe something. It could be really anything. Then he/she will ask themselves a question. Like how does it do that? Or why does it do that?
Then they will form a hypothesis. This is where you will ask yourself what will be the outcome of the experiment.
Next you actually perform the experiment. If the experiment comes out as your hypothesis predicted, then you accept your hypothesis.
If not, you reject your hypothesis.
Of course, in science you just don't do one experiment. You do it multiple times and even with different circumstances.