Consider a person with sickle-cell trait. Can you think of a test to determine whether this is the result of random mutation rather than the insertion of an engineered gene inserted by space aliens?
Can I, personally? No. Somebody who does genetic engineering for a living would have a far better chance of proposing such a test, were one to exist, as he'd have some idea of what to look for.
Now, given that I readily acknowledge that random mutation plays a role in biological phenomena, I am not bothered by the possibility that random mutation could be responsible for sickle-cell traits. (And, given that sickle-cell traits confer some degree of immunity to malaria, I can see a mechanism by which this trait would be passed on naturally.) So a lack of a suitable corresponding test for "alien induced sickle-cell traits" would be no big deal to me.
Then again, we know that humans can at least pursue similar results -- for example, a great deal of progress is being made in the field of gene therapy for cystic fibrosis.
The question in that case would be: could one think of a test to determine whether the results of the cystic fibrosis gene therapy came as a result of random mutation? At the same time, could one think of a corresponding test to determine whether the gene resulted from intelligent agents?