I know that it's sci-fi, that there were a limited number of episodes, they only had 43 minutes etc. etc. -- but I still find it hard to ignore all of the egregious jumps in logic in this plot.
I watched this show as a kid, and I credit it for fostering an interest in science in me at a formative age. Now I watch this as an adult who works in research, and I'm cringing every time 'alien DNA' is mentioned. What does that even mean? So now we know how to identify alien SNPs? If Scully had just said that she had sequenced the sample she had used for the southern blot back in season 5 (Redux, I believe) and identified a novel, unique locus that hasn't been found in any known individual human genome, then I would have been satisfied. Otherwise to me it just sounds like throwing out techniques (genome sequencing, CRISPR-Cas9) to be relevant.
This sort of thing feels like something that would have been better explained in the original run. The southern blot was equally implausible within that timeframe (no, not even a white hot probe would produce results that fast), but the concept was solid. It made sense. This? It just felt sloppy considering the obvious thought that went into science techniques previously. I do really appreciate the effort, but it's clear that there's a crunch for time and the 'science' in the plot really takes a hit for it.
But Scully getting upset about the failed PCR tickled me greatly. 'There's nothing there!'
Because sometimes that is just my life.
