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Einstein and Scully
FBI Agent Einstein (Lauren Ambrose) takes a blood sample from Dana Scully (Gillian Anderson) in the season finale of “The X-Files.” (©2016 Fox Broadcasting Co. Credit: Ed Araquel / Fox)

Spoiler Alert! This post doesn’t reveal any major plot twists, but it does explore significant elements of the “X-Files” season finale. Stop reading now if you want it to remain a surprise.

This week’s season finale of “The X-Files” is one of the first prime-time TV shows to reference the revolutionary gene-editing technology known as CRISPR-Cas9, but it won’t be the last.

We won’t delve into the details of how CRISPR figures in the alien conspiracy. Let’s just say that the ability to snip out and insert genetic coding with molecular-scale precision is as good a match for the “X-Files” mythology as Scully is for Mulder.

The technology takes advantage of a cellular defense system that was first studied in bacteria. Researchers were intrigued to find that the genomes of many types of microbes contained snippets of DNA that matched coding for the viruses that attacked those microbes.

They eventually learned that those snippets, separated by standard spacers, were used as templates for hunting down the viruses. These “wanted posters” of viral snippets are called clustered regularly interspaced short palindromic repeats, which is where “CRISPR” comes from.

The other part of the defense system is a set of enzymes called CRISPR-associated proteins, or Cas proteins. One enzyme in particular, Cas9, is great for making a precise cut in a DNA molecule. When a CRISPR-Cas9 complex encounters a virus that matches one of its wanted posters, the bad guy’s DNA is snipped away.

Scientists have been able to reprogram the system to go to a specified spot in virtually any genome, cut the DNA, and then coax the DNA molecule to incorporate a custom-made genetic sequence as it heals itself.

“You can use it to not only delete a gene, you can use it to add a gene,” said Anne Simon, a biologist at the University of Maryland at College Park who serves as a scientific adviser to “X-Files” creator Chris Carter.

Previously: Meet the ‘X-Files’ biologist who puts the scientific truth out there

Scientists are using the technique to develop new kinds of treatments for cancer, blindness and other diseases. It’s also being used on plant genomes to make crops more disease-resistant and drought-tolerant. Eventually, the technology could lead to new methods for producing biofuels and diagnosing diseases.

But there are legal and ethical concerns. CRISPR technology is the focus of a patent fight that could go on for years. And Chinese researchers stirred up a controversy last year when they used CRISPR to edit the genome of non-viable human embryos. The prospect of making permanent modifications in the human germline sparked a global scientific summit in December.

It also sparked the plot for this week’s “X-Files” episode. Simon highlighted one gene in particular as the target for conspiratorial skulduggery: the ADA gene, which plays a key role in producing adenosine deaminase for our immune system. If your ADA gene were to get snipped, that would leave you vulnerable to a host of infectious diseases.

“Effectively, we’re giving people ‘boy-in-the-bubble’ syndrome,” Simon said.

The TV series’ writers put CRISPR and ADA deficiency into the script, and then added some woo-woo plot twists having to do with stem cells, smallpox vaccines, chemtrails and aluminum nanoparticles. The bottom line is that the end of the episode poses a huge cliffhanger that Carter and other members of the “X-Files” team (including Simon) can only hope they’ll have the opportunity to resolve in future shows.

Some folks are already talking about continuing “The X-Files,” with the focus shifting from Agents Mulder and Scully (David Duchovny and Gillian Anderson) to next-generation Agents Miller and Einstein (Robbie Amell and Lauren Ambrose).

However it turns out, Simon wants it made clear that in the real world, CRISPR and other genetic engineering techniques are tools for good, not evil. “The X-Files” may be spooky, but it’s just a TV show.

“The whole idea of trying to get something into everyone’s cells – that’s not a viable system,” she told GeekWire. “We keep trying to say these are aliens doing this. … It’s aliens, OK? Aliens can do anything.”

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