14 years after we’ve last been fascinated by Mulder and Scully’s investigations of paranormal activities on prime time, the duo went back to work at the FBI’s X-Files in a 6-episode mini-season.  This season was just enough to whet fans’ appetites with fond memories of their favorite stories (Eve, anyone?) and infuriate us with a cliffhanger ending.  But it was the bookended storyline linking episodes 1 and 6, that made my scientist blood boil (FYI–just a saying, tissues would be incinerated long before blood could boil).

This “long” arc was an homage to the mythology of the entire franchise, which has always contrasted with the popular monster-of-the-week design beloved by fans and critics alike.  This time, it starts with Tad O’Malley (Joel McHale), a conspiracy theorist on The Truth Squad soliciting Fox Mulder and Dana Scully to help him “blow open the biggest conspiracy the world has ever known“.  This meeting has Scully running tests on her blood, which we later discover reveals anomalies in her sequence–alien DNA.

So far so good and pretty much on par with what I’d expect from the X-Files:  alien cover-ups, crazy pseudoscience involving insertion of alien DNA, and Scully being the reasonable counterpart to Mulder and O’Malley.

But this goes a bit sideways in episode 6, the season finale, with Scully quickly jumping off the deep end into conspiracies involving anti-vaccination sentiment.  First, Scully blames the smallpox vaccine for mass insertion of alien DNA.  That this idea is “not far-fetched and within the realm of accepted science” from the generally objective Dr. Dana Scully had me cringing.

Second, the anthrax vaccine is blamed for lesions and sickness in military personnel whose immune systems have been decimated by what is assumed to be alien DNA, but turns out to be the Spartan virus (more on that below).  In reality, the anthrax vaccine (AVA) contains proteins from anthrax, but doesn’t harbor any living bacteria, meaning that it can’t cause disease, even in those with weakened immune systems.

In a matter of minutes we discover that the smallpox vaccine has introduced Spartan virus DNA into the germline (meaning our eggs and sperm).  Then, years later chem trails releasing aluminum into the environment cause the Spartan virus to activate an enzymatic reaction called CRISPR/Cas 9, which deletes the adenosine deaminase gene, leading to weakening of the immune system.  Got all that?  Here’s a graphical depiction to help:

We know from patients with diseases in their immune systems (called immunodeficiencies) and infections like HIV that destroy a critical immune cell type, that a broken immune system can be tantamount to death from all sorts of infectious diseases.  So, mass immunodeficiency is definitely quite scary and could leave us susceptible to opportunistic infections (those that we’re normally resistant to) and epidemics of easily transmitted infections such as flu.

Scully and a few select others have been given a gift, alien DNA (also strangely in their germline) that inhibits CRISPR/Cas9 from functioning and thereby protecting them from the affects of aluminum in the chem trails.

Setting aside the rapid discovery of this complex plot, with Scully enlightening newcomer agent Dr. Einstein in every scene with new information, there are a few other problems with this scenario.  The most relevant is that CRISPR/Cas9, despite being a hot topic of late and a great buzz word interjected into not just The X-Files but also the CW series Arrow, is not present in people.  It’s a defense system for bacteria that allows them to chop up foreign DNA and protect them from viruses.  Yes, it has been used for gene editing in human cells–an ethically-charged endeavor–but, and this is important, in a test tube.

There is a scenario in which this complex plot might work, though this hypothesis was not corroborated by Scully in the episode, so it’s complete conjecture (like that matters at this point).  Consider this:  if the Spartan virus itself contained the gene for Cas9 and CRISPR sequences that inserted themselves around the adenosine deaminase gene, then expression of Cas9 induced by aluminum in chem trails (how that’s regulated I have no idea) could theoretically cause the deletion of adenosine deaminase.  Like so:

It’s important to note that scientists recently discovered the CRISPR/Cas9 system, so it would have had to 1) been discovered prior to the end of routine smallpox vaccination in 1972 and kept a secret and 2) cloned into the smallpox vaccine using genetic engineering methods not yet available at the time.  So even my theory is dubious, at best.

Then there’s the issue with where the smallpox vaccine inserted the Spartan virus DNA.  Not where in the genome, but in what cells.  They say it’s in the germline, which makes it sound scarier because it can be passed on to children.  But if its only in the germline, then the adenosine deaminase gene would be deleted from your eggs or sperm and wouldn’t have any affect on your immune system at all.  The smallpox vaccine is given on the skin of the upper arm and often forms a pock at the site.  The vaccine or perhaps the Spartan virus itself would have to infect stem cells or immune system cells to cause immunodeficiency.

Since the alien DNA protects Scully, she hypothesizes that her alien DNA sequence could be used as a cure.  Performing a PCR with primers from Scully’s sequence to do this actually makes sense (good for you X-Files writers!).  She had previously sequenced her genome and discovered the alien DNA in chromosome 17.  So all Dr. Einstein would need to do is find the alien DNA in the sequence and select flanking areas of Scully’s DNA to create her primers.  The problem arises with the process of PCR.  If alien DNA contains different nucleotides (the building blocks of DNA–the A, T, C, and Gs), and I’m assuming it does or else wouldn’t be detectable as “alien” or anomalous from the sequence alone, one would need to add those alien nucleotides to the test tube to make the PCR work.

All of this lab work interspersed with scenes of packed hospitals and many sick people steamrolls to a climax with Scully creating her cure, scaled up to IV bags within moments, and healing the sick.  Yay!  Except that if CRISPR/Cas9 deleted the adenosine deaminase gene, how does the alien sequence, that blocks CRISPR/Cas9, rescue those already afflicted?  They’ve already lost their ADA gene.  A more reasonable therapy would be reinserting the adenosine deaminase gene into the genome or supplementing the protein.

If you let this all go and just appreciate a story–even a far-fetched one–that entertains you without thinking too much about the details, I commend you.  But it seems irresponsible  to center this storyline around a current and dangerous movement.  It’s doubtful that anti-vaxxers will directly use The X-Files to support their claims, but planting seeds of doubt in those on the fence and providing rational-sounding examples of conspiracy is dangerous ground on which to base their story.  Finally, it’s highly unlikely that someone already believing in government conspiracies would truly appreciate the self-deprecation of Chris Carter and the X-Files writers:

“It’s fear mongering, clap-trap, techno-paranoia so bogus and dangerous and stupid that it borders on treason.  Saying these things would be incredibly irresponsible.”
-Dr. Dana Scully (S6-E1)