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Posts Tagged ‘anne simon (science advisor)’

Some Complementary Season 10 Mythology Elements

Season 11 is less than a month away! Its two-and-a-half mythology episodes promise to be very dense: a lot of plot to go through, a lot of returning and new characters, William, flashbacks, the ungrateful task of attempting to reconcile this new mythology direction with what we considered to be “the truth” in seasons 1-9… and conclude in a cliffhanger for season 12! Season 10’s mythology’s lukewarm reception motivated FOX to downplay the mythology this season, however the new mythology doesn’t sound more welcoming to new fans and still has to convince old fans. Since My Struggle II aired, fans have been trying to connect the dots in the hope that the mythology would make sense, once more — theorizing is a typical x-phile occupation.

Follow and comment the #46DaysOfMythX (FB, t) as we count down to season 11 by reviewing the “classic series” Case Files — and finish transferring material from the old version of EatTheCorn to this modern version!

A shout out to the incredibly ambitious X-Cast Podwatch project, with one hundred 20-minute podcasts covering two episodes at a time released daily (or even more than daily)!

We analyzed in detail the complementary mythology elements in the book “The Real Science Behind The X-Files” by virologist, X-Files science advisor and Chris Carter friend Dr. Anne Simon here.

Carter’s other science advisor, for the second film onwards, is Dr. Margaret Fearon, a medical doctor and microbiologist, and Simon’s friend; the sick boy Christian Fearon in I Want To Believe is named after her.

Simon & Fearon contributed with ideas and suggestions to Chris Carter when writing the season 10 mythology episodes. For their work, they were credited for co-writing the season finale My Struggle II! On February 22 2016, Anne Simon hosted a viewing party for the finale in the University of Maryland, where she works.

What follows is commentary on the behind the scenes info and bits of information that she revealed during the Q&A session that night — long before season 11 was a reality and long before Carter put fingers to laptop to write the My Struggle III script!

The making of My Struggle II

  • About The X-Files returning after so many years, Simon says: “I heard Chris many times saying he would never do it again. I never thought it would come back.
  • Carter asked Simon: “I want you to come up with a way to kill everybody off – everybody except the chosen few“, among whom Scully. Simon: “I was really surprised when he asked me to kill everybody off. Because then who would be the audience? And how would you get out of it?
  • This is the third time she’s been asked something like that in the series [I suppose the other two refer to bees carrying smallpox in 4X21: Zero Sum, and the Black Oil virus itself in Fight the Future]
  • In the beginning there was a misunderstanding: Simon had Scully be the victim. But Carter said no, that alien DNA has “got to be the key“.
  • Simon had the idea of the threat not being an alien virus again, but something that would remove the immune system. She came up with a mechanism to lose one’s ADA gene. Carter was very happy with the idea and kept asking “write a lot more“, “I want more science“. The use of actual science is one of the distinguishing marks of The X-Files.
  • Anne Simon and Margaret Fearon together came up with involving Crisp-Cas9: to have the smallpox vaccine with a second virus that would deliver the DNA that would then deactivate ADA gene. [Simon certainly remembers her own contribution in making the smallpox vaccine a tagging device in 4X01: Herrenvolk; we still don’t know how this new use of the smallpox vaccine articulates with what we learnt before, and why the conspiracy would know how to use this virus from at least the 1970s but then focus on using the Black Oil virus.]
  • How is this activated? Carter wanted it to be chemtrails and aluminum [following recent conspiracy theories]. Simon thought it could be the level of CO2 in the atmosphere, which is rising; Carter didn’t like that idea. [The trigger remains unexplained.]
  • Margaret Fearon came up with the symptoms observed in the first victims, and using anthrax as an example.
  • Simon was helping with My Struggle II at the same time Carter was shooting Babylon. Every day there were pages going back and forth with corrections and suggestions, it was a difficult time for Carter. [This is the actual script; we do not know how far ahead the story was conceived.]
  • Simon says that My Struggle IItakes place 6 weeks after the first episode” [as mentioned in the dialogue]. In My Struggle Ithere are some hints that something is going wrong. So it’s really taking quite a while before thew immune system is starting to go down“, it is “very gradual” [but this connection between the two episodes is never made explicit in the scenarios].

Gillian Anderson calls William, the presumed pilot of the UFO/ARV!

What could come next

  • Carter cut the final 10 pages of the My Struggle II scenario to create that cliffhanger. [We could then say that season 10 and season 11 mythology were conceived as a single story arc, if not in the details then at least in story directions.]
  • Simon knows what happens after “that close encounter” at the end of My Struggle II. [This would mean that the occupants of that craft could be alien, and that the arrival of the UFO/ARV was not something that was added after the first draft in order to create a cliffhanger for next season.]
  • Simon and Fearon had mapped out the science for the next episode [My Struggle III] already.
  • With Scully’s vaccine, we all have alien DNA now. Simon: “could this be what they wanted all along? Maybe this is their plan.” [This gives credence to the theory that the Spartan virus is a ploy and the real objective is to have people vaccinated with Scully’s cure, which will prove to be a biological Trojan horse of some kind. The alternative would be that there are several kinds of aliens, and those would be benevolent towards humans.]
  • About producing the vaccine with Scully’s extra nucleotides on an industrial scale for the whole world: “The idea is that then they would be able to synthesize this. But initially it would require Scully’s blood. That was all worked out. Chris was asking about that, but how long would it take… So where are the last 10 pages?” [Does that mean that a general cure for the entire world’s population is what we will see in My Struggle III and only necessitates 10 pages? This is asking a lot of suspension of disbelief! Scully would presumably get some slight help from the CDC and the WHO — perhaps even from the occupants of that UFO/ARV as well?]
  • Simon wrote more material: “I had a dream kind of thing, where you go back and the Cigarette-Smoking Man takes his first puff, he was really young, I thought it was good. And Chris said no, you cannot do a back in time thing, because he was doing it with Monica and I didn’t realize he was planning on that.” [But then My Struggle III seems to be all about flashbacks to a young CSM! Perhaps Carter kept Simon’s ideas for My Struggle III.]
  • And finally, about My Struggle II and the coherence of the mythology: “I hope people can see how this episode fits in with the mythology. I think it explains a lot. What was the conspiracy? This is the conspiracy. Now, did Chris know that this was the conspiracy? Obviously not because I told him what the conspiracy was — but he knew there was a conspiracy, he just didn’t know what it was.” When she sent ideas, Carter was happy: “Chris could see that it fit what had been done before.” [My Struggle I & II present lots of problems of continuity with earlier episodes: the purpose of the Syndicate, the absence of Colonist aliens, the absence of Black Oil in greys, the credulity of Mulder, the absence of Supersoldiers, the chronology of the Syndicate using the smallpox vaccine to introduce this Spartan virus since the 1970s while spending decades afterwards to find a way to use the Black Oil virus as the trigger of the Apocalypse instead and developing hybrids immune to it, the inconsistency of the CSM’s behavior if he manipulated everybody from 1947, and more. Some of these problems depend on future twists in My Struggle III and so forth, but it is likely that is will not be possible to reconcile everything.]

An otherwise useless zoom-in into Scully’s eye echoing the closing shot of the episode

Would the original conclusion that Simon is referring to actually take place right after what we saw in My Struggle II? How could we switch from a UFO/ARV suddenly appearing and menacing Scully to Scully saving everyone by mass-producing her vaccine, thus cancelling that particular Apocalypse? — until…”could this be what they wanted all along?

Recent season 11 promotional material seems to confirm a theory that started as hearsay mentioned by Jonathan Maberry all the way back to October 2016: that starting from the zoom-in in the first scene in the X-Files office until the zoom-in in the last shot, My Struggle II would be a sort of vision of the future that Scully had. This could be a premonitory dream, a vision given to her by somebody who has psychic powers (spiritual beings, aliens, William?), or a vision projected on her by someone via her implanted chip, which can be tele-operated (e.g. to call her to a specific place, as in 5X13: Patient X) — perhaps so that she would know of the future and act to prevent it. This is not the retconning of Millennium end of season 2 to beginning of season 3 (the viral Apocalypse was actually a local event with low death toll), but it is a way out.

My Struggle I cut scene

The DVD/BluRay (released in June 2016) included some excellent making of documentaries by Julie Ng, whose love for the series shows on every frame! — some additional anecdotes that did not make it in the final edit of the documentaries can be found here and here (originally a feature for X-Files News, it has disappeared there?).

“Our lives are at danger now.” echoes Deep Throat’s “Your lives may be in danger” from 1X01: Deep Throat in the same way the Old Man’s “You’re nearly there. You’re close.” echoed Deep Throat’s “Don’t give up on this one. Trust me. You’ve never been closer.” from 1X23: The Erlenmeyer Flask!

This included a cut scene for My Struggle I. In it, Mulder is waiting to meet the Old informant a second time in the same spot. Instead, he meets who pretends to be the informant’s daughter, who tells Mulder that her father was dead — presumably killed by the conspiracy because he was feeding Mulder with presumably true information. My Struggle I was a very dense episode and this short scene was cut for no other reason than for time; we can thus consider this information as canon (until proven otherwise).

This scene explains why we do not see the Old informant in My Struggle II, something that would have made narrative sense given the important impact of his information on Mulder’s beliefs, and given the informant’s promise of revealing more secrets to Mulder in the future. Instead, this character was of one-time use: Carter introduced him, he told Mulder what he needed to say, served his purpose, and was written out, all of which in the same episode. (Sadly, the actor portraying him, Rance Howard, passed away just days ago, on November 25 2017, making the return of this character impossible without a recast.)

This is one more example of the issues Carter’s recent scripts have with pacing, and Carter’s tendency in most of his post-season 5 mythology episodes to have characters tell the plot and not have Mulder and Scully actually investigate to uncover the truth.

Carter took a bold leap into the unknown by choosing to do a cliffhanger without a guaranteed season 11, which, with two years’ negotiations versus five months for season 10, nearly didn’t happen. Nevertheless, he created an X-Files cliffhanger like no other where everything — characters’ fates, humanity’s survival, the very meaning of the narrative of the mythology that makes the fabric of the show — is up in the air, and got people talking. We will know shortly how, and if, it all comes together!

Mythology elements of The Real Science Behind The X-Files

Dr. Anne Simon is a researcher in virology and professor in the University of Maryland. She also has in her curriculum the no less respectable title of science advisor for The X-Files! Anne Simon got involved in the show from the very first season, 1X23: The Erlenmeyer Flask, through a family connection — her mother’s best friend is Chris Carter’s wife and writer Dori Pierson — and has remained involved to this day, even earning a writing credit on the show’s last episode to have aired to date, 10X6: My Struggle II. She is also the daughter of screenwriter Mayo Simon, who wrote several science-themed or science fiction features (Marooned, Phase IV).

In 1999, Simon wrote “Monsters, Mutants and Missing Links: The Real Science Behind The X-Files“, a book that mixed episode stories with her own scientific knowledge and participation in the making of the series. Simon’s contribution in the series as a scientist elevates this particular book above the usual “the science of…” tie-in books that get released to ride on a pop culture phenomenon’s success. The book makes for a great read for the science amateur and informed X-Files fan, it invites the reader to enter the mindset of a scientific researcher questioning everything and attempting to reconcile facts in order to come up with theories — a quintessentially x-philian activity. The X-Files, after all, tried to balance Mulder’s encyclopedic knowledge of paranormal phenomena with Scully’s no less encyclopedic knowledge of medicine and more.

The US cover

The book covers seasons 1-5 as well as Fight the Future and the first episode of the sixth season. It would be interesting for Anne Simon to do a second edition of this book, with additional chapters not only covering seasons 6-9 (and importantly, as will be seen below, the revival) but also offering an updated view on the science: medical sciences and biology in particular are very lively fields that have seen great advancements over the past 15 years. Scientific truth is an ever-expanding, ever-shifting landscape!

By her own account, Simon only helped Carter with the science of the mythology episodes, the only stand-alone exception being 5X06: Post-Modern Prometheus, also a Carter episode. The science in other X-Files episodes must have been the writers’ own work or Ten Thirteen’s in-house researcher. Thus, the book’s science can be broken down into three types:

  • The book attempts to provide a scientific background for the phenomenon seen in an X-Files investigation. These are more akin to more or less wild sessions of theorizing and of attempting to put science where scientific accuracy might not have been the writers’ concern. For example, finding a biological basis for Virgil Incanto’s need for fat matter (from 3X06: 2Shy).
  • Scully (mostly) and Mulder explicitly reference a scientific concept in an episode, and the book offers further background to that concept. If the concept made it into the script, then it’s likely that the writers used this concept as the basis for their script, or at least they were aware of it and wrote it in in order to strengthen the scientific accuracy of the script. For example, the Chupacabra fungus launches a discussion of how fungi and enzymes work (from 4X11: El Mundo Gira).
  • A third category is Simon’s own contributions, which are first-hand accounts of what research was done to give these episodes scientific verisimilitude and what were the writers’ (well, Carter’s) intentions by including some elements of the research and not others. For example, identifying alien DNA with the two extra nucleotides (from 1X23: The Erlenmeyer Flask).

Anne Simon circa 1999

Sometimes, the additional research that didn’t make it into the final script and the behind-the-scenes discussions Simon had with Carter provide interesting insights into the script-writing process and valuable information about the mythology that cannot be found elsewhere. This mythology information could be described as “secondary” canon information: although not in the episodes themselves, it is certain it was in Simon’s and Carter’s minds and intentions when the episodes were being written and this extra information does not contradict the episodes. I used this extra information for EatTheCorn’s Mytharc Primer. This will be the focus of this article.

Are all of these elements below things we were to ponder on purpose as part of the larger mysteries of the mythology, or are they fan theories extrapolated from trying to inject too much science into a scripted piece of entertainment?

Mythology elements

The DNA to create an alien is already existing in humans and the Black Oil/Purity virus switches on this junk DNA


Chris Carter, the movie’s scriptwriter, originally wanted to connect the black oily slime and the lizard-like entity in the following way: the black slime carries a virus, which is infectious when the slime enters a person; in the warmth of a person’s body, the virus develops into the monstrous creature..
Very imaginative, yes.
Minutely possible within the framework of biology, no.
After reading the movie script in early 1997, I hoped that Chris would change his mind. Having a special place in my heart for viruses, I discussed with him why a virus couldn’t possibly develop into anything. Viruses are, after all, just a bag of genes. A bag of genes that turns into a lizard with large black eyes and long pointed nails wouldn’t fit even my expanded definition of an extraterrestrial virus. I explored with Chris an idea for tinkering with his scenario. What if the black slime virus is responsible for the development of the creature but is not the progenitor of the creature? The virus, carried into a human by the black slime, could invade a cell in the person’s body and cause the cell to lose its identity. The cell could then be enticed by the virus to enter a new developmental pathway. That cell, together with its descendent cells, would regenerate into the hideous alien monster. I was thrilled that Chris liked the changes, since I wasn’t enthusiastic about the ribbing I would have taken from my fellow virologists if viruses changed into lizard-like aliens on the big screen — with me credited as science advisor.

The concern for scientific realism here is remarkable. A virus is a simple strand of DNA, much, much shorter than the DNA of a single-celled organism let alone of a complex multi-cellular organism like humans or grey aliens. For a virus to turn a human into an alien monster, it would have to carry much more information than a simple virus; so much so that it would not be categorized as a virus at all! The solution Simon found was to have the virus just be an activator of genes that are normally inactive in humans.

It would be have been simple to ignore that and just handwave the science away and make the virus do what viruses can’t do, but Carter was more than willing to incorporate this into his script.

Victim of (a strain of) Purity

Implications: human origins

This has large implications. If the information to create an alien were already present in human DNA, how did it get there? What happens if random genetic mutations switch part of that DNA on but not all of it? Gibson Praise and the Biogenesis trilogy storylines are the results of this idea. Super-human abilities such as mind-reading are the result of select genes in the so-called junk DNA being switched on (5X20: The End, 6X01: The Beginning). The alien DNA was put there by design because we are creations of aliens (6X22: Biogenesis). It would make sense then that the Ships with inscriptions on them containing a transcript of human DNA on them would belong to that same alien race that created us (7X03: The Sixth Extinction): Purity.

Implications: Black Oil virus origin

The Black Oil virus can thus be understood as a biological tool to transform a human into an alien. Could that mean that the Black Oil virus itself is manufactured, a tool of biological warfare on humans? The Purity aliens then would, in their natural form, be humanoid greys, the end result of the Black Oil virus’s life cycle. The Black Oil virus and its derivatives (see the creation of the Supersoldiers) would just be a tool for the Purity aliens to spread.

Extending this concept further, the Black Oil virus arbiters the mixture of active human genes and active alien genes in an organism, i.e. determines how much of an alien/human hybrid that organism is. Could that mean that hybridization experiments that result in our well-known green-blooded hybrids consist in finding out which genes to switch on and off? In the study of 5X14: The Red and the Black I theorized that the green blood in Alien Bounty Hunters and Faceless Rebels would mean that this race was created by Purity using some Purity genetic material in the same way humanity was, and that the green blood in alien/human hybrids is proof of that: could it be that this race of Shapeshifters actually be the result of earlier genetic experiments on humans?

Scully is not buying that viruses can think

Implications: virus vs. sentient organism

And so Carter and Simon thus went out of their way to present the Black Oil as a virus, behaving like a real virus. In most episodes we see it, the Black Oil infects people like a normal virus and at most put them into a coma (depending on things like temperature conditions, exposure of the host to a vaccine, potential weakness of the Black Oil strain). What doesn’t jive well with this is that the Black Oil, at times, behaves as if it has sentience: once it is inside a host, at times, it makes the host behave as if he is controlled by an intelligence other than his own. A simple virus would be very far from having the complexity necessary to do this. At best it could influence the behavior of the host in a specific way, like the worms wrapped around the brain in 1X07: Ice made the host violent. Could this be anything else than artistic license?

To be fair, the only times when the Black Oil virus shows real intelligence all by itself is in 3X15: Piper Maru / 3X16: Apocrypha, when for example it drives Krycek to negotiate with the CSM in order for it to reach its UFO — and the writers might not have yet settled their minds about what this black fluid was or that the “black cancer” they introduced in 4X09: Tunguska was the same entity. The other instance is in 8X16: Vienen, where the infected try to get more people infected. Interestingly, it is only in these two instances of the Black Oil that we see the host emit a flash of radioactivity to protect and attack, as if this were a different entity altogether. In both these instances, it could be that the Black Oil merely manipulates the brain to usher the host to rejoin with more of its kind, and the host uses the resources at its disposal — the host’s intelligence, memories, capabilities — to achieve that. This would not be unlike what some real parasites do when they control the host to their own benefit, for instance by ingesting more food or by moving to a safe place for the parasite to mature (see these or this lovely example).

How the Black Oil operates inside the Alien Bounty Hunters would be a different issue entirely.

The Black Oil/Purity virus doesn’t have extra nucleotides: is it terrestrial or extra-terrestrial?


In ‘The Beginning’, the opening episode of the sixth season, Mulder’s convinced that there is a connection between Gibson and the virus involved in activating the development of the lizard-like creature. Unfortunately, hard evidence is lacking. Gibson is gone and the creatures have vanished. Muider’s only piece of evidence is a trace amount of the virus that he believes is extraterrestrial. Mulder is crushed when Scully cannot support scientifically the alien nature of the virus. After running tests, Scully reveals that the virus, although of an unknown species, has the same four nucleotides in its DNA and the same 20 amino acids in its proteins as earthly viruses. She therefore concludes that Mulder is mistaken. The virus comes from Earth.

Here Simon just summarizes how 6X01: The Beginning unfolds, but doesn’t counter Scully’s argument. Throughout the book, the Black Oil virus is casually referred to as alien and there is no question that aliens are here to colonize. There is just this catch: the Black Oil virus doesn’t contain the two extra nucleotides that was the most convincing proof of alien biology! Simon explains in detail her idea of two extra nucleotides to the usual four found in all earthly organisms, and how Carter integrated this idea in his script for 1X23: The Erlenmeyer Flask involving alien gene therapy on humans (i.e. inserting bits of alien DNA in the DNA of living humans). Surely, this is the best evidence Scully should have to make her believe in aliens. By Fight the Future and 6X01: The Beginning, Mulder believes the Black Oil virus and the clawed creature it spawns to be alien, but Scully’s analyses do not show something out of the ordinary apart from the fact that humans share a large part of their genome with it.

Southern blot DNA test in 5X02: Redux

Does that scientific result insinuate that the Black Oil is, in fact, terrestrial in origin and the entity with extra nucleotides is the only thing that is alien? The extra nucleotides are encountered in 1X23: The Erlenmeyer Flask and 5X02: Redux (and again in 10X6: My Struggle II; and since it is inside Scully, presumably it is what the Lone Gunmen analyze in 2X08: One Breath). What this would imply for the overall mythology is unclear. The Syndicate obtained the alien fetus with the extra nucleotides DNA from a deal with the aliens (6X12: One Son), the same aliens that are identified with the Black Oil/Purity colonization effort in many instances. Are the extra nucleotides necessary only in the mature grey form of the alien but not in the virus and first “clawed alien” forms? Is the Black Oil race in fact also seeking protection from the extra nucleotides race and conducting hybridization experiments as well? Did the Black Oil race originally evolve on Earth before leaving and now returning once more?

Gibson Praise’s DNA test in 6X01: The Beginning

This raises more questions than it answers, and unless it is building up to a future revelation about multiple races I will categorize it as an oversight on behalf of Carter for now.

The Syndicate’s endgame was the depopulation of the planet


As Kurtzweil explains to Mulder in the X-Files movie, the corn is for production; the virus is the product; and the bees are for transportation. A deadly sting that the conspirators thought would depopulate the world but instead will repopulate it with virus-induced alien life-forms.
And that’s all the buzz on bees, corn and viruses.

Although there were talks of plagues and viruses and Apocalyptic warnings, the Syndicate’s purpose as it was exposed in Fight the Future and again in 6X11: Two Fathers / 6X12: One Son and 9X19/20: The Truth was to spread the Black Oil virus and see the world be taken over by the alien colonists, with the Syndicate members themselves surviving as immune hybrids. Indeed, if the Black Oil virus didn’t do anything else but put people in a coma or kill them why term it “colonization”? Why would the aliens collaborate with the Syndicate if they didn’t get something in return? In Fight the Future the Syndicate discovers the Black Oil triggers a gestation of a “clawed” alien. Well-Manicured Man: “This isn’t Colonization, this is spontaneous repopulation!” “We believed the virus would simply control us, that mass infection would make us a slave race. Imagine our surprise when they began to gestate.” We thus discover that the aliens perceive colonization as using the human population to reproduce themselves and increase their numbers, at humanity’s expense (and extinction).

The Well-Manicured Man spills the beans (that he knows about) to Mulder

Simon’s sentence could have been a shorthand — what effectively happens whether humans become hosts to Purity for life or humans die giving birth to the clawed alien form is that humans as such decrease in numbers. The mention of “depopulation” in Simon’s text is not backed up by anything in the series’ canon and would not mean much more — right until depopulation was presented as the (a?) conspiracy’s endgame in 10X6: My Struggle II. It could be then that the conspiracy’s initial objective was depopulation and choosing who would survive. Then came along the colonist aliens who offered the conspiracy with a means to achieve this objective: a potent pathogen, the Black Oil virus. In 1973, the conspiracy became the Syndicate by agreeing to share the spoils with the aliens in a post-depopulation colonized Earth. The Syndicate might have believed that the Black Oil virus would make humans into slaves that they, as new world leaders, would control jointly with the aliens. When the Syndicate discovered the aliens’ true purpose, the agreement was off and what remained of the Syndicate returned to the original plans of depopulation we see in season 10, using the Spartan virus injected into the population before 1973 along with the smallpox vaccinations.

Scully’s cancer was not cured, it only went into remission thanks to chip


In the summer of 1997, I discussed with Chris some cool new treatments for curing Scully’s cancer. Scully’s health was getting progressively worse, until she lay near death in the sequel to the episode ‘Redux’, called ‘Redux I’. Chris decided to have Scully ‘cured’ when a synthetic chip was placed at the base of her neck. While watching the episode, I groaned. I knew what would happen the next day when I faced the 500 rabid X-Files fans in my Introduction to Biology class. Hands flew up as soon as I entered the room. ‘How could a computer chip in the neck cure cancer, Dr Simon?’ I was asked repeatedly. When I talked to Chris later that week, he said ‘It’s not a cure! It’s only remission!’ I remain hopeful that some new neat medical technology will prevail in the end.

The Redux trilogy ended in an excellent way synthesizing the core themes of the X-Files. Scully’s cancer disappeared, and it could have been due to her prayers being answered by God, or due to the conventional treatment she underwent, or due to the chip that was put into her again, a symbol of unconventional science and perhaps of the existence of aliens.

Studying Scully’s very first implant

That it would be just a remission instead of a cure makes some pseudoscientific sense. Scully’s cancer was caused by the experiments done on her during her abduction (radiation exposure to trigger hyper-ovulation? contact with alien genetic material?). A cancer is certain cells losing their constraints and duplicating endlessly growing into an unwanted tumor. The chip put inside Scully during her abduction put shackles on these cells and stopped their spread. The removal of the chip in season 3 caused the spread to begin anew; the addition of a similar chip in season 5 stopped it. Scully only has to remove the chip and her cancer could return; or, the chip could be reprogrammed to kill her by permitting the cancer to grow. Carter’s quote above could be both an acknowledgment that the chip did not magically cure her cancer, and a tease for a potential future development — one story thread that has not yet been pulled back to the fore.

Some additional short tidbits that have their significance

Dr. Anne Carpenter

In 1X23: The Erlenmeyer Flask, Dr. Anne Carpenter’s name comes from Anne Simon’s first name and not legendary director John Carpenter, but after Anne Simon’s husband name.


Magnetite is mentioned extensively in the description of the (real) Mars meteorite that might have contained fossilized bacteria, which served as inspiration for 4X09: Tunguska. Magnetite is of course a widely common iron compound found on Earth and elsewhere and there is nothing particular about it, however magnetite’s importance as the aliens’ weak spot introduced in season 9 does make this research relevant. One theory would be that the presence of magnetite in the Mars meteorites is what weakened the Black Oil’s potency and allowed the research into a vaccine to proceed faster in Russia compared to other, more potent Black Oil strains, like the ones in Fight the Future and 6X01: The Beginning.

Black vermiforms

Foum Tataouine

Discussing Mars meteorites, Simon also mentions the Tatahouine meteorite, which was analyzed in the wake of the potential bacteria find in the ALH84001 meteorite from Antarctica. That meteorite fell in the Foum Tataouine/Tatahouine/Tatawin region of Tunisia in 1931. This is the same place where we find Conrad Strughold at the end of Fight the Future. It is possible the Syndicate installed GMO corn fields above findings of Black Oil, some of which might have landed on Earth with meteorites.


In Scully’s and Pendrell’s analysis of smallpox vaccination tags in 4X01: Herrenvolk, the aminoacid sequence that appears onscreen is not random: it is that of the cowpox virus, as could be expected from a smallpox vaccination!

Look what Pendrell found inside Scully

The chimera organism

The chimera organism in 5X02: Redux that develops under Scully’s microscope and could be alien is actually footage of a proteus urchin!

Alien urchin

Genetically modified plants

Fight the Future and colonization in general is based on genetically modified corn that carries the DNA from the Black Oil virus, which is passed on to bees when the bees come into contact with the corn’s pollen: the transfer of genes from one organism to the other is something that is observed in nature with Agrobacterium tumefaciens, which transfers its genes into plant cells and has been used to insert specific genes and thus create genetically modified plants.

Black Oil worms

The Black Oil coalescing into worms was inspired by dictyostelium slugs. It looks like the Black Oil behaves intelligently, for example when it forms worms that “attack” a host in Fight the Future. There is however a real nature counterpart to such behavior, as odd as it seems. One could imagine the Black Oil virus organizing itself and the hydrocarbons in the oil it is bathing in order to behave like a multi-cellular organism looking to infect a host, in a broadly similar way to the ‘dicti‘ organism.

Dictyostelium discoideum life cycle

ADA enzyme & gene

There is mention of the severe immunodeficiency syndrome caused by a faulty gene producing the ADA enzyme. Years later, Simon would use that knowledge to come up with the mechanism with which the conspiracy would depopulate the planet with the ADA-removing Spartan virus, in 10X6: My Struggle II.

Southern blot

Simon is well aware that the Southern blot test conducted by Scully in 5X02: Redux was done way too quickly because the narrative of the episode demanded it, and it has become a bit of a recurring joke that she has received criticism for this. (To accelerate the test, more heat is needed, thus the mention of a “blazing hot probe”: little did she suspect that FOX censorship might take issue with that expression!) I wonder how the same people would react to 10X6: My Struggle II and its extremely quickly produced alien DNA vaccine.

Annex: Book contents

An overview of all the information in the book’s six chapters:

1: Hidden and Hungry
Episodes: The Host ; Ice; Darkness Falls; Firewalker; El Mundo Gira; F. Emasculata
Described: extremophiles; pathogens; antibiotics; hypothalamus & hormones; flukes & worms; hermaphrodites; reviving extinct species; spores; silicon-based life; fungi & enzymes; immune system; parasites & outbreaks

2: Visitors from the Void
Episodes: The Erlenmeyer Flask; Tunguska; Piper Maru; Ice; Gethsemane/Redux
Described: bacteria; microscopes; DNA, RNA & nucleotides; virus replication; Human Genome Project; ALH84001 Mars meteorite, PAHs, carbonates & magnetite; dicti slugs; Tunguska event; life in space & panspermia; ammonia-based life; chimeric organisms; Piltdown Man hoax; RFLP DNA test; mitosis & somatic development

3: Mutants and Monsters
Episodes: Post-Modern Prometheus; Home; Small Potatoes; 2Shy; Leonard Betts; Fight the Future; The End/The Beginning
Described: fruit flies; genetic engineering; DNA mutations; epidemics & mutant gene spread in human population; birth defects & genetic disorders; chromosomes, autosomes, sex chromosomes; dominant & recessive genes; extra chromosomes & chromosome inactivation; inbreeding; PCR DNA test; enzymes, proteases, lipids & digestion; regenerating limbs & repression by the immune system; cancer, proto-oncogenes, p53 gene & mutation suppression; bacteria redirecting the identity of cells & viruses activating genes; junk DNA; God module

4: Releasing the Genetic Genie
Episodes: Eve; Memento Mori; The Erlenmeyer Flask; Redux; Zero Sum; Herrenvolk; Fight the Future
Described: cloning; genetic engineering; chemotherapy & radiation treatment for cancer; gene therapy; Southern blot test; cloning & extra chromosomes; reproduction by cloning; forensic entomology; smallpox, immunization with cowpox, Smallpox Eradication Program; immunohistochemical staining & protein amino-acid sequence “tagging”; adding genes to plants & Agrobacterium tumefaciens

5: Seeking the Fountain of Youth
Episodes: Young at Heart; Dod Kalm; Roland; Synchrony; Our Town
Described: immortality & cell life ageing theory; HeLa cells; Hayflick cell division limit; human experimentation & consent forms; ‘wear and tear’ ageing theory, progeria, Werner’s syndrome, helicase enzyme; gene therapy; telomeres; cancer & telomerase enzyme; free radical ageing theory; antioxidants; male/female longevity, hormones & metabolism; cryonics; cells freezing process & ischemia; cryopreservants; vitrification; nanotechnology; brain diseases, Creutzfeldt-Jakob disease; prions; cannibalism & kuru disease; ‘mad cow’ disease

6: Fooling with Mother Nature
Episodes: War of the Coprophages; The Jersey Devil; Blood; The Pine Bluff Variant; Quagmire
Described: environmental problems; invasive species; species extinction from loss of habitat; mutations, global warming & Hsp90 protein; insect sterilization for pest control; man-made insecticides, DDT, environmental oestrogens & link to cancer; artificial chemicals & health problems; animal & human pheromones; adrenaline; biological warfare & US & USSR programs; flesh eating bacteria, Streptococcus, anthrax; terrorist groups with biological agents (Aum Shinrikyo & nerve gas sarin, domestic terrorism in 1998); amphibians extinction; Endangered Species Act; coelacanth; chytrid fungi

[Unknown]: X-Files: Science Fact or Fiction?

X-Files: Science Fact or Fiction?
Kristen Philipkoski and Brad King

This Sunday, FBI agents Fox Mulder and Dana Scully hang up their badges after nine tumultuous years on the The X-Files, where the dynamic duo helped thwart a government conspiracy to help aliens recolonize the Earth, oftentimes at great personal peril.

Every other week, in fact, the pair were getting knocked around, kidnapped, bushwhacked and downright messed up by aliens trying to create a slave race of human-alien hybrids.

Right, OK. No problem. Assuming that aliens ever landed, maybe that could happen, considering the quantum leaps in science over the last decade: sequencing the human genome, cloning animals and developing the first round of genetic medicine.

But surely series creator Chris Carter was pushing the bounds of science, right? Frankly, that’s the only way we’ve been able to sleep at night, believing it was all some science fiction nightmare.

Unfortunately, that’s not entirely true, according to Frank Spotnitz, an executive producer for the last eight years, who walked us through the show’s plot.

Spotnitz explained that on the show, the government conspiracy began in 1947, when a spaceship landed in Roswell. The aliens were coming back home after a brief respite in space to avoid the ice age that covered the Earth millions of years ago. They were happy we kept the planet warm, but they wanted the Earth back.

This time, to take over the planet, they had brought a little weapon called the black oil virus, which invades the human body. The virus not only allows aliens to control an infected person, but also implants an alien fetus in the human. Anyone who’s seen Alien knows that doesn’t end well for the host. As if that’s not enough, the aliens also want to create a race of human-alien hybrids to do all their dirty work.

So they start to experiment, hoping to find a way to engineer “worker people.”

Here’s the kicker. If we run across aliens some day and they are DNA-based critters, scientists believe that cross-species hybridization could happen. Certainly lots of mice are running around with human genes, engineered as test subjects for potential human drugs.

However, there is another way to create a hybrid race, called chimerism, which is a process of combining embryos from two species to create a brand new one.

“The cells of the species then cooperate with each other to form an organism that hasn’t existed before,” said Stuart Newman, a New York Medical College professor of cell biology and anatomy.

Although he doesn’t have plans to make one, Newman has filed a patent application on his own chimera: the “humouse.”

Scientists have purposely developed “geeps” — sheep crossed with goats. And they say they’ve learned quite a bit about human and animal development from these chimeras.

But all that genetic manufacturing is a royal pain, as anyone who has ever tried to create a hybrid race of human-alien slaves knows. So, our alien visitors developed the black oil virus.

In The X-Files universe, humans have both a human genetic program and an alien one. The black oil virus can flip a “gene switch” to turn off the human program and turn on the alien one.

“The idea was that this virus inside this black slime would actually get into the cells, inactivate the human program and start the alien one,” said Anne Simon, a virologist, University of Maryland professor and scientific adviser for the show.

Simon, who wrote the book The Real Science Behind the X Files, was inspired to come up with the idea of a genetic switch by the large amount of so-called junk DNA in humans. Only about 1.5 percent of human DNA is made of actual genes that have a known function, and the rest is relatively mysterious — or even alien.

Like the appendix of genes, junk DNA doesn’t have any recognizable uses. Which isn’t to say science won’t one day unravel that mystery. However, Simon said that the black oil virus could essentially re-sequence junk DNA to create new, alien genes within living humans.

“Viruses are able to do a lot of fascinating things,” she said. “They can activate and inactivate genes, integrate into the genome, shut down the manufacturing of all the host proteins.”

On The X-Files, the black oil virus and the hybridization tests laid the groundwork for colonization. Mulder and Scully continually come face to face with the Syndicate, a group of rich white dudes helping the aliens in exchange for their freedom. Mulder nearly buys the farm several times, but Scully — poor Scully — she can’t buy a break.

Scully is abducted in 1994. Once captured, she is subjected to experiments that render her unable to have children. Her eggs are harvested so the aliens can try to create hybrids. But that’s not the end of Scully’s problems.

She’s eventually stung by a nasty swarm of bees that carry the black oil virus. The bees picked up the virus from pollen, which the aliens engineered.

Frighteningly, this would be a piece of cake for any virologist.

“Expressing a virus in plant pollen would not be a problem,” said Simon.

Once she’s infected, Scully is kidnapped and put into a cryogenic freeze where the alien baby inside her can grow. But Mulder rescues her and kills that nasty alien baby. Afterward, Scully is chilly, but fine. Except she’s sterile.

Nothing is ever as it seems on The X Files. The aliens weren’t quite finished with her. Soon, she’s pregnant.

Before childless women putting off parenthood until the last possible moment rejoice, they should be reminded: First, Scully is a TV character. Second, fertilization technologies are improving, but even they couldn’t help someone whose eggs have been completely depleted by aliens.

In fact, several fertilization experts have recently warned women not to wait too long to try having children because the fertilization techniques might not be as good as they hope.

Aliens, however, have the fertilization game down. When little William — Scully’s baby — starts levitating his toys and the meteorites that mysteriously appear in his dresser drawer, it’s pretty clear he’s no regular baby.

This is where we leave our hero and heroine, heading into their final small-screen adventure, with a baby that could be not entirely human, a mysterious black oil virus possibly floating around the universe and some honked-off aliens.

“I’m very sad that this is the last episode,” Simon said. “The life of a professor, as fun as that is, is always in need of some comic relief — and this certainly provided some.”

Sure. Alien invasion. Comedy. Sleep well.

Written By: A Viral Inspector: The science advisor to Chris Carter's The X-Files takes no credit

Written By
A Viral Inspector: The science advisor to Chris Carter’s The X-Files takes no credit
Richard Stayton

By Anne Simon, Ph.D. (as told to Richard Stayton)

This is Chris’ show. He writes it. He’s the creative force behind it. All I do is help with the science. I’ve occasionally gotten some of my original ideas on the show, but the most is a line, and it’s up to him to use it or not. He’ll call me and say, “How can I tag someone with their small pox vaccine?” I didn’t come up with tagging someone with small pox vaccine. He did. I just gave him some science.

I always say, “Oh, just e-mail it to me. Let me look at it first, and I’ll make sure that the science is correct.” But it’s his storyline. His story. His idea. He writes the scripts. All I do is help a friend.

It’s because of my dad [writer Mayo Simon]. I’m very sensitive to how little control that you have in Hollywood and how upset my dad got when people were taking credit for things that he had written. And in science we really don’t like it when people take credit for our ideas, and we’re very careful to attribute things in science. We’re careful about what we’ve done and what we have not done. I understand the pain that writers go through.

When people take credit for your writing, it’s terrible. You’ll have this wonderful movie, and who gets the credit? It’s the director who did it, and it’s the actors who did it, and who mentions the writers? And it’s ridiculous. It’s the writer who did it. The director is just going from the script, and the actors are just doing what the director says that’s in the script. I grew up with that.

During my book tour, I’d make reporters swear that they would not say that I wrote for the show. “I’m a science advisor,” I’d tell them, “I help with the science.” They end up writing, “She writes for The X-Files.” And I think, My God! I know what my dad would think. So I began the interviews by saying, “You’re a writer. You know what it would be like if somebody took credit for your writing. Well, think about how I feel when people write that I am doing the writing and providing the creative ideas behind what somebody else is doing.”

Contacts and Connections

When I was much younger and living with my parents in Pacific Palisades, Chris’ wife was a friend of my dad’s. So Chris was over at Thanksgiving, Passover, the usual affairs. I got to know him as a really cute surfer, which was what I thought of him. He was gorgeous: blond and always tan. I didn’t think about him as a writer at all. His wife was the writer.

Then when I got my assistant professorship at the University of Massachusetts, I didn’t really think about Chris until five years later. I was going through the TV Guide, seeing if there was anything on, and I read this description for this show on Fox: two FBI agents investigating cases of the paranormal. I like science fiction, and I thought this could be a really interesting show, especially because it describes the woman as a medical doctor and scientist. I was watching the show every week, and about halfway through the first season I get this call from my mother and she says, “Do you know that Chris has a new show called The X-Files?”

Chris is a real fan of science. In another life he would be a scientist.

Once I had corrected a script. But I said, “Do you realize this term is incorrect? Do you want to have it wrong in the script?” He said, “Yeah, it’s more conversational.”

Chris and I discussed whether or not you could have virus in pollen. I said, “Sure, I could do it. It would have been tricky. But you can do pretty much anything.” So he sends me this film script. And I’m number 10 to see it because the scripts were all numbered. Our names stamped on every page. Mine was spelled incorrectly. I got to look at my incorrect name on every single page.

I’m reading the script, and Chris starts talking about how the virus gets into a person and turns into this horrible alien organism. Chris’ idea was that the virus was the original inhabitant of the planet. But when I’m reading it, it’s like the virus turns into this horrible creature. And he’s describing the big black eyes of the virus. And I’m going, “Oh my god!” I work on viruses. Viruses can’t turn into anything. If a virus turns into something, it’s not a virus. I was really horrified. So I read the rest of the script, and I came up with a different science that would only change a few conversations, but it would change the idea of what the virus was. And I had my fingers crossed that he’d go for it. If Chris wanted that virus to turn into something, he would’ve done it whether I wanted it to or not. But he loved the new idea: The virus integrates itself into the DNA of the person. That’s what a lot of viruses do, activate a resonant program in the cell. There’s a program in all our cells, in our DNA that starts with that single egg and turns us into a person. And that’s encoded in our genes, in our genetic makeup.

The problem is that there’s a huge amount of DNA we don’t have a clue about. There’s a whole lot of DNA that we call junk DNA. We don’t have a clue what this junk DNA is doing. My idea was the virus activates a resonant program in the junk DNA, and that the junk DNA is actually there to turn a cell into the horrible creature, which means that we are the aliens.

Once Scully was so upset when she had this horribly deformed baby that she accidentally misspoke and called the illness an autozomal dominant disease when it’s really an autozomal recessive disease. There’s a huge difference because if it’s dominant, the parent had to be dead at birth. And that can’t happen if you’re talking about the baby, so obviously you can’t get around that. But there are some people who nitpick and say, “The writer obviously made this bad mistake here.” But I say, “So what? Writers aren’t scientists. I see plenty of mistakes in grant proposals from professional scientists.” It’s not my job to sit here and go through the problems. These are not scientists. They do a terrific job of making the science look real, and occasionally there’s a little problem. So what.

Anne Simon, Ph.D., is Professor and Associate Head of the Biochemistry and Molecular Biology department at the University of Massachusetts and author of The Real Science Behind The X-Files: Microbes, Meteorites, and Mutants.

Sci-Fi Flix: Simon Says Science

Sci-Fi Flix: Simon Says Science
[Anne Simon]
Melissa J. Perenson