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

Quote:

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?

Quote:

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

Quote:

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

Quote:

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

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.

S.E.P.

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