Clock King Orange: The Pyschosis of Batman Villians

Batman is my favorite DC Superhero.

The minute I write that I start arguing with myself, though. I mean, it’s actually probably Martian Manhunter… he’s just so adorable and we both love oreos… I mean “Chocos”…

Seriously though, DC used to use the term “Oreo”, but abruptly changed it to “chocos” due to a trademark violation… ALSO Chocos “produce a physical addiction in Martian anatomy” (REF).

I suppose I really appreciate Batman though, as he stands out as just a man amongst gods and aliens. DC, more than Marvel, is full of characters that are not of this world. This is my theory for why making a financially/critically successful movie is difficult for the company (though I completely disagree with this and think the DC movies have been superior to most Marvel ones, but… that’s a rant for another day). However, the benefit of this is that Batman really stands out as being exceptional, he relies on his logic and deductive reasoning skills. A man after my own heart.

Though I love the Nolan movies, I think it has lulled the public into an impression that Batman is just a rich guy who’s very good at Krav Maga. When in reality, he’s a detective. He’s Sherlock Holmes, but with gains. Here is a great article explaining my feelings on this.

Look at those obliques…

Another big reason why I love reading Batman comics (Dark Knight Returns, The Killing Joke, Hush, Year One, A Death in the Family… all are seriously in my top 20 comic books storylines) are the villains

Bane, Joker, Catwoman, Harley Quinn, Penguin, Scarecrow, Riddler, Poison Ivy, Ra’s al Ghul, Two-Face, even Clock King… All of his villains are just humans too, they aren’t particularly gifted or powerful, and yet they all terrify (and intrigue me) way more than Ares, Doomsday, Sinestro, etc…

I think it’s because humanity’s unprecedented ability to destroy and the depth of depravity of some humans is one of my deepest fears (I’d like to see a Bogart tackle that one).

Abby boggart.jpg

Perhaps my boggart would just be Daria

I suppose it’s also that the villains are so relatable, it really speaks to my fear that I am part of the problem, that I could easily become the villain in the story. The Batman universe (and comics in general) is a great place to play with these very real fears, as in this universe true good and true evil are very clear and definable. It’s harder when you’re in the real world and these lines become blurred.

And of course, the fact that they each represent a different type of mental illness is pretty scary too. It is increasingly becoming clear, as it becomes socially acceptable to discuss happy lights and Xanax, that we all struggle with some form of mental illness. Thus I think if most people were to look at the Batman universe they could find a character, or idea, that they identify with.

The most used resource for professionals when diagnosing individuals with various mental disorders is the “Diagnostic and Statistical Manual of Mental Disorders”, it is currently on its 5th Edition. Please note that this manual is constantly evolving with more and more studies conducted, and has been egregiously wrong in the past. For example, it took until the sixth printing of the 2nd edition to remove homosexuality as a mental disorder. So, by no means is this manual perfect, but it is as close as we have come to quantifying the deviations of the human mind and I will be using it as my main reference for these analyses.

The manual splits up disorders into sections:

  1. Personality disorders
  2. Neurocognitive disorders
  3. Substance-Related and Addictive disorders
  4. Disruptive, Impulse-Control, and Conduct disorders
  5. Sleep-Wake disorders
  6. Feeding and Eating disorders
  7. Somatic Symptom and Related disorders
  8. Dissociative disorders
  9. Trauma and Stressor-Related disorders
  10. Anxiety disorders
  11. Bipolar and Related disorders
  12. Neurodevelopmental disorders

For the sake of this blog post (and my own sanity, HAHA), I will only give a character one disorder. It is very easy to attribute a ton of disorders to one person, and though it may be accurate, I want to focus on the root of their personalities.

Okay, let’s get started…


According to the Knightfall storyline, Bane’s father was a revolutionary leader (think Che Guevara) that escaped persecution by the fictional tyrannical Santa Prisca’s government. The government decided that the young boy (Bane) would carry out his sentence in a rough prison. During his incarceration, Bane read all the books he could, learned a variety of languages, and pumped some serious iron. He had no friends and had to constantly defend himself from the other inmates. He ultimately rises to become the “king” of Peña Duro prison. As if that wasn’t bad enough, the prison doctors decide to test a new drug “Venom” on the prisoners, it almost kills him and causes an immense amount of pain. However, once he survives the initial dose, he finds that it has increased his strength. Of course, it comes with a catch. He needs to take it every 12 hours, or he will die from the horrible side effects. Throughout his life and episodes of drug-induced pain, Bane suffers from horrible terrifying nightmares featuring a bat-like creature.

UGH! NO! Not that venom… is the world ever going to forget about SM3??? 😦

So, Bane obviously has some Anxiety disorders (mainly a phobia of bats), and he also obviously has a Substance-Related Addictive disorder (specifically a stimulant use disorder), but I think the main disorder are various Trauma-related disorders, specifically PTSD (post-traumatic stress disorder).

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Yeah, I’d say Bane would score high on that checklist. Here’s some “textual” evidence…

He obviously has a VERY traumatic childhood (Knightfall):


#1, #3, #4


#2: He has recurring nightmares of a bat demon…


#9, #13, #17, #18: “Always there is someone seeking to take what is Bane’s. As in prison so it is outside. All I own is challenged. A challenge that must be met with overwhelming force.” -Prime Earth

#15: um… yeah… he’s got some angry outbursts…



I think the best Joker backstory is from The Killing Joke. So, I will be using that. Here’s a clip from the movie adaptation of The Killing Joke (great film, check it out… but the graphic novel is much better).

The Joker is an engineer, who quits his job at a chemical plant to pursue his dream of being a comedian. Problem is, he’s not very good. On top of that, his wife is pregnant and he is feeling the financial pressure. He decides to help a team of criminals rob the local playing card company (I didn’t realize playing card factories were such a hot spot for robbery). However, his wife and unborn child are tragically killed before he can provide. The criminals force him to go along with the plan anyway, dressing him up as a known villain in order to act as a decoy if they are caught. They are caught and the terrified engineer jumps into the plant’s waste while attempting to avoid Batman and the cops (what waste is generated by playing cards I wonder?). The chemicals disfigure the engineer, giving him the Joker’s trademark skin and lips (so THAT’S HOW HE GOT THOSE SCARS!). The physical and emotional trauma then cause him to go “insane” and the Joker is born.

I almost didn’t diagnose the Joker, as I feel it’s been done to death. Everyone says he’s “psychotic”. But, I don’t know if I agree with that vague diagnosis. I think it’s more likely that he suffers from a Dissosiative disorder, specifically “depersonalization/derealization disorder”. According to the textbook Abnormal Psychology: An Integrative Approach by Barlow and Durand (I really hope I don’t get sued for showing this…) this is the diagnostic criteria for depersonalization/derealization disorder:

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Barlow, D. H., & Durand, V. M. (2011). Abnormal psychology: An integrative approach. Nelson Education.

A) Throughout The Killing Joke you see the Joker reliving moments from his traumatic “pre-Joker” past. In this panel, in particular, you see him looking into a reflection where his pre-Joker image is reflecting back at him, though his hand is white and clad in the iconic purple gloves. Suggesting that he has some sort of disconnect from who he was, and who he is now. I think these “flashbacks” are an example of moments where the Joker breaks through his mental illness and returns to his original personality. However, they are always brief and get less frequent as his depravity deepens throughout the novel.


I am especially interested in the criteria of seeing objects or surroundings as “dream-like” or “distorted”… this is portrayed very well visually throughout the novel (Moore and Bolland are total geniuses…). The colors become more and more vibrant as the tension of the plot, and the Joker’s madness (and perhaps Batman’s) heightens.

Here is a panel from early in the book:

And here is one at the very end:

B) The Joker does seem to understand what he’s doing in the current timeline. He seems to understand he is the one responsible for all the carnage. He even seems to show remorse at times. This is why I don’t think he’s simply had a “psychotic break”

And yet… he seems to be able to dissociate himself from this past…

C) Um… yeah, I’d say the Joker is not socially functional… in fact I think The Killing Joke shows his journey in becoming more and more detached from society as he increases the viciousness of his crimes, ultimately culminating in the scene with Barbara Gordon. I think that scene (I’m being cryptic on purpose, and no, the movie doesn’t do it justice) is actually the event that makes him completely morally unredeemable. The reader, along with Batman, goes from sympathizing with him… to wanting to break Batman’s cardinal rule: to kill him.

One of the best scenes in comic history.

D+E) These points are probably the ones that weaken my theory the most… this is because The Joker is inherently an unreliable narrator. Though we can assume his pregnant wife and the horrible accident at the factory did happen in this storyline, we really don’t know if these are just lies… We also don’t know what was in that chemical waste, perhaps it did cause some sort of medical condition. Also, though he seems to be mentally stable in his flashbacks, it is unclear what his medical history really is, perhaps he is a diagnosed/undiagnosed schizophrenic.

The Joker is notorious for changing his backstory.


Catwoman’s backstory is complicated. She’s been a character since the 1940’s, and thus her background has evolved many times. Femme fatale, a flight attendant with amnesia, a battered wife, blackmail victim, dominatrix, and of course: Anne Hathaway.

I love that line.

The evolution of Catwoman is actually very interesting from a feminist perspective. She goes from a victim who Batman takes care of and ultimately reforms (pre-Frank Miller makeover):

To being her own woman (or at least her own boss), in Frank Miller’s Year One storyline.

For the purposes of this post I am going to use the storyline established in Batman: Year One, it’s (sort of) sister comic Catwoman: Year One (written by Mindy Newell), as well as Nolan’s interpretation in The Dark Knight Rises. For the record, I don’t really recommend reading Catwoman: Year One… it’s not the best. But it pretty much follows the same storyline as Batman: Year One (which is a great read), just filling in some (somewhat unnecessary) blanks.

Selena Kyle is working as a common prostitute in Gotham. One night her pimp beats her up so badly that she is sent to the hospital. There a sympathetic cop gives her the card of a former prizefighter Ted Grant. Grant teaches her martial arts and she eventually (inspired by Batman) puts on the suit and becomes Catwoman. It also seems like she leaves the streets and becomes a high-end dominatrix (which would explain the leather suit and whip). Though there is some guesswork here, the theme of Catwoman “gaining control” over her power (sexuality and physical abilities) is clear. The Batman: Year One origin storyline seems to be the one that Nolan used for Anne Hathaway’s character in The Dark Knight Rises, though Nolan evolves it much further.

A scene from the Batman: Year One movie, where Eliza Dushku voices Catwoman. A casting choice I am still fangirling about 7 years later.

This diagnosis is really interesting, as I think Catwoman is probably the least mentally ill of all the Batman villains… which is probably why she and Batman have an on/off romantic relationship. In many ways I think she serves as a foil for Wayne. They both have extremely tragic paths (though Kyle’s is more ambiguous), but Wayne comes from money and has an Alfred, and Kyle is poor and alone. It serves as an illustration of why some choose good or evil, and how sometimes there isn’t much of a choice.

Though it seems like maybe she finally got Wayne to put a ring on it…

However, I do think she may be a good candidate for kleptomania which is a Disruptive, Impulse-Control, and Conduct disorder.

“The impulse control disorder kleptomania is characterized by: 1) a recurrent failure to resist an impulse to steal objects that are not needed for personal use or their monetary value; 2) an increasing sense of tension immediately before committing the theft; 3) an experience of pleasure, gratification or release at the time of committing the theft; and 4) stealing that is not performed due to anger, vengeance, psychotic symptomatology, mania, or antisocial personality disorder.” [Grant, J. E., & Potenza, M. N. (2008). Gender-related differences in individuals seeking treatment for kleptomania. CNS spectrums13(3), 235-245.]

In Nolan’s portrayal of Selina Kyle her motivations for stealing is a bit ambiguous. She is obviously “lower class”:

She would definitely be at the 99% protests…

However, seeing as she can crack “an uncrackable” safe, has amazing acrobatic skills, and is desperate to erase a significant criminal record, I’m willing to bet she has enough financial stability that she doesn’t have to continue to steal, but rather she wants to. Furthermore, notice what she steals. Yes, she is at the Manor to get Bruce’s fingerprints, but she just can’t resist also stealing a necklace.


Look at how satisfied she is…

In fact, she seems to use the excuse of “being poor” to justify her stealing to others, and sometimes it seems almost to herself.


Yes, it could just be her being snarky. But it could also be a pathologic compulsion to steal. She does seem to have some deep resentment towards society, specifically the upper class. But that resentment seems to disappear throughout the film. In order to truly know if she’s a klepto, we would have to see if she continued to steal post-credits. That’s actually a storyline that has been explored a lot in the comics. After Catwoman switches to the light side, does she stop stealing completely?


Batman’s villains are interesting to diagnose psychologically, but Batman himself is just as fun to poke and prod philosophically. One angle I’ve always found particularly interesting (that I don’t think has ever been explicitly examined) is that Batman’s villains are all symbolic of his own insanity, his own psychological issues. Batman has one of the most traumatic backstories of all comic book heroes, and yet he somehow turned out morally righteous.

An optimist could say that Batman is an exception to the rule, and is thus a symbol of hope for all of those raised in the dark. A traumatic past does not doom you to a life as a villain.

However, a pessimist could say that Batman is only a hero in his own mind. In fact, perhaps Batman himself is mentally ill. Is Batman suffering from a narcissistic personality disorder? Is he a reliable narrator?

Okay, but seriously… let’s take a look:

(1) has a grandiose sense of self-importance (e.g., exaggerates achievements and talents, expects to be recognized as superior without commensurate achievements) 

You could argue that Batman being a part of the Justice League could be an example of this.

Seriously… royal merman, intergalactic policeman, demi-God, OP alien, the defier of physics, walking AI… and Batman? He’s definitely not on par with these guys powers wise, and though I think he deserves a place on the team, how he doesn’t suffer from constant self-doubt when in the presence of his teammates is a bit puzzling.

(2) believes that he or she is “special” and unique and can only be understood by, or should associate with, other special or high-status people (or institutions) 

Batman is definitely a loner, and he definitely seems to be comfortable feeling “misunderstood”. That’s actually a large reason why I really enjoyed the Lego Batman movie as it illustrated the ridiculousness of Wayne’s loner complex by making it a major comedic point in the film.

(3) requires excessive admiration 

Two words for you: Bat. Signal. Batman is definitely pretty obsessed with building a “bat brand”. Why couldn’t he just give Gordan a phone to call him on? Or, just simply a light in the sky. I would really love to hear why that bat signal is necessary. On top of that there are “batarangs” and “batmobiles”… I seriously think he’s just begging for a royalty deal with Hasbro.

(4) is interpersonally exploitative, i.e., takes advantage of others to achieve his or her own ends 


In Justice League: Doom Batman is revealed to have come up with a secret plan to take down each member of the Justice League in case they go rogue, even a plan for himself. Though I can admire his ability to remain detached from personal feelings, and his desire to keep the public safe at all costs, this is a little morally grey, and his teammates feel betrayed and angry when they find out Bruce is behind it.

(5) lacks empathy: is unwilling to recognize or identify with the feelings and needs of others 

This may not seem obvious at first. How can a guy who has committed his whole life to fighting crime lack empathy? Well, sometimes I’m not quite sure why Batman fights crime. His motivations have been examined many times in various storylines. It could just be a sense of duty, it could be out of retribution for his parent’s death, but I don’t think it’s 100% empathy for other people. In fact, ironically, I think Superman’s main motivator is empathy. At the very least Bruce shows over and over that he lacks empathy for the person closest to him: Alfred.


Raise your hand if you ugly cried at this part…


And though he does make up for it in the end (sort of)… you have to admit he kind of uses Alfred as an emotional punching bag. In fact, I think most of his interpersonal relationships fail because he is incapable of true selflessness/empathy. His teammates, his girlfriends, his former sidekicks, a lot of his relationships are dysfunctional.

So I don’t know, is Batman a narcissist? Either way, it doesn’t really matter, because even if he is mentally ill, he is “good” for society. In fact, Batman, and his villains, really illustrate the power of choice. Because when it really comes down to it, the villain that chooses to be evil is much more terrifying than the villain that just inherently is evil (looking at you Doomsday).

And similarly, the hero that chooses to be good is perhaps the best.



Alfred Dumbledore for the win!






Schrödinger’s Rick (and Morty)

Most people are familiar with the thought experiment Schrödinger’s cat, however, few people understand the physics behind the analogy.

Schrödinger was a pretty cool cat.

Erwin Schrödinger was a leader in the field of quantum theory, a field which aimed to model and predict how subatomic particles existed and interacted with one another. Yeah… they were super nerds.

Many fellow scientists were discovering that the electrons of different elements produced differing wavelengths. These wavelengths, or emission spectrums, are unique for each element, almost like a finger print. Spectroscopy is still used by scientists to determine which elements are present in an unknown sample.

I’ll go into the details of what is actually being ’emitted’ in a post soon, but all you need to understand is that each element has a unique ‘wave function’. When this exciting discovery was made physicists were eager to find a mathematical equation to describe the shape of the various waves produced by electrons and they sought to interpret what these different shapes meant.

Schrödinger devised this wave equation and won a Nobel Prize in physics for his work. You know… no big deal…

The wave equation allowed scientists to predict shapes of various waves and plot them on graphs.

Here is the wave function for hydrogen

In an attempt to interpret what the wave function of a given electron meant, Schrödinger proposed it could be the density of the charge over time. SPOILERS: It’s not.

Another physicist with a funny name suggested that the wave function was said to represent the probability of finding an electron at a given point in space. When a wave function is graphed, the points where the function is at x=0 represent a 0% probability that an electron will be found in that space. Points with a larger absolute magnitude represent a greater probability of finding an electron in that space.

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This meant that if an experiment was performed where a scientist observed an electron’s positioning over many time points, some positions would be more common than others, and this should match the wave equation plot derived from Schrödinger’s equation.

Screen Shot 2017-08-31 at 3.42.33 PM.png

Imagine the grey dots are data points corresponding to electron locations, there are more points closer to x=0.

It was still unclear what the physical interpretation of the wave function was, does it only represent electrons individually, or does it describe groups of electrons? These questions still exist today. And until we have Professor’s microscope from Futurama, we may never fully understand.


A problem that is inherent in Schrödinger’s equation is that it gives you the probability of discovering an electron in a certain location, but an experiment is required the know the exact placement. This means that prior to observation, an electron exists in multiple probable places all at once, or as scientists call it: the electron is in ‘superposition’. This state of superposition goes away once the electron has been measured.

Here are all the different forms electrons can move in for hydrogen, unless you observe where the electron is, it is in all of these positions simultaneously.

This was a ground breaking concept in physics, and even now it sounds more like philosophy. Even fellow physicists had a hard time grasping this interpretation. In an attempt to make this more clear Schrödinger devised a thought experiment to explain the behavior of subatomic particles. Most people know this thought experiment very well, it is commonly referred to as Schrödinger’s cat. Here is his description of the experiment:

“One can even set up quite ridiculous cases. A cat is penned up in a steel chamber, along with the following device (which must be secured against direct interference by the cat): in a Geiger counter, there is a tiny bit of radioactive substance, so small, that perhaps in the course of the hour one of the atoms decays, but also, with equal probability, perhaps none; if it happens, the counter tube discharges and through a relay releases a hammer that shatters a small flask of hydrocyanic acid. If one has left this entire system to itself for an hour, one would say that the cat still lives if meanwhile no atom has decayed. The first atomic decay would have poisoned it. The psi-function of the entire system would express this by having in it the living and dead cat (pardon the expression) mixed or smeared out in equal parts.” (source)


(The Oatmeal)


A wave function could be drawn for the probability of the cat being alive/dead much like the wave function of the placement of an electron, with equal probabilities for both outcomes.

Schrödinger’s work was, and still is, essential to the field of physics as I have established above. It allowed scientists to understand and predict the function of subatomic particles and created a new subfield of quantum mechanics.

However, it is just as well known to the non-physics community. Even if you don’t realize you’ve heard of this concept before, unless you live under a pop culture rock, you probably have. Popular books, films, shows, etc. that portray alternate realities would never have imagined such a concept if it wasn’t for Schrödinger’s equation and his thought experiment.

Speaking of alternate realities, this wonderful piece of television would not be possible without  Schrödinger.

Perhaps the most recent example of pop culture using Schrödinger is the Rick and Morty episode “A Rickle in Time”. In a nut shell, Rick freezes time initially to give him, Morty, and Summer enough time to tidy after their giant intergalactic party before the parents get home. Of course, the three of them get distracted/have existential crises and keep time frozen for six months. Because time has been frozen for so long Rick warns the kids not to touch their parents until the timeline restabilizes. Hijinks ensue and a rift in time is created and two realities are created. Now none of that is particularly scientific, more fiction than anything. But then Rick explains that Morty and Summer’s ‘uncertainty’ has caused time to fracture into two equally possible impossibilities. He proves this by opening the front door and it is revealed they are floating in darkness surrounded by Schrödinger’s cats.


Rick tries to fix the situation but his grandkid’s continued ‘uncertainty’, his asshole-ry, and a fourth-dimensional being, causes more and more rifts until there are 64 different alternate realities.

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All of these possible realities are happening at once due to character’s uncertainty, just like how all of the electron configurations of hydrogen is possible until they are observed. The solution in R&M is to strap on time-stabilizing collars on all three characters and restoring the certainty of the timeline. However, in this episode, and many other episodes, it’s established that multiple timelines are all occurring at once all with different versions of Rick and Morty.

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The council of Ricks is like the different electron configurations of hydrogen.

I think Schrödinger would have been approved of his rival being beaten up by fourth-dimensional beings.

Would Darwin play Pokemon Go?

I will admit, I am one of the few people in the world still playing Pokemon Go.

And because I’m a double nerd I’ve also already used Pokemon Go to explain the life cycles of S. mansoni.

The fad was crazy popular for a couple months and then seemed to have fizzled out over the last year. But I still am driven by the collection aspect of the game (yes, I seriously HAVE to catch them all), and I find that it motivates me to get a good hour of walking the dog in a day.

However, as a biologist, every time I click the ‘evolve’ button I feel pretty dirty.

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Though Pokemon Go, and Pokemon in general, succeeds in entertaining kids and ahem… adults, it may have damaged the average person’s understanding of what evolution means. And that’s saying something because evolution is already one of the most misunderstood concepts around.

In Pokemon Go an individual can be ‘evolved’ when a certain amount of species specific candies have been collected, this ‘evolution’ causes them to physically transform and increases their power. Some Pokemon species have multiple ‘evolution’ opportunities (look at you Eevee), where as some have none.  Usually, the art depicts the creatures as looking somewhat similar, or as having a similar theme. However, this isn’t evolution, it’s an organism’s growth and development.

Amphibians are one the best (and most interesting) example of an organism with distinct developmental stages. I actually wrote an honors thesis in college examining how the skin microbiome shifts over developmental time in Boreal toads, so I’m an expert at Gosner staging toads/frogs (one day I’ll explain what that distinction means).

Spoiler alert!

Much like the Bulbasaur, the frog begins its life cycle newly hatched from the egg as a tadpole with fully functional gills and a body type perfect for swimming. As time goes on, the gills begin to disappear, limb buds begin to form, and the tail is reabsorbed and the amphibian is now a ‘metamorph’, an analogous stage to Ivysaur. As the frog begins to navigate the life of a land creature, they grow bigger in size, reach sexual maturity and are finally considered an adult, much like Venusaur.

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This is a very simplified version of amphibian development, in reality, there are 46 distinct morphological stages identified by a cool dude named Gosner.

Now that I’ve established what’s going on in Pokemon Go is development/metamorphosis, let me explain why it’s NOT an example of evolution. It’s actually very simple. Evolution does not occur within an individual’s lifetime, it occurs in a population over time. Usually a lot of time.

This is a pretty common misconception. An individual fish did not decide one day: ‘oh this seems like a lovely day for a walk on the beach’ and crawled on shore. Well, maybe he did, but he didn’t live to procreate. The experience probably went a little like this.

Instead, this process took millions of years and required a ton of little mutations to be successful. Not just 50 species candies and a sun stone.

And no, this doesn’t disprove everything I just said.


So let’s be real, that button shouldn’t say evolve, it should say metamorphosize. But I’m assuming it wouldn’t fit, or someone on the design team had a poor science education.

I know what you’re going to say, “it’s just a game!”, but misconceptions over evolution are very much real, and they have very serious consequences. Don’t believe me? We’re getting better, but we still have so far to go.

It’s well known that Darwin was an avid walker, seriously look at his daily routine. Just imagine how many eggs he could have hatched.

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About Darwin’s Finch:

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A scientist by day, and a nerd by night!

I’ve gotten into the habit of using nerdy analogies to explain complex scientific topics, and I get a kick out of exploring the nerdiest of things using the best super power of all: science.

Only here can you get nerdy knowledge known nerdily.

The Epidemiology of Greyscale: Is Ser Jorah Patient Zero?

Someone may accuse me of trying to take advantage of the current GoT hype to make this blog post popular… and they would be right. But I must point out that I’ve discussed the GoT universe twice before: once when discussing the Targaryen’s freakish complexion and eye color in my evolution of pigment post, and another time when I hypothesized that the GoT universe was in a Dyson sphere.


I found myself, like most people, screaming while watching the scene where Samwise… ahem I mean Samwell Tarly… operates on Jorah’s greyscale. But, I was screaming for a different reason, and when Sam shook Jorah’s hand I about lost my shit. I had always been confused about the epidemiology of the disease, but this episode just confused me more. How could a disease with 100% virulence, little to no cure, and that is spread through contact be so rare? How did removing the physical greyscales result in being cured? Was this disease caused by a pathogen, or more hand-wavey magic?


That pie transition was probably the best transition I’ve seen. (Sorry Star Wars scene wipes).

Okay, just a little background about greyscale. The disease has casually shown up in multiple seasons afflicting mainly Princess Shireen Baratheon and later Ser Jorah.

In Season 5, Shireen tells Gilly that she was diagnosed with greyscale as an infant, was thankfully cured, but has a disfigured face due to it. Gilly mentions she had sisters that were diagnosed with a similar affliction, but unfortunately, their greyscale covered their entire bodies until they were no longer coherent and were mercy killed/burned by Craster. Later in the season Stannis embellishes the story of Shireen’s contraction as he explains she contracted the illness from an infected doll that he bought somewhere in Dorne. Dolls: 2, humanity: 0.

Everyone told him to send her away to the Narrow Sea (it is unclear if this was to prevent an epidemic, or allow her to die among the Stone Men in Valyria), but he ignored them and recruited every healer to help his daughter. Somehow, vaguely, she was cured, but left forever disfigured.

This foreshadowing of the dangers of greyscale happens just in time for a season end Ser Jorah cliffhanger. Jorah and Tyrion are sailing through Valyria when they are attacked by stone men. Jorah fights them off and saves Tyrion, but is secretly touched, and infected, in the process.

In Season 6, Jorah’s disease is spreading, but only Daario seems to notice. Jorah goes to his queen Daenerys (a scene that had me screaming: DO NOT GO NEAR HER WHEN YOU’RE INFECTIOUS!) and tells her that he’s going to emo around and kill himself before the disease progresses and wishes to be released from his service. She refuses and commands him to find a cure… which is sweet, I guess? But mostly just douchey…

In Season 7, Samwise… ahem I mean Samwell Tarly… is wiping up poop at the Citadel when Jorah comes seeking a cure. Samwell finds instructions on how to cure Jorah in books from the restricted section… oh darn, wrong fantasy series…


Samwell decides to try the procedure on Jorah despite:

  1. Never performing a serious medical procedure before.
  2. Putting himself at serious risk of greyscale infection.
  3. Putting the entire Citadel, and the world, at risk of an epidemic.
  4. Putting his patient at risk of extreme pain, infection, and death.
  5. Slughorn explicitly telling him not to… darn wrong universe again.

    Unfortunately, this is as close as you get to a surgeon in the Game of Thrones universe.

 For some reason getting the greyscale literally off his body satisfies everyone enough, including Maester Marwyn, that they LET A POTENTIALLY INFECTIOUS patient go back into the world. Sam even shakes hands with Jorah. Thank god he gives up on being a doctor after this episode.

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Then Jorah goes on to reunite with Daenerys. While everyone else was probably tearing up a bit, I was screaming “Don’t touch her, don’t touch her… dear god he touched her.”

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Okay, I think we’re caught up now on the plot, and hopefully, some of you are starting to understand why I’m so frustrated. But to really understand how little sense this disease makes let’s sum up what we know about it.

Let’s first discuss the etiology of this disease: where did it come from? Is it intrinsic, extrinsic and idiopathic? Intrinsic diseases occur due to a change or problem within the body, these include genetic diseases and predispositions, hormone dysregulation, cancer, and autoimmunity. Though a genetic predisposition may explain how such an easily spread disease hasn’t infected the whole world, there isn’t specific proof of this in the show/book. Extrinsic diseases occur due to an individual’s exposure to a harmful substance/organism in their environment. This is a better description of greyscale as all of the infections described can be traced back to touching an infected person or object. Idiopathic etiologies of diseases are the kind that gets sent Dr. House, when there is no clear cause of the disease. This may be an even better way to describe greyscale as there seems to be some unrealistic, nonbiological, even magical element to it that we may never get a good explanation for.


The disease’s pathology is pretty narly. Some of the best descriptions come from the books where the disease is actually talked about in depth. The disease begins pretty mildly and symptoms become more dramatically at a pretty consistent pace, for a more scientific description we will describe it in four phases. The first phase begins days after the initial infection: the extremities are the first to be affected as fingertips begin to blacken and feel numb. If a patient thinks they have been exposed they should prick their fingers and toes with a knife preferably a sterilized one) daily, if the prick hurts they have not contracted the disease. For some reason in the show they show Jorah immediately shows symptoms after being touched. The second phase of the disease is when the skin of the body begins to turn grey, stiff, and cold. This is the phase the stonemen that attack Jorah and Tyrion are most likely in. The third phase results in blindness/deafness/muteness as the disease reaches the face and turns it to stone rendering it non-functional. In the final stage, the disease starts to affect the organs and death follows shortly after. Though we haven’t seen a character experiencing the last two phases, it was described by Gilly and at the Citadel as always resulting in madness.

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Virulence is a measurement of how much damage a pathogen does to a host. So in this case, um… 100% virulence if not treated. There is no reference in the show/book to anyone naturally curing themselves of the disease. Interestingly enough greyscale seems to confer complete immunity to a worst disease: the grey plague, which is a quicker and more intense form for greyscale. Perhaps the children of the seven kingdoms should be vaccinated with greyscale… imagine those anti-vaccination campaigns!


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Unfortunately only 20% of this is fictional.


The transmission of the disease is probably the most unclear part for me. It is consistently stated that you can only get the disease from touching an individual. This seems to indicate that the pathogen cannot survive outside of the body, or that perhaps it’s not a pathogen at all. This is a pretty strange form of transmission and I can’t think of any real disease that follows this strict contact only transmission. For example, staph infections are transmitted by touching, but it’s also transmitted by using an infected person’s towel. However, Stannis mentions that Shireen was infected from a doll. This seems to indicate that the cause of the illness is some sort of organism or ‘germ’ that can be transmitted from people to objects. If this is the case it makes the pathogen way less difficult to control and once again makes me question how there aren’t more people infected, especially since those that are infected don’t know until days later after they’ve touched swords, food, THE MOTHER OF DRAGONS.


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If the second hypothesis on the transmission is true then that belt is infected, those gloves, that scalpel, even the shirt Jorah was wearing when he first came to the Citadel.


The infectivity of a disease is a measurement of how effective the pathogen is in establishing an infection. Though there isn’t any specific evidence, the infectivity seems to be pretty high as every character we’ve seen exposed has been infected. However, how we define “exposed” is very confusing (see above). If the disease can spread to objects the infected individual’s touch, then the infectivity must be very lower as a small amount of the population actually becomes infected. It is mentioned that the affliction is most common in children who live in cold climates, though this doesn’t seem to be represented in the show. This could mean that individuals with naive, or depressed, immune systems are most likely to contract the disease.

We discussed this briefly already, but it is established that treatment is very hit or miss and survival is very rare (most likely less than 1%). Some treatments recommended are: limes, scalding hot baths, praying, mustard, sacrifice, fasting, and vinegar. However, these seem to only slow the progression, not completely cure the patient. Severing the limbs afflicted, or literally removing the greyscale infected tissue is suggested, but explicitly said that it is not always effective. With our best case study (Shireen) now in ashes we have no way to know how she was cured, and how long it lasted for. Furthermore, she was largely isolated from the world, so we have no idea if she was still infectious.

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If I was to assume that this disease does make medical sense, but we simply don’t have all information yet there are three hypothetical models of how the disease works.

  1. You can only contract it by touching an infected person. Most infectious people are killed or isolated, so this interaction only occurs rarely. This isn’t biologically common and may have a more magical origin.
  2. The disease can be spread airborne, through objects, and through contact, but most people with healthy, mature immune systems are immune to it.
  3. The disease is becoming more infectious, but due to the shunning of infected people and the relatively quick mortality, it has not caused a pandemic. Ser Jorah represents patient zero.


Convergent Evolution: Knights and Samurais

Convergent evolution is a process where organisms that are not closely related independently evolve similar traits. This usually occurs because they live in similar environments and must adapt to these ecosystems in similar ways. This is the opposite of divergent evolution which we’ve discussed before. Let’s not worry about parallel evolution yet, but keep it in mind.

The most popular example of this concept is wings. Think about it: insects, birds, bats they all have evolved wings for flight independently. Now, there are specific anatomical and functional differences in the structure of their wings and how they actually fly, but theyare considered analogous structures. When nature has a problem (we need to fly) and a species engineers the same solution (how about these flappy things?) that’s convergent evolution, baby! There are other biological examples: opposable thumbs, the structure of the eye, the development of fruit in plants, etc.

The most common mistake when learning convergent evolution is forgetting that the two organisms with analogous traits must be distantly related. For example, opposable thumbs in primates and humans is not an example of convergent evolution because we have a common ancestor that evolved this trait, and then we diverged into different species. However, the opposable thumb in the panda is a perfect example. Their hands have a completely different structure than primates, they have five fingers and a thumb, and the thumb structure develops from the wrist bone. This structure developed independently as primates and pandas both live in the jungle and thus climb a lot of trees and need to grasp their food, simple as that. Thumbs are good for this. If you don’t believe me try using a fork with only four fingers.

Many people believe that the development of the thumb was one invention that ultimately led to our unrivaled success as species as it allows us to use tools. On the other hand, pandas seem to use it primarily for sucking and making people go “awwww”… which isn’t a horrible strategy… after all, who is cleaning their poop?

There are examples of convergent evolution that aren’t structural or even biological, in fact, there are a lot of societal and cultural examples. One of my favorite examples has to do with samurai and knights.

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Japan and most Asian countries were largely isolated from the rest of the world, especially from Europe, until the 1800s give or take. This means that medieval England and medieval Japan are a perfect example of societies that evolved socially independently, much like the panda and the ape. There are many similarities between their cultures, but perhaps the most interesting one is the creation of the knights and samurais.

The amount of similarities between these social classes is remarkable considering they evolved separately. For instance, their role in society was almost identical: they were both feudal lords who received land and the people on it from an Earl/the Daimyo. In return for this land, they were required to pay taxes and pledge troops to the Shogun/Emperor (depending on which was currently in power) or to the King.


How they acquired power was also similar: both knights and samurais were granted their land by inheriting it through birth or marriage. They both lived by a code, bushido for samurais and chivalry for knights, which encouraged the moral values of chivalry, bravery, honesty, etc.



However, they both regularly took concubines/mistresses and had usually had impunity to kill any of the people that lived on their lands.

Perhaps most interestingly, they both were the subject of great tales that are still told today: 47 Ronin and King Arthur and the Knights of the Round Table. In fact, both of these tales were just recently retold in Hollywood… though both had pretty horrible tomato meter results…

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Much like the evolutionary tree above examining the origin of the thumb, a tree can be made to describe the convergent evolution of samurais and knights. Note that much like primates and humans, the ancient Romans and Medieval Europe both utilized a militaristic class in their feudal governments.

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Rogue TNF-R1: An Apoptosis Story

Apoptosis. One of my favorite scientific words. Perhaps, one of my favorite words period. It’s mostly because it provides an appropriate sound effect for the cellular concept. Don’t worry, you’ll understand by the end.

Perhaps the most common example of apoptosis, or rather the failure of apoptosis, are webbed hands or feet. When people are born with this abnormality it is due to failure in apoptosis, or “programmed cell death”.


This is because apoptosis plays an important role in early growth and development. Most animal embryos have similar looking hands (in this case chickens and ducks). However, as developmental time goes on apoptotic events, or lack there of, cause dramatically different ultimate phenotypes. For a duck, webbed feet are normal, even beneficial, and thus years of evolution has selected for a suppression of apoptotic associated gene expression. For a human, they can be darned inconvenient (unless you are trying to win the second task in the Triwizard Tournament).nrg1159-f2.jpg

This is a pretty powerful developmental tool. It can allow a tadpole to swim away quickly enough from a predator before they become prey, it could inhibit an early humanoid from picking up and using a stone as a tool. Yet, this pathway is usually remarkably reliable, only 1 in every 2,000–3,000 babies is born with webbed fingers or toes, which from an evolutionary perspective, is pretty impressive. Apoptosis doesn’t cease to be important once you are born however, it continues to be essential in removing faulty, and even potentially cancerous, cells through out your body. In fact, apoptosis is responsible for the death of 50 and 70 billion cells each day in an average human adult. Even more impressively, that is only 0.5% of the TOTAL cells you kill in a day through other methods.

Because apoptosis occurs so frequently and is unable to be stopped once the process begins, there are two different pathways which regulate the process: extrinsic and intrinsic. In order to explain this properly we have to introduce the destruction of the death star in Star Wars Episode IV: A New Hope… and Rogue One: Episode… 3.5…

The Extrinsic Pathway, let us consider this scene in the movie. The Rebels have analyzed the Death Star’s plans and have identified an exhaust port that connects to the main reactor. Luke, thanks to good old Obi-Wan, successfully shoots into the exhaust port and destroys the Death Star from the outside!

Well, this is a lot like the extrinsic pathway, where other cells, usually T-cells, use a surface molecule known as the FAS ligand (FasL) to bind to FAS receptors on the surface of the unwanted cell. This then activates intracellular factors which result in the caspase cascade. These caspases then break down essential cellular materials, thus killing the cell.

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The T-cells are a lot like X-wing starfighters, and the FasL surface molecules are like the lasers they are firing at the death star, the Fas receptors are the exhaust ports. I supposed the caspase cascade is then the fire and energy released by the destruction of the main reactor.






For many decades us nerds joked about the poor exhaust port engineering, what a silly plot device, as if super geniuses would have made a silly mistake like that.

“Marshall: The but the Death Star is gonna get built either way, and don’t you think the architect of the Death Star is pretty psyched to have that thing on his space resume. I mean, yes, his design was flawed in the sense that he let a single bullet fire into a particular vent that would explode the whole thing…

Ted: For all we know, that was the contractor’s fault.”

However, in Rogue One we discover, it wasn’t a poorly conceived plot device after all! It was totally intentional!!! Thankfully this makes for a perfect analogy of the other type of Apoptotic pathway.


The Intrinsic Pathway, as the name suggests this path of destruction is initiated from within the cell, specifically in the mitochondria. The mitochondria contain anti-apoptotic proteins (BCL-2 and BCL-X) and pro-apoptotic proteins (BAX and BAK). In a healthy cell, these proteins are bound together, preventing either from being activated. However, if the cell experiences damage or does not receive the normal survival signals, then the anti-apoptotic proteins will be blocked from binding and BAX/BAK can be free at last. They then punch holes in the mitochondria and allow all the fun juices to leak out, these juices activate the caspase cascade… and well you know the rest…

When I picture the inside of mitochondria, I definitely think of Galen’s Imperial research facility on Eadu, who doesn’t?


Here, Galen tells Jin of the small weakness in the Death Star, this encourages her to get this information to the Rebels. This is a lot like how the cellular damage signals activate the BAX and BAK proteins. As we know the Rebels then send fighters to “poke holes” in the Death Star until it explodes.


Both processes result in cell death, both narratives end in Vader’s anguish. However, for decades we thought this was a story of an extrinsic pathway, but all along it was an inside job.

Rest well Stardust.



The Hardware of the Cell

This blog post is a bit of a 2 for 1 sale on learning. You’ll learn about the hardware parts that make up your computer (you can go into any Apple store and intimidate the employees), and you’ll also learn about the various organelles that make up eukaryotic cells. So whether you’re learning about what CPU means, or what cilia are you’ll be entertained.

When you walk into Best Buy, the Windows store, etc. you are first struck by the visual similarities and difference between one computer and another. Some are gray and shiny, others black and matte, most have an emblem of some sort whether that be fruit, a cartoon alien, or simply the brand name. Computers also vary significantly by size. The largest computer ever built is the Sunway TaihuLight which has the average computing power of 93 petaflops (yeah, that’s a measurement), check out this video below to have your mind blown. The smallest computer is the Michigan Micro Mote, at one millimeter cubed it’s the smallest autonomous computer in the world.

Similarly, the outsides of eukaryotic cells come in many shapes, colors, sizes, and textures. Some have flagellum or cilia (bacterial cells), others have a rigid structure (plants cells), and others are amorphous (animal). Members of the Ostreococcus genus rank as the smallest eukaryote. They have an average size of 0.8 µm, a genome 13 Mb long, and contain only four organelles: a nucleus, a single chloroplast, a single mitochondrion, and a single Golgi body. (Fun fact, their genome is still 13 Mb which four times the size of smallest recorded genome of 2.9 Mb). The largest eukaryotic cell (sorry slime molds, I’m disqualifying you) are neuron cells found in particularly large animals. A  published in Progress in Neurobiology found some neuron cells in the blue whale to be 10 cm long!


Laptops have varying degrees of protection and rigidity. The kind used by the military (you know, the ones Samuel L. Jackson is usually holding in movies) are water and shock absorbent and are extremely rigid. On the other hand, companies are actively working on creating computers with flexible displays. Cells are also highly variant in these qualities with plant cells being very rigid and highly structured, and animal cells being shapeless and fluid. This difference is due to the cell wall/membrane. In plant cells, the cell wall is made of sugars (cellulose and chitin) and can range in thickness from 0.1 to 10 µm. Animal cells have a cell membrane made of fats (phospholipids) which make the cell have more of a flexible form.

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Both types of cells have what is called a cytoplasm. The cytoplasm is mostly made of water and nutrients and fills the cell in and gives it its shape (picture the water in a water balloon). It helps the organelles stay in place and allows proteins, chemicals, etc. to move around the cell. Much like the cytoplasm, every good computer needs a cooling system to circulate through the entire computer to ensure all of the parts do not overheat and fail. There are two main cooling systems for computers, either air (usually made by installing fans, this is the noise you hear when your computer is working hard), or the riskier option for hardcore gamers: water.


The cytoskeleton is usually referred to as the skeletal structure of the cell, it’s all of the proteins that maintain the cell structure and organelle organization. The motherboard doesn’t actually do anything, it relies on the processor to give the machine power, relies on the RAM to store memory, but it is the circuit board of the computer that ensures all of the electrical signals from the various parts of the computer go in the most efficient and correct direction.


The endoplasmic reticulum is the highway of the cell, a network of membranes that is connected to the nucleus, to the golgi apparatus, etc. It comes in two flavors, smooth and rough.The smooth ER contains various enzymes to aid in creating lipids, detoxifying noxious chemicals to make the soluble in water, and stores ions the cell may need later for energy. The rough ER is covered in ribosomes (hence its name) and is essential to the synthesis and packaging of proteins. The ribosomes are the organelles specifically responsible for creating polypeptides out of amino acids. When the ribosomes are finished synthesizing the leave the ER and move to the golgi apparatus. A major component of computers is wiring. Wires that connect the motherboard, the case, the power source, the fan, etc. all together, there really is a ton of wires… Much like the ER which is responsible for shuttling genetic information through the central dogma process, the wires in a computer are essential in sending data and electrons throughout the machine making all of the independent pieces work together.


The golgi apparatus takes the proteins and lipids made by the ribosomes in and determines and directs where the proteins should be sent. The golgi puts the components in a vesicle that will be able to get around the cell or through the cell wall without being damaged or degraded. This is very similar to what a hard drive does. The hard drive is where data is stored and retrieved in a computer, data is placed on the hard drive via electrical currents on a bit as a 1 or a 0, and the these 1’s and 0’s are read, converted back into electrical currents and the data is retrieved. The number of bits used is dependent on how complicated the data is. For example, an average photo is made of millions of bits. Hard drives keep getting smaller and smaller as more bits can be placed on smaller surfaces. See here for some helpful visualizations. The golgi and the hard drive both act as temporary storage and go-betweens in shuttling data (in the case of the cell, genetic data) around the cell/computer.


Lysosomes attach to old organelles such as mitochondria, or to foreign particles, and break them down so it is easily digested by the cell. The cache acts as temporary storage, the data stored on the cache is usually old or duplicated data which is kept in order to faster serve future requests by the user, however, when the computer is turned off this data is completely erased.

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The nucleus is the most familiar organelle, it’s usually referred to as the brain of cell. It is where all of the genetic material is kept. When an environmental factor outside of the cell is sensed (most likely a change in chemistry) by the nucleus and the nucleus directs the organelles to respond to the stimulus appropriately. DNA is relaxed from it’s normal compressed form and various proteins flow into the nucleus to transcribe the code and take it for translation into proteins. The nucleus decides when the cell divides, when and what proteins are made, and even when the cell should self-destruct. The nucleus is a lot like the processor of a computer. The processor receives input data (the click of a mouse of instance), processes this data, and provides output data (opens an application). Without the processor, the computer could not be able to respond to stimulus which would make it useless, much like a cell without a nucleus.


The phase “Mitochondria are the power house of cell” is so common and lame that it makes my skin crawl, but it is true. The mitochondria supplies the cell with energy in the form of ATP by breaking down nutrients and utilizing the electrons. ATP is then released into the cytoplasm so the other organelles can perform essential functions. The process is much more complicated than that, so I will bore you with it another time. This is a lot like how the computer uses the PSU (power supply unit). The PSU converts the alternating current power supply you get from sockets into the low-voltage direct current power the computer needs to run, much like how the mitochondria converts nutrients into ATP.


I have no clever conclusion, my computer and I are both very tired.