Deep Sequencing: The Bomb

Or the moment that destroyed me and its historical context in The Manhattan Projects: Volume One
By Jonathan Hickman, Nick Pitarra, and Jordie Bellaire; Image Comics

Before The Manhattan Projects took a sharp turn to completely fantastical, gruesome Mad Science, it briefly flirted with the real life history of The Manhattan Project and the development and deployment of the Atomic Bomb. The chapter of Volume One, The Bomb, which tells an alternate story of bombing Hiroshima, is one of the most tense, arresting single issues of comics I have ever read: the way it plays with true history and the bizarre carnival mirror of the comic is profound and horrifying and a thought provoking look at the intersection between Science/Technology and Society/Politics. (You really ought to read it; if I were teaching a Philosophy of Science class I'd make my students read it.) That said, there is a single moment in tThe Bomb that is so rip-out-your-heart perfect that I still think about it more than a year after reading it. And I would like to explain why.

This post will have *SPOILERS* for Manhattan Projects: Volume One. Be warned.

In this sequence amoral-mirror-Richard Feynman goes to evil-parallel-universe-doppleganger-Albert Einstein with the engineering question of whether the Manhattan Projects should focus on constructing a relatively simple "gun-type" nuclear fission bomb, or a more complex "implosion-type" device. The part of this that resounds with me and absolutely guts me, is that not-Einstein replies simply that they should "just build both".

Which is just so completely fucking, oh my god brilliant and awful and perfect.

Because the real-life Manhattan Projects really did build both.

The thing about nuclear bombs is that they are perversely simple. For a nuclear fission explosion, all you need is enough stuff, a sufficiently massive lump of high purity fissionable material will undergo a runaway nuclear chain reaction and explode. So all a nuclear fission device is, is a machine that takes  a chunk of radioactive material which is too small to have this exponentially growing nuclear reaction and pushes it over the mass threshold needed to explode. The simplest way to do this is to hold two chunks of fissionable material apart, and then rapidly stick them together to make a big enough chunk to blow up. And this is literally what a gun-type device is.

The real challenge of nuclear bombs is the fuel for the explosion. Naturally occurring high quality fissionable material is exceedingly rare, and even then the most reactive isotopes have to be painstakingly separated from slightly more common less or un-reactive isotopes. Many of the better nuclear fuels are not naturally occuring in sizeable amounts and have to be produced in labs, usually using other nuclear reactors. (Incidentally a bunch of super important medical isotopes are becoming increasingly rare as many countries shut down their reactors.) So the real life history of The Manhattan Project is shaped by the history of the production and availability of high quality radioactive isotopes.

Initially, the project lacked sufficient pure radioisotopes of any kind of fuel to build any type of bomb. However, the project did have access to naturally occurring Uranium from a variety of mines and over time developed the a technique to separate desirable Uranium-235 from the inert, majority Uranium-238. This meant that The Manhattan Project had the capability to construct an enriched-Uranium nuclear device. Because the The Manhattan Project was in a rush to build atomic weapons to use in the war, they opted to keep it simple, and build a gun-type device that shoots a small chunk of U-235 into a larger chunk to set off an explosion.  This is the first bomb they built called the Thin Man and later, The Little Boy.

However, during development of this first bomb, a new, better fuel source, Plutonium, became available. While The Manhattan Project was developing the bomb, another portion of the project was developing nuclear reactors. Some nuclear reactors make, as a byproduct of fission, plutonium, which is a higher energy fissionable material and so useful amounts of Plutonium became available to The Manhattan Projects. (Science brag: Ive held a warm sphere of lead lined Plutonium in real life.) However, Plutonium did have one other problem: it was too reactive to be used in a gun-type device. A gun-type Plutonium device would "fizzle" by tearing itself apart before a significant amount of the bombs fuel could be reacted, and so the device would lead to a much smaller explosion. And so the real-life Manhattan Project was forced by engineering reasons to develop an implosion style device that basically crushed a ball of Plutonium into a dense enough ball to set off an exponentially growing nuclear reaction and explosion. Trinity and The Fat Man were this type of bomb.

The thing is, this device was, by comparison to the gun-type device, super complicated so The Manhattan Project was not willing to suspend the development of the simpler Uranium gun-type device. So in the end, they built both a gun-type bomb and an implosion-type bomb.

And then they fucking used both.

The bomb the US dropped on Hiroshima Japan was The Little Boy, a uranium gun-type device. The bomb they dropped on Nagasaki three days later was Fat Man, a plutonium implosion-type device. In real life, they built both types of bomb and USED both types of bomb. 

And that is at once a perfectly logical, practical Science and Engineering decision and excruciatingly horrifying.

With this real life context, this line by evil-Einstein is just so perfect and so completely awful. This moment encapsulates the mercenary practicality of the decision to develop both devices, the near sociopathic disregard for the consequences of this choice, and the inevitable finality of this decision. It's a carnival mirror reflection of the frigid, inhuman extremes of Science and Engineering. 

And so it sticks with me.

Previously:
The Manhattan Projects: Volume 1
The Manhattan Projects: Volume 2

Super Science: The Beat That My Heart Skipped

Or representations of heart rate in comics and my crazy pet peeves surrounding them, using examples from Daredevil.
By Mark Waid, Javier Rodrigues, and Chris Samnee; Marvel Comics

A not uncommon trope in comic books is that a character with super hearing can assess the honesty of other characters by listening to their heart beat. The idea is that someone with something to hide will have their heart rate unconsciously increase when they are being untruthful or when they confronted and be betrayed by their telltale heart beat. For characters like Wolverine, Superman, and especially Daredevil, it can be quite common to see our hero confront a potential liar and see the squiggly wave pattern of their heartbeat flash across the panel.

And on the surface this is fine. Liars DO often have an unconscious increase in their heart rate, a response to confrontation that activates their fight-or-flight nerves (Sympathetic Nervous System) which stimulates a faster heart rate. As a result, heart rate is one of the physiological responses that are tracked during a Polygraph lie detector test. This idea actually works to a certain extent in real life. So I really have no issue with the overall concept of using heart rate as an indicator of duplicity in comics.

No my issue is that the sound of a heart beat is portrayed as an electrocardiogram (ECG) waveform.

Now, in my day job, I'm a Science graduate student who studies how heart muscle cells work: specifically how their electrical signalling (which controls contraction and heart rate) influences the rate at which they convert fuel (fat/sugar) to energy (ATP). So I know a bit about how hearts work, and spend more time than an average person looking at and thinking about ECG's. So as a result, I have a crazy person pet peeve about using an ECG waveform as a stand in for the sound of a heart beat. And here's why:

An electrocardiogram measures changes in voltage in the heart. The heart, as you probably know, is an electrically active organ: on a cellular level it moves charged atoms (ions) across cell membranes in such a way to create voltages which in turn turn control heart contraction. During a normal heart beat, a cluster of pacemaker cells, which spontaneously change their voltage, activate themselves by "depolarizing", and start a cascade of electrical signals that will spread around the heart and cause it to contract. Heart cells are joined end to end in a way that lets them carry this electrical signal and activate one another, so once the pacemakers "fire" their activation signal, that signal will eventually travel to every healthy muscle cell in the heart during a single heart beat. And every heart muscle will, when it sees this activation signal, activate and contract, which makes the heart compress and pump blood. Now, the heart has to contract in a coordinated way: different parts of the heart will contract in a sequence, and within those parts thousands of cells have to work all at once. To make this happen the controlling electrical signals in the heart follow a specific, regulated path around the heart. The electrical signal starts in the pacemaking area, travels around the top chambers of the heart (atria), slows down for a tiny moment at a fusey structure to give the atria a chance to contract and empty, and then races down specialized signalling pathways that spread the signal evenly throughout the big lower chambers (ventricles) of the heart so that this part of the heart contracts all at once. What this all means is that if you stick electrodes on opposite sides of the heart you will see regular, repeated patterns in voltage changes, and this pattern is an ECG.

And ECG are awesome tools for measuring heart rate. You get a regular waveform with a small upward tick during atrial depolarization, a complicated down-up-down squiggle during ventricular depolarization, and another upward tick when all the ventricle cells reset themsevles by "repolarizing" (if you measure an ECG in the stereotypical way). You can get all kinds of information from these ECG patterns, including, from how close together or spaced out they are, the heart beat of a person. Which is how they are used in comics.

My crazy-person problem is that voltage changes in the heart have NOTHING to do with how a heart sounds: an ECG is not related to the heart beat sounds at all. And this bothers me a little.

Hearts make a pretty distinctive sound when they beat, a kind of "Lub-Dub" (or, in the words of Johnny from dirty dancing, "Guh-Gung"). This sound is made by the valves in the heart snapping closed during a heartbeat. Heart valves, the doors between the four chambers of the heart and the heart and the rest of the body, function as one way valves that let blood travel one way through the heart and body. So during a heartbeat you get a sound, "LUB", when your ventricle chambers compress, making one pair of valves located between chambers to loudly snap close. Then after the heart stops contracting and relaxes, you get a "DUB" as the other set of valves snap close to stop blood from flowing back into your heart. And this cycle of "Lub-Dubs" directly relates to heart rate and is LITERALLY heart beat. So a slowly beating heart sound something like "Lub-Dub....Lub-Dub...Lub-Dub" while a rapidly beating heart would have a beat like "Lubdub-lubdub-lubdub...". Comic artists could literally just use the onomatopoeia of the sound to make a more realistic portrayal of a racing heart.

But, admittedly that isn't very visually satisfying or efficient comics.

But there is a visual solution that is also accurate. The lub-dub sound is so regular, so characteristic that its waveform, the shape of the sound itself, is so visually distinct that it is a diagnostic tool in medicine. (Literally the first test for heart function, before and ECG or Echocardiogprahy (visuallizing the heart with ultrasound) is a doctor with a stethoscope listening for regular lub-dubs, skipped beats, and weird leaky sounds. And even later in the diagnosis game a more complictaed sound analysis test is sometimes used.) Anyway, this waveform, just like an ECG keeps the same pattern, bigger initial collection of squiggles ("lub") closely followed by smaller cluster of squiggles ("dub"), over and over. Heart rate is defined by how wide the gap between repetitions of the pattern, also just like in an ECG. So really, with the heart sound waveform pattern you get a distinct looking thing that describes heart beat just as well as an ECG waveform that is LITERALLY the sound of the heart beating.  So, if an artist wanted to represent the sound of heart rate in a super-detailed and Scientifically correct way they could draw the actual waveform pattern of the heart.

Now, I'm aware how crazy, pedantic, and unfair this pet peeve is. Normal people don't care about the distinction between heart sounds, heart muscle contraction, blood pressure, and electrical activity when measuring heart rate. I suspect for most people an ECG is just as valid a way of representing audible changes in heart rate as my purposed "lub-dub" sound waveform. In fact, from a comics-as-visual-media perspective an ECG is probably a BETTER way of representing heart rate than the sounds: it is much more universally recognized as a heart specific thing and directly relates to heart rate in the human imagination. Hell, it is even tied to sound with the "bleep-bleep-bleep" of heart rate monitors in hospital settings (and the "bleeeeee...." of a stopped heart). The ECG as a symbol conveys much more visual meaning with more efficiency than the Scientifically accurate sound diagram, and since comics are about telling stories in visual ways and not appeasing internet jerks using ECG's is probably the right choice.

The right choice that I find irrationally annoying.

(Oh, and while I am on the topic of ECG's in comic books, I recently tried the first issue of the new Superman/Batman comic by Brain Azzarello and Lee Bermejo, and there is a use of ECG in here that is all kinds of wrong. While trying to portray a racing heart in a terrified man fighting (to contrast it to the cool as cucumbers steady beat of Bruce Wayne) they used a crazy erratic ECG trace. This is how an ECG would look if you were having a SERIOUS ahrrythmic/ventricular fibrillation event. Seriously, this is how an ECG would look if you were DIEING of "Sudden Cardiac Death". A racing heart keeps the pattern's shape: sound and ECG patterns don't change, they just repeat faster. An ECG drawn this way isn't just me-being-a-lame-pedant-wrong, but is meaningfully factually wrong.)

Marvelling at Captain Marvel #9

Or an excuse to talk about Science in the context of comic books.

There be *SPOILERS* in this one. So go read Captain Marvel #9 before reading this post. Don't have it? Shame on you, this is an amazing comic.

First let it be said that Captain Marvel #9 kicks so much ass. I mean, I've really enjoyed every issue of Captain Marvel so far, but this one is fantastic. To the point where if someone were to ask me "Why do you read superhero comics?", I could answer "Because Captain Marvel #9". It's based around a slice-of-life ordinary day for Carol and is filled with satisfying character moments, little snippets of great comedy, a broadening supporting cast, and a gun point standoff. And a ridiculous "lucky" touque (I'm Canadian, we have a word for that). AND dinosaurs in downtown Manhattan. In Captain Marvel #9 Kelly Sue DeConnick manages to turn what could kind of be considered a setup/logistical issue into a beat perfect superhero comic. Filipe Andrade, this issue's artist, has a kinetic and kind of exaggerated style that is pretty great and completes the package. Did I mention I really like this comic?

Anyway, on the last page *SERIOUS SPOILERS* it's revealed that Carol has a lesion in the Suprachiasmatic Nucleus of her brain.

You might be wondering, what is a Suprachiasmatic Nucleus (or SCN). Well, since two of my favourite non-human things are Science and comics, I'll try to defuse this jargon.

Structurally the SCN is a small collection of neuron cells that live kind of behind the optic nerve and some visual signalling structures (one of which is called the optic chiasm) in the brain. In the brain, small clusters of neurons are referred to as a nucleus (not to be confused with the nucleus that contains DNA; Scientists are the worst at naming things). So we have a collection of neurons that lives close to the optical chiasm: hence Suprachiasmatic Nucleus. 

But brain structures only matter in so far as they do something. So what does the SCN do? Well, it's where our bodies' internal clock lives.

People evolved on a planet that has light and dark cycles; day and night. A consequence of this is that our bodies adapted to do certain things at certain times of the day. Like to sleep at night and wake up in the morning or to get hungry during the day, but to fast and slow our metabolism at night. To manage this our brains contain a time keeping mechanism that counts out almost exactly 24 hours before resetting. And this time keeping mechanism lives in the SCN. Which is pretty cool. But how does it work?

So a clock works because some part of it is able perform a motion in a consistent, regular way. A grandfather clock has a pendulum (a big ass weighted chain) that sways back and forth at a regular interval (which is maintained by a slowly uncoiling spring). Old pocket watches work by winding a spring that slowly and regularly uncoils and spins gears that turn with a certain speed to keep time. Modern watches use a piezoelectric crystal (essentially a cool rock that will physically oscillate in size (a little) when you run an electric field through it from, say, a watch battery) to mark the regular, periodic passage of time. Well, the SCN works in a fairly similar way, except it oscillates protein levels to tell time.

In the SCN a protein called CLOCK ("circadian locomotor output cycles kaput"... because sometimes Scientists DO name things well) is produced. CLOCK is something called a "transcription factor", which is a protein that can bind to DNA in a cell and turn on or off the production of other proteins. They are kind of like control switches. Anyway, in the SCN, CLOCK is made at a steady rate. Initially it has a low concentration and is stuck in the main compartment of the cell (called the Cytoplasm). Eventually CLOCK reaches a high enough concentration to enter the Nucleus of the cell and bind to DNA. CLOCK can turn on and off a lot of different protein making pathways, but some key genes that get turned on are the ones that manufacture  Period (PER) and Cryptochrome (CYC) proteins. PER and CYC are also transcription factors, and when they are turned on they bind to DNA and turn off the production of CLOCK. This causes CLOCK levels to fall (because cells recycle things), which eventually means CLOCK can't turn on PER and CYC, which means PER and CYC can't turn off CLOCK, which means that CLOCK production starts up again. The cycle repeats.

So to recap, in the SCN during a 24 hour day, CLOCK is made until it turns on production of PER and CYC which turns off CLOCK which eventually will turn off PER and CYC which turns on CLOCK. And then this repeats during the next 24 hours. Which is, in a basic sense, how your brain keeps track of time.

Of course, it's WAY more complicated than that. There are other proteins in the SCN that also fluctuate during a 24 hour period and interact with CLOCK to help keep time. (such as BMAL1, REV-ERBa, RORa etc). Your brain also takes in environmental information and uses this to fine tune the clock. So things like light and dark are used to alter the clock and make it run even more accurately. (Which is why it is important to sleep in a DARK room and why when my dog needs a 3am emergency bathroom run involving a well lit hallway my sleep gets ruined.)  But all of this action takes place in the SCN.

Information from the clock in the SCN gives timed instructions to other areas of the brain, like centres that control wakefulness and hunger or regulate the release of hormones like insulin, melatonin, and growth hormone. So it's a pretty important little structure that affects pretty much every other system in your body.

Which makes the SCN not a great place to have a lesion.

Did I mention I love this comic book?

Heart Attack!

Or the implausibly plausible Science in the Heart of Hush storyline by Paul Dini and Dustin Nguyen

Two of the things I love in this world are comic books and Science. Sometimes I like to write about both. This... Is one of those times.

In a recent post, the internet's foremost Batmanologist Chris Sims panned the character of Hush, criticized his origin and also the "Heart of Hush" storyline. Critically he dismissed the latter story for its entertainment value as well as its Scientific believability. I am here to tell you, in my capacity as an actual heart scientist, that as far as comics go, it's actually not too unbelievable.

Okay, gotta lay some caveats and addenda down here. While I might tease Mr. Sims for his knowledge of heart Science/Medicine, his Batman knowledge is encyclopedic and incredible and his taste in comics is impeccable. His thesis that Hush is a silly character with bizarre motivations and contrived story uses is totally correct. Hush stinks. The Hush origin books, while visually appealing are derivative and ultimately a base amalgam of much better comics. And yeah, the Heart of Hush storyline, wherein Hush literally steals Catwoman's heart is pretty ridiculous. (Although, I thought the Catwoman-Batman love story part of it was kind of nice; much better than the anatomically bizarre rooftop fucking of the New 52.)

The crazy thing is though, is that the Sci-fi of the story (Hush surgically removes Catwoman's heart, then keeps both Selina Kyle and her heart alive with machines, after which her heart is replanted) is actually not as far fetched as you might think.

A Scientific discussion of the Heart of Hush storyline after the cut: 

The Amazing Spider-Goat

Or the real life goats with amazing spider-powers.

Scientists genetically engineered goats which produce spidersilk proteins in their milk by adding spider DNA to their genetic makeup.

Let me reiterate that: Scientists made goats that produce spidersilk IN REAL LIFE.

Producing milk with extra proteins admittedly isn't much of a superpower, but it is a genetically engineered goat that can do something regular goats can't. It's also a case of giving spider traits/abilities to a non-spider creature, which under the Spider-Man paradigm is superhuman (well, supercaprids).  Also, given the caveat that this is real life where things have to behave in scientifically valid ways and I think this is considerably awesome.

It’s also a hypothetical proof of concept for making humans that can produce spidersilk. (although they would have to be lactating females…)¹

How did they create these sins against nature? The first thing they did was to create a synthetic chunk of DNA with a spidersilk gene (specifically for a dragsilk protein, which is the strongest kind) under the control of a mammary tissue² specific promoter (a genetic on/off switch that controls how much a gene is turned into a protein). My money is that the promoter they used is one of the casein ones (proteins in milk, that are only made in mammary tissues). They then took the synthetic DNA and injected it into a bunch of goat embryos, some of which added the DNA to their genome.³ They put the embryos into mummy goats an got goat babies with amazing spidersilk milk powers. SCIENCE!!!

Of course Nexia, the Montreal based biotech company (which may or may not be a front for Department H) that made these goats apparently couldn't spin the spidersilk well enough to use it for industrial/medical applications and subsequently went bankrupt. Apparently they sold the last spidersilk goats, Sugar and Spice, to the Canadian Agriculture Museum. So you can go see the amazing Spider-Goats in person!

Also, apparently a researcher in Utah has made his own spidersilk producing Spider-Goats too... So the dream lives on? I hope so.

1: It would also be SOOOO unethical.

2: Udders in goats, breasts in humans.

3: It’s a bit more complicated than this… but that’s the basic idea of how it works. They have also used retroviruses, but that can be kind of messy/cancer causing.

In Theory The Iceman Cometh

Or a Scientific Treaties on the Plausibility of Mr. Freeze

Mr. Freeze from Batman and Robin. Campy!

I think Mr. Freeze is one of the more interesting characters in Batman’s Rogues Gallery. He has a cool gimmick (ice powers, has to stay cold to live), a chilling and tragic backstory (gets powers from lab accident while trying to cure terminally ill wife),¹ and like all of Batman’s best villains Mr. Freeze acts as a foil for the caped crusader (loss of loved one motivates revenge instead of heroism). He is also one of the few Batman villains who can contend with Batman both intellectually and physically making him a good candidate for being a major villain in a potential future Batman film. Unfortunately, due to his supernatural/sci-fi nature and his campy Batman’66 and Schumacher escapades, it is very unlikely we will ever see him in another movie.²

I’m here to tell you that Mr. Freeze does not have to be campy and unrealistic. In fact, with some relatively cosmetic changes, Mr. Freeze can be made into a serious and Scientifically plausible villain.

An extensive treatise follows after the cut: