Biochemistry of Michael Bay‘s “The Rock”

Michael Bay is not particularly known within the scientific community as someone who cares about accurate representations of scientific principles (e.g. Armageddon… All of it). Nonetheless his 1996 release, The Rock, is one of my favorite action films and probably his best ever film release in terms of quality movie-making. Without spoiling too much of the plot, it involves a disillusioned U.S. army general that steals a bunch of rockets armed with poisonous gas to hold the city of San Francisco under ransom for compensation for his soldiers whom had fallen in combat and had been disavowed by the U.S. government due to the covert and reticent nature of their reconnaissance mission. Yikes. The FBI enlists the assistance of a biochemist played by my own personal hero and spirit animal, Nicholas Cage, and James Bond.

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Not even kidding. There is no other way of putting it. Sean Connery plays a British secret agent who was captured by the American government and held without trial ever since. The way I see it, The Rock and the James Bond movies take place in the same universe where Connery’s Bond is captured sometime after his last exploits in the 007 franchise. But I digress.

The plot is perfect. The casting is perfect; the music is especially perfect, the pacing, the action, the climax, the heroes’ and villain’s arcs. It’s all exemplary. It is the perfect action movie… except for the science perchance. But it’s still damn close.

The aforementioned toxic gas is called VX-gas and even though it sounds made up, it is entirely real. Its systematic IUPAC name is ‘Ethyl ({2-[bis(propan-2-yl)amino]ethyl}sulfanyl)(methyl)phosphinate (pictured below).

VX-S-enantiomer-2D-skeletalVX-S-enantiomer-3D-balls

(Right) 2D molecular structure of VX. (Left) 3D molecular structure of VX.

The film allows this toxin a corrosive nature that results in exposed characters being melted prior to death by asphyxiation. The deliquesce, face-melting property is, however, completely made-up, albeit pretty cool. (Movies are allowed a dose of artistic license here and there, right?) However, its toxic properties are quite real and are adequately represented in the film. I.e. this is a severely potent neurotoxin.

To explain how the toxin works, we need a crash course in neurochemistry. Bear with me.

The human body withholds an immense network of interconnected neurons; cells who are excitable by electric charges and thus have the ability to receive, process, and transmit information through electronic and chemical signals. In layman’s terms you can imagine an electrical domino effect, where an external stimulus (like a kick in the nuts) leads to a sudden local response in the affected area. Electrical charges (i.e. aforementioned local response) are moved from one neuron to the next all the way up to the brain where signal is interpreted as atrocious pain.

One of the principal molecular components that allow the electrical signals to be transferred from neuron to neuron is called Acetylcholine (ACh).

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2D molecular structure of Acetylcholine (ACh).

ACh is a neurotransmitter used at the neuromuscular junction, i.e. it is released by the nervous system to act as a motorboat for the activation of muscles. On top of that, ACh is also a neurotransmitter in the autonomic nervous system that governs e.g. the function of the internal organs, fight-or-flight response, etc., as well as acting as a neurotransmitter in the brain.

In biochemistry, usually every molecule has its associated enzyme whose sole purpose is to break the molecule down into (relatively) inert components. For ACh, that would be Acetylcholinesterase (AChE).

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4.order structure of the enzyme, Acetylcholinesterase (AChE).

Briefly, AChE’s job is to break ACh down into acetic acid and choline which cannot perform the molecular task that ACh has.

Now, the function of ACh in terms of transmitting neurosignals is as follows: (i) ACh is released into the region between neurons or a neuron and a receptor cell (called a synapse), (ii) ACh binds to receptors at the adjacent neuron, (iii) the binding of ACh causes ion channels to open and allows positively charged ions (plus-charged sodium atoms) to flow into the adjacent neuron or other cell, (this is sort of the chemical equivalent of opening a door with the right key) (iv) the ACh in the synapse is then broken down by AChE into acetic acid and choline, (v) and finally choline transports back into the neuron where it is transformed back into ACh with help from another enzyme called Acetyl Coenzyme A.

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Schematic of the molecular role of Acetylcholine in the synapse between neurons.

Phew. So, where does VX come into this picture?

Well. It is an acetylcholinesterase inhibitor (AChEI). It works by blocking the function of AChE. The original purpose of breaking ACh down is to avoid a state of constant muscle contraction. If ACh is not broken down, it keeps the aforementioned ion channels open and thus would induce muscle spasms by constant charge flow.

What VX does is that it binds to AChE without being broken down the way ACh would be. Therefore ACh can’t be broken down by AChE and which results in the accumulation of ACh in the synapses. This leads to constant stimulation and eventual fatigue of all ACh receptors. As a result, anyone affected by the toxin exhibits violent contractions and muscle twitching. Prolonged exposure leads to flaccid paralysis of all of the body’s muscles, including the diaphragm muscle that causes death by asphyxiation.

The potential fatal dose of VX is only slightly higher than the dose having any effect at all and the effects of a fatal dose are so rapid that there is little time for treatment.

Coming back to The Rock I want to give credit where credit is due. Nicholas Cage’s acting. Yes. I am going to actually complement Nicholas Cage’s acting.

faceoff

In one of the last scenes of the film where his character is subjected to VX poisoning, he does exactly what the toxin is expected to do. He convulses, spasms, and finally lies on the ground expecting to die, utterly fatigued. Cage must have done his homework on the effects of VX gas because his reaction to the toxicity is utterly believable.

On the other hand, another creative license the film took to up the ante, was to make the only defense against VX be an intracardiac injection (needle to the heart) of atropine rather than intramuscular injection (e.g. into the thigh or buttocks). But let’s be honest, watching Nicholas Cage stabbing himself in the chest with a needle is much cooler than watch him inject a needle into his ass. That’d be more appropriate for his film choices of the past 10 years rather than his flawless 90’s career.

 

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„Dodge this“ …. Okay!

Right off the bat, I love The Matrix. It’s one of my all-time favorite sci-fi movies (along with The Animatrix… the sequels suck) and was one of the first films that got me into the genre of sci-fi and still feels very nostalgic to me (I saw it on video when I was twelve).

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On the other hand, it is definitely flawed, riddled with plot holes, and the Neo is basically another Jesus Christ inspired main character that countless other sci-fi (and non-sci-fi) films based their basic plot on. But despite its shortcomings, its style, special effects, action scenes, etc. more than make up for the relatively lame story and hole-punctured plot.

But this brings me to one specific scene I’d like to nitpick. It’s nearing the end (spoiler alert) when Trinity momentarily saves Neo from an agent. In spectacular special-effect fashion, Neo dodged the agent’s bullets just as the agent had dodged his by moving his upper body extraordinarily fast while standing still. Walking up to Neo who’s laying on the ground, the agent points his gun at Neo. That’s when Trinity points her gun at the agent’s face and says: “Dodge this” and shoots him in the face (which somehow sends the agent jumping into the air. Uhm hello, conservation of momentum… someone???).

My problem with this, albeit cool scene, is that it makes no sense. Exhibiting the kind of reflexes the agent just showed us, the three seconds that it takes the agent to notice the gun being put to his face and Trinity coolly saying her line should be more than adequate time for the agent to simply move away and shoot her in the face. I mean, It’s cool, but nonsensical.

So here’s my input. A simple calculation to why this doesn’t make sense.

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Okay. Let’s say the agent is standing 10-15 m away from Neo (d = 12.5 m ± 2.5 m). When Neo fires at the agent, he lets out 20-24 shots (22 ± 2 shots) in a time-frame of 7 seconds (7.0 ± 0.5 sec). If we are to believe Mythbusters, bullets travel approx. 2500 feet per second or 760 m/s ± (say) 20 m/s. Let’s assume that the time between Neo’s shots is approx. equally divided, i.e. 7 seconds divided by 22 bullets = 0.32 ± 0.04 sec/bullet**. The time it takes Neo’s first bullet to travel the space between Neo and the agent is then the distance divided by velocity of the bullets, i.e. 12,5 m / 760 m/s = 0.016 ± 0.003 sec. This demonstrates the initial reaction time of the agent where he dodges the first bullet. The time elapsed between bullets (0.32 sec) is therefore more than enough for the agent to dodge the previous bullet and anticipate the next one. In summary, the agent dodges a bullet in under 0.016 seconds and has 0.32 seconds to react and dodge the next bullet.

The time it takes Trinity to put her gun to the agent’s face (nota bene, the gun touches his face before she delivers her line) is approx. 2-3 seconds (let’s say 2,5 ± 0,5 sec). In that time the agent could theoretically dodge 2,5 sec / 0.016 sec = 160 ± 40 friggin bullets! I.e. at least over a hundred. Nice one Trinity. Nice one.

Remember kids. If you’re going to play it cool. You are mathematically more likely to die… sooner.

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**Uncertainties were performed with a general error propagation formula as described by H. H. Ku.

Next stop: SOLEIL

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Over a year prior to finishing my PhD I have been hunting for postdoc positions in the field of astrochemistry. I have written a bunch of grant applications (including Marie Curie fellowhsips and VENIs) and gotten a whole lot of disheartening rejections. Recently I came across a pretty good quote that was supposedly by former Indian president A. P. J. Abdul Kalam. (By the way, try Googling his name and you will stumble upon a plethora of inspirational quotes).

“Sometimes not getting what you want is a brilliant stroke of luck.”

[Tangent] However, once I started googling the quote itself, I found inspirational posters that trace the quote back to either Dalay Lama or Lorii Mayers. Thanks internet. Here, have another A.P.J. Abdul Kalam inspirational quote then![/Tangent]

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The way I see it, I believe I have hit the jackpot with all these prior rejections. I have, namely, obtained a postdoc position at the distinguishing and world-renowned SOLEIL synchrotron in Saint-Aubin, France.

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The SOLEIL synchrotron functions by accelerating electrons up to high speeds (near the speed of light, at which point they become relativistic). The electrons then start to loose energy in the form of photons are variable energies. These photons (or synchrotron radiation) are used on many installed user stations at SOLEIL, each of which dedicated to a certain wavelength region of the electromagnetic spectrum.

I will be working within the Atomic and Molecular Physics, Dilute Matter, Universe Science division on the DESIRS beamline ((Dichroïsme Et Spectroscopie par Interaction avec le Rayonnement Synchrotron) under the supervision of Laurent Nahon and Gustavo Garcia-Macias.  The DESIRS beamline focuses on ultraviolet radiation in the 5-40 eV photon energy range and my projects will concern combustion chemistry and interstellar chemistry.

According to the researchers themselves:

„DESIRS provides new opportunities for the study of photon-induced processes via the valence shell on mainly isolated gas phase samples, such as cold molecules, radicals, laser-excited species, biomolecules, large ionic biopolymers, clusters and nanoparticles, as well as on condensed matter. This includes high resolution spectroscopy, molecular dynamics and reactivity, and photoionization dynamics studies. In addition, the availability of calibrated versatile (linear, circular) polarizations of the photon beam is a unique specificity of the beamline allowing the study of molecular chirality and anisotropic properties of matter via different types of dichroism experiments.“

My first day at SOLEIL will be September 1st. I can’t wait!

What is astrochemistry?

The short answer: Chemistry in space.

Sounds awesome, doesn’t it? A completely unbiased answer would be: “Yes”.

But in all seriousness, for me personally, this is indeed the case. In my view, astrochemistry abides by the abstract. Weird chemistry. Chemistry that, to the novice, makes absolutely no sense. In a sense it constitutes a “chemical objet d’art”.

Untitled.pngObjet d’art is fancy talk for ‘ curiously artsy thing’. 

To get our heads around why this supposedly doesn’t make sense, we should break down our predetermination of “space” and “chemistry”.

Space isn’t entirely empty. Despite the vast regions of black edifices between the stars in the night sky, those dark prairies are full of diffuse matter. Our presuppositions may dictate that besides the galaxies, stars, planets, planetesimals, asteroids, etc., space is a vacuous hollow. This is a major misapprehension that may dilute our imagination in terms of the potentialities of chemistry in these parts of space.

But how could chemistry proceed in environs ruled by almost zero temperatures, strong ultraviolet radiation fields and cosmic rays whilst simultaneously being scarcely populated by atoms? This is where our preconceptions of general chemistry may involuntarily hinder our perception of the possibility of astrochemistry.

orion-frontpage2028129Weird molecules in space. Figure is totally stolen without permission from the home page of Robert J. McMahon’s research group at the University of Wisconsin. http://mcmahon.chem.wisc.edu/  

Chemistry, we learn, is full of rules that are specifically designed and put forward to help us understand the characteristics, behavior, and physical properties of the elements and their molecular amalgamations.  The Periodic Table, the Octet Rule, classical (“Arrhenian”) kinetics, the laws of thermodynamics; all are used to train our chemical instincts and insights. These give rise to our gut feeling that space and chemistry shouldn’t mix. UV radiation destroys molecules. Atoms stop moving at almost zero temperatures. Etc.

This was indeed the prevailing consensus amongst scientists until the late 1960’s when small molecules like water, carbon monoxide and formaldehyde were discovered in interstellar clouds. These discoveries were made by detecting and analyzing spectroscopic fingerprints of these molecules by analyzing microwave spectra from stellar objects, recorded by terrestrial telescopes.

herschel20100304-browseA plethora of molecules have now been detected in space.

The presence of these molecules cascaded in a new research paradigm; searching for molecules in space, how they could be formed, and how they would affect the development and evolution of molecular clouds in space. These objectives currently represent the trichotomy of modern astrochemistry, namely observations (where astronomy meets spectroscopy), experimental work (where experimental physical chemistry plays a central role), and astrochemical modeling (where Newtonian and quantum mechanical behaviors of atoms and molecules are accounting into sophistical computer models of various environments in space).

Spectroscopy further revealed the omnipresence of dust particles, silicon dioxides. Their presence was particularly conspicuous in stellar nurseries, the birthing pools of stars. Around nascent stars, an envelope of dust particles is gravitationally suspended by the star’s mass. The gravitational pull from the star causes the dust cloud to spin around it, just as the planets revolve around the sun in our solar system.

In the furthest reaches of the cloud, where the stellar radiation is dilute, the temperatures can range from 3 – 50 degrees above absolute zero (3 – 50 K). Under these temperatures, small molecules such as H2O, CO, NH3, O2, N2, H2CO, etc., accrete onto the surfaces of these dust grains, from the extremely diffuse gas phase, that mostly comprises molecular hydrogen, H2. Upon processes such as UV-irradiation, atom bombardment, electron / ion scattering and X-ray irradiation, reactive radicals can form in these ices that start to react with other present compounds, or recombine with other radicals to form larger, more complex molecules.

iceThe anatomy of an interstellar dust particle and the processes which its accreted material undergoes.

The most pertinent research questions of modern astrochemistry include: “Can biological precursors or life’s building blocks, form in space?”, “How did life begin on Earth?”, “How are abstract and weird molecules, observed to be present in the interstellar medium, formed?” What are the compositions of planets around distant stars?” And more.

Astrochemistry seeks answers to some of the fundamental questions humanity is yet to answer. It is by nature and necessity, a collaborative effort of astronomers, physicists, chemists and everybody who identifies themselves somewhere in betwixt.

I, for one, can’t wait to see where astrochemistry will lead us and what mysteries it will uncover.

P.s. Check out the website http://www.astrochymist.org/ for reviews of various books of astrochemical relevance (many of which I’ve read and would recommend but even more of which I’ve yet to read), a comprehensive Astrochemistry FAQ, a nexus of the latest astrochemically relevant publications, and a hell of a lot more! Honestly, I just found this website while writing this post. I believe I’ve found a new favorite website! (Sorry dictionary.com)

Mathematical Curiosities: A Treasure Trove of Unexpected Entertainments

Mathematical Curiosities by Alfred S. Posamentier & Ingmar Lehmann

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I promise not to tell a lie. I found this book a bit frustrating to read. The frustration stems from the fact that half of the time I was mesmerized by the mathematical curiosities promised by the title while the other half of the time I found them rather tedious and tiresome. This may be because my affection for beautiful mathematics is perhaps not as high as I myself expected, but the problems I found with the book also stem from its basic structure. Therefore, this review’s structure will be a bit binal in nature.

(Get it? Bit… binal…binary… Sorry, I’m just finding myself unendurably funny these days).

The book is divided into five chapters, each one devoted to its own branch of mathematical curiosities, kind of.  These are entitled “Arithmetic Curiosities”, “Geometric Curiosities”, “Curious Problems with Curious Solutions”, “Mean Curiosities”, and “An Unusual World of Fractions”. The chapter on problems and solutions was a most dissatisfying travail. The chapter is set up as a series of 90 mathematical problems with very contrasting levels of curiosities. Some are kind of obvious, some are interesting enough while yet others just… aren’t (in my opinion). My disgruntlement with the chapter is that I wanted to know the answer once I tried solving the puzzle in my head. The authors, however, don’t trust the reader enough to show the solution right after the puzzle because one might have an inkling to sneak a peek. This I found insufferable. Once I thought I had the solution (or didn’t want to spend more time of a particular puzzle, flipping back and forth between the puzzles and the solutions is just tiresome and defeats the point anyway of separating the puzzles from the solutions.

Besides this major disagreement between myself and the authors I found their gratuitous self-citations a bit bothersome. „I you want to know more about some interesting stuff, we’ve already written about so buy our other books too. I mean. I’ll admit to self-citing my previously published papers for the citation stats. But in book form, I think it’s kind of lame.

Despite all my aforementioned grievances, I want to give credit where credit is due. The good parts of the book (which accounts to roughly 70%) are electrifyingly interesting. The authors show verve and passion in their presentation of especially the arithmetic curiosities, which are just breathtaking. Strange, weird, hypnotizing. Arithmetic can take the form of artistry and mind boggling magic. When the book is good, it’s magnificent. When it’s not, it’s frustrating.

There is a wealth of number patterns that are explored that left me amusingly bewildered and bewilderingly amused.

number_pattern_10number_pattern_9Courtesy of: http://blogupiel.blogspot.co.uk/2009/08/suprising-number-patterns-iv.html.

The concept of the Japanese Sangaku tablets are examined and many examples dissected. Sangakus are geometric problems that are presented as geometric puzzles, comprising multicolored triangles, polygons, circles, circular arcs, etc. There is an inscribed geometric beauty about them and a deep mathematical intrigue. When Sudoku falls out of favor. Sangakus could replace them.

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Left panel. Ancient Sangaku tablet. Right panel. A modernized Sangaku puzzle. 

The harmonic triangle also makes an appearance. The harmonic triangle is very similar to Pascal’s triangle only it makes use of fractions rather than whole numbers. Each member of the triangular arrangement of unit fractions will be such that the sum of the two fractions below it – the one to the right and the one to the left of the member – will be equal to that fraction. The similarities between the two triangles are quite peculiar and intruiging in their own way as is explored in further detail here.

581098eb5e9213bf6c66e932ed218e08The Harmonic Triangle

In summary, the peculiar numbers, sequences of arithmetic operations, and even some of the curious problems, do tilt my opinion so that I would recommend it to anyone. But I will expect different people to have different reactions to the book. There are enough interesting numbers for anyone I suppose.

71/100

Reevaluations of the adjunct vagabond

In January this year I set myself high goals. Maybe even lofty ones. Some I have managed to achieve splendidly, others… not so much. One of my resolutions in the New Year was to allot time every Sunday to write for the purposes of this website-blog-thinga-majigg. This essay has turned out to be rather cumbersome, evidenced by my lack of blog posts for the past couple of months.

Other aspirations I set myself was to be more active in reading research articles. I thus included in my daily schedule 30 minutes during my lunch break, which I diligently dedicated to reading scientific papers. This endeavor has proved to be extremely fruitful and I have read several dozen research articles in the first three months of 2017, by reading in my lunch break. Several of these have been long and extensive review articles, mind you. This added injection to my daily routine in terms of reading habits has been extremely useful as (i) I now have a much better grasp of the theory and technical details of my current measurement setup, (ii) I have read several papers from numerous different research groups whom I have recently applied for postdoc positions, and (iii) I am mentally prepared for upcoming writing responsibilities aimed at dissociative electron attachment (current research) results.

As a part of my reevaluation of my changed habits regarding what works and what does not, I have decided to change things up a bit regarding my writing habits. Instead of trying to write every Sunday for a lengthened period of time, I want to try and write every day for 15 minutes (for my blog). That’s it. Change one thing and evaluate the results. If I manage to agglutinate these 15 allotted minutes to my daily schedule, I believe I can get a great deal more of writing done.

The reasons for my lack of writing for the past two months has, however, not been because of idle hands. I am currently waiting for responses for four different postdoc applications and my personal life has been in bloom during the past weeks and months. I am well aware that as an academic, my personal life should be non-existent, but I am also aware that I risk severe burnout if I aggrandize my stress levels over my website which I initiated out of interest and enthusiasm. I don’t want to force the things that make me happy, especially if they require capacious workloads like researching and writing about what interests and intrigues me.

For the past few years I have found happiness in working hard and achieving my goals. But I also have to stay grounded and take good care of my head; not to belittle myself for requiring a break here and there. I recently learned about myself that I in all likelihood suffer from imposter syndrome so I already have severe tendencies to corrosively think of what I do and do not accomplish. (I’ve been in therapy in this regard which is going very well, thanks for asking).

At the moment I am looking for ways to escape the Icelandic academia. Well, not so much escape but elevate myself out of it. If I sound derogative, it is not my intention. I’ve had both the pleasure and honor of working with brilliant scientists and I’ve learned so much from everybody here. But I have spent thirty years living in the same place and I need to leave to further my career. And I’m sick of the weather. To which I am physically adjusted. Crap.

As previously mentioned I have a few postdoc applications of whom I am currently awaiting judgement but I have already received an invitation for one interview. Things are getting exciting and I feel that I can see a light at the end of the tunnel. I may finally get out and fulfill my dreams of working on state-of-the-art apparatuses at well-equipped facilities employing the best of the best worldwide.

[Rambling] Of course growing roots is not something one does at this stage in an academic’s career. (At least I do not plan that way). Postdocs, more than anyone else, come and go. Traverse the world, gain experience working in different research fields, work themselves to the bone in hopes of getting to the next level. Tenure. Well, at least this is my perception of how the postdoc life is. I’ve been a postdoc for a year or so, but I merely changed research groups in the same institution. I didn’t even move office. Laboratory wise I moved 30 feet tops.

Living in Iceland, one feels a deeply engrained sense of isolation. You are geographically isolated from the rest of the world and if you want to get out, then you have to be good. Really good. Excellent. I’m rambling. [/rambling]

I’ve been writing this blog post in three 15 minute sessions. That’s more work than I’ve done for the past two months. Kudos to myself and to a new and improved way of writing.

Women in Science: 50 fearless pioneers who changed the world

Women in Science: 50 fearless pioneers who changed the world by Rachel Ignotofsky

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Fact #1. The history of scientific discovery is a vast sausage fest, layered with facial hair of varying majesty.

Fact #2. Historically, the scientific contributions of the double-X-chromosomed half of humanity have often been disregarded and even discredited in lieu of the chauvinistic status quo.

Fact #3. This book helps set the record straight. And it is delightful, beautiful and interesting. My own personal holy trinity.

You know what? I am going to keep this review short and sweet, because it’s exactly what I found the book to be. I was delightfully surprised by its character, low tolerance threshold for B-S-misogyny, and its gorgeous illustrations. It is inclusive and hits precisely the right mark of amount of information to be enjoyed by adults, children, and everyone in betwixt.

4Seriously. How can you not just fall in love with this artwork and honorific presentation?!

Rachel Ignotofsky is an experienced illustrator and crafted everything in the book. The written word and painted picture. I highly recommend all her other scientific illustrations that are available on her website. They are enchantingly informative, gorgeous, and they just fill me with joie- de-vivre.

downloadI just… wow. 

In fact, another book by Rachel Ignotofsky entitled I Love Science: A Journal for Self-Discovery and Big Ideas comes on sale March 17th and can be pre-ordered here. I, for one, can’t wait to read it.

96/100

Science of the Alien franchise I – Xenomorphic blood

The Alien franchise is among the most successful sci-fi franchises ever spawned out of Hollywood. It even commingled with the Predator series (famously through one camera shot of a Xenomorph´s skull in the Predator´s spaceship in Predator 2) allowing for Hollywood to exploit our obsessions for details with a series of video games and an Alien vs Predator movie franchise. The film series have even inspired a wealth of Alien comic series with even more outrageous cross-overs such as Batman/Aliens, Judge Dredd vs Aliens, Green Lantern vs Aliens and even Aliens vs Predator vs The Terminator. As the actual science that is swathed throughout the series is extensive; from hypersleep to space travel to the Xenomorph´s life cycle, I will have to contain myself and start with one of the most discussed topics; the Xenomorph´s blood.

                                              avpvtt                                                  This actually exists. How friggin awesome!

The actual aliens or Xenomorphs were designed and developed by Swiss genius/weirdo H. R. Giger, who has crafted some of the world’s most creepy, unsettling, disturbing, and FUBAR imagery (ever!) put on paper. Their big sinister smile, eyeless exoskeleton, and complete indifference and apathy for other lifeforms, make the Xenomorphs among the scariest villains ever put to film. Notwithstanding their genetically weaponized defense mechanism; corrosively acidic blood.

bob-ross-giger“And we’re just gonna put a happy little biomechanoid right here.”

The films themselves cleverly gave as little information as possible as to the chemical composition of the blood, all that was mentioned pertained to “molecular acid”. (What type of acid is not molecular by the way?) The original purpose of this article was to introduce the concept of superacids to display the possibilities of the corrosive nature of the aliens´ acidic extravasate. After a few Google searches, however, it seems like this idea has been done to death. Which isn’t anything bad, but in a nutshell, superacids have the capability of protonating alkanes (which is quite the feat) and the strongest known acid, magic acid, is a combination of hydrofluoric acid (HF) and Antimony pentafluoride (SbF5). I highly recommend this video by Nerdist but the video cements my original idea for this particular blog.

So. All acquainted with magic acid? Good. Now I will take this idea even further to illustrate some more interested aspects of the Xenomorph´s physiology and cosmic origins.

hunter_aliens_colonial_marinesSciencing the scariest of scary fucking bastards.

The exact composition of the Xenomorphic blood is a hotly debated topic… on the internet, particularly on Reddit. If we take a chapter from the Aliens vs Predator wiki community, however:

“The specific composition of the acidic blood remains a mystery, with its incredibly corrosive properties no doubt limiting the degree to which it may be studied. However, it has been theorized that the blood could be some type of “hydrosulfuric” or hydrochloric acid composition due to its corrosiveness and its conspicuously toxic effects on living human tissue. It has also been proposed that the Xenomorphs are immune to their own acidic blood due to an endobiological build-up, similar to the human stomach’s ability to protect itself from its own digestive fluids. It has also been theorized that the blood is fluorine-based, and that the Xenomorph’s protection system against its own toxic acid is essentially a bio-organically produced Teflon insulation within its body, since polytetrafluoroethylene (PTFE, or Teflon), being a fluorine-based compound, does not react with hydrofluoric acid. It is known that Xenomorph chitin is resistant to the acid even after it the creature has died or its chitin has been removed.“

In short the superacid HF*SbF5 does not necessarily have to be the main culprit. If anything, it may just be a minor component in the blood considering the prevalence of atomic Antimony in outer space. There may in fact be other various acidic components in much higher fractions than magic acid, like the aforementioned hydrofluoric acid but also sulfuric acid (H2SO4), hydrochloric acid (HCl), nitric acid (HNO3). Considering the relative solar system abundances of these acids´ constituents, they are likely culprits of the acid blood´s corrosive nature.

alien-acid-for-blood11…And just a dash of the Universe´s most heinous molecules…

But is the acid the actual blood of the Aliens? Our blood serves a specific purpose, namely to carry oxygen and carbon dioxide molecules around the body´s organs and tissues and thus enable our metabolism to take place. What is purpose of the Xenomorph’s blood?

Here we need to delve into the comic book lore of the Aliens. In the comic books, a multinational conglomerate called Lasalle Bionational (a subsidiary of the Weyland corporation) that focused on biologica research managed to unravel some the physical properties of the acidic blood. To again quote the Aliens vs Predator wiki:

“While Xenomorph acidic blood is primarily thought of as a passive defense mechanism used to deter attackers, studies show that it in fact plays a far more integral role in the creature’s biology. Research by Lasalle Bionational indicates that the acid is primarily a component of a biological “battery”, generating a powerful bio-electric charge by means of chemical reaction that provides the Xenomorph with its energy, replacing the need for traditional respiration and digestion of food altogether. This would would help to explain how the creature is apparently able to survive in the vacuum of space for significant periods, and also helps to explain how the Ovomorph stage is seemingly able to remain dormant but alive for vastly extended periods of time. However, the means by which the creatures may “recharge” this battery remains a mystery. It is quite possible it simply cannot be renewed, and that Xenomorphs will eventually die naturally as a result of this energy source depleting.”

Buck-ark.pngAlien blood as energy source?

This brings up an interesting point. If this is true, then these species have found an more efficient power source (in an evolutionary sense) than us humans with our food. The purpose of eating is essentially to break down large molecules such as carbohydrates into simpler molecules via burning (reactions with oxygen). This is an oxidation/reduction reaction that involves a simple exchange of electrons. The purpose of eating is to release energy to power our bodies by exchanging reactions. In the process the energy can be used for mechanical and kinetic purposes which (in a nutshell) make up the extent our corporal faculties.

ImageJ=1.33u unit=pixelElectricity breathing aliens? Yes, we’ve discovered some of those. 

Recently, organisms have been discovered that do not require food per se, but rather use a stream of electrons as a power source. This means that actual life forms exist that do not require nutrition, only a steady stream of electrons to grow, regenerate, and repopulate. Give beings this kind of efficient natural power source and the proper evolutionary environment and you may end up with the cosmically internecine and malignant species of the Xenomorph family. Facehuggers and all.

The question of the appropriate cosmic environment where this kind of life may evolve gives, however, merely tenuous answers. This is purely speculative, but a water based world like our Earth’s surface is probably an unlikely scenario and a more hostile environment is required for such a tenacious and perniciously resolute creature to evolve. If it puts your mind at ease, I don’t believe space travel will be furthered enough in the coming years to meet such creatures, given that something even worse lurks in The White House.

10gesk

The Quantum Enigma

The Quantum Enigma by Bruce Rosenblum & Fred Kuttner

qenigma

Quantum theory is the most successful theory of our time. No question. Every prediction it has portended by its rigorous mathematics has been experimentally verified.

And even though it contains leagues of strenuous calculations that only the formally initiated (mathematics, physics and some chemistry graduates) can aspire to take on manually, it produces science’s greatest of mind-f***s we’ve encountered in nature. As it turns out, nature is weird. And though nature itself definitely doesn’t mind, some of us do!

The Quantum Enigma is written by Bruce Rosenblaum and Fred Kuttner, both experts in quantum theory and its applications. Bruce is Professor Emeritus at the University of California, Santa Cruz and Fred is a physics lecturer at the same university. The Quantum Enigma addresses the inherent weirdness of quantum theory and the different approaches physicists take to interpret or reconcile its evoked enigmas.

To the uninitiated, the book may be difficult at times, but it is an extremely rewarding reading experience. I don’t believe I’ve ever had to ponder so much reading a single book. I often found myself reading for 15-20 minutes, only to pause and think about what I’d just read for an additional 10 minutes. To be completely honest, this is the first book in a decade I’ve now read twice.

The book is intelligently structured. It begins with an anecdote from when on of the authors (Bruce) met Albert Einstein during his physics graduate studies. Einstein famously disliked quantum theory because of its implications. Two of his most quoted phrases, “God does not play dice” and “I like to think the moon is there even if I am not looking at it.” are particularly enlightening about his antagonistic view of the theory. Both phrases are quoted from intense discussions between him and his ‘frenemy’, Danish physicist Niels Bohr, who was a staunch defender of quantum theory AND its implications. (Tangentially, there are several more quotes about quantum mechanics by notable physicists to be found on the book’s web page. I particularly like the one by Richard Feynman: “Nobody understands quantum mechanics.”)

feynmanFeynman: That’s right I said it. Nobody!

What follows the short anecdote is an intriguing fable of a physicist who encounters a shaman who supposedly can reproduce quantum experiments on a macro-scale with humans. This evidently disturbs the physicist and plants the seed for the coming discussions of quantum weirdness.

The tell-tale physics fable is followed by a logical historical perspective in tandem with the historically relevant experiments and natural phenomena (oscillating electromagnetic fields, wave mechanics, etc.) that laid the foundations for quantum physics.

More to the point, the enigma itself stems for the fact that a conscious observer irrevocably influences a system under inspection. The act of observation yields a result, created by the observation itself! Up until the point of observation, the results are correctly predicted by quantum mechanics. But without the observation, the results are superpositions of possibilities, coexisting synchronously. A wave of probabilities, suspended between objective realities. The discussion of these intangible facets of nature in The Quantum Enigma are coherent, well written, and engaging. It renders you perplexed yet curious of what we consider reality and where the line is drawn in the sand what constitutes reality and what doesn’t.

This is inherently weird for humans. Our brains did not evolve to account for nanoscale mysteries. They evolved to help humanity hunt and survive the entropies and onslaughts of the wilderness. Niels Bohr said once: “Anyone not shocked by quantum theory, has not understood it”. You totally get where he is coming from, but it is also a bit clouded by a sense of bias, that the world should be the way it is, because that’s how we see it. Reading this book has helped me overcome this intrinsically biased view. Nature is strange to us, and it’s okay. Either way it is fascinating.

Without going into any more specific details, The Quantum Enigma addresses the role of consciousness in quantum theory, explores some of its technological applications and quantum entanglement, which includes transporting information faster than the speed of light… in a nutshell. If you are interested in learning more about the book’s contents (without actually reading it), you can check out the aforementioned website dedicated to the book. There you will find all sorts of additional goodies such as amusing quotes, a complete chapter walkthrough, and original drafts of the chapters along with a bunch funny little illustrations the authors drew to accompany the text. It’s really quite endearing.

untitledA couple of examples of the writers’ creative drawings. As I said. Endearing.

I highly recommend this book, but only to those who are ready to have their minds blown.

Rating: 95/100

Reading and writing habits

I think it was about time to start writing again. For my website that is. I’ve been keeping myself busy with writing postdoc applications and preparing my teaching schedule for the coming semester which includes one half of a single course. This means my teaching workload will be a mere quarter of last semester‘s. (Yay!). More time for science!

But I have been reading and writing a bunch (in regards to the aforementioned postdoc applications) which I consider to be a good and healthy practice since I am trying to secure my future in the academic research sector. Not the easiest of career choices.

At the moment I have plenty of stuff to write about as The Cosmic Chemist; everything from lasers to cosmic acids.

What I really wanted to do for now, though, is share with you my reading schedule. Yes, reading schedule. Let me explain.

A few years ago I realized I was piling up books I was dying to read but my reading habits were, well, non-existent and rather unbalanced or patchy. I would read diligently for a period and then completely lose focus and not read at all for a while. I wanted to get back on track but realized that I needed to do so in a more efficient manner. Thus, I reshaped my reading schedule, so that every day, I would start my day by reading for half an hour. That’s it. Just make time in the morning for myself to read for a little while. That way, I’d read every day to nurture that unquenched thirst for the books I’d been piling up. (I am a frequent Amazon customer with a penchant for hoarding books.)

At this time (around 2012-2013) I was starting my PhD so most of the reading material was in some way scientific; both papers and large lexicons on spectroscopy. This was also the time when I was really getting into popular science books, e.g. Carl Sagan, Michio Kaku, bibliographies of famous scientists, etc. I realized that half an hour was not enough for me in the morning so I upgraded my reading schedule to two times thirty minutes. That way I could ready popular science for half an hour and then thick heavy set school books for a half an hour.

On a tangent, I actually set my timer to 31 minutes for each session as I allot an extra minute for glossaries. English isn’t my first language (though it’s still quite proficient, I assure you) and I continually want to extend my vocabulary, so I keep with me a small notebook for words I’m unfamiliar with and I want to add to my regular diction. After an hour of reading in the morning I look through the words I’ve glossed and add them to a magisterial Excel spread sheet I’ve organized over all the glossed words amassed over the past three years.

Anyway, once I finished my PhD I had made myself the promise I would get back to reading fiction again and there have been some big ones I still haven’t read. The first works of fiction I would read would be the Harry Potter books. Then The Hobbit and The Lord of the Rings. Then Game of Thrones. Then the complete works by Douglas Adams and… something. I haven’t decided what should follow Adams.

My morning reading schedule thus consists of 30 minutes of fiction and 30 minutes of popular science. (Don’t get me wrong, I still read scientific papers, but I do so at work, as it still constitutes as work.)

I finished the Harry Potter books last November. The Hobbit followed in December and now I’m halfway through The Fellowship of the Ring.

What writing is concerned, I have copious amount of material to cover. I have three book reviews pending (The Quantum Enigma, Women in Science: 50 Fearless Pioneers Who Changed the World, and Mathematical Curiosities: A Treasure Trove of Unexpected Entertainments). I have planned sci-fi blogs on the aliens from the Alien franchise, the “science” of Flash. And as an added bonus, I plan on writing about lasers and high-tech spectroscopic methods I worked on during my PhD as well as some astrochemistry related material. But more on that later.

I usually write my science blogs on Sundays though I do tend to research the blogs on and off during the week or during evenings, depending on my schedule. I like to assign a particular day to writing because… I pretty much have to. I’m a creature of habit, and I enjoy habit. It keeps me productive which releases dopamine molecules in my brain. Or in other words, it makes me happy.

The inspiration for my writing schedule actually came from reading some of Ryan Holiday’s work. He’s one of the most interesting people to follow on Facebook because he is just brimming with useful advice on reading, writing, life stratagems, and… stoicism. I may end up writing about stoicism in the future once my ideas for everything else science related dries up.

Even though my reading schedule is pretty solid at the moment, I’m still looking for ways to enhancing and upgrading my reading habits. I’ve tried to squeeze in 20-25 minutes of reading during my lunch break and I do confess that many of my evenings are spent aimlessly on social media. My aim for next week is to read for something like 20 minutes every lunchbreak and then 15-20 minutes before I go to bed.

Ready, set, go!

P.s. I’ve made a few adjustments to this page, most notably I’ve added all my scientific publications under ‘Research’. Feel free to browse if you’re interested.