Nerds vs. Breaking Bad

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I love chemistry.

My late grandfather was a chemist who worked in dyes at a local mill. He was apparently some kind of impoverished prodigy, and the Dow corporation once tried to recruit him (he turned them down for reasons unknown.) And far back in the mists of the 19th and early 20th centuries, both sides of my family produced a few other chemists and engineers. We don’t know where their money went, but they existed. So chemistry is in my blood. Well, it’s in everyone’s blood, but you know what I mean.

I enjoyed chemistry in high school. My teacher was a boring old man everyone hated, but that didn’t stop me from poring over my textbook every night. I even started to use Lewis electron dot structures as a form of emotional expression; “I am in an octet today,” I would say when I was feeling withdrawn. I should have signed up for AP chemistry, but the rich kids in the AP classes were snobby and mean and surprisingly stupid, and I had taken college prep algebra instead of honors algebra, and so on. My lack of formal education did not stop me from buying a periodic table poster and developing a deep obsession with Primo Levi, however.

Now I’ve picked up the thread using online resources, and when I finally get my butt back in school I plan to study chemistry. I’m nuts about it. It makes me happy. Yesterday I wrote a song about the spin quantum numbers, based on “This Magic Moment”:

This magnetic moment
So different and so new
Was like any other
Until I spun you

And then it happened
New quanta we surmised
I saw that you had spin too
By the double emission spectra lines

Wolfgang Pauli just knew (Pauli just knew)
What an electron could do (electron could do)
He could do everything (do everything)
To make Mendeleev sing

This magnetic moment
Will keep the orbitals aligned
Maybe forever
Depending on space and tiiiiime

Someone told me this song means I’ve hit Peak Nerd. They are wrong. Bohemian Gravity is Peak Nerd, and I only wish I’d done something like that.

Unfortunately for nerds, the unethical applications of chemistry are having a bit of a cultural and historical moment.

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645 evils/mol

Breaking Bad, AMC’s beloved series about a cancer-afflicted chemistry teacher who becomes head of a meth-dealing empire, comes to an end tonight. It’s all anyone’s been talking about. I must say that I admire this show’s style and its determination to get the chemistry right (see related articles), but a big part of me can’t wait for the final curtain to fall. Other chemistry-lovers see Breaking Bad as thought-provoking entertainment, and can easily laugh off the facetious assertions lobbed by their non-nerd friends. A white lower-income East Tennesseean may be forgiven for laughing a little less. When the head of my public housing development dropped by my apartment for a brief inspection, I considered hiding my science homework. “You’re cooking!” is not a joke where I live – it’s an allegation.

This must have been what physics nerds felt like in the 1950s, when Albert Einstein died and the mutant ants from Them! replaced him in the national consciousness. Conversations about the shady side of science are important, so very important, and yet for nerds they can grate. When media depictions of science become frightful enough, the line between “Caution, nerds, don’t let yourselves become power-hungry greed-monsters” and “All nerds are power-hungry greed-monsters” can become blurred. I hate them blurred lines.

I can’t help but be reminded of Primo Levi, my favorite writer and in many ways the anti-Walter White. Levi (1919-1987) was an Italian-Jewish chemist who got involved with anti-Nazi activities in the Italian Alps, and was sent to Auschwitz as a result. The tale of his survival is tied up in chemistry – he had fever dreams about carbon atoms that briefly and crucially reminded him that life was worth clinging to; a comparatively cushy job as a slave in an IG Farben chemistry lab kept him from starving to death, and also provided him the bizarre experience of meeting German chemists who were working in Auschwitz. And of course the threat of being gassed, as his girlfriend and comrades had been, hung over him ever hour of every day. When he returned to Italy and began working in the paint and varnish industry, he found that his sense of morality was fine-tuned, almost painfully exquisite, as a result of his suffering.

Just as the scientific character leaked into his writings on the Holocaust (Cynthia Ozick referred to him as “a Darwin of the death camps”; she meant this as a dig but Levi would consider it a compliment), the Holocaust leaked into his writings about science. When The Periodic Table is not busy being brilliant and amazingly fucking beautiful, it often concerns itself with what it means to be a good chemist in a world of gas chambers and meth – though he does not mention the latter. What to do when reason is a tool of fascism but also, oddly, its antidote?

Chemistry…let to the heart of Matter, and Matter was our ally precisely because the Spirit, dear to fascism, was our enemy…After being force-fed in liceo the truths revealed by Fascist Doctrine, all revealed, unproven truths either bored me stiff or aroused my suspicion.

In Other People’s Trades, he concluded that knowledge is a form of redemption, an imperfect redemption but one that could cover a multitude of sins.

The future of humanity is uncertain, even in the most prosperous countries, and the quality of life deteriorates; and yet I believe that what is being discovered about the infinitely large and infinitely small is sufficient to absolve this end of the century and millennium. What a very few are acquiring in knowledge of the physical world will perhaps cause this period not to be judged as a pure return of barbarism.

This is my view as well. Yesterday I was outside reading The Greatest Show on Earth when a young boy approached me and started chatting with me about science. He was a little professor who knew things about whales and insects that I, 21 years old and counting, did not know, though I was able to make up for it by sharing my knowledge of birds and minerals. He also got a perfect score on the math section of the T-CAPS despite going to a dismal inner-city school. His goal is to become an engineer who works with vehicles and renewable energy. This is my portrait of redemption: two geeks from the projects trade nature facts and become friends, illustrating what Breaking Bad gets wrong. In Breaking Bad, education makes you a great meth dealer. In life, it keeps “meth dealer” off the list of career options.

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The science of calico cats

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Why is it that when you cross a black cat and a ginger cat, you get some black male kittens, some ginger male kittens, and female kittens with a calico pattern?

It has to do with X chromosome inactivation, something all female mammals (including you, ladies) go through as embryos. A male cat embryo has a fat X chromosome bursting with relevant genes and a puny, shrunken Y chromosome that gives him nothing but balls, to be blunt about it. Meanwhile, a female has two of those fat X chromosomes. She can’t express the genes on both in the same cell – it would create too many proteins and gum up the system.

Her DNA has an ingenious way of protecting itself from such disasters. Early in gestation, one X chromosome in each cell gets “deactivated” – bound up in proteins and effectively closed for business – through a fascinating process I’ve been learning about in an online class called Epigenetic Control of Gene Expression. The details are not for those uninitiated in molecular biology, but the gist is that female cats have different cell lines in their bodies. In some lines, the paternal X chromosome (the one from dad’s sperm) will be active. In other lines, the maternal X chromosome (the one from mom’s egg) will be active. Since the genes for coat color are on the X chromosome, female kittens will express mom’s genes in some areas and dad’s genes in others. That’s what gives calico cats their trademark patchwork look.

It’s also why you rarely see calico toms. Male cats don’t need X inactivation because they only have one X chromosome to begin with. As cat breeders know, there are exceptions – sterile male calicos with an XXY karyotype, the feline equivalent of Klinefelter syndrome.

The study of calico cats was important for the development of epigenetics, or the study of how genes get turned on and off inside cells. In 1949, Murray Barr was examining cells taken from calico cats when he noticed tangled blobs at the edge of the nuclei. These “Barr bodies” were inactivated X chromosomes, and Mary Lyon would describe them in a 1961 paper that foreshadowed decades of epigenetic discoveries to come. So if you own a calico cat, you own a piece of scientific history…kind of.

In humans, X chromosome inactivation has profound implications for diseases where the pivotal gene is on the X chromosome (like hemophilia) and diseases which result from a person having too many chromosomes (like Down syndrome.) Down syndrome is an interesting case because researchers just figured out how to silence the extra chromosome that causes it using a process that mimics X inactivation – in a test tube, at least. Let’s hear it for the scientists!

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Meow!

The great rainbow caper

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Snell’s Law governs the order of the colors we see in the rainbow. Art courtesy of Wired Science.

2013 has been a difficult year for people who don’t like gay people. The Supreme Court struck down Prop 8, America got its first openly gay pro athlete, and now it looks as if the United Kingdom will make the leap from civil unions to full marriage rights. This may be the gayest year on record, narrowly beating out 1897 (don’t act like you don’t know about 1897!)

In the face of major legal battles lost or nearly lost, homophobes on the internet have taken a maudlin and pathetic tone, seizing upon minutia and moaning so pitifully that I can’t help but be reminded of Adrien Brody’s weepy performance as Władysław Szpilman in The Pianist:

Don't cryyyyyyyy out looouuuud

Don’t cryyyyyyyy out looouuuud

Just keep it insiiiiiiiide

Just keep it insiiiiiiiide

Learn how to hide your feeeeelings

Learn how to hide your feeeeelings

As you can see, a lot of this whining and bitching centers on the idea that gay people “stole” the rainbow. For this to make any sense whatsoever, you have to assume that Christians owned rainbows in the first place. I called the US Copyright Office about this and they laughed me off the phone.

Perhaps I should illuminate this situation with a little factoid not known to many: rainbows are as important to physicists as they are to Christians, if not more. Many advances in physics, from Newton’s work on light to the much later invention of the laser, owe a lot to experiments involving PRETTY COLORFUL RAINBOWS. They’re among the most important objects in the history of science. It’s unsurprising that physicists can develop deep feelings for them – in For the Love of Physicsheterosexual MIT professor Walter Lewin claims to schedule showers around the possibility of seeing rainbows in his bathroom.

Yet I have never encountered a physicist lamenting the gay conquest of the visual spectrum, or the use of rainbow imagery in the Old Testament for that matter. Perhaps this is because physicists are confident that the visible spectrum exists outside of any cultural narratives humans may provide for it. A Christian looks up in the sky and sees a symbol; a physicist looks up in the sky and sees a fact. Something that’s woven into the fabric of Nature itself cannot logically be stolen by a group of hairy bipeds. Apparently, God is weaker than Nature – His symbolic rainbows are vulnerable to theft.

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This is the visible spectrum. These are the photons we can see. This was here before the Israelites told spectacular tales of an ark-builder named Noah, this was here before the gay rights movement erupted out of a little Village bar in 1969, and this will be here long after we are all dead. No political or religious movement is going to pay royalties for this. Only those unaware of their cosmic tininess would be willing to fight gay people for the use of the rainbow – or worse, find themselves poisoned by spite against the wonder of naturally-occurring rainbows. I don’t want to socialize with anyone who would get angry about this. It’s a sign of a cramped, miserable mind.

It’s been hot and stormy here in Knoxville, good rainbow weather, and a few days ago I saw one. Well, part of one, suspended in the steam above a street. I didn’t think “Ohhh, hello gays!” the way I do when I see a rainbow flag or bumper sticker – I thought “Ohhh, hello rainbow! About 40° upwards from the car’s shadow, just like Dr. Lewin said! I wish I could get a better look at you! You’re so awesome!”

This vibrant yet ethereal parallelogram of color brightened my day in a way that was totally apolitical, totally secular. I have knowledge to thank for that. If the universe were so small that petty human squabbles about symbolism were all that mattered, I think it would be suicide for me.

Where do sunburns come from?

Vintage Sunburn Ads (1)

Last Monday, I reached over the stove while I was cooking and bumped my wrist against a hot saucepan, sustaining a semicircular blister burn. That Saturday, when my thermal burn was nearly healed, I went to Knoxville Pridefest in a sleeveless blouse and got a sunburn on my shoulders. As I write this, my week-old sunburn is shedding little pieces of skin onto the inside of my T-shirt.

These annoying but altogether normal experiences had me wondering: why do sunburns and thermal burns look and feel so different? Why did my thermal burn heal without peeling everywhere? Why do thermal burns hurt immediately, while sunburns glow warmly but painlessly for hours before you really feel them? And why does one increase the risk of skin cancer while the other does not?

As it happens, science has the answer! Well, science still has to work out the minute details, but on the basic level it has the answer.

When sunburn occurs, ultraviolet radiation penetrates the nuclei of the skin cells and mutates the DNA within. The mutant DNA gets transcribed into mutant bits of non-coding microRNA, which disseminates and triggers an inflammatory response. This inflammation is what makes the sunburn red and warm. If the mutations are pronounced enough, the cells in the first layer of skin will die and eventually peel off. The body has processes that stop the crazy sunburn mutations from spreading, but every time you get a sunburn it increases the statistical possibility that mutations will stick around – and that’s why sunburns increase the risk of skin cancer.

So sunburns are caused by DNA mutations from radiation. Real life is so much less glamorous than superhero comics.

A thermal burn from a hot stove, by contrast, happens when excessive heat melts the proteins inside the skin, causing it to break down. You feel this immediately, which is a good thing when you think about what would happen if you just left your hand sitting on a hot saucepan. Thermal burns have nothing to do with skin cancer because they do not mutate DNA.

It just goes to show that even common experiences can be an opportunity to learn some fascinating science – or, if you’re really smart, to come up with some fascinating science.

Ring Nebula

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The Ring Nebula’s hot new profile picture

This 1998 pic of the Ring Nebula entranced me when I was a child. A spooky cloud of gas and dust, measuring a whole light-year across…and to think that I only had the privilege of seeing a 2,000-year-old version of it, because the light took that long to travel over 120,000,000,000,000,000 miles of space! Rather than inducing existential angst, these numbers made me happy: the universe was so much bigger than whatever idiocy was going on in my life.

Now there is a new high resolution image of the Ring Nebula, and it gives us all the cold, ancient beauty we’ve come to expect from Hubble, as well as some new insights into the structure and formation of the nebula. The space in the middle, once thought to be almost empty, is webbed with low-density material, suggesting that the nebula is barrel-shaped rather than ring-shaped.

The best MOOC ever just ended

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This week marks the end of a massive open online course called Introduction to Biology: The Secret of Life. This course, an adaption of human genome unwraveler Eric Lander’s Bio 101 class at MIT, was offered (and may be offered again) by all-star online education platform edX. And as it happened, it consumed my life for three whole months.

I am going to miss it so much.

The principle joy of taking this course was Dr. Lander’s feisty, creative teaching style. I’m sure that I missed out on some things experiencing it on video only, but the elitists who snub MOOCs on this basis forget that most of us are never going to know what it’s like to attend an MIT lecture in person – the effect of a charismatic hologram professor on the student is diluted, but still valuable. I admired Dr. Lander’s manner of structuring the material, which involved tying the textbook material to the historical progress of genetics, biochemistry, and molecular biology. The few MIT chemistry lectures I watched before accepting that I needed to take calculus first followed a similar multidisciplinary-historical approach, suggesting that this may be part of the MIT model of education in general. If so, MIT is awesome.

English: Professor Eric Lander teaching the fi...

Platonic crush ahoy!

I loved how current some of the material was. At one point, Dr. Lander was discussing RNA-induced silencing complexes, and he said “This isn’t in your textbook, but it’s in your body.” That’s how fast the discipline of biology is moving, and that’s the value of having MOOCs in STEM fields. A rockstar prof involved with cutting-edge research is going to have access to the most recent advances and know how to teach about them. S/he will also have amazing stories to tell – this year, Dr. Lander wrote a brief to the Supreme Court regarding the pitfalls of gene patents, and it was cited at the hearing!

Please grant me one more paragraph of shameless gushing: some of the software available with the course was incredibly cool. It allowed students to solve problems involving actual protein structures and genome sequences. Now, there were a few bugs that drove us all crazy in the beginning, but all in all it was a good system – there is nothing like solving a biology problem with a real genome. There is nothing like knowing that one’s homework is real.

I came within five points of earning a full certificate in this course as opposed to an auditor’s certificate, but I didn’t make it. This is only, and I mean only, because I went through a disorganized period in May where I missed the second half of the midterm exam. I guess I learned some lessons about writing things down on my calendar. Depressing, certainly, but I cannot consider it an outright failure, as it is not going to be carved in stone on any transcript. The point of most MOOCs, as they currently exist, is what knowledge one can take away from them; 7.00x was stellar in this regard. I’m happy to take the auditor’s certificate as a souvenir/physical token.

Earlier this year I took a MOOC called Introduction to Genetics and Evolution, courtesy of Dr. Mohammad Noor of Duke University in partnership with Coursera. I did earn a full certificate in that one, as well as two hours of college credit and a distinction badge. When I was banging out Hardy-Weinberg equilibrium problems as part of Introduction to Genetics and Evolution, I remembered thinking, “Wow, I could do this every day for the rest of my life!” Normally statements like this are just hyperbole (“Mmmm, Miss Carrie, I could eat this cornbread every day for the rest of my life!”), but when they concern things like biology, computer programming, sewing, writing, or fixing cars, that’s an inner voice to which one should pay heed. It reminds me of being that little girl who would only listen to fairy tales if her mother replaced all the characters with anthropomorphic viruses and bacteria. Seems I’m still that little girl.

To close with a quote from Dr. Lander’s lecture on gene patents:

There are choices we have to make as a society, and different societies make different choices. It’s done in different ways in different places, and they may value things in different ways. But it’s important that as much as we may focus on alpha helices and proteins and telomerase and things like that, we recognize that what we’re doing does spill out and affect the rest of society, and as scientists, or people just learning about science, it’s important to think about bringing that knowledge to these social questions…That’s what we want people to be able to do, to be able to take knowledge from science and then go apply it to different social situations, combining with real human values. In the end, the values make a big difference to where you’re going to come out. But if you’re not informed by good science, values alone aren’t going to be enough to get you to a good answer.

Indeed, indeed.