I…I miss the lab

There. I said it. I never thought I would.

But something going on right now, Real Time Chem Week, is making me jones for my chemistry lab days a bit. For those of you who don’t want to click that link, Real Time Chem (or rather #realtimechem) is a hastag people are using to tag their tweets about doing everyday chemistry. Or rather, the chemistry they do every day. It’s mostly chemists doing the tweeting, but anyone who’s doing any kind of chemistry is welcome to play. And reading them is really filling up my nostalgia beaker. Here are some of the ones I think are the funniest/most representative/most relatable so far:

https://twitter.com/cjsobers/status/326511862697062401

And it’s only Monday night! But it’s pretty fun so far. And, as I said, making me miss the lab a little. For me, this is really saying something because my grad school experience/lab work was on the miserable side. I have narrowed it down to what I really miss, though.

Problem solving.

I really miss figuring things out, especially stuff that nobody knows the answer to.  I’m actually right now thinking fondly of that project where I had a beautiful clean NMR that made no sense (right number of protons and everything!) that I could. Just. Not. Figure. Out. Until I did. (It was a perfect 1:1 ratio of 2 almost structurally identical porphyrins, and some of the peaks overlapped perfectly. The paper’s here if you’re interested. Check out the subdat for an assload of amazing 2D NMR. If you’re into that kind of thing.)

MY POINT is that I don’t really problem solve any more. Sure, science writing and editing makes me use my brain, but it’s not the same. And I am still only working part-time, and doing the child rearing thing the other part of the time. Which, don’t get me wrong, I love spending time with my kid. And it’s challenging and rewarding and takes a lot of patience, but it’s not exactly stimulating to the intellect. I’m doing more crosswords now to help fill in the gaps. It works, to some extent.

So Real Time Chem people–I am living vicariously through you. Don’t let me down.


The Chem Coach Carnival!

It’s National Chemistry Week! I’ve decided to honor the 25th year of this most sacred event by coming out of baby-induced blog hibernation. Don’t expect it to be permanent.

What prompted this head peek back into the land of the living was See Arr Oh and his blog carnival. I missed the last few, so that’s why I’m procrastinating paid writing and doing this instead. He’s collecting posts on what people with chemistry backgrounds do for a living. People who maybe want to be science writers ask me about it a lot. So here’s my story.

Your current job: Freelance science writer, part-time. Also, stay-at-home mom. With no childcare. My work hours: naps, nights, and weekends.

What you do in a standard “work day.” Oy. Very little of what I do is standardized. The kid is now seven months old, and a lot of what I do during the day is try to entice him to sleep so I can work. (That usually goes very poorly. His unofficial motto: Nunquam Dormio!)

But, it depends on what I’m working on. I mainly write/edit for the ACS at the moment. So a lot of what I do is reading chemistry papers and try to glean out the essence/important bits of what the research is, then writing about it for about a chemistry student’s level. Scope is a very important word for me. Why is this research important? What are the main ideas/directives/reasons behind the research?

Most freelancers spend a lot of time looking for story ideas, and pitching them to editors. I don’t do this. I wait for editors to assign stories to me. Lazy? Maybe. But since I have very little work time during the day, I have to minimize the bullshit and maximize the actual writing time. Looking for stories and pitching can be very time consuming. And if you can’t get anyone to pick up your idea, that’s potential earning hours wasted. Plus, I rarely write stories where I have to interview anyone right now. That’s due to the no childcare thing. I can’t schedule the sprog’s naps (or even if he’ll take one), so I can’t usually schedule an interview. That will change when he goes into daycare part time in January. But for now? Research synopses and editing for me!

What kind of schooling / training / experience helped you get there? I have a PhD in Inorganic Chemistry, which is required for most of what I do. I also started writing early on in grad school, first for my university paper, then as a AAAS Mass Media fellow, then some freelancing, then blogging for CEN, then as an intern at Reuters Health. I couldn’t have gotten to each step without the one before. And most of what got me to the first step was just talking to people and writing. (My first column for the university paper was on National Chemistry week, actually.) I got to know some people at CEN through Jyllian Kemsley, who was a friend of my PI’s wife, so he asked if she would talk to me about being a science writer. And a lot of the work I get now came though knowing people at CEN.  Other work I’ve gotten from friends I made though the AAAS fellowship. Network, people. Seriously.

How does chemistry inform your work? Since I write about chemistry research, I of course use the six tons of chemical knowledge that I acquired in grad school on a regular basis. But probably the most valuable skill I learned was how to read the literature, and how to become well-versed in a topic I only have marginal knowledge of in a short period of time. And talk about it in an intelligent way. Yay for all those lit talk group meetings.

Finally, a unique, interesting, or funny anecdote about your career.  A really important tool as a science writer (especially a freelancer) is being able to jump around between different ways of writing, depending on what you’re doing. An encyclopedia article requires a different voice than a research spotlight for a chemistry audience, which is different than a blog post, for example. I left the lab to intern at Reuters for four months, where I was writing about medical research for the general public, then came back to write my thesis. When my adviser saw an early draft, he was so disturbed that he pulled me outside to talk about it.

“It’s just, the way you’re writing is so…so…” he trailed off and scowled at the side of the building.

“Conversational?” I suggested.

“Yeah!” he yelled. “That’s really bad!*”

So I added more passive voice and threw in as many long words as possible. Then he was happy as a pig in shit. Voice matters.

_______________________________________

*That thumping noise? That’s the sound of a thousand science writers banging their heads on their desks.


Big girls don’t cry

Nope. Instead they hack, retch, and struggle to breathe. Or pour Coke on their face?

Tear gas was a hot news topic back in February or so, when protestors in Egypt where getting hosed down with the stuff. It’s coming back up now, since police around the country are using it to clear out Occupy Wall Street camps and such.

And so with this surge back to the forefront of the news is the popping up again of urban myths surrounding tear gas. The one I’m talking about in particular is that acid (eg vinegar, Coke, etc.) can protect a person from the effects of tear gas. But before we get into if that actually works, we need to first define what tear gas is.

There are a fair few of lachrymators out there. The most common are CS, CN (aka Mace), DM, CR, and CA. Aren’t those names helpful? Most are called after the initials of the inventors. CS, synthesized in 1928 by Corson and Stoughton, is what is usually called tear gas and is most commonly used in the US (according to this book chapter about riot control agents, pdf). The chemical name is o-chlorobenzylidene malononitrile and it looks like so:

The structure of CS. I think I've given up on ChemDraw.

Okay, so what do we have here? We’ve got a benzene ring, a carbon-carbon double bond, two cyano groups, and a choloro group. According to this article (pdf), tear gas works by reacting with the water in our mucous membranes–that is eyes, nose, throat. The choloro group is the culprit here. It combines with water to make hydrochloric acid (HCl), which as you might imagine, is quite the party pooper. [ETA: CRAP! This is actually not right, as was pointed out by an astute commenter. I will update soon with the actual mechanism. Sorry about that.]

So would adding a mild acid to your face keep the stronger acid from forming? Well, Coke has phosphoric acid in it, which is a strong acid. Vinegar is a weak acid. Water is an even weaker acid. Of all those, phosphoric is the most likely to donate an H+ over to the choloro. But, in water (such as your eyes), hydrochloric acid falls apart to make H+ and Cl- anyway. So is pouring acid into your eyes really going to help you? Not sure about that.

Coke is it?

I suppose that it could have the same protective as sunscreen. That is, give the sun something to break down on your skin other than, well, your skin. But I think that dousing your face with a can of Coke is not the best way to go here. It probably won’t do too much, except attract bees. (Amirite, chemists? Weigh in here.) I think a bandana soaked in some acidic substance and draped over the face may work better. Sure you won’t be able to see, but if you’re teargassed you won’t be able to see where the heck you’re going either, because of the tears. Alternatively, according to the paper I cited above, drying out the eyes after you’ve been teargassed is the best way to make it go away fast. Hear that OWSers? Make sure to keep your hair dryers with you at all times.

Also noted in the book chapter about riot control agents is that animals are not so susceptible to the aerosol effects of tear gas, because they are covered in fur. So, best defense against tear gas: turn into a bear. Then the bees probably won’t bother you anyway.

Oh, for those of you getting hyper about those cyano groups up in the CS structure, they aren’t particularly harmful. Quoth the riot control agents chapter:

“If one were to absorb completely all the CS during a 1-minute exposure at 10 mg/m3, and if both cyanides on the molecule were liberated — and evidence suggests that only one is liberated — the
total amount of cyanide received would be equivalent to that received from two puffs of a cigarette.”

I think the big picture here is that you shouldn’t smoke.

No seriously, you really want to avoid tear gas if possible. Yes, you can imagine that it sounds nasty and all, but I’m telling you it really really sucks. I should know, as I’ve been tear gassed three times.

I should say in my defense that in two cases I was an innocent bystander. The third was from malfunction of safety equipment. Um. Sure, that’s what I’ll call it.

The first time was at a Grateful Dead concert. (Hey. Don’t judge me.) Some geniuses decided to jump the back gate at Deer Creek, the police came and set off tear gas canisters, and I happened to be on the wrong side of the wind at the wrong time. Really, I was in the parking lot, I wasn’t even at the show. The most horrible thing about that is there was a woman next to me holding a baby that was maybe 6 months old. Hearing a baby choke on tear gas is something I don’t ever want to repeat. Ever. Being teargassed feels like you are breathing needles. Fortunately, I only got a very light dose that time.

The second time was only marginally my fault. I was working at a bank, as a teller. Do you know that in all cash drawers is a pack of $20s, sometimes real, sometimes fake, that you’re supposed to hand over if you get robbed? It’s called a bait pack. In some cases, all the serial numbers are recorded so the bills can be traced. But in other cases, such as this particular bank, the bait pack consists of a rectangular packet of dye and sensor, sandwiched between two $20 bills, called a dye pack. The dye sensor, I was told, is ONLY SUPPOSED TO GO OFF WHEN IT GOES PAST THE OUTSIDE DOORS. This is important.

An exploded dye pack. Yep, it really looks like this.

I had just started working there, and was talking to the manager about something at my window, training type stuff. She mentioned the dye pack, and me being me said, “Wow, that’s cool. Can I see it?” Sure, she said, so she deactivated the police alarm on the drawer (the bait pack is in a special slot attached to a silent alarm, at least it was at this bank), pulled out the dye pack, and handed it over. I gently lifted up one of the $20s to look underneath, and the thing started making popping noises at me. The manager yelled, “Aaaaah!! Get rid of it, get rid of it!” So I chucked it under my desk and we both bolted for the back room. She slammed the door and we watched, with the other tellers, as a giant magenta plume filled the two story marble lobby. And the funny thing? It wasn’t just dye, there was tear gas in there as well.

Fortunately, it was about five minutes to five so there weren’t any customers in the lobby. Unfortunately, my dad also worked at the bank (vice president of something, which is how I go the job, yay nepotism), and it was kind of a small bank. Word traveled fast. Approximately three minutes after the dye pack went off, the phone rang on the teller line. “So,” my dad said, “I hear you tear gassed the whole lobby.”

The worst part was that we all had to walk through the lobby to get out, which meant also through the tear gas. I put my sweater over my face and ran for where I vaguely remembered the door to be. Amazingly I didn’t crash into anything, but got a HUGE dose of the tear gas. I had to wash my clothes three times to get rid of all traces.

The last time was after Bobby Knight got fired from IU. Again, wrong place wrong time for me. I was downtown with a friend, there was a kerfuffle going on, and for some reason she wanted to see what was going on. We walked a block towards the noise, then I saw the cops and caught a whiff of what was now a familiar smell, so I grabbed her arm and dragged her the hell out of there. Our lips and eyes burned a bit, but that was all really. Narrow escape.

Big big take home message: don’t get teargassed, even if you do get amusing stories out of it. I intend to avoid it from now on.


That chair thing

This is Chemjobber’s fault.

And Carmen Drahl’s and UnstableIsotope’s too. See, Carmen is collecting hand drawn propofol structures over at her blog. (I didn’t draw those yet, but I might.) But then UnstableIsotope said we should do chair conformation too, and I can’t resist a good chair conformation. And then Chemjobber put his up on his blog so then I was really spurred to action. Here’s mine. (And yes, it was the first try.)

Forgive the different C-H bond lengths there. I’m at the public library, and all I could find to write with was one of those tiny library/golf pencils that don’t have erasers. This one almost didn’t have a point. I guess I need to refill my bag with writing implements.

I other news, I’m slowly recovering from defending my thesis earlier this month. I’m working as a full-time freelance science writer now. And I hope to get back to blogging as soon as I can get some kind of reliable internet access installed at my house. That’s why I’m at the public library, by the way. The wireless keeps going in and out and there’s a really old guy who keeps hacking into a handkerchief right next to me. It’s awesome. I guess I should be glad that he at least is using a handkerchief.

Anyway, revel in my lovely chair confirmation. And I hope to be back soon.


The ‘O’ word

For those of you that didn’t get here from there, this post is the last in the series of CHEMisperceptions bloggy roundtable. Please read the other entries at ScienceGeist, Chemjobber, and ChemBark for your own enlightenment and entertainment.

Organic. What the hell does that word mean?

As with many things in life, the answer depends on who you are. Are you a chemist? (I am!) Then organic makes you think benzene, hexane, methane—almost any chemical compound that contains a carbon atom. Perhaps you’re a gardener. (Again, me.) Then organic means a way of tending your plants, using bat poo and insecticidal soap instead of Miracle-Gro and Roundup. Are you a writer of dictionaries? Then organic might mean something like this to you…

“of, relating to, or derived from living matter.”

So twigs, leaves, chipmunk carcasses, eyeballs, your wool socks, cat whiskers, whatever, all organic materials. Things that are not organic: Rocks. Metal. Whatever beats in Rupurt Murdoch’s chest. These things are known as inorganic, the opposite of organic. In the chemical sense, they (mostly) do not contain carbon. Some very familiar inorganic substances are water (H2O) and salt, table or other. (Table salt is sodium chloride, NaCl. The salt they put on the roads in winter is usually potassium chloride, or KCl. There are also numerous other salts that don’t contain chloride ions.)

By the way? That organic = natural definition is the oldest one. So if we want to be purists about it, that’s what organic really means.

However, in colloquial language terms, we are not purists. As such, organic means whatever we say it means. So what do we say it means? To most people, when they hear the word organic they think produce. The Farmer’s Market on Saturday mornings. The first thought of organic is in the farming sense. And that actually, is something very specific.

According to the USDA, if you’re a farmer or a food-seller, you have to meet very specific guidelines to call your food or product or whatever ‘organic.’ And they are thus:

“Organic crops are raised without using most conventional pesticides, petroleum-based fertilizers, or sewage sludge-based fertilizers. Animals raised on an organic operation must be fed organic feed and given access to the outdoors. They are given no antibiotics or growth hormones.

The National Organic Program (NOP) regulations prohibit the use of genetic engineering, ionizing radiation, and sewage sludge in organic production and handling. As a general rule, all natural (non-synthetic) substances are allowed in organic production and all synthetic substances are prohibited. The National List of Allowed Synthetic and Prohibited Non-Synthetic Substances, a section in the regulations, contains the specific exceptions to the rule.”

I think that last line is the most important there. That list? Is huuuuge. And some of the things on it are surprising (such as oxytocin). However, the point is that organic doesn’t necessarily mean natural, or non-synthetic. (The USDA even says so right here.)

So the general public somehow seems to have combined the older definition (organic = natural) with the farming definition (organic = non-synthetic, except for when it doesn’t). Because the general zeitgeist does seem to be that organic somehow means better for you. It does not. However, I’m not going to go into that here. It’s a complex and fascinating topic, and I highly suggest Christine Wilcox’s excellent post about the myths of organic here.

In this context, I’m more interested in where the term ‘organic farming’ came from. And the biggest name in organic farming is certainly Rodale. The Rodale Institute was started in 1947 by J.I.Rodale. The Rodale Institute publishes a lot of books on organic farming practices, as well as runs a series of farming trials comparing organic farming practices to conventional ones.

Rodale is considered by many to be the father of the organic farming movement. These ideas did not come from nowhere into his head, however; he was highly influenced by Sir Albert Howard’s An Agricultural Testament, published in 1940. (Here is a pdf of the whole thing, if you’re interested.) Lady Eve Balfour also wrote upon the subject in 1943, in a book called The Living Soil (but that one’s out of print).

Regardless, no one’s really sure who coined the term ‘organic farming.’ However, it was a term used to differentiate between conventional farming techniques that used many inorganic salts as fertilizers. The big deal with Howard and Balfour and Rodale was the use of manure to add organic matter back into the soil. The use of inorganic salts on cropland will, over time, kill the millions of organisms that live in dirt, leading to ‘dead’ or inorganic dirt. You want your dirt to be alive to have healthy plants. Hence, ‘organic’ farming. It actually makes sense if you think about it.

So, I imagine that all the chemists reading this are gnashing their teeth about now. Because in chemistry terms, ALL farming is organic farming. Remember, organic to a chemist means containing carbon, and you’d be pretty dang hard pressed to find a plant without carbon in it.

Supposedly, the term ‘organic chemistry’ came about in 1807, named by Jöns Jacob Berzelius for compounds that were derived from living things. (I say supposedly because I can only find one source that says that, Wikipedia.) So it does outdate the use of organic for farming. But that means chemists win? Do we own the term ‘organic’?

So that’s the question I’m throwing out to you reader-types out there. Should organic farming be called something else? Or should we just all get along, and share the word?

Here’s my $0.02: let the poo lie. Organic can mean different things to different people. Although I am speaking as both a chemist and an organic gardener. (Yep. Before grad school, I used to teach organic gardening to kids in the summer. I also did soil science research as an undergrad, so I’ve got a lot of views of the issue.) So maybe it’s easy for me to see both sides.

Although this is what does piss me off: the use of the word ‘organic’ when it’s not government approved, or even reasonable. For example, those dry cleaners who put signs up in their windows touting their ‘Organic Practices!’ Or this organic water crap. This is just preying on people’s ignorance about the subject to make a buck. Or as it’s otherwise known in the modern world, “marketing.”

Unfortunately, it seems the only way that people can avoid being duped by this is by education: being aware what organic means, when it is applicable, and if it actually has any benefit. And the jury’s sure out on that last one.

Oh, organic. What an obstreperous obstacle you are.

Photo sources: chipmunk, cat. The other pictures are mine, that I took in my garden. So no stealing.


Plagiarism—is it ever okay? No, really.

I’m writing my thesis. Therefore, I am temporarily non compos mentis. Sorry.

Logic dictates that along with the crazy comes obsessive fixation. And the current one? Plagiarism. I’m trying desperately to avoid it, which isn’t as easy as it sounds. Because first of all, what exactly is it?

Copying someone else’s words verbatim and claiming them as yours, okay that’s obvious. But how many words do you have to change before it becomes your own? For example, take this sentence, from from the onlineyest of online sources, the Huffington Post:

Separate from the inspector general’s power to ban, the FDA has resurrected something called the “Park Doctrine,” which makes it easier for prosecutors to bring criminal charges against an executive.

So that’s from an AP story on the HuffPo site, In Shift, Feds Target Top Execs For Health Fraud By Ricardo Alonso-Zaldivar.

Trying it verbatim, dustball.com and plagiarisma.net (using yahoo) labeled it possible plagiarism. Yay, them. Duplichecker (using msn search) came up with a bunch of links that were similar, some of them the AP story, some not (like the Wikipedia page for Inspector General). So now let’s change things up a bit. How about…

Distinct from the inspector general’s authority to prohibit, the FDA has revived something termed the “Park Doctrine,” that simplifies lawyers bringing charges against senior business people.

What I did was just change a lot of the words for synonyms, and rearranged a bit. What do those free web checkers think? Again, duplichecker came up with a bunch of links, but this time none of them were the original AP article. It was likewise hunky-dorey with dustball.com, and called unique by plagiarisma.net.

But what do actual flesh and blood people think? Is my bastardization of the AP sentence plagiarism? Or not? Where’s that hazy line in the sand? How different does it have to be to be considered…different enough?

And why the hell am I asking?

As I mentioned above, I’m up to my armpits in thesis right now. And I’m finding myself in the situation of having to re-visit some topics, specifically ones I’ve recently written papers on. As such, how I worded intros, discussions, and conclusions is quite fresh in my mind. So fresh that I find myself writing them exactly the same way in my thesis. I’m trying to avoid it whenever I can, but sometimes still catching things that slip through. But I have a feeling I’ve been missing some.

To add to the confusion, I’ve been reading the theses of other people, from my lab or not, to see how they did things. And when I go back to some of their original sources, I’m finding some…remarkable similarities. Some in places where it’s probably not okay, and some in places where it might be.

But where are those places? When is self-plagiarism okay?

Of course I’ve already asked my adviser this. His response? “It depends.”

Helpful.

When pushed to his limit, he told me, “try not to do it too much.”

Sigh.

Look, I realize that I’m being neurotic about the whole thing and probably overthinking it to boot, but I’m trying to stay above board here. No, I don’t think I’m going to end up as a Retraction Watch post or anything, but I do want to Do a Good Job. So where and when is self-plagiarism okay? Really.

In lieu of your opinion on the matter, you also may tell me to lighten up or take me out for a drink. All are welcome.


Why take iodide for radiation poisoning?

Earthquake and Tsunami damage-Dai Ichi Power Plant, Japan

The picture above is an aerial view of the Fukushima Daiichi power plant. As we all know, it was knocked about in the huge earthquake that hit Japan yesterday morning. At the time of this writing, it seems like there was some radioactive material leakage at the Fukushima Daiichi power plant, but it may have gone down. There’s a lot of confusion about what’s going on, not surprisingly. It does seem like authorities are handing out iodide tablets as a precaution against radiation poisoning, however.

So why would taking extra iodide protect against radiation poisoning? To answer that, we need to take a pretty big step back.

Many nuclear reactors get their energy by smacking uranium-235 with a neutron, called fission. And in a turn of events that is both crazy and amazing, a single act of fission can create more than 200 million times the energy of the neutron that kicked it off in the first place. I’m not going to go into why here, but it has to do with the famous Einstein equation.

So when uranium-235 decays, it gets broken into a lot of smaller fragments. One of these is iodine-131. It’s also radioactive. Out of the most common fission products of uranium, iodine is the only one that’s present naturally in our bodies.

There are actually fourteen major radioactive isotopes of iodine. The majority of them are not considered dangerous, because they have very long half-lives. That’s the time it takes for half the radioactive material in the element to decay.

For example, iodine-129 has a half-life of 15.7 million years. So its decay might be something like this:

Blam!…wait an extremely long time…Blam!…wait an extremely long time…etc.

However, the half-life of iodine-131 is 8 days. So it may look something more like this:

Blamblamblamblamblamblamblamblamblamblamblamblamblamblamblam
blamblamblamblamblamblamblamblamblamblamblamblamblamblamblam!

I’m simplifying here, but you get the general idea: iodine-131 has the potential to do a lot more damage to the body, because it gives off more radiation in a short period of time.

And where it’s going to do that damage is mostly in the thyroid.

That little butterfly-looking thing in your neck is the only part of the body that can absorb iodine. It pulls it out of food and, along with the amino acid tyrosine, converts it into the hormones thyroxine (T4) and triiodothyronine (T3).

T3 and T4 go off into the blood stream and the rest of the body where they oversee the conversion of oxygen and calories to energy. Every single cell in the body relies on these hormones to regulate their metabolism.

So imagine if the iodine absorbed by the body were radioactive. That would be way, way bad.

Triiodothyronine and thyroxine: hot or not?

Iodine is pretty volatile (in a very purple way). So if a nuclear reactor were to leak, iodine-131 might be in the air. Which people might breathe in. Which could get into their thyroids. Which could cause radiation poisoning in the short term. In the long term, breathing radioactive iodine can cause thyroid cancer, especially in kids.

To minimize the damage, people who may be/have been exposed to radiation from a power plant can take iodide pills. These work by saturating the thyroid with nice, non-radioactive iodide. That way, if any radioactive iodine does come along, the body won’t absorb it–the thyroid can only absorb a finite amount of iodine at a time.

If people can get these pills 48 hours before or eight hours after radiation exposure, it can reduce thyroid uptake of iodine-131 and decrease the risk of radiation-induced thyroid cancer.

[ETA: I do want to point out that this will ONLY protect against internal iodine radiation poisoning. Not radiation from cesium-137 and strontium-90, extremely dangerous fission products of uranium-235.]

These pills contain about 100 milligrams of potassium iodide. You can overdose on iodine, although it takes several grams. But burning of the mouth, throat, and stomach, fever, nausea, vomiting, diarrhea, and/or a weak pulse may be preferable to getting cancer later.

This treatment was used in the the 1986 Chernobyl nuclear reactor accident. There were fewer cases of childhood thyroid cancer in areas that had access to iodine tablets, compared to areas that didn’t, or got them too late (pdf link).

Hopefully, people near the Fukushima Daiichi power plant will have access to iodide pills, and be able to get the hell out of there. Radiation’s not something you want to mess around with, especially if you’re pregnant or a kid.

UPDATE: There are now rumors that one of the reactors has exploded. Follow Reuters for breaking news, and keep your fingers crossed.

Photo credit: Digital-Globe imagery, Wikimedia Commons.


So much to love

So Chemjobber, the reigning potentate of goofy lists, sent out an edict yesterday to hear other people’s favorite things in chemistry. Here are some of mine:

Tetraphenylporphyrin crystals! Although honestly, I've never made batch this small.

  1. The lovely purple sparkliness of tetraphenylporphyrin
  2. Bantam ware
  3. Using that three-neck 3L flask that looks like a giant glass udder
  4. Running columns that would match the decor at a six year old girl’s birthday party (ie, fractions that are pink, purple, and orange)
  5. Beer at group meetings
  6. Short group meetings
  7. When my husband picks me up so I don’t have to drive home from group meetings
  8. Clean separation of compounds on only one prep TLC
  9. Beautiful, clean 2-D NMR spectra
  10. Fresh bottles of tetrakis(triphenylphosphine)palladium (0)

Although, I think my most favorite thing about chemistry is having a finished thesis. Oh wait! Hang on! I don’t have that! I must be hallucinating again. Repeated banging one’s head on the wall will do that, I guess.

Check out some other contributions: The Boiling Point, ScienceGeist, Curious Wavefunction, LabMonkey4Hire.


The persistence of Barry White

Isn’t it funny sometimes, when you start out trying to do one thing, and you end up doing another?

A lot of science goes that way. The guy who invented post-it notes was supposedly trying to make a stronger adhesive. Teflon was supposed to be a refrigerant. And Viagra? Well, they were trying to make a drug to control blood pressure.

It makes sense if you think about it for a minute. High blood pressure is a problem because it increases pressure in the arteries (duh), which means your heart has to work harder to get the blood everywhere it needs to go. But if you took a drug that made your arteries wider, your heart wouldn’t have to push so hard, problem go bye-bye, yes? More or less.

All right, let’s talk about penises now.

A selection of penises from the Iceland Phallological Museum. Yet another reason to visit Icleand. Photo by Wellington Gray.

A guy gets an erection because blood flows into his penis, then stays there. Most men with erectile dysfunction have a problem with their penises filling up with blood. The arteries don’t open up enough, not enough blood can get in, hence no stiffy.

The body regulates arteries widening and constricting, like it regulates pretty much everything else, by chemical cascades. In this particular case, the brain sends a signal through a nerve cell, which triggers the release of nitric oxide, or NO. This turns on an enzyme called guanylate cyclase, which starts making this stuff called cyclic guanosine monophospate, or cGMP for short.

NO

This cGMP is the Barry White in the equation here. It puts those arteries in the penis at ease, so then they relax and open up. Then, schwing! Blood can get in, dude can pitch a tent, and make some sweet sweet love.

Of course, it’s not great biologically to walk around with a constant boner, so there’s something else floating around to make the cGMP go away. It’s yet another enzyme called phosodiesterase, or PDE. There are a lot of different PDEs in our bodies, but the one that rules in the wanger is PDE 5.

PDE 5’s one job is to break down cGMP. No cGMP, no more blood flowing into the penis, and eventually, no more erection. So here’s the pretty cool part: Viagra works by throwing a wrench in PDE 5’s machinery. It’s also known as 5-[2-ethoxy-5-(4-methylpiperazin-1-ylsulfonyl)phenyl]-1- methyl-3-propyl-1,6-dihydro-7H-pyrazolo[4,3-d]pyrimidin-7-one. It looks like so:

chemical structure of Viagra

Generic structure for Viagra--the pills actually contain sildenafil citrate, which is slightly different than what I've shown here. That convert name to structure button on ChemDraw just made things a bit too easy for me.

And this is what cGMP looks like. See the resemblance?

cGMP

Resemblance to the Viagra molecule. Not to Barry White. But you can kinda see him too if you squint just right.

So PDE 5 is an enzyme, and those work by kind of a lock-in-key type way. A molecule of a certain shape fits into the enzyme, and then the enzyme does what it will with it. In this case, breaks some bonds so the molecule can’t do its job anymore.

But when is sees Viagra floating around in there, it gets confused. That bit in red there? It fits into PDE 5 exactly the same way that cGMP does. So when there’s a lot of Viagra around, the PDE 5 chews it up, instead of the cGMP. So then cGMP can build up in the penis, which makes sure the arteries are opened up. Barry White persists, and the guy gets a chub. Long live Barry White.

Viagra induced woodies can also last up to four hours. So for those of you who can’t get enough? You’re in luck.

Happy Valentine’s Day.

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For further reading (with diagrams!) I suggest Discovery Health’s How Viagra Works page. For the chemists in the crowd, the original paper by Pfizer is pretty interesting: Terrett et al., Bioorganic & Medicinal Chemistry Letters, Vol. 6, No. 15, pp. 1819-1824, 1996.

Oh and btw: the Icelandic Pallological Museum. You’re welcome.


Chemistry: this shit’s important

What’s the most important scientific discovery ever?

I put this question up on facebook, and people came up with some pretty good answers. Electricity was the most popular. Fermentation and antibiotics were also good suggestions. But when you think it in terms of having a direct impact on the largest amount of people, there’s really only one answer: the Haber-Bosch process.

Yeah, I know. You’ve never heard of it. But you may be alive because of it.

The Haber-Bosch process is how you make ammonia out of nitrogen and hydrogen gasses. I’m simplifying it a wee bit, but here’s how it works:

You take your hydrogen and nitrogen,

HB before

Figure 1. Nitrogen and hydrogen gasses. Blue = nitrogen, red = hydrogen

squish the crap out of them and make them really really hot,

HB during

Figure 2. An approximation of the Haber-Bosch process. Please note that squish = approximately 250 times the pressure of the normal atmosphere at sea level, and way hot = anywhere from about 900 to 1600 degrees F. Maybe I should have said way way hot.

and poof! You have ammonia!

HB after

Figure 3. Ammonia (NH3) is a happy molecule. Please note the the happiness factor of each molecules has been approximated using standardized procedures published elsewhere.

The thing about this process–chemists had been trying to do this for more than 100 years when Fritz Haber figured it out in 1909. As living things, nitrogen’s pretty important to us. Our bodies are about three percent nitrogen by weight, and we get it from eating plants and other animals. But plants, having no mouths (for the most part), have to get it either from the air or the soil. The problem is that even though N2 (the nitrogen molecule, Fig. 1) makes up almost 80% of the air we breathe, it doesn’t react with anything. That triple bond you see up there is quite strong, and it takes a lot of energy to pull it apart, more than plants generally have at their disposal. So plants can’t break it down1 and recycle it into things like amino acids and cell walls and all that useful stuff. For it to be usable, nitrogen has to be “fixed.”

Ammonia, NH3 (Fig. 3), is a fixed form of nitrogen. That means that its bonds are breakable, and it can react with other things. Generally, it’s used to make nitrates, NO3, which is used for both explosives and fertilizer. Natural forms of fixed nitrogen are rare, but it’s found in bat and bird poo, and saltpeter. These things were some seriously in demand fertilizers before the Haber-Bosch process was discovered. In fact, The Guano Islands Act of 1856 was passed so people could claim any uninhabited, poop-covered island they found as a US protectorate. Wars were fought over poo. Really. So when Haber found a way to finally make fixed nitrogen, it was quite a big deal.

bird poo

Figure 4. Americans get the poo. The Guano Islands Act of 1856 is allegedly still on the books. Get your flag and go! (With apologies to Eddie Izzard.)


Then Carl Bosch and Alwin Mittasch came along and figured out how to make Haber’s system workable on an industrial scale. Haber had originally used an osmium catalyst to make ammonia, but that’s pretty expensive. Mittasch went through about 4000 other catalysts until he found one that worked as well—a mixture of iron and metal oxides. The Haber-Bosch process was officially rolled out in the industrial world in 1913. Haber won the Nobel Prize for it in 1918. Bosch shared the prize with Friedrich Bergius in 1931 for figuring out how to deal with high-pressure chemistry.

So this was a great chemical breakthrough and all that, but the really important thing? A lot of people stopped starving to death.

Figure 5. Effect of the Haber-Bosch process on world population. Graph from Erisman, J. W.; Sutton, M. A.; Galloway, J.; Klimont, Z.; Winiwarter, W. “How a Century of Ammonia Synthesis Changed the World”. Nat. Geosci. 2008, 1: 636-630.

The above graph shows how the world’s population changed after we got cheap, available fertilizer. Look at the difference between the solid black line and the dashed red line. According to this chart, about 3 billion people are alive today because of this. Because of one chemical reaction.

The Haber-Bosch process is used to make about 500 million tons of artificial fertilizer per year, and sustains about 40% of the population. It uses about ONE PERCENT of the world’s total energy supply2. If the population continues to grow as expected, then by 2050, about 270 million tons of coal (or equivalent energy) will be needed to make enough fertilizer to keep us all from starving to death.3

One chemical reaction.

On the flip side, nitrogen runoff from fertilizer is choking lakes and rivers with algae and messing up the ecosystem. Keeping the Haber-Bosch reaction running is filling the air with carbon dioxide, carbon monoxide, and other combustion byproducts that are changing the climate. I’m not even going to go into the potential impact of a hugegrowingwayfast population. (Tangentially, Haber’s discovery also kept the Germans in explosives during World War I. He’s known as the father of chemical warfare, and his work led to the use of Zyklon B in Nazi death camps.The Alchemy of Air is a fascinating book about the whole history. The writing is a bit dry, but I still highly recommend.)

Even taking these things into account, it cannot be argued that the Haber-Bosch process has had an ungodly huge impact on all of our lives. Go ahead, try to deny it. Try with both hands.

This year is the International Year of Chemistry, “celebrating the achievements of chemistry and its contributions to the well-being of mankind.” And believe it or not, there are a lot of them. Way too many to mention. Way too many for us to even know about.

Chemistry: this shit’s important.

…………………………………………

For more reading on the Haber-Bosch process, I suggest of The Alchemy of Air, In the shadows of greatness, Jürgen Schmidhuber’s page on Haber and Bosch, and World Population: How Did It Get So Big?

1Legumes (eg beans or peanuts) have bacteria at the base of their roots called rhizobia that can pull nitrogen out of the air. They’re the only kind of plants that do this, and that’s why you’ll often see soybeans as a rotator crop with corn. Beans put nitrogen in the soil, and corn pulls quite a bit of it out.

2Science 297(1654), Sep 2002.

3Biological Nitrogen Fixation – National Research Council . National Academic Press 1994.


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