Tag Archives: chemistry

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.

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:


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.

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


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

HB during


and poof! You have ammonia!

HB after


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


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.