Category Archives: biology

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.

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.




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


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



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.

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.

The Immortal Life of Henrietta Lacks: something I didn’t say

So my Science review of The Immortal Life of Henrietta Lacks by Rebecca Skloot came out today. It’s here, although you’ll need a subscription to get through. I’ll have a secret back door link in a couple of days, which I’ll post from my Clips page.

Anyway, I wanted to spend a moment talking about the something I didn’t say in the review. Is Rebecca Skloot a badass or what?

It took her *ten years* to write this book. She had doors repeatedly slammed in her face. People refused to talk to her, hung up on her, and generally treated her as untrustworthy. An entire town disappeared while she was writing Henrietta’s story. But she still made it happen, seemingly bringing it into existence by a mixture of stubbornness and passion.

Reading between the lines, it also seems that Skloot may have had some problems with editors. (I think it was in the prologue where she mentioned there was an editor that wanted to completely remove the Lacks family from the book? Seems odd, since their story was the part that really dug into your chest and squeezed.)

Well, maybe that’s normal. I don’t know, I’ve never had a book published. But I do know this–if I ever do write a book, I’m going to use Immortal Life as an example of how to do it right. It was the type of book that hangs around a long long time after you put it down, the kind of story you experience rather than read.

Okay, enough. I’ll chuck my Rebecca Skloot pompoms and megaphone into the corner now. But really–go read it. It will not be a waste of your time.