Earlier this week, I showed you how scientists can use a simple, hand-operated tool to collect stratified core samples of mud at the bottom of a swamp. The deeper the samples go down, the older the mud is—until, eventually, you're looking at 6000-year-old muck, the remains of a lake bed that filled in with sediment and became swamp.

The core samples are narrow logs, each 50 cm long. (In all honesty, they looked like less-colorful versions of the 3 pound gummi worm I ordered for my 30th birthday party last year.) For the most part, they're some variation on the shade of brown, with occasional streaks of red and burnt umber, until you get to the very bottom. There, the samples turn grey. Put a bit in your mouth, as I was encouraged to do by Harvard Forest director David Foster, and you'll taste clay and feel grit between your teeth.

That's all well and good. But what do you do with core samples once you have them? For this installment of Dispatches From Harvard Forest I'm going to leave the woods and head into the lab, to see what happens to the parts of the Forest that scientists take home.

Step one: Make dirt cupcakes

We cut samples out of the samples. (Insert your "yo dawg, I heard you like samples" joke here.) Every 25 cm, so twice for each core, we cut off a little hunk from the side. We put the pieces into ceramic cups that had been weighed and labeled, so we'd know later where in the chain each sample had come from and what the samples weighed.

Then we baked them.

Seriously. The Marine Biological Laboratory (or MBL as it prefers to be known these days) has a great big industrial oven. The cups went in a roasting pan. The roasting pan went into the oven. Several hours later, all the liquid had been cooked off and we were left with dry samples.

Out of all the little samples, there were really just three main types. Near the top, we had a lot of crumbly black earth, studded with roots and sticks and fibers.

Further down, that petered out, and you ended up with solid lumps. The lumps had some stuff in them, but not nearly as much. By the time mud is this old, a lot of the biological material in it has decomposed. These samples looked brown when we first cut them off the mud cylinders. After baking, they turned greyish-green, mottled with brown spots.

Finally, at the very bottom, was the grey clay. After baking, I could see that the grid I'd tasted was actually mica. It made the whole sample sparkle.

Step 2: Record the color

We weighed the baked samples and we wrote down a short description of what they looked like. This being science, "I think this lump of dirt looks kind of bluish-green" was not considered to be an accurate description.

How do you take something subjective, like color, and bring it into the world of the objective? This looks like a job for official color charts.

The Munsell Soil Color Chart book is like Pantone for dirt. You just take your sample and match it up to one of the color chips. The number of the chip is what gets recorded. That way, other people can go back and verify (or challenge) your interpretation.

Step 3: Burn off all the carbon

Next, the samples go back in the oven and the heat gets turned way up—hot enough to burn away all the organic material. What your left with is stuff like minerals, metals, and rock. If you weigh the samples and then compare that to what they weighed after first baking, you know how much of the sample was organic material and how much wasn't.

Naturally, the results changed as you moved from the surface down. Barely any weight remained in the uppermost samples. The lowest ones had barely changed. That's the difference between soil filled with plant material, and lumps of mica-filled clay.

This is, to say the least, probably not a huge revelation. But it leads to something really cool. After the carbon was burned off, the samples looked amazing. Some were chalky moonscapes, others had turned into piles of dark red fibers.

The fibers, pictured above, are what you should be paying attention to. Because they don't really make sense. We just burned off all the carbon-based material…which should include plant fibers. So, then, what in the sam hill are those things?

According to Rich McHorney, one of my advisors in the MBL Science Journalism Fellowship, the red color is from iron oxide—rust. What you're seeing here isn't plant fibers, but a shell of rust that had formed around plant fibers that were on their way to fossilizing. We burned away the plants. But the iron oxide remained. In a way, it's a bit like the casts of bodies from Pompeii. How cool is that?

Read the rest of my Dispatches from Harvard Forest