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You know about fossils, but what other secrets are lurking in the ground beneath our feet?

Hosted by: Hank Green
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Hank: You probably think most of what we know about ancient life comes from fossils. Y’know like, bones and stuff in the ground. Well, it turns out that there are lots of other clues about the history of living things that are just waiting to be dug up. It’s just that they’re a lot smaller than even your tiniest fossils.

Like, I-definitely-can’t-see-them small. I’m talking about ancient DNA. These little bits of really old DNA are in soil -- as well as other places like ice, and at the bottoms of lakes or oceans -- and together, they’re what scientists call sedimentary DNA.

They’re leftovers of long-departed plants and animals: sloughed-off flakes of skin and pieces of hair; dropped feathers and eggshells; and fallen leaves. And because of advances in our ability to purify, amplify, and analyze DNA, we can now use these remnants to re-create what Earth looked like tens or even hundreds of thousands of years ago, all without fossils like bones or teeth. Someday, sedimentary DNA may even tell us about life on worlds beyond our own.

And it’s kind of amazing that scientists can find this ancient genetic material at all. Because DNA isn’t exactly a robust molecule. Once it’s exposed to the elements outside of cells, DNA breaks down easily, especially in hot temperatures.

So it’s no surprise that some of the oldest sedimentary DNA comes from samples taken from the coldest places on Earth, like glaciers in Greenland or Siberian permafrost. But there are other ways DNA can stick around. DNA can bind to charged particles in the soil -- specifically in clay -- which protect the molecules from getting chewed up by enzymes that are released by microbes in the dirt.

And sometimes those microbes can help save the DNA, too. Instead of breaking it down, bacteria can actually incorporate sequences of other organisms’ DNA into their own genomes for safekeeping. But to unlock the secrets that are kept in sedimentary DNA, scientists have to find it, and amplify it.

For this, paleobiologists use a technique called polymerase chain reaction, or P-C-R. They extract the DNA from a sample of mud or ice, or whatever they’re interested in, and then make lots of copies of certain stretches of it, so they can get a closer look. To do this, they add a bunch of nucleotides – compounds that are the basic building blocks of DNA -- along with an enzyme called DNA polymerase.

The enzyme uses those blocks to replicate the DNA, ultimately making millions of duplicates. Armed with those copies, scientists can then sequence the DNA and find out what sorts of plants and animals once occupied that little spot of mud or ice many years ago. Unfortunately, PCR isn’t perfect, and sometimes DNA polymerase amplifies the wrong thing, like DNA from the researcher and not from the soil sample.

With a small cough, a tiny droplet of saliva can make it into the tube. And PCR is so good at what it does, that it takes a minuscule amount of outside DNA to ruin everything. But if researchers can keep their samples and workspaces impeccably clean and keep out unwanted DNA, they can find amazing things.

A lot of these things have to do with what really happened when, in Earth’s history. Because sedimentary DNA is really helpful in giving us a sense of how old a certain bit of genetic material might be. It’s not perfect, but because scientists generally know how old the layers are that they're digging in, if they find DNA in it, it's a good guess that the genetic info is that old, too.

So for example, in 2009, a team of researchers drilled a sample of sediment from the Yukon Flats in central Alaska. And they found sedimentary DNA in that sample that showed that woolly mammoths roamed mainland Alaska just 10,500 years ago -- that means the hairy pachyderms survived at least 2,600 years longer than we originally thought!

Another study found that bacteria were evolving ways to be resistant to antibiotics 30,000 years ago, well before we ever came with the idea for modern drugs.

And in 2015, researchers reported that they had found sedimentary DNA evidence of 8,000-year-old wheat in the British Isles, suggesting people were farming the land a full 2,000 years earlier than previously thought. But other scientists have since contested these results, arguing that the samples were – you guessed it – contaminated.

Because we are DNA-based, too, contamination is a constant concern. But some researchers think that the growing science of sedimentary DNA, may help us find signs of life on other worlds, like Mars. It’s super cold there, after all, so if DNA is or ever was around, there’s a good chance it’s preserved somewhere. We just need to find it, and either then bring it back, or analyze it there, without contaminating it with any of Earth’s very abundant genetic material. You know, easy peasy. So many secrets, right under our feet!

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