Kenya 2012: Bones, Bodies, Misbehavior*

Note: The internet comes and goes at Kenya in the moment. Mostly goes. As such, this post is a few days late. Pardon our tardiness. We’ll get back on schedule lickety-split.

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I would say the weather in Nairobi is temperate. Gray clouds floated by today without dropping their contents, except for the short but violent tantrums when they did. It’s the sort of taunting atmosphere that makes the decision of whether or not to wear a jacket a real existential crisis.

I’ve been told that it’ll be chillier in Laikipia. That should make these things clearer cut.

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That’s how you start conversations, you know, at least in the States. You talk about the weather. It’s a pretty safe bet that wherever there are people, there is weather nearby.

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Now that those formalities are over, let’s get to some more formalities. My name is Paul Mitchell and I’m in Kenya in order to put some of the parts of at least one person in a few bags. Of course, there’s more to the story, but we’ve got to introduce the dramatis personae first. It’s a convention to do so, but perhaps an informative one.

At this point, what you need to know is that I’m a student at the University of Pennsylvania in Philadelphia, a major in biological anthropology and philosophy, am twenty-one years young and work at the Penn Museum in the skeletal collection. As such, perhaps you can now contextualize why I’m interested in people parts. Keenly interested.

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Dr. Kathleen Ryan has been to this part of the world many times. When we checked into the United Kenya Club in Nairobi, the porters and receptionists and drivers recognized her, shook her hand and asked how she was. A whole bunch of folks did the same thing when we were at the National Museum. She greets them back in a fantastic accent, grown organically in Ireland. She motions to me, “This is my colleague, Paul.” They shake my hand and hang giant smiles to dry for minutes on a line between their ears.

Kathleen is a woman of many hats, but you can call her an archaeologist if you want to affix a single label. Her archaeozoology lab neighbors one of the rooms of the human skeletal collection in the research wing of the Penn Museum. If I recall correctly, I first met her as she popped out of her office, very spryly, as she does, while I was carting skulls through the hallway. I don’t know how it happened, but she asked me to go with her to Kenya some time ago. There are human skeletons to be excavated and examined and samples to be taken for genetic analysis at one of her sites, she explained. My ears perked.

I’m sort of secretly in love with Africa from afar, so I said “yes” at some point. So, that’s why I’m here now with a mosquito net over my bed and a stomach full of coffee that could have been picked only down the road, just as happy as a clam.

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My final exams ended on the eighth of May. On the ninth of May, mostly braindead, I was leaving with Kathleen. We got on a plane in Philadelphia, heading to Nairobi by way of a connecting flight in London. I was reading Lolita and bothering the stewardesses all the time for more coffee. A towheaded toddler behind me cried and cried. I sat next to a fellow Penn student. He was a sophomore and from Nairobi himself. He studied finance. I decided that we wouldn’t talk about academics.

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We had four hours to kill in Heathrow. Kathleen declared that we needed something to eat. It was breakfast time, vaguely. We stopped at a cafe which had tall, orange plastic giraffes, twice a person’s height, in the middle of the dining area. She ordered something with bacon and eggs and toast and home fries. I ordered something with avocados and cherry tomatoes and hummus and sourdough. I think she chuckled at me.

Kathleen couldn’t weigh more than one hundred pounds when carrying two full bags of groceries in a monsoon.

“As much as one hundred and three pounds,” she marmishly retorted when I was brazen enough to broach the subject. I want to get the facts straight.

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We met Louise in London. Louise is a chemist and will be joining us in Laikipia. She’s from New York but just got back from the Caribbean. Erika and Jen and her retinue are supposed to be here later, too. Holy smokes, all the people, dead and alive. The dead people will come into the story later. All the actors in the play so far are alive, alive, alive.

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We got to Nairobi without difficulty. As we flew in, I watched the sun set out the window over the southern tendrils of the Sahara. Justus and Kamande met us at the airport and drove us to our accommodations at the United Kenya Club. While Kamande drove and chatted with Kathleen up at the front of the van, Justus told Louise and I all about his thoughts on politics, religion, and the medicinal applications of the local flora.

It was late by the time we got in. We drank these bottled beverages called Tangawizis on the porch. They’re ginger beers and they’ll clear your sinuses. The club is great. It has a big porch where you can drink things. Like soda.

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We had to do a whole mess of things on Friday before we leave for Laikipia on Sunday. First, there were permits to be gotten at the National Museum. I saw a statue of Louis Leakey. I got excited.

We journeyed to the archaeology department’s main office. Some other folks who looked as if they had similar prurient archaeological ambitions and needed permits, too, were milling around. They were a cheery lot. Mary is an archaeozoologist like Kathleen. She invited me to help her wash her microfaunal bones sometime. Oh yeah. Susana spends the lion’s share of her time digging up rocks that chimpanzees used to crack nuts hundreds and thousands of years ago. She’s going to Koobi Fora now to look at lithics. Little stone tools. We all must have been strange children.

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Dr. Purity Kiura, Head of Archaeology at the Museum and Professor Mulu from the University of Nairobi helped Kathleen get the permits. There were letters to be written and fees to be paid. After scribbling the necessary signatures, we got a tour of the osteology department. See?

Paul and Kathleen

Louise and the warthogs

Osteology crew at the NMKN

Paul loves gorillas.

Here’s my favorite box at the museum. I think it wouldn’t be a terrible idea to install some of these in D.C.

We ate at the museum. Louise ordered tilapia. Mary joined us for lunch and looked at the tilapia bones after Louise was done.

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It took us all afternoon to get what we needed at the mall. The ATM wasn’t working and the air conditioning was out. It was significantly hotter inside than outside under the mercurial Nairobi sky. Laikipia is a six hour drive away, so we needed to ensure that we have water and food and all that jazz for the journey there. I got a bunch of instant coffee and chewing gum. Priorities, you see. It was something of a hectic experience buzzing around a Kenyan mall, looking for this and looking for that. People pour over everywhere and it isn’t always intuitive where they’ve stashed what you’re looking for. Kathleen bought some sunglasses, which I think are very stylish. The height of fashion, my little droogies.

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Soon, we’ll be out of Nairobi. The skeletons we’re supposed to sample in a place called Mpala on the Laikipia Plateau are west of here, between Mt. Kenya to the south and Lake Turkana to the north. We’ve been here since Thursday evening. One more day at the museum before Erika arrives, we can get out of here, and the work can begin in earnest.

Kathleen showed me a photo of one of the burials at Laikipia. Brittle bones in the earth. They dug up one of the many burial cairns in Mpala a year ago. The skeleton isn’t in anatomical position. At risk of sounding irreverent, it looks like someone sprinkled those bones on the grave like potpourri on a the centerpiece of a dining table in a kitschy interior decorating magazine. Normally, you can expect bones to fit together in a pretty predictable way. There is no natural articulation in which you’ve got an ectocuneiform articulating with an ethmoid. Know what I mean?

***** WARNING: Technical Details *****

At this point, let’s get into some of the nitty-gritty, but truly delicious, details of the science of what the heck I’m doing out here in Kenya:

There are certain parts of the skeleton that I want to put in our very official sterile containers and send to the lab. Some parts are better than others. Buried like storied treasure in the collagen of bone and in the pulp of teeth is the thing we seek: acid. Deoxyribonucleic acid, that is. DNA. We hope to grind up these bones into little pieces and look at these people’s genes. That’s the big idea. Big ideas are composed of little ideas, all sorts of devilish details. Let’s unpack them.

I figure there are two ways to talk about this project. We can ask “why?” and we can ask “how?” For the moment, even though it’s a little pedantic, let’s take the “how?” stance.

In the barest bones sort of way, here’s what we’re talking about: getting DNA from dead people in the ground.

The big issue is making sure that we don’t have any contamination in the bones that we’re digging up. Of course, I’m dropping my own DNA at record pace with little strands of hair, globules of mucus, and the constant shedding of dead skin cells which I very liberally drop everywhere so as to create a genetic trail of the places I’ve been. You do it, too, so don’t look at me like I’m weird.

The best way to avoid contamination of our sample is to not touch the bones from the site without sterile gloves and to not cut them in the field, and have as few folks as possible getting up close and personal with the skeleton. That’s my job, you see. Getting up close and personal with the skeleton. Communing with the dead. If there’s only one person likely to contaminate the skeleton and you take his or her DNA, then you only have to test for contamination by one person.

Of course, it’s not just human DNA that can contaminate this thing. All over the place, little bacteria swarm about in hordes the immense number of which human minds don’t have the capacity to entertain. Those suckers get into the bone and leave their DNA, contaminating our samples with the genes of those fantastically complex microscopic slimeballs. Human genes, the genes of the person to whom the skeleton used to belong, are what we’re after, however. We’re trying to avoid sequencing bacteria genes.

Our best bet is to get bits of the skeleton that have a lot of cortical bone, which is the hard part of the structure and essentially the part that we can see from the outside. The deepest part of the inside of bones is hollow but has trabecular, also known as spongey, bone, but there’s not much hope of getting any DNA from that stuff. Cortical bone is dense, with a lot of collagen around the osteocytes, the bone cells. Since it’s so dense, it’s harder for bacterial or human or whatever contamination to get into it. That’s the key.

Some bones need to be cut if we want to fit them into the containers we have, which can introduce all sorts of nasty contamination into the sample. No, no. We’re looking for the most cortical bone for our buck on the smallest bones that we don’t need to cut. What do we want? First ribs, clavicles (collarbones), metatarsals (the rays of the foot), metacarpals (the rays of the hand), phalanges (fingers and toes), and maybe some tarsal (foot, ankle) and carpal (hand, wrist) bones are what we’re looking to snag.

Of course, there’s no guarantee that the collagen didn’t get washed away in the water in the soil or destroyed due to temperature or any number of other things. What we’ll have to do before we can even think about looking at the genes is testing to make sure the collagen is there. It’s in the nucleus of the collagen cells that the genes do dwell. What we’ll do is have the lab folks test these guys for nitrogen content. There’s nitrogen in collagen, which is a protein, but not so much in the mineral structure of the bone made from calcium, which contains no DNA. If there’s a good deal of nitrogen there, it means that we’ve got some collagen. So, having collagen is a necessary condition for getting at the genes. But, as you’ll see, it is not sufficient.

The skeletons we’re looking at haven’t been properly dated, so we don’t know how long those little strands of genetic material have been sitting there ever so compactly in the nuclei of those cells. During life, if something goes wonky with the DNA, there are little machines in your cells called polymerases which fix the problem. Those machines stop working when you’re dead, but plenty of things can still go wrong. Among other things, heat makes the DNA fall apart, and the little particles of background radiation that generally pass through our bodies little BBs through latticework occasionally knock a nucleotide or two. This changes the structure of the DNA and messes up our ability to put things back together like they were when the person actually had these genes working in their body. Things fall apart. We futilely fight entropy, folks. We can have a bunch of bones stocked to the brim with collagen, nice and uncontaminated, but the DNA will be just too degraded to use. Let’s all cross our fingers that such isn’t the case. Kathleen has had some folks scout these sites and it looks like the ground in which these skeletons are buried is very favorable to DNA preservation and they’ll be recent enough that we won’t have too many issues. Fingers crossed, eh?

We have to keep the skeletons clean, we have to hope we’ve got collagen, and we’ve got to hope our DNA is nicely preserved. A lot to ask of the universe, but we may have luck yet.

Since the skeleton that was previously excavated is not in anatomical position, as I mentioned way above, that means that the graves we’ll be looking at were likely disturbed by animals long ago. I’ll have to search for the bones I want as I dig. I can’t expect to follow the radius to the carpals and metacarpals that I want, you see. The complexity of things never, ever ceases to amaze me. There’s delicate work to be done.

And, before I forget, we’ll take some teeth. You can do different things with teeth and bone. They’re made of different stuff. The mineral structure of bone grows and remodels, changing through life. The enamel on teeth doesn’t. Ever break a bone? It heals. Ever chip a tooth? Tough luck. Since enamel only grows once, it contains a chemical record of the first decade or so of life, since, in sort of simplified terms, the body uses the chemicals it has to make the teeth. There is no DNA in enamel, but there is DNA aplenty in the pulp in the middle of teeth. The pulp is the part that contains the nerves that hurt real bad when you have a tooth infection or get a root canal. I think I’ll carefully collect some molars to get at their DNA. That should do the trick.

***** END of Technical Details *****

I’ve been writing this thing for a while. It’s early in the morning and I’m hungry. I think I’ll go to the dining hall and get breakfast. They make pretty good semolina porridge here and the papaya is out of this world.

* Title inspiration.

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  • Beverly Mitchell

    I am in AW as I am sure you feel you are in Heaven. Enjoy every moment of this wonderful experience. I am so happy for you PJ..I will follow your blog. Stay safe and healthy..Bev

  • Abby Grant

    I know this trip is old news to you but it’s totally amazing to me. As is everything that you’ve accomplished Paul! I hear you’re headed to California now. I’ll be praying for you and all that’s ahead.