Cleaning the ancient DNA lab

When I start lab work, I'll be in the ancient DNA lab: a dedicated space for working with ancient samples. Yesterday I joined in with one of the regular deep cleans. It was quite exciting.

First, I had to shower that morning and get into completely clean clothes. Then, once in the little ante-room next to the lab, I put on all of the protective equipment:

• Hairnet
• Gloves
• Plastic suit
• Crocs
• Plastic booties
• Facemask
• Hood
• More gloves

With me, the other new student, one second-year student and our mentor post-doc, there were four of us trying to cover ourselves with plastic in a space the size of a lift. Then we filed into the lab proper, which is more like living-room sized, and wiped everything with bleach followed by 70% ethanol, including the ceiling. The air smelled like a swimming pool, even through the mask. It is vitally important to clean with bleach and then ethanol, in that order, because if you mix alcohol with one of the nasty chemicals used for DNA extraction, it makes mustard gas. If anyone sees a yellow smear appear on something they've just cleaned, we have to evacuate the lab and possibly the building. So yeah.

The large amount of plastic, though, is less for our protection and more to protect samples. Ancient DNA comes in tiny amounts, so you have to be very careful to not let any contaminant DNA get into your work because it will completely swamp any ancient stuff. And, depending on the circumstances, it can be difficult to tell what's contamination and what's genuine. So we packaged ourselves to reduce the amount of us in the lab, and these deep-cleans are to regularly remove the small bits that do escape.

The plastic overalls are affectionately referred to as bunny suits:

Me, in the standard pose of 'I love science'

It's a bit culty but I'm enjoying it so far.

Overdue roundup

Hello again, dear reader(s). Long time no see.

A year ago, I started this blog with cautious optimism about how often I'd post, and I don't feel too disappointed, but I do regret not doing a summary last weekend. Now I have real work to do again!

Since the last post, I have:

• Finished the Siberian grave helminth project
• Moved out of London
• Signed up to stage manage two plays
• Handed in my dissertation on the project
• Given a presentation on the project
• Sat a viva on the project (like an interview about why you deserve to pass)
• Confirmed enrolment for a PhD at Warwick University, right next to my hometown
• Joined a new Brownie group
• Had the Warwick induction
• Made a to-do list that fills a page of A4 (font 10)
• Made six cakes, 24 mince pies and 30 fig rolls that were not on the to-do list

Apart from official results and graduating in May, my MSc is over! I'm now officially educated in taxonomy and biodiversity. Oddly, what I feel I've gained most from the year isn't actually much more knowledge about taxonomy or biodiversity than I had before. Instead, I took a risk and did a project on DNA, which involved some molecular biology, which I previously avoided like the plague. But it was great fun. And I took the even bigger decision to do sign up for something similar in a PhD, which will take at least three years of my life.

I read a book on learning that argued that whether you're interested in something just depends on whether you have enough background knowledge for it to be accessible. Now I've had a go at DNA things, and can actually read the papers without looking up every other word, I am finding it interesting. Warwick has been great so far, and I'm really excited to apprentice myself to some more real scientists and do something useful.

I said goodbye to my wonderful NHM supervisor with carrot cake and am still emailing Smith as she embarks on the complicated world of American postgraduate study. My birding photographer friend is hanging on at the museum, hopefully for the long term. My heart breathes a sigh of relief to be back home. My pancreas takes a worried look at the baking equipment.

Wildlife in Imperial College library

A few months ago, during one of my wonderfully quiet early mornings in the library, I did a double take as I spotted two mice running up and down the aisles. I've since seen traps. Clearly there are more mice around than the staff would like. Today I made a rare afternoon visit and, sitting at a desk, something small and brown on the carpet caught my eye. I was secretly happy to have seen a mouse again. But on closer inspection, it was no mouse!

It was a robin!

Unfortunately, it didn't look like it was going to get out any time soon. The open window was tall and narrow, and after the robin fluttered past it a few times I got the impression it was deliberately not going through. I reported it to the very excited librarians and, as I left, one was considering using her sandwich as bait. I will check in tomorrow to see what happened.



UPDATE: The next day I asked what had happened, and the staff had managed to get it out without much trouble. Fast forward to the 16th of September, my next visit, and the robin was back again. I don't think it was trapped. I think it was clever.

More grave goods: blowflies

While awaiting feedback on last week's draft, I've mostly been collecting references and formatting. But I also went back down to the lab to take some pretty pictures. The entomologist has finished identifying the fly puparia from one of the grave samples: they turned out to be Protophormia terraenovae, the northern blowfly. They eat bodies! It confirms that there really was a body, which isn't exactly groundbreaking but is nice to know.

The entomologist wants to do some high-tech imaging of some of the best preserved puparia later on. But for my project, I decided it would be nice to have some simple photos just to show what they look like. Not many people see blowfly puparia, and even fewer up close. I borrowed a lovely microscope and camera setup from the schistosomiasis people, who use it to photograph the little water snails that carry that nasty nasty parasite. Here are two of the best in the finished figure:

The lower one actually has a little fly face poking out! The two flat discs are its eyes, and the little lumpy bit southwest of them is the proboscis. It looks like it was starting to emerge when it died, because that's the part of the puparium that they hatch out of. I don't know enough about flies to say more than that. But it was quite a surprise!

Blowflies only feed on carcasses, so the puparia can't have just ended up in the soil long after the person was buried. They must have been there from the time of burial. This site is at least 100 years old, possibly 200, making this a very old fly indeed.

Drafts

A girafft. Source: https://en.wikipedia.org/wiki/File:Giraffe_standing.jpg

For the last few weeks, I've been working increasingly hard and long to get a draft of my thesis done. I've done so many analyses that didn't work, come to so many conclusions that turned out to be irrelevant or wrong, and agonised over some beautiful graphs that didn't actually show anything helpful.

Like those graphs. Beauty is ephemeral.

 But yesterday, a draft was done. I sent it off at about two and was out of the building by three thirty. Today I've been working on fiddly formatting and referencing bits, satisfyingly monotonous admin that requires very little thinking, and it has been great. The end is near!

A pot of snake worms

All was quiet yesterday afternoon. My usually busy office was empty but for me, the two single-office researchers and the curator on my floor were away and nobody was using the labs. So when a visiting retired scientist came wandering up looking for somebody, he came to me. He said he was in the process of slimming down his collection of parasitological paraphernalia and wanted to donate some specimens to the museum. He handed over an ancient hummus pot filled with specimen jars:

Each containing snake worms: parasitic worms from snakes. Needless to say, these are rather difficult to come by. They're now on the curator's desk, hopefully destined for the vaults.

Big pretty moth

I saw a big pretty moth last night:

Fingertip for scale. I have normal-sized fingers.

Accidental flash probably blinded the poor thing.

A quick Internet tells me it was probably a swallow-tailed moth, otherwise known as a 'flying post-it note': https://www.ukmoths.org.uk/top-20/ (number 9)