TCJ – 09: Field Museum, Data, and New England

The Chicagoland Journals

One perk of working at The Morton Arboretum are the Monday lunchtime Tree Talks – short lectures presented either by a member of staff or a visiting scientist. Although I spend most of my time at The Field Museum now, it’s nice that the perk has seemingly carried over. Although not on a regular schedule, there have been numerous interesting talks over the past few weeks. From Dr. Tyrone Lavery and the “Tree-Dwelling, Coconut-Cracking Giant Rat” to Dr. John Novembre’s work on the human genetics mirroring geography. Another great talk was presented by Dr. Corine Vriesendorp’s, for the Women in Science’s February meeting, on the creation of a new national park in Peru – Yaguas National Park – which took 15 years to be recognised! Dr. Robert Hart also spoke on the topic of ethnobotany and the value of local knowledge when assessing change in biodiversity. Yet another perk – the dollar-beer happy hour on Fridays isn’t bad either!

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The Field Museum’s mascot, SUE the T. rex, has now been dismantled and is being moved out of public display until Spring 2019. Taking up their mantle is a titanosaur, Patagotitan mayorum, which, according to The Field Museum’s website, is “25 Danny DeVitos in length.” Whilst I’ll miss walking past SUE at work, their twitter account, @SUEtheTrex (Specimen FMNH PR 2081), will keep their legacy alive hopefully for years to come – even whilst they’re out of the public eye.

One big event last month was the Super Bowl. Despite having seen half a game of American football last year, I still didn’t really understand the rules – Molly and I were mainly there for the halftime show – but now, after watching most of the Super Bowl, I have a better idea. We had a little beer tasting whilst the game was on, with one beer from the Lagunitas Brewery, which I actually visited towards the end of January! It was pretty huge – although it is the only brewery I’ve had a tour of, so maybe I don’t have a good standard of measurement.

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My house at the arboretum, surrounded by snow.

Also, after six months in the US, I’ve finally had my first repeat Uber driver, a zoology-major who remembered me as “The Botanist” which I can only assume means that I’ve made it as a plant scientist, coupled with the fact that I used “carex” in a game of Words With Friends the other week.

Although I’m working at the Field Museum most days, I still work at the arboretum on Thursdays. The main purpose of this is for the individual and group lab meetings, but it’s also a good time for me to focus on analysing the data from the prairie restoration project, this includes the biomass data I collected in autumn, as well as NDVI and soil data collected previously by Lane and other researchers. Towards the start of the month, Andrew and I sat down and worked through the data, analysing the NDVI readings from one section of the experiment, with particularly deep soil, to their replicates in other sections. Later in February, I cleaned up the code and set aside what worked, making use of RStudio notebooks that use markdown – I’m finding them very handy. Next up is checking to see if the results observed from the NDVI data are reflected in the biomass data.

 

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In the middle of February, I took a trip over to New England, specifically Mount Holyoke College, to visit some friends. Although I didn’t get to see much of Boston, Massachusetts seems like a beautiful state and reminded me more of home than anywhere else in the US so far. Mt Holyoke College is also remarkable, being a fairly old women’s college that features grand brick buildings and a variety of trees, such that they form the Talcott arboretum. It was nice to hear that they’re also a progressive women’s college, accepting trans and non-binary students, perhaps unsurprising considering the college’s gay history. The nearby town of Northampton (or ‘Noho’) even features a rainbow zebra crossing. Everyone I met was friendly and welcoming, letting me join them in some interesting lectures and also indoor rock climbing – something I’ve missed doing whilst being over here.

 

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TCJ – 08: Holidays and Beyond

The Chicagoland Journals

If it feels like a long time since my last blog, that’s because it is! It has been just over a month, and with Christmas and New Year’s sitting right in the middle, that’s only made it seem like longer. I’ve had a variety of tasks at work as the prairie project has been finishing up for the winter, and my other duties have just started taking off.

My celebrations over the fieldwork being done were slightly premature, as I still had bags of biomass that needed to be distributed back to various plots in the prairie (and still do have remaining bags). This was back on December 20th-21st, when the Illinois landscape didn’t resemble an arctic tundra. Although cold, it was still possible to get the biomass dumped – unlike now, where snow has covered the tags indicating the ID number of the plots! A one-off task I assisted in was sonic tomography. Marvin needed a little help one day so I got some experience knocking on wood. To measure the density of trees in a fairly non-invasive way, sensors are hooked up to some permanent nail fixtures in the trees, then are tapped with a hammer. The sensors record the vibrations around the ring and calculate the internal structure.

On the eve of Christmas Eve, I volunteered for Illumination again, this time as a fire pit monitor! Counter to my initial thoughts, this was colder than the Illu-medallion distribution, as that was in a heated marquee and this was obviously out in the cold. Christmas away from home was a strange and new experience, however, it was nice to see some family over a video call after their Christmas dinner (and just after I woke up). I spent the actual holiday with two friends from work, we went to the cinema, got a meal, and had some drinks, so a good day was had.

IMG_20180111_150052In the strange not-quite-holiday days between Christmas and New Year’s, I made an attempt at dumping the final portion of biomass, but the plot numbers were completely disguised underneath snow and soil. Without the map, which was back at the office, it wasn’t productive. Instead, I worked that week on DNA quantification, using a Qubit fluorometer – this was a good exercise into getting back into the lab practice.

With the coming of the new year came the beginning of my time at The Field Museum. Although I haven’t got started on the core of the work yet, I have started lab work there. Mira and I performed some DNA dilutions in preparation for the next generation sequencing (NGS), specifically HybSeq, that will give us the results of this project. As well as the dilutions, I performed some more DNA quantification – I’m certainly getting a lot of practice with Qubit.

During my time not in the prairie, or at the Field Museum, I’ve been working on a project with another research assistant, Lane, comparing data from the prairie that she collected with her drone’s multispectral imaging camera with the biomass data I collected last semester. Processing both datasets and importing them into “R”, the software we use for analysis, was quite challenging, but in the end, we succeeded. The results seem promising so far but more analysis is needed, although it’s no groundbreaking research it’s very exciting! I even got to fly the drone the other day, something I’ve never done before. They’re amazing pieces of technology, although hearing one up close (it sounds like a swarm of bees), I can understand why some people might be wary of them.

Despite being all the way over in the United States, I’m still technically on four modules at Edge Hill University, placement modules. These modules cover personal reflections and activities, as well as two assignments on the placement organisation – specifically an issue with the organisation, and the solution to this issue. Although I would’ve much rather just carried on with the work at the arboretum and museum, they’re important assessments to show something has been gained by the time spent working in indsutry.

Halfway through the month of January, I took a trip over to Utah to visit a friend, Avery. We had originally planned to drive down to California, visiting more friends in Los Angeles but unfortunately that plan fell through. Instead, we’ve been based around central Utah, a couple hours south of Salt Lake City. So far we’ve watched many films, including The Last Jedi and Mary and The Witch’s Flower in the cinema; driven around the local mountains, specifically the Skyline Drive near the Manti-LaSal National Forest; and visited the Loveland Living Planet Aquarium and Natural History Museum of Utah. Although it was sunny and almost warm when I arrived, snow has now hit along with sub-zero temperatures. Seems like I brought the Chicagoan winter with me! It’s been a nice break from work, but I must say that I miss Chicago – the city must’ve really grown on me in the past few months.

Reflection/Anticipation

Almost two months have past since the end of my ERASMUS+ journey in Sweden. Umea was very kind to me, as was everyone at SLU! It was an experience that I was greatly looking forward to, and one that I will always remember. The most memorable event was probably my first night out in Umea – the night I went out to Droskan for the TQ event. That night spurred many memories as well as being the root of new friendships. The most valuable aspects of my time in Sweden were probably the trip to Gällivare and the beetles experiment – both events on either end of my journey. The hard trekking through snow with cumbersome window traps on my back showed me the physically taxing side of fieldwork, whereas the beetles experiment demanded patience and determination.

I’ve been back in the UK for less time than I was in Sweden, and already I’m off again – this time, to Chicago. I’m writing this in Rejkavik, after having flown the first leg of the journey, and will have landed once this post goes live. I’m incredibly excited to spend roughly 8 months in the US, at the Morton Arboretum as a research affiliate. I know that I’ll be involved with two main projects relating to prairie restoration and the phylogeny of Oak trees. Although less different to the UK than Sweden, I’m sure there will be some aspects I’ll have to adjust to.

Day 4: Just Getting Started

Deciding to take the cheapest flight available also meant dealing with the longest layovers possible – and three separate flights. In total, Charlotte and I spent about 3 hours in the air and about 25 waiting for the next flight. This did, however, mean we got the chance to take a good look around Copenhagen. We walked around the city, visiting the botanical gardens and walking up to see The Little Mermaid which – after a quick Google – I discovered has had her head sawn off twice, and also been exploded off her rock. She’s quite the target for political activism it seems. After a long day of walking, we found as comfy a spot as any (four chairs in one of the terminals) and decided to sleep. Not the best night’s sleep I’ve had, but actually not the worst.

The old glasshouse at Copenhagen Botanical Garden

The next layover in Stockholm was around 5 hours – too short for us to comfortably leave the airport. I’ve got to say, terminal 5 of Stockholm airport is lovely: great seats, plug sockets and desks, a whole array of shops and restaurants… It’s a shame our flight was from terminal 4, which turned out to be a further distance away than we assumed. Fortunately, security wasn’t busy and we made it to our gate with plenty of time to spare – but we were panicked for a moment! I decided to take a nap on the plane to catch up on some lost sleep, and only really woke up when we were touching down – but Charlotte described Umeå as being surrounded by forest, something I’ve seen for myself after the few days I’ve spent here.

Sunset over the runway from Copenhagen airport

It’s been a quiet first week, having been in on only Monday and Wednesday so far, but everyone I’ve met so far has given us a warm welcome. We visited one of the closest experimental sites on Wednesday, taking a look at where some of the data the university has collected came from. Unfortunately, we didn’t manage to see any moose (despite finding evidence of them), but I’m hopeful we’ll spot one, or at least some reindeer, in the coming months.