A Visit From Home and A Paper In The Works

Around mid-April, I was visited by a friend from home – Hollie, who went to the same sixth form as I. Fortunately enough, I had a few days off to show Hollie around the city and make the most of their time over here. Having come over in early Spring, Hollie got to experience Midwestern weather at its most capricious – with the weather nice enough for shorts bookended by light snow and heavy rain. Whilst the sun blessed us with heat, we trekked around the city, visiting The Bean and shopping in some indie “thrift” stores that didn’t seem to be entirely secondhand. I also took another trip to the Neo-Futurists to see The Infinite Wrench. As per the nature of the show, in the time between my two viewings, the individual plays had changed entirely. Although I preferred the shows during my first viewing, I did get to go up on stage this time, which makes two for two on ‘member of my party being directly involved in the show’!

On the rainy days of Hollie’s stay, we still braved the cold outdoors to visit the Shedd Aquarium and Adler Planetarium. Honestly, a highlight of the day we went to the planetarium was Pokemon Go Community Day – we both caught some gems including our first shinies of the game and the North American regional exclusive Tauros. On the last full day, I showed Hollie some of the best and worst that Chicago has to offer – the Impossible Burger and Malort – one being a delicious vegan meal, the other a harsh drink that has a lasting bitter flavour.

During my days back at the Arboretum, I’ve been making progress on the work that’s going into the upcoming paper I’m working on with Lane and Andrew. I’ve already managed to create a few nice boxplots and we’re starting to see some interesting results from our analyses – time to get it written up into a suitable format! Working inside at the arboretum whilst it’s sunny and fairly warm outside makes a change from last Autumn when I was working in the prairie. Over at the Museum, I’ve assisted on the bait capture stage of the experiment, a stage that is similar to using the Bioanalyzer in that although it’s a simple procedure, the pressure is on with timing and expensive reagents.

Board-Games and Field-Work

Towards the start of April, I went to not one, but two board game parties – both for the birthdays of some Chicagoans. Sarah from the Arboretum and Katie who is Arb-adjacent, the housemate of someone who works at the Morton. I finally got to play Settlers of Catan, a game I’ve wanted to play for about a year but never found the opportunity to – although simple in its basic rules, a lot of strategy can be implemented. Lately, I’ve come to realise that I enjoy these kinds of events much more than going out to a crowded club or bar, something that I certainly enjoyed during the previous two years at university. Maybe it’s the fact that I’m in a new place with new people that has pushed me to enjoy a more quiet setting over a high energy one.

I enjoyed my first Seder at the start of Passover, complete with vegan Matzah ball soup and many cups of wine. There was a condensed reading which was very informational and interactive – a piece of Matzah, the afikoman, was hidden before the service and since there were no children present to look for it, we did. Also, being the youngest at this dinner meant that I read a specific part of the text.

Over the at the Field Museum, I used the Bioanalyzer for the first time, which was slightly daunting if only for the fact that each individual chip costs around $60. I also attended another talk, this one by Nathan Lord on jewel beetles, their incandescence, and how and what they see. Fascinating stuff, stretching over a broad range of disciplines from biochemistry to taxonomy. Another Super Speaker, Meg Staton, was at the Morton Arboretum in early April also, presenting on a citizen science app, TreeSnap, which aims to help affiliated scientists gather data on specific trees such as the American Chestnut or Ash trees.

Back in the field, I was put to work outside as the prairie restoration project is coming alive again after Winter. The prairie needed to be burnt to rid the site of last year’s dead growth, and I assisted Mary-Claire in readying the plots so that they were in the best condition for ignition. Sadly, I missed the actual fire, as the conditions were so good that the burn team completed their work in a flash.

New England Thoughts

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 RStudios 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.

Working in R again got me thinking back to second year, when myself and Heather tackled a small research project during our Research Methods module. Our study was on leaf morphometrics and involved ~80 samples from 6 sites. This, of course, pales in comparison to a full dissertation but was a very useful intro to the world of research. My dissertation next year is still something I need to be thinking about, as are my module choices for third year. Currently, BSc Genetics students only have one optional module in their final years, making this decision particularly difficult – I’m considering at least 4 modules right now.

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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, which accompanies the Mt Holyoke College Botanical Garden (which has a corpse flower!). 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 LGBT 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.

Life at The Field Museum

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!

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.

Earlier this month was of course 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.

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.

New Year, New Work, New Adventures

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 that show that you’ve gained something from your time in industry.

 

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.

 

Holidays in Chicago/New Field & Lab Work

If it feels like a long time since my last blog, that’s because it has! It has been just over of a month since my last Chicago post, 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 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 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 my 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 still had.

In 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.

Soon, I’ll be moving over to The Field Museum to assist my colleague Mira on some more lab work, but not before I take a brief respite in Utah, where I’m visiting a friend!

Winter Approaching In Chicago

In my last blog post, I was excited to have all the biomass collected and waiting to be dried – hopefully before the end of December. Well, that was certainly a low bar, since all the biomass was weighed by the 13th December! My house is now empty of plant matter – and looking slightly empty for it. Looking back, it’s almost unfathomable how many bags I ended up weighing, I’m incredibly grateful to Lindsey and the volunteers for helping out in the field, collecting just wouldn’t have been possible without them. Now all that’s left to do is empty the remaining weighed bags of biomass back onto their original plots.

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It may not be visible, but it was snowing when this photo was taken.

In addition to collecting all the biomass from the prairie, it has also been winterized – the hoses, sprinklers and electric fence removed, as well as data from the weather station downloaded. It certainly feels like winter has arrived, to me at least, with light snow every other week, temperatures regularly dropping below freezing, and winds that often cause my phone to flash a “Weather Warning” alert at me, however, I get the impression that the worst is yet to come! I’ve received numerous sets of thermals from family as presents for my birthday, however, so I feel suitably prepared.

The past few weeks have seen Thanksgiving – which I spent with my supervisor, Andrew Hipp, and his family – and my 21st birthday, which I spent with my dad, doing various touristy things over the weekend, such as visiting the Art Institute of Chicago, Field Museum, Shedd aquarium and Skydeck. For my birthday (observed) the following weekend, I went out for drinks and a meal with many of the other research assistants (RAs) at the Arboretum, since I am now legally allowed to drink (odd since I have been able to drink since 18 back in the UK). Since it was also the third night of Chanukah, menorahs were lit and dreidels were spun.

 

I also got to see Molly again, as she visited to see Illumination (which I have started volunteering for). Finally, after my last attempt was left incomplete by the threat of the setting sun, we took the trip over to Big Rock – it was conquered. We also baked pie and visited a mall, where I saw my first Hot Topic – an unexpected American Bucket List item.

During Molly’s visit, I was disappointed by a store-bought vegan pizza. Thankfully, my faith in fake cheese was restored the following weekend when I visited the city with Diana, one of the RAs. We saw some local theatre and a drag show – I think the first I have been to. Both shows were great, but Lizzie, the punk, feminist, musical preceding the drag show, blew me away.

Aside from the prairie work and social activities, I’ve got a university assignment to focus on, which is proving harder than I thought! Identifying problems at the Arboretum that can be discussed and solutions proposed is challenging when the place is pretty shipshape!

Fieldwork season – Finished!

On November 2nd, I experienced a very important, personal life event. Something that was not on my American Bucket List, but my actual bucket list. I saw a tardigrade. Tardigrades are otherwise known as water bears or moss piglets, and are one of the hardiest animals known to exist. Although not true extremophiles, they can survive the harshest of conditions including extreme temperatures, pressures, and radiation, mainly by entering a state of cryptobiosis where they decrease their water volume to 3%. Some individuals have even survived being in outer space. Marvin, a Research Assistant here, discovered a few on a piece of moss from the arboretum grounds, and plated them up for us to look at under a microscope. It was a good day.

Whilst in the field, collecting biomass, I’ve spotted a few more deer and also some other native wildlife – sandhill cranes and a possum! I was very excited to see a possum, honestly, it was also on my American Bucket list. Another item to tick off was going to my first potluck! It was a bit of an impromptu event for me so I didn’t take anything myself, next time I shall be more prepared!

I’ve made a couple of trips into the city in the past few weeks, once to check out a shopping mall (American Bucket list – check) and again to revisit the Field Museum and check out Brain Scoopin’ LIVE, a demonstration of a specimen preparation – in this case, a beaver. I also stumbled upon a charming used bookstore – I waited out the time until my train, reading on my Kindle (I did feel slightly guilty reading my own material there, I figure I’ll go back and contribute to the store another time). It’s a real shame I didn’t bring my camera over here because the fog and snow I’ve witnessed in Chicago has been breathtaking at points.

Another breathtaking event coming up is Illumination, an event focussed on lights and trees and the arboretum. I’m volunteering for the event and recently went to the training evening, where we got a quick tour. It really is spectacular and can’t wait to experience it properly, soon.

Back to biomass, we reached a huge milestone yesterday – all the collecting is done! Biomass from all the monocultures and treatment plots has been successfully collected. Unfortunately, yesterday was also the last day we had access to the large cooler, meaning half the remaining biomass is being stored in the office and half at my house! Space really is an issue, but the dryers are the true bottleneck. Slowly, the material is all being processed, and hopefully, we will have all the data written up by the end of December!

East Side Story: Big Rock

Since Mary-Claire had her last day on the 13th October, I’ve been working independently on the prairie restoration project. This was a little rocky at first, as I got used to the method of identifying and collecting the plants – but after a little advice from Andrew and practice with another research (and herbarium) assistant, Lindsey, I got the hang of it. It’s still a time-consuming process however, especially when the plot has monsters such as Helianthus pauciflorus, where the plant easily fills two of our large brown bags. Also, as expected, we have been collecting biomass at a quicker pace than we can dry the material. With limited oven space available, fresh biomass must be stored in the coolers until it can be dried. But space in the cooler quickly gets used! The weather has also been a factor we’ve sometimes had to fight against since we cannot collect biomass if the plants are wet from the rain.

On the days when it has been too damp to collect material, I have been assisting Mira with some lab work, preparing me for the work I will be doing after my time on the prairie restoration project has come to a close. I helped with a DNA extraction and also a gel run, both techniques I have done before albeit only a handful of times. This also got me accustomed to working in the lab and biohazard room.

Towards the end of October, the trees finally realised it was autumn, and started showing their rusty, scarlet hues. I saw an equally vibrant cardinal flitting about the trees near the visitor one day after collecting in the morning. On the evening of the 26th, after work, I cycled around the East Woods. Having been here around a month and a half, it was about time I saw the larger side of the Arboretum, having only really seen the West side until then. There were some beautiful lone trees and the woods as a whole were lovely. Sadly, by the time I reached the far side of the East Woods, by the Big Rock visitor station, it was already dusk and I didn’t have time to actually take the trail out to see Big Rock. I got home before dark with the lure of Big Rock still calling to me. Another day, Big Rock. Another day.

Autumn Fieldwork in Illinois

Dried biomass in pre-weighed bags.

Over the past few weeks, I’ve been given more responsibilities in the field and more exciting work to do! Whereas before I was helping with the vital job of weeding, and watering, the time has come for us to collect data from our prairie restoration project. To assess how well different plots of mixed species are performing, we need to collect, then dry and weigh, biomass. Since the project leader has now taken maternity leave, I have been left in charge of this next phase of the project.

I’ve taken to cycling down west to the prairie in the mornings, but this becomes an issue when returning biomass to the lab – I currently have to rely on the cars of others. Outside the arboretum, I’ve noticed that a car seems like a necessity in the United States, since public transport is not widespread, yet everything here is spread wide apart! The country seems scaled up compared to the European ones I’ve visited, everything is just somehow further away…

Map of the West side of The Morton Arboretum, showing rough location of A: My house and B: Prairie Restoration Project

In the week following my last American entry, I moved house, since I had accidentally been placed in the wrong one for my first few weeks – it’s smaller, but I am the only one currently living there, plus, the WiFi is stronger!

The lab meetings on Thursdays have also become a book club, we’ve been reading Improbable Destinies by Jonathan B. Losos, and we’re now about four chapters in. So far it’s been very engaging and has included some interesting ideas about the commonality of convergent evolution yet also the randomness of evolution, with compelling arguments on either side.

On the weekend before last, I took the train down to see Molly again, and this time visited her home in “The Boonies,” to check out the Spoon River Valley Scenic Drive. Although most food along the drive wasn’t vegan, I did manage to eat an obscene amount of popcorn and a delicious apple cider slushie. I also had a “lemon shakeup” a still, sugary lemon drink. Still on my American Bucket List is trying American lemonade, which is different from the lemonade back across the bond that is synonymous with Sprite or 7-Up. After driving back to Molly’s home, we cooked up some funnel cake made with soy milk, which was enough to induce a food coma combined with everything else from that morning. We also visited the Wildlife Prairie Park – it harbours rescued animals and plants native to the area, as well as telling the history of the area. It was a bit windy that day, as the night before we had been under a tornado warning – exciting times!