TCJ – 10: City Excursions and Super Talks

The Chicagoland Journals

Shortly after returning from Boston, I took a trip to Garfield Park Conservatory. The conservatory hosts a number of rooms, each with a different theme – the front room is home to palms, the centre room to ferns, and another to aroids. The showroom at the time of my visit was featuring the Spring Flower Show, “Hashtag No Filter”. Next up on the list is the Chicago Botanic Garden, hopefully, I’ll make it up there in time for their orchid show.

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Also towards the end of February, I saw a reading for a play written by a new friend, Hannah Verdon, called Eleanor Absolute, which is based on true events and tells the story of a journalist, Lorena Hickok, and her romantic relationship with Eleanor Roosevelt – whilst questioning who gets to decide on a person’s legacy.  I went to another show in March, this one with Molly, who drove up for the weekend. This show was called The Infinite Wrench and was by a group called the Neo-Futurists. The show is an hour long and the aim is to perform 30 short plays, with interrupting “wrenches” that add a new dimension or obstruction to the performance. Some plays were silly and short, others were longer and heartfelt, Molly was even chosen to dance in one of the shows. It was worth enduring the cold for as we queue to get in (we arrived far too early).

The following day, Diana and I made it down to Maggie Daley Park on the final day of ice-skating on their rink. Having not skated in years, and never being proficient at it anyway, I think I faired fairly well by simply not falling over. Diana pointed out that it was easier to skate with speed and, although far more nerve-wracking, she was right – we picked up a decent pace as we made a few loops around the ribbon. Our time on the rink was cut short by the Zamboni, but it was a nice day out and the park was nice to walk around.

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Whilst I spend most of my time in the city now, since I work in the Pritzker Lab at the Field Museum labs instead of at the Arboretum, I do work at the Arb on Thursdays. During this time I’ve been analysing the data gathered from biomass and vegetation indices in R, working on a potential paper. I’m quite proud of the various graphs I’ve made, utilising the “ggplot” package. Since this is a group effort, we’ve taken to using GitHub to streamline our workflow. Although I’ve used GitHub to access other people’s data before, I’ve never used it to upload my own data and collaborate on others’. The process has been largely straightforward and we’re making good use of the system.

I made an exception to my usual schedule the other week when I worked at the arboretum on Monday. This was because there wasn’t just any Tree Talk happening, there was a Super Tree Talk. Presented by Nathan Swenson from the University of Maryland, this talk was on the structure and dynamics of tree assemblages, from traits and phylogenies to transcriptomes and functional phylogenomics. Back at the Field Museum, I’ve recently also attended talks on indigenous archaeology and the root microbiome.

Just down the road from the Field Museum is Adler Planetarium. I’d never been to a planetarium before until a few weeks ago when I went to “Adler After Dark” with Diana. As you might suspect, the event was in the evening, at a time when the planetarium would usually be closed. Although there was a theme (game-night), we’d never been to the standard exhibits or shows, so those were the priorities of the evening. The two shows we saw were on the “Cosmic Wonders” of the observable universe and of the sky as seen from Chicago on that night. The first showed the many deep sky objects humanity has observed, including the incredible photo of 5,550 galaxies from Hubble’s eXtreme Deep Field, featuring galaxies formed just 450 million years after the big bang, and a photo of gravitational lensing on a galactic scale. The second pointed out the many asterisms and constellations visible in the night sky. We also were given a tour of the telescope and got to turn the roof – very fun. That night also marked the second time I’ve held a piece of the moon and Mars!

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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.

 

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.

TCJ – 07: Biomass? Weighed.

The Chicagoland Journals

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. Described as “American mythology set to a blistering rock score with rage, sex, betrayal and bloody murder” by the theatre, it was like nothing I’d ever seen.

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!

TCJ – 06: Wrapping Up

The Chicagoland Journals

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. (picture below!)

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.

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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!

TCJ – 05: East Side Story

The Chicagoland Journals
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The greenhouse corridor at 6:20pm, after a long day of work.

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.

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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.

TCJ – 03: Fieldwork Firsts

The Chicagoland Journals

Time for the Prairie Rundown: Last week started with my first (and then second) day in the field alone – I cycled down to the prairie in the morning, set up the sprinklers, and weeded. I repeated this on Tuesday, except the watering was taken care of by the weather, leaving me with a rather wet bike and not a whole lot of time to weed (lesson learnt about trusting the weather forecast). Wednesday was another rainy day, but not enough to keep me and the others from weeding, it was merely spitting until around 10am. Thursday saw me take charge in the field, leading two volunteers – this wasn’t as hard as I’d expected, I suppose that over the course of these two-three weeks I’ve come to understand the project and the imminent plans for it. On Friday, I began weighing the paper bags that we’ll be using to collect the biomass in – soon, we’re going to collect a portion of each plot, separated by species for the mixed plots, and dry the plant matter in an oven, this dry biomass will then be weighed to determine its productivity this growing season.

In “un-prairelated” news (apologies for the pun), last Monday’s Tree Talk was presented by Christina Carrero on the importance of building a community around arboreta, and how the Morton Arboretum’s ArbNet helps do just that. It was a very enjoyable lecture highlighting how important communication is to maximise our conservation efforts.

A surprising event unfurled on Tuesday – due to a mix-up when I arrived, I was in the wrong housing for the first two weeks! Meaning that when my third week rolled around, I had to be moved from one house to another. I am now in the house I was originally meant to be in, and although smaller, I think I prefer it (the WiFi signal is stronger here).

TCJ - 03Also, this week was another lab meeting, this time focussed on the book that we have been reading: Improbable Destinies by Jonathan B. Losos. The intro and chapter one really sold the book to me, some very interesting points were made about convergent evolution and the nature of adaptation.

Friday also saw me start work in the lab… sort of! I was taken on a safety tour, then helped rearrange some vials from the freezer. Still, it was good to see the lab properly and spend some time there helping out. Next week we’re looking to start biomass collection if the weather permits and pretty soon I’ll be taking over in the field as Mary-Claire, the project leader goes on maternity leave. Exciting times ahead!

TCJ – 02: More Of Illinois

The Chicagoland Journals:

I’ve been in the US for just over two weeks and when I think about it, I’ve packed a fair bit into that time – lots of new experiences. One such experience was my first visit to The Field Museum of Natural History! After walking through the city, alongside the huge mass of water that is Lake Michigan, I received my own lanyard and ID, along with a set of keys for the Arboretums office space. It’s official. I’m a research affiliate at one of the largest natural history museums in the world, with roughly 30 million specimens! As I walked the corridors behind the scenes of the public museum, the sheer number of resources available began to sink in. Admittedly, I got lost walking back to the office.

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“Sue,” the largest, best-preserved, and most complete Tyrannosaurus rex ever found.

During the rest of the weekday mornings, I was back out in the prairie doing the necessary work of weeding plots that had seen undesirable species encroach, as well as sowing some eco-grass along the walkways to held guard off against the more nasty weeds and to prevent soil erosion. Wednesday and Thursday afternoon held a training session on R and a lunchtime meeting. The R training lecture was largely things I already knew, however, there were a couple of techniques which I was unfamiliar with. Also, different ways to achieve the same results – just goes to show how people have their own solutions to situations. The lunch meeting was helpful in further orienting me with the work being completed at the Arboretum and who by. Listening to people talk about their research is a wonderful thing, and I’m very excited to help out with more projects, specifically the work relating to the hybridisation of the Quercus genus. Another fun thing we established that meeting was the book that we’re going to read, hopefully before Christmas. I’ve read the introduction already, and if the rest is anything like it then I think I can say that I will enjoy it.

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“Root beer,” a non-alcoholic soft drink.

I read the introduction on the train, Friday night, as I was going to Macomb to see my friend, Molly, who was studying abroad at Edge Hill last year. Fortune has it that she lives in the same state that I am currently working in, so it’s almost easy to meet up! The time it takes me to get the train over to see her, across half the state, is roughly the amount of time it takes me to travel from my hometown to my university – that’s roughly half the country. Since I arrived quite late, we had a meal, went shopping, and then hit the hay. But not before I tried both root beer, and spiced apple cider (both non-alcoholic, despite their names) for the first time. The cider was truly delicious, especially when warm.

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Myself (left) and Molly (right).

Another reason for visiting Molly when I did, was that is was her homecoming. Along with trying various soft drinks, going to the homecoming parade and football game were valuable entries on my American Bucket List. Although I’m not all too familiar with the rules of American football, it was fun to watch, especially for the halftime show – the band sounded wonderful and the baton twirling was a sight to behold as well. Molly had even altered a bear mascot head to represent Rocky, the bulldog mascot of Western Illinois University.

I finished off that busy week with walking three and a half miles to the shops, bumping into an exceedingly complimentary man whilst waiting for my Uber back to the arboretum. Once again, I have to wonder if the next week will be quite as packed with activities as these first two.

TCJ – 01: Getting To Know The Prairie

The Chicagoland Journals:

So I’ve been in the US for a week now! That’s four days of work down at the prairie – weeding, digging and planting – as well as two-three days exploring the city. It’s been hard graft in the field, especially after the flight; jet lag is a real pain. But really just getting back into the fieldwork mentality and adjusting to the heat is the main issue.

During my first week here at the arboretum, I’ve been shown around the research building and introduced to many new people – colleagues, you could say, because i’m actually working here! (I’m still absorbing it all.) Everyone has been very friendly and welcoming, and I’m told that’s partially a midwest thing, but also that the arboretum staff really work together, so there’s almost a familial sense about it. I’m excited to start doing work with more members of the team.

Before I arrived, I knew I was to be doing work relating to the prairie (and how phylogenetic diversity affected the restoration of it) as well as work relating to the phylogeny of oaks. Now that I’ve got here, I know the immediate plans and some of the specifics of what I’m to be doing. I know that I’m going to be focusing on the prairie up until roughly January, and that when the current project leader goes on maternity leave, I’ll be filling her shoes to keep things running. Also on my agenda is to help figure out how to measure the biomass we’re to collect from the prairie to assess the level of restoration – and from that, if there’s a way to incorporate data from drones as part of a method.

Despite only being here for a week, I’ve managed to get into the city and attend VeganFest with a colleague, as well as get the train into (and the loop around) Chicago to see a film at the Reeling Film Festival (the film was Cat Skin, which was filmed in the UK so was a nice reminder of home). More locally, I walked down into Lisle, visited a 7-11, to get a slushie (something to check off my “American Bucket List”), and the local Aldi – again, a reminder of home.

It’s been a busy week and I am thoroughly exhausted. At this rate, I should be able to give a nice update on my activities in another week! Then again, perhaps this week has been so packed because it was the first.