TCJ – 11: Games & Visit

The Chicagoland Journals

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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.

This year, I enjoyed my first Passover Seder, 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.

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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.

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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!

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 – 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!

Day 34: Traditions and Updates

This week saw the beginning of one line of work, and the continuation of another. We began work with some small logs that are part of a global study looking at decomposition rates – on Tuesday morning we collected the logs for this year’s measurements, and Wednesday afternoon we made the initial measurements before leaving them in the drier for the next few days. It’s quite incredible to think that we helped in a study that is being performed globally. Tuesday afternoon’s excursion was to collect some beetles (which, if I recall correctly, were Phratora vitellinae) from young aspen trees that will be later used in an experiment on the GM aspen seedlings back in the greenhouse. We also gained a valuable insight into the “fish people’s” work on Tuesday morning, and how their catch, tag, and release projects operate.

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Yesterday also happened to be Midsummer’s Eve, as the Swedish celebrations of this holiday always occur on the Friday between June 19th and June 25th. The weather was lovely and sunny, matching the warm atmosphere that surrounded the festivities. The day started with wreath making, which we missed out on until Charlotte decided to give it a shot later in the day. What we were in time to see was the dancing around and raising of the maypole. Whilst at Västerbottens Museum, we also ate some traditional sour bread and had a look at some of the Sami structures. 

Midsummer’s Eve also coincided with the update of Pokémon GO’s GYMs, meaning I was once again on my bike, catching and battling with the pocket monsters much like I was last summer after the launch of the game.

Day 27: More of Umeå

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It’s been a quiet few weeks since I returned from Gällivare, which has left me with plenty of time to explore the city of Umeå and experience life here. A few days after my return, it was the weekend of Brännbollsyran – a music festival that has grown quite large in recent years that also sports a tournament of Brännboll (rounders) during the daytime. As well as the official event, there are many unofficial happenings that occur over the weekend, one of which was an outdoor DJ basically on our doorstep. After meeting some more wonderful people at pre-drinks, we arrived the party outside our apartment and I ran into some friends I met the week before! A coincidence that made the night even greater. There was a slightly harrowing part of the night, however, where we entered what we thought to be a regular party bus, but was actually full of Swedish nationalists. A Swedish-speaking friend clocked what was happening (as they understood what the bus-people were shouting), then led us swiftly back off the bus and explained the situation.

Back in the lab, Charlotte and I had been tasked with transferring the previous year’s insect collection from their containers filled with glycol to specimen jars with ethanol – tedious work, but important nonetheless. Another production-line-esque job was the transplanting of aspen seedlings from agar to soil. Charlotte and I switched roles of uprooting and replanting a few times so we each got the full experience and, working together with another researcher, we completed this task pretty swiftly. I found this much more enjoyable than the insect bottling, and really quite rewarding – I look forward to seeing the plants grow during the next few weeks.

 

 

 

Around a week ago was when I got my first pang of longing for home. It hit me that, after being in Sweden for around 2-3 weeks, I was really missing Ormskirk – a town I’ve grown to love – and my university friends that live there. After being surrounded by them since September 2016, this was probably the longest I’d gone without seeing them. I know that the two months of summer I have before (hopefully) heading out to the US will have to be spent seeing at least a few of them. This was also around the time of the snap general election and the unfortunate events at London Bridge.

A problem that we didn’t encounter in Gällivare which struck me the other day in the field was that of mosquitoes (and other flying insects). I can’t stand them. I was warned that there would be many, but I was not ready. The incessant buzzing of the flies as they whizz past your head, the omnipresent cloud of mosquitoes in your vision and the occasional bite together made it an unbearable experience. Next time I will be adequately equipped with a head net; hopefully, that will lessen the torture of the mosquito cloud, but will, unfortunately, do nothing to the sound of flies as they barrage obnoxiously close to my ears.

Snapchat-630975932Back to exploring the city: I went into the centre of town to witness the last part of the Swedish Gymnasium graduation – a parade with students on floats fitted with birch bundles, handmade banners, and music. It’s quite a sight coupled with their unique graduation caps and other traditions. That week I also experienced a BBQ by the lake, where BBQ means open fire in a concrete container whilst balancing food on sticks. Having such fire pits available to freely use allowed that event to take place a lot easier than a BBQ in the UK, and was really enjoyable. Another aspect of Sweden which I was informed about but not prepared for was the price of a drink in a bar, it rivals London on New Year’s Eve!