Undergraduate Research Fellows Blog

  • When One Door Closes, Another One Opens.

    Landscape of Oak Savanna, displaying burr oaks and an open green prairie field at Pleasant Valley Conservancy- Madison, WI
    These are some of the burr oaks I had the chance to collect leaf foliage from for a co-worker's research project.

    If someone told me two years ago I was going to be working in a prairie, and switching my major to environmental science, I would have thought they were crazy. I was always focused on the biology track. When people asked me what I wanted to do with a biology degree, my mind was blank. I never had a clear answer to give them. So, going into last summer with no idea of what I wanted to do in the future, had me applying to various internships. I knew I was interested in animals and the environment, so I wanted to do something with wildlife. I applied to several places late spring, so either the position was filled or they wanted more ecology experience. After being turned away at numerous places, I explored the option of volunteering somewhere. I originally went to The Grove looking for a wildlife volunteer position, but those were all taken, so they directed me to volunteer at the Kent Fuller Air Station Prairie. I was a little apprehensive about working with plants because I was always so focused with animals. However, I had a feeling that I was meant to be placed there.


    My first week in, I started learning about all the different prairie plants, and why it is so important to restore the prairie ecosystem. Prairies are a vital ecosystem to not only many plant species, but many animal species as well. This sparked my passion for restoration ecology and led me to switch my major to natural resources and environmental science. Ever since I made the decision to work at the prairie, and switch my major, so many doors and opportunities have opened for me. I had a great opportunity to assist a graduate student’s research project and I was accepted to be a part of the NRES ambassador program. After having such a successful summer and spring semester, I knew I wanted to continue my passion for the prairie and restoration work. I looked vigorously for the right internship that allowed me to continue my passion. Morton Arboretum was the place to do so.


    I have only been here at the Morton Arboretum for a couple of weeks and the amount of opportunities I have had, the information I have learned, and the people I have met is remarkable. I am mainly focusing on Dr. Andrew Hipp’s prairie project, but I had the opportunity to collect data from burr oaks, and attend a sedge class. Also, I never thought I would be conducting my own research project, but the Morton Arboretum URF program offers undergraduate students a chance to do so. If someone told me a few years ago I would be conducting my own research, I would have thought they lost their mind. Research was never my first choice as a career path, but this program has sparked a feeling of excitement inside of me to want to further my career in the research field. For my research project, I will be analyzing plant survivorship within a range of phylogenetic and functional trait diversity. I feel honored to think that my little bit of research will be able to help with the restoration of prairies for the future. I am no longer nervous about conducting my own research, I am very excited to see where it takes me. The opportunities I have been given at the Morton Arboretum has helped me to build confidence to pursue my career goals. So, when someone asks me what I want to do after college, I no longer have a blank mind to that question. I cannot wait to see what offers are behind the number of doors I will be approaching at the Morton Arboretum. 

  • From Fish to Trees

    Two Mongolian Oaks on the west side of the Morton Arboretum.
    Two Mongolian oaks that I will be studying for my research.

    Hi everyone! My name is Alyssa Gao, and I am one of the Undergraduate Research Fellows working for the Morton Arboretum’s Center for Tree Science this summer.

    What better way to start off a post about me by reminiscing about my childhood? 

    I have been fascinated by wildlife for as long as I can remember. When I was young, I used to drag my entire family to the Batavia Public Library every weekend and spend hours pouring over Zoobook magazines. Something about getting up close and personal – well, as up close and personal as a kid in the Chicago suburbs can get – with animals from every corner of the world took my breath away.  

    Coming into my freshman year at Dartmouth College, I knew I wanted to try my hand at scientific research. Working as a research assistant turned out to be one of the highlights of my freshman year. Based on the title of this post, I’m sure you can guess what I was working with.  

    Conventional aquaculture diets use fishmeal and fish oil extracted from ocean-caught fish, which is financially, socially, and environmentally unsustainable. My research investigated the feasibility and sustainability of farming tilapia on marine microalgae-based diets. My first experience with research was absolutely amazing and I am excited to continue working in this lab when I return to Dartmouth in the fall. 

    I think that the importance of engaging youth is often underestimated. My love for Zoobooks serves as a reminder of the importance of science communication and outreach – reading this magazine was what really made me care about the natural world and inspired me to pursue a major in environmental studies. This type of media, which breaks down and explains information in a child-friendly, yet engaging manner, is exactly what we need to foster an interest in the environment in future generations early on. The Women in Science Project at Dartmouth, the program which funded my research, provides first-year women with early hands-on research experience and the opportunity for mentoring from a faculty member and research scientist. By exposing freshman to research in action, this program allowed me and countless others to supplement our education and develop our awareness of science career possibilities.

    The Center for Tree Science seeks to accomplish a similar mission by training the next generation of tree scientists, a goal that drew me to this fellowship. I am conducting a project under Dr. Chuck Cannon which will examine the accuracy of allometric estimates based on the predicted and observed measurements in a dying Mongolian Oak. Allometry is using an easily measured variable such as diameter or height to determine other characteristics that may not be as easy to measure, such as biomass. I  will also compare properties between Mongolian Oaks of varying states of health. Through this project, I hope to provide insight into the accuracy of allometric estimates and investigate the variation within a species. I hope that this experience will inspire me to continue learning and exploring for the rest of my life. I am excited to try new things and contribute to the on-going research at The Morton Arboretum! 

    Until next time!


  • Fieldtrip to The Field Museum

    2016 Fellows and Staff on the steps in front of the Field Museum of Natural History
    2016 Undergraduate Research Fellows and Staff enjoy the Field Museum

    On August 8th, interns from The Field Museum of Natural History hosted interns and fellows from the Chicago Botanic Garden and The Morton Arboretum.  Throughout the day, we were given the unique opportunity to learn about the projects that the Field Museum interns were working on with their mentors and colleagues.

    As we shared lunch together, Dr. Corrie Moreau gave an informative seminar, “How to apply for graduate school in the Sciences”.  Before we headed home, many of us took the opportunity to see The Terracotta Warriors exhibit, currently on display until January 8, 2017.  Our thanks to the Field Museum staff and interns for a great day!

  • Wrapping up the Summer at the Morton Arboretum

    Four undergraduate research fellows standing next to posters.
    Having oodles of fun at the symposium!

    It’s hard to believe that the summer is almost over and the Undergraduate Research Fellowship is coming to a close. I'll use this final blog post to tell you about the results of the science I did here this summer and how this fellowship impacted me as a scientist and a person. Let’s start with the science! One of the main things I worked on in my time at the Arboretum this summer was science communication. I have been learning and studying science for years, but it’s harder than you think to communicate that science to others, especially to people in different fields. One of the ways we practiced this was communicating our research using only the 1,000 most commonly used words in the english language. So here’s my attempt of telling you what I did this summer using only the 1,000 most commonly used words.

    Controlled burning is a way to control the woods and help trees grow. However, little is known about how burning changes the ground. Studying the ground under our feet will help to better understand how burning changes the entire woods. We looked at the ways the ground changes when the woods are burned in areas with different types of trees. We asked two questions: (1) Does the ground change with controlled burning? (2) Does tree type change the what burning does to the ground? We found that the ground in burned areas is different than not burned areas, but different types of trees do not change the the ground or change the burning. Humans need some stuff in our bodies to grow and live, trees also need stuff from the ground to grow and live. We think that there is more of some stuff in the ground in burned areas, which may help the trees that need that stuff. Burning also lets in more light which can help some trees grow. What we found in this study should be considered when deciding if we should use controlled burns.

    Forested area with thick green vegetation and lots of light.
    One of the burned areas at the Arboretum


    Besides learning a whole lot about soil, field work, lab testing, and communicating, this fellowship gave me a better idea of what it’s like to be a scientist and think like a scientist. I got a lot of great practice asking questions about the world around me and trying to figure out how it’s working. I learned that scientific research always produces more questions than answers. In this project, we found some changes in the soil with burning. This raises many new questions. How are those changes are affecting trees and other plants and animals in the forest? Does burning always make these changes to the soil or only in some areas of the world? Is buning changing things other than the soil too? When these questions are answered, they will raise new ones. We will never fully understand the entire world, so there will always be more questions and more scientists to try to answer them.

    This research experience taught me to think about the world in a different way, and see beauty in the details of an ecosystem. I find it truly amazing how every little piece is necessary for the world to be the way it is.

    Undergraduate research fellow with a scientific poster.
    Giving a presentation at the Undergraduate Research Symposium was a great way to practice science communication

    I will wrap up this post by thanking everyone who made this summer so amazing. Dr. Meghan Midgley was an amazing mentor and taught me so much about soil and about being a scientist. Many people helped immensely with lab and field work including, Michelle Catania the Soil Science Research Assistant, all the phenomenal volunteers in the Soil Science Lab, and Ali McGarigal. Christine Carrier ran this program very smoothly I thank her tremendously for everything she has done. Jessica Turner-Skoff was a wonderful resource to have and taught us all so much about science communication. All the other fellows were a great support system and marvelous people I am so happy to have gotten to know them this summer. My time at The Morton Arboretum has been oodles of fun!

  • Me and my Laptop: A Love Story

    A person with a bored expression at a desk, using a drawing tablet and laptop.
    Me, working at my desk. That may be a dead-eyed expression on my face, but I swear my brain's still working hard.

    Here it is, the last post of this three-parter on my project!  Since I skipped posting last week, I'm doing a double post this week!

    To summarize, I’m interested in looking at interbreeding oaks, using their chloroplast DNA, nuclear DNA, and their geographic location.  Since I work with DNA sequences, file sizes can get quite large, quite fast!  For example, my chloroplast DNA dataset is the smaller of the two, and it contains 91 different samples, each of which have a 130,000 base-long sequence.  If you do the math, that’s almost 12 million individual bases!

    On one hand, most professionals work with much more data than this, but on the other hand, I can’t settle down on the couch with my trusty abacus and a pencil and paper to work, either. 


    A visual representation of a set of DNA sequences. Nucleotides (A, T, G, and C) are color-coded on a screen.
    My oak chloroplast DNA sequences. The sequence continues waaaaay off the screen. It's 136000 bases long – this is a small genome!
    Kasey Pham


    The data in this study was previously generated for other studies that my mentors and collaborators have been working on, so I’ve been working solely on the data analysis.  Everything from processing the gene sequences, to building the phylogenetic trees, to modeling the equation takes computational power, from a few second’s worth to a few days.


    This is where the second part of why my research is important, at least to me, comes in.  Back in the old days, computer science and biological science were separate fields with little in common.  Of course, that’s drastically changed with the shifts that biological science has taken towards doing molecular work.  Biological studies can generate so much data, especially using DNA sequences, that there’s no way to handle the volume except by computer.  Ecological fields have also benefited from computers, which can help us link geography to years of study data more easily than ever.  With computers, we can tackle problems and answer questions that couldn’t be answered just thirty years ago.

    I want to work at the interface of computers and biology, so this project is important to me, personally, because it brings me closer to that goal.  I’ve learned so much from Andrew and my other collaborators about how we manage biological data and what we can glean from it.

    Of course, working with computers isn’t always so glamorous.  This is my usual sight for seven and a half hours of my day:


    A screenshot of what can usually be seen on my computer screens.  There are multiple coding environments and visualization programs open.
    A screenshot of my usual working environment on my computer. Yes, I have two screens to fit all my stuff. Yes, that makes me a huge nerd.
    Kasey Pham


    I spend the majority of my time coding (read: hunched over a computer).


    A picture of a desk with a laptop, extra monitor, and drawing tablet.
    My workspace all summer. Isn’t it absolutely riveting? Perhaps not as beautiful as the experimental plots or the lush forests of the Arb, but at least I have a spiffy ergonomic mouse!
    Kasey Pham


    My interest in computers, however, is fairly recent.  Last summer, I didn’t know how to code at all.  Heck, I didn’t know what the purpose of coding was.  The extent of my computer knowledge was that if my computer froze, I should turn it off and turn it back on.  (I’ll admit, this is still my most important computer skill set.) 

    Yet, I needed to totally re-evaluate my goals and interests when Andrew tossed me a project where coding was a necessity.  I found that I needed to learn how to code, and fast, if I wanted to finish my project.  I wasn’t expecting to find that coding was a puzzle, almost like learning a new language, or that it was actually fun.  All for a college student who’d never so much as tried to jailbreak her phone. 


    My experience taught me that you don’t need to be a “computer person” to code.  Until I’d had no choice, I had vehemently denied my mother’s encouragement to try computer science using that very excuse.  Yet, if I had to choose anything else to study now, it would be computer science for sure.  I’d definitely encourage anyone who’s even vaguely curious to give comp sci a chance!  You may be pleasantly surprised, not just at how useful coding is, but more importantly, how fun it can be.

    While I may not have many thrills from getting to see trees growing before my eyes, or testing branch strength by tearing them off dead trees with heavy machinery, I do get to experience the thrill of finally getting a script to work, after hours of frustration.  I get to see patterns come out of the woodwork of a sea of data.

    And that thrill?  It’s totally worth the glowing screen eye strain.



    A cartoon of a person hunched over a computer in the dark, with only the light of a laptop shining.
    Bonus: me in my coding cave – Oops – uh – I mean, my office. I'm not saying I'm Batman, but have you ever seen he and I in the same room?
    Kasey Pham
  • More on Those Pesky Oaks

    A mug that reads "The Morton Arboretum" in front of a laptop
    My trusty Morton Arboretum mug, which has seen many a tea stain over the years. Oaks are so important to the Arb that there's even one in the logo!

    Hi guys, this is a continuation of my last post, explaining what I’m doing at the Arboretum this summer.  I’ll be jumping off straight from there, so please give it a read if you haven’t yet!  Unlike what I said last week, I won’t be getting around to talking about how computers tie into all of this just yet.  Instead, I want to explain my research question in a little more detail.  To recap, my research question is:


    How can we use an oak’s nuclear DNA and its physical proximity to other oak species to predict differences in its chloroplast DNA?


    Breeding results in the exchanging and mixing of DNA, which leads to similarity of DNA over time.  As you may recall, the more similar two living things are genetically, the closer they’ll group on a phylogenetic tree.  There are two factors to consider when you think about the likelihood that two living things will breed:

    1.       How compatible are the two living things?

    2.       How close in proximity are they?


    Compatibility, in this case, means that they have to be related enough in their DNA that, to speak figuratively, the socket matches the plug.  The sex cells and mechanisms of breeding of the two living things have to be able to produce living offspring.  For oaks, even other species of oak are compatible, though the degree of compatibility depends on how closely related the two oaks are. 


    An analogy for hybridization in oaks. A circle block labeled as bur oak lies in front of a hexagonal gateway.  A large square block labeled as red oak lies in front of another hexagonal gateway.
    A visual analogy of breeding compatibility in oaks. The circular bur oak block is still a similar enough shape to fit, but the red oak block is not. It should not surprise you that bur oaks are more closely related to white oaks than red oaks are.
    Kasey Pham


    Proximity is probably a little more intuitive.  Plants can’t move, so the closer a plant is to its breeding partner, the easier it is for them to exchange pollen and breed.

    Both of these factors are important!  Chloroplast DNA and nuclear DNA in oaks give us two different types of information.  Chloroplast DNA tells us what oaks have been recently interbreeding.  Oaks that group together on a chloroplast tree are supposedly interbreeding more often.  Nuclear DNA, an oak’s main DNA sequence, tells us how related oaks are evolutionarily, so oaks of the same species will group together on a phylogenetic tree made with nuclear DNA. 


    A phylogenetic tree based on the chloroplast (right) in which oaks of different species that live in the same area are more closely related.  A nuclear phylogenetic tree (left) shows oaks of the same species as more closely related.
    A comparison of simplified chloroplast and nuclear phylogenetic trees. The leaves signify different species of oaks, the abbreviations are the states the trees were found in. The two trees cluster the samples differently.
    Kasey Pham


    You can probably see where this is going; I have data for the sequences of both chloroplast and nuclear DNA for a set of about 30 oak trees, and GPS data on where they are living.  Using this data, I can investigate how important relatedness and physical proximity are to how oaks hybridize.

    Or, if you like equations:

    Chloroplast distance = Phylogenetic distance + Geographic distance


    A visual representation of the equation "chloroplast distance = evolutionary relatedness + geographic distance"
    A visual representation of the equation driving my research question, stated above.
    Kasey Pham


    So why does all of this matter?  This type of work is important for two reasons.  I’ll talk about the first of those reasons now and leave the second for next week, when I talk about the role of computers in my project.

    There are two categories that many people use to explain their research.  The first is applied research, and the second is fundamental research.  Applied research is the investigation of how to change and improve the way that people do things.  It seeks to streamline, improve, and build upon human ingenuity so that our lives will be easier, addressing practical problems that people encounter in their lives.  An example of applied research would be a study testing the effectiveness of several cancer treatment regimens on hepatitis C-linked liver cancer.  It’s easy to see with these kinds of studies how people’s lives are bettered.


    A diagram of the applied research cycle.  An arrow points from a scientist to the Congress building and a factory, saying "solutions". An arrow points from Congress to a person wearing a shirt that reads "public", saying "policy".
    How applied research helps society. Studies affect business practices and policy affect the public, which brings problems back to researchers.
    Kasey Pham


    Fundamental research is the investigation and understanding of the underlying workings of nature.  It seeks to understand why and how things happen.  A recent, well-known example of fundamental research is the search for the Higgs-Boson particle, spearheaded by particle accelerators such as the Large Hadron Collider and Fermilab’s Cyclotron.  While finding evidence for the existence of this particle may not directly impact you and me in our daily lives, it has big implications for our understanding of how objects in the universe interact.  This kind of work, aside from expanding human knowledge for its own sake, forms the foundations of understanding that are necessary to support applied research.

    A common example of fundamental research which has ingrained itself in every part of our society is relativity.  Albert Einstein’s theory pertained to the interactions of huge objects interacting through gravity, the size of planets and suns.  However, relativity has very real impacts on our society.  The equations that resulted from this theory allow us to use satellites for our GPS systems and our cellphones.  As my high school physics teacher used to say, you never know what people will be using our knowledge for in the future.  Research that may seem frivolous or obscure in the present could be vitally important to new technology just a few decades in the future.


    A diagram of fundamental research. Same as the diagram above, but a field scientist researching leaves is the source of an arrow saying "theories" that points to the applied researcher.
    How fundamental research helps society. Studies affect other studies affect applied science affect business practices and policy affect the public.
    Kasey Pham


    Of course, the line between fundamental and applied research is fuzzy, and not every project will fit neatly in one of the two boxes.  However, using these terms does connote what kind of impacts the research makes and who it affects.

    The research I’m doing, while definitely not as glamorous as these famous studies, is also fundamental.  I won’t claim that it’ll change the world or the larger biological community.  However, I’d like to think that my collaborators and I are doing our part to help understand the way trees grow and spread.  With the way that we make phylogenetic trees of oak trees, I guess you could say that we’re Champions of Trees of Trees!

    Sorry, that was pretty bad.  I’ll just stop while I’m ahead.

    (Next up: What does this tree look like again? Or, Kasey’s torrid love affair with her computer.)

  • Stubbornness and Flexibility

    A stock of bright purple flowers in focus, with a young woman looking through the lens of a camera on a tripod in a lush open forest out of focus
    Lane collecting data using the photography method on a sunny summer day

    I must apologize for not writing for two weeks! I keep trying to write this blog post, and I keep getting side tracked. Anyways, at the beginning of the week, when I originally started writing this post, I started off by stating that this week was going to be my last week in the woods collecting data. Of course, because I wrote that, the world (or the weather) decided that it was not going to let me finish my data collection this week.


    The week started off well, and I was completing all of the plots I planned to each day. Then Thursday came. That day, I was prepared to be super productive, complete my last three plots and finish my data collection. I must admit, I did notice that the weather forecast said that it could storm in the afternoon, but since they have been consistently wrong, I didn’t worry too much about it. However, right around noon, as predicted, the sky started to get dark, and the rain started to gently fall from the sky. Drew, Sean’s research assistant, was helping me collect data that day. When it started to rain, he and I were under a fairly dense canopy, so we barely noticed. We continued measuring trees, and the sun even started to come out.


    A picture of a large trunk with deep ravines in it's grayish brown bark with a yellow measuring tape rapped around it
    This was a very large dead ash tree that was measured this week. The Emerald Ash Borer is a real problem in this part of the US right now.
    Alison McGarigal


    After we finished measuring the plot the old fashioned way, we started the photography method. Since it looked like it was clearing up, I thought it would be wise to check what the storm looked like on the radar. There was lightning a little ways away, but not close enough to need to abandon our plot. However as I watched the radar, the thunder started getting noticeably louder and the rumbling started to sound more menacing. I unfortunately had to make the call that it was time to abandon the plot for now due to safety concerns. So we sat in the car eating our lunch waiting to see if it would pass. But instead of passing quickly like storms here normally do, the sky just kept getting darker, the thunder kept rolling closer, and the sky started to spit out big fat drops of water. It took me a while to finally admit to myself that the weather just wasn’t going to let me finish my data collection that day.


    However, my decision to head back in for the day was reaffirmed when the sky literally opened up and poured down on us as we drove back to the research center. I walked about five steps from the car to the building several times to unload gear, and got completely drenched from head to toe!


    Looking out of a car windshield that is splattered with rain drops with a dark cloudy sky in the background
    Drew and I safe and sound in the car, driving back through a rainstorm that we could have been stuck in. We were lucky we didn't take the open air cushman out that day!
    Alison McGarigal


    Anyways, since Friday’s weather wasn’t looking any better, I had to come to terms with the fact that this week was not going to be the last week of data collection. Which is really not a big issue because I still have plenty of time before the symposium to figure out what all the data means. It was more of a psychological thing. The main thing that got me through this past week was that I could see the finish line. After seven weeks of being out in the woods almost everyday, and having to repeat the same three tasks at my plots day after day for almost five weeks straight, I admit that I was a little worn out. But I also admit that I can be a little bit stubborn when it comes to completing the goal I set out to do. (Side note: Kirsten wrote a great post on the importance of repetition in science that you can read here!)


    In some cases, like in this project’s data collection process, it can be seen as a good trait. However, in other circumstances, I would be much better off letting go. For instance, last weekend, I was determined to walk to downtown Downers Grove from our hotel so I could get some exercise, a change of scenery, and find a coffee shop to get some work done. Unfortunately, it was a ridiculously hot, humid day in Chicagoland, and I made a poor decision on what shoes to wear. After an hour and a half, I finally made it to the downtown. In retrospect, when I realized the unideal weather conditions I was walking in and just how far of a walk it was going to be, I should have got an uber to take me the rest of the way. But because of my stubbornness, I walked the whole way, ended up with two huge blisters on my heels, and was drenched from head to toe in my own sweat.


    I guess the lesson from all of this is that it is good to have goals and to see projects through to the end. However, it is also good to be flexible and to know what is important and what can be let go. I have found that these lessons can be pretty much applied to all aspects of life. You have to find a balance between determination and compromise, between stubbornness and flexibility, between stability and change.


    Till next week (probably… maybe the week after…)



    A young woman wearing a bright orange shirt holding a large tube covered in QR codes stands in front of a field of wild sunflowers in bloom
    The wild sunflowers started to bloom in the burned section of the forest! They were so beautiful that I had to take a picture with them ;)
    Lane Scher
  • Science is BIG! (and small)

    soil samples with a pH probe
    Testing the pH of some soil samples

    Hello there blog readers! I have been doing a lot of lab work in the past few weeks. I decided to use this blog post to tell you about the BIG and the small of my project. Let’s start with the small. Lab work is small. Some of the things I am looking for in my soil samples are the carbon and nitrogen concentrations. There is a really fancy machine in the lab that I can use to figure this out but, in order to get the soil ready to go in the machine I have to weigh out 25 milligrams of soil and wrap it up in tin foil. Just for reference, 25 milligrams is less than the weight of two grains of rice, tiny.

    small foil ball about 1/10 the size of a penny
    One of the tins with 25 milligrams of soil in it, and a penny for size reference.

    Another one of my lab analyses is determining the ammonium and nitrate concentrations in the soil. I go through a long procedure that results in lots of plates with tiny little wells that have pink or blue liquid in them. I put these plates in a machine that uses light to measure the color in each well to determine the ammonium and nitrogen concentrations. In the end, there are many plates with 96 wells on each plate and about 2 drops of liquid in each well, tiny.

    Varying shades of pink and blue liquid droplets on plastic plates.
    The colorful ammonium and nitrate test.


    Lab work is small, but science is big! It is easy to get caught up in my tiny soil samples and little droplets of colored liquids and forget about the big picture, but all the small comes together to mean something big. Each tin of soil or drop of liquid represents a different area of the woods. When the results of these samples are combined, they represent an entire part of the woods that has been burned or not burned. That can give a good idea of how the soil reacts to burning practices in the arboretum and any other forest in a similar climate and environment. My results are limited to areas that are similar to the woods I sampled, but they can be combined with results that other researchers find in other areas. When put together, this can tell us something big about the world around us. That’s my favorite part about science, it is small, but when the tiny results are all put together it can mean something big!

    Researcher using test tubes with soil and liquid in them and funnels over them.
    Filtering samples for phosphate analysis under the watchful eye of the lab dinosaur.
  • Oaks: A Tricky, Promiscuous Genus

    Oaks: A Tricky, Promiscuous Genus
    A frog sculpture in a white oak tree. Its name is Edward.

    This is the first of a two part blog post!  More to come soon.

    This is my ninth week here at the Arboretum.  It’s a little scary how quickly this time has gone by.  Sometimes, I’ll catch myself feeling insecure about what I’ve gotten done so far, but I try not to let it get me down.  Thinking back to the beginning of the summer, I’ve learned so much since then about coding, writing, and looking at data!

    Unlike the other fellows, I didn’t start the summer with a fresh project devoid of previous data.  Since I’m interested in learning how to tease out hidden relationships in data, Andrew’s modus operendi for both this summer and the last has been to put me on projects that have fallen by the wayside.  For the most part, these projects have had preliminary datasets already collected, and it’s been my job to clean them up and analyze them.  That being said, I’ve done my share of data collection. (The summer after I graduated high school comes to mind.  So many… leaf blades… to measure…)


    A scientific scale
    Our lab scale. I bet my hands will still automatically tare this scale and go for a leaf blade of sedge to weigh by muscle memory.
    Kasey Pham


    Rather than sedges, this summer I’m studying oak trees.  As I explained in my last post, systematics is the science of studying biodiversity.  I’m interested in looking at how different species of oaks are related to each other, and how their DNA can tell us more about these relationships.

    At this point, it might be helpful to have a little background.  For those who’re familiar with genetics, please bear with me!  DNA is the code that provides a plan for everything that goes on in our bodies.  The unique sequence is different for every living thing, and changes over generations.  As DNA is copied and passed from parent to child, differences crop up.  They’re very small – a change of a single part of the sequence here and there.  Then the former child will pass its DNA onto its offspring, and once again, a few changes will be made.  Changes in DNA lead to changes in how organisms look and how their bodies function.  This is called evolution, and it’s the backbone of systematics. 


    Illustration of cladogenesis
    Evolution at work. The very famous picture of a monkey growing more upright to walk as a man is actually incorrect! I’ll definitely be writing about that later.
    Kasey Pham


    Over thousands and millions of years, changes in the DNA of all living things lead to groups of organisms that have more similar DNA, and are therefore more closely related to each other.  They breed with other organisms in the group, because it is nearly impossible to make offspring if the two parents have DNA that is too different.  These groups of organisms are called species. 

    Similarities and differences in DNA sequence allow us to group individual living things into species, species into genera, and so on.  For instance, all animals will have more similar DNA than an animal and a plant.  The degree of similarity between any number of living things can be represented by a phylogenetic tree.


    A simplified phylogenetic tree of canids and felines
    A simplified phylogenetic tree. The animals within a circle are more closely related to each other than to the animals in the other circle.
    Kasey Pham


    My job is to take DNA sequences from different species of oaks and make phylogenetic trees with them.  Then, I use the trees to investigate the research questions that I’m interested in.

    My research question for this summer is the following:


    How can we use an oak’s primary DNA sequence (called its nuclear DNA) and its proximity to other oak species to predict differences in its chloroplast DNA?


    That might need a bit more explanation.  Plants use the process of photosynthesis to produce energy for themselves.  This requires a special set of machinery, found in a part of plant cells called the chloroplast.  This special set of machinery is coded for by a separate set of DNA that is unique to the chloroplast.


    Simplified illustration of the chloroplast, including the thylakoid membrane and grana
    The chloroplast, with all the machinery necessary for making sugar from sunlight.
    Kasey Pham


    Oak chloroplasts are weird.  This is because oaks act very strangely when it comes to breeding.  Certain oak species interbreed pretty commonly.  This is the equivalent of us humans commonly procreating with chimpanzees.  Bizarre, right?  This interbreeding causes their chloroplast DNA to reflect a different evolutionary history than their nuclear DNA.  Where nuclear DNA will group all oaks of the same species as being the most closely related to each other, the chloroplast DNA may group them with other oak species that live close to them, rather than with other oaks of the same species that may live farther away.


    Illustration comparing hybridization rules for apes and oaks
    While humans and chimpanzees can’t and won’t mate under any circumstances, oaks have no such qualms.
    Kasey Pham


    I’m investigating how we can predict relatedness of oak chloroplast DNA to other oak species.  We think that differences in the chloroplast DNA of two oaks can be modeled by a mixture of how related they actually are, according to their nuclear DNA, and how close they live to each other.  I’m investigating that relationship for different species of oaks that interbreed with each other to varying degrees.

    While I’d love to explain how I investigate this question, I think I’ve gone on long enough.  Look forward to the second post of this two-parter, where I’ll be explaining why my laptop is my very best friend in the entire world.  Until next time!

  • Fieldtrip to Chicago Botanic Garden

    Morton fellows and staff enjoying the Waterfall Gardens at the Chicago Botanic Garden
    Morton fellows and staff gather at the Waterfall Gardens

    On July 8th, Undergraduate Research Fellows joined Field Museum interns on a field trip to the Chicago Botanic Garden.  We spent the morning on a guided tour through many of the gardens and natural areas, with stops at the Bonsai Collection and greenhouses.  We spent the afternoon in the Plant Science Center learning about the research being conducted by interns at the Chicago Botanic Garden.  Our thanks to the Chicago Botanic Garden staff and interns for a fantastic day!    

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