Month: February 2017
One in a Million
by Lindsay, 12th Grade Research Student
A lot of people dream about winning the lottery, choosing a few numbers and instantly becoming unimaginably rich. Despite the enormous odds against each player, people trade their cash for slips of paper that could be the key to a whole new life. However, there is one lottery that no one wants to win, and yet, millions of people are stuck with the jackpot each year.
A person’s life is irreversibly altered when they are diagnosed with a rare disease. According to Global Genes, a rare disease patient advocacy organization, approximately 30 million people in the United States are currently living with one. Many factors can cause a rare disorder, but most of the time, a person is born with it. Whether genetic or otherwise, rare diseases are often debilitating and frustrating for those who have them; I can say this from personal experience because I was born with one myself.
Before my first birthday, my parents found out that I have X-linked hypophosphatemic rickets. It’s not as complicated as it sounds; I promise. XLH, as it’s known by patients and doctors alike, is caused by a mutation on the PHEX gene. In other words, there is a critical mistake in the letters on one very small portion of my DNA. However, not every person with XLH has the same mutation as me. There are many different recorded mutations, and even some that have not yet been discovered.
For my project in the Minnetonka Scientific Research program, I am extracting the DNA from my cheek cells and preparing it for sequencing so that I can identity my own specific mutation. I might have a variant that no one has ever seen before! Even though I’m not discovering any new scientific theory, my results could add to the current studies being done on correlations between a patient’s physical symptoms (phenotype) and DNA sequence (genotype). However, the importance of research for my condition extends far beyond the cellular level.
This tiny mutation of XLH leads to a domino effect of problems. It causes the body to produce too much of a hormone called FGF23, which makes the kidneys get rid of phosphorus that is critical to bone health. As a result, patients often end up with bone deformities, weakness, and pain.
The current treatment for XLH is daily intake of phosphorus and vitamin D as well as surgery to prevent or fix any bone deformities that may occur. However, there’s a catch. This method does not prevent bone pain and can lead to a dangerous buildup of calcium deposits in the kidneys and in some cases, kidney failure. Even so, XLH patients are some of the lucky ones. Global Genes states that 95% of rare diseases have not one single FDA approved drug treatment.
This is one of the many reasons we celebrate Rare Disease Day on the last day of February each year. It is a day dedicated to raising awareness for over 7,000 rare diseases. This year, the theme is research.
With seemingly nowhere to turn, scientific research brings patients hope. Because of research efforts, there is currently a treatment for XLH that has made it to clinical trials with promising results. It has been shown to reduce bone pain and prevent the threat of kidney failure because patients would no longer need to take so many pills each day. Even more exciting, young children with the condition could face leading a “normal” life. Research has given everyone in the XLH community hope for a brighter, pain-free future.
Being in the Minnetonka Research program means that I can be a part of this critical point in the history of my condition. It has given me and the other students an early opportunity to see the wide range of positive impacts research can make on the world. In the lab, we are doing so much more than filling test tubes and looking through microscopes; we are practicing changing lives and bringing hope. We are one in a million.
Help Is Closer Than You Think
by Dylan, 12th Grade Research Student
While working on my research, I learned that people who know very little about your subject can be just as helpful as an expert in the field. Many times it is important from a person who has more experience in that field. That should be common sense, what I didn’t expect was that you can learn as much from trying to answer peoples’ questions as you can from someone who knows a lot more than you do.
The first time this happened was at the very beginning of the year when I was trying to come up with my topic. I felt completely stuck; any topic that sounded interesting was not possible for me to do at the school in one year and the practical topics did not sound very interesting. I was looking at doing something with hydrophobicity,a property in which a surface repels water but that did not sound like something I could stay interested in for a year. I was talking to a classmate about this and, knowing that I like biking, he asked me if there was anyway I could improve a bike using this property. Even though he didn’t know a lot about bikes or hydrophobicity, he gave me the idea I could research an application of a surface on something I am interested in. After more research into both subjects I found that by applying principles of hydrophobicity in order to increase the length of time it takes for the brakes to overheat.
Another way that my classmates have been helpful to me, despite researching very different topics, is by sharing their experiences with similar tasks. Most of the tasks we need to do are the same on a surface level in the early stages of the research. Finding materials, researching experimental design and contacting companies about products are just a few of the many daily things we have to do. Even though the details of accomplishing these tasks vary for each project, I have been able to talk to other groups and find out what has worked well for them. Contacting companies with a phone call versus using email to get a more immediate response is one of the many things that I have learned from peers who have had similar struggles while working on a very different project.
Even though learning from someone more experienced is still one of the most effective ways to solve a problem, it is important to accept help from anyone who is offering it. In some cases you will receive the best help from someone you didn’t expect to have any answers.
How a Doubtful Kid Became Driven – Without Deadlines!
by Will, 12th Grade Research Student
Hearing about this brand-new research course here at Tonka, you might get the impression that our class entirely consists of totally put-together, diligently self-motivated students. I assumed the same thing, and I was worried to death about it; everybody I talked to was telling me this was the perfect opportunity to explore my passions! – But what if I don’t know what my passions are?
I’m Will, and as my mom would be eager to tell you, I’m not always a paragon of organization; one look into my bedroom or backpack and that would be abundantly clear. Oh, I’ve passed plenty of AP classes, but you can probably guess whether my academic success so far has come from neatly filed folders and a balanced workload or from a combination of deadlines and lots of commitment.
To be honest, it surprises even me how far I’ve progressed in my education while seeming to lack the faintest idea of what I intend to study the next few years of my life. Because of this generally uncertain nature of mine, doubts about Minnetonka Research raced through my mind the majority of last summer. If I don’t even know whether I’ll become a graphic designer or an environmental engineer, how can I decide on a single question to devote a year’s worth of research to?
As the year started, I was comforted to see students in the same boat as I was. We had to get started quickly, though. Since I’m a pretty deadline-motivated student, I knew it would be way too easy to let time slip away from me; I knew I was going to have to change my habits. Instead of waffling between fields of science for weeks on end, like I naturally would, I sat down at Caribou with my girlfriend and we brainstormed over coffee for a good hour. I spent the next few nights searching scientific news websites to find something that would align with my interests, and sure enough I found out about types of bacteria that can naturally degrade oil spills: something we had questioned the existence of that night at the coffee shop!
Having cleared what I was sure was the biggest hurdle, I still had to maintain a rigorous organizational attitude about this whole thing if I was going to be successful. I bought a planner and started a clean Table of Contents for my brand-new research notebook, taping in each piece of notebook paper I used for my crude preliminary research. As the weeks went by, I got into the swing of dating every entry in my lab notebook, writing down the title of every research paper I took notes on (and keeping its link saved in my iPad), and even checking my school email multiple times a day. I know for most adults this is a given, but for me it took self-discipline to train myself to check, read, and reply to my emails. I already feel more put-together, and it’s been easier than I thought!
Honestly, I think the fact that this is my very own research has made everything I’ve learned about organization come much more smoothly than I would have expected. Turns out, when punctuality has a direct impact on my personal goals, it feels a bit more important! After being assigned to my amazing mentor Willow Coyote-Maestas, a graduate student at the University of Minnesota, I quickly got used to sending a few substantial emails a day; his dedication to my project means a lot, so there’s good reason to stay on top of things! I have so much yet to learn about microbiology, even with such a specific topic as studying one gene from one bacterium, but I’m really thankful that this course has motivated me to become more professional in my communication and self-motivational skills.
‘TypeError’: A Tale of Data Reduction
by Sky, 12th Grade Research Student
While other sciences can go out and test their theories directly, astronomy is totally reliant upon observation. Despite the wishes of astrophysicists worldwide, space remains rather far away, and until technology catches up, it just isn’t feasible to perform experiments with supernovae or colliding galaxies. Until then, we’ll have to rely on what we have: the ground-based observatory. My project involves developing software tools to analyze the light spectra of objects such as variable stars in order to classify them and inspect them over time.
A month or so ago, my mentor sent me a folder full of raw data and the instruction to calibrate them, a preliminary task to occupy my time while we wait for more images to come in. When you think ‘space photos,’ you might picture beautiful full-color images, the kind that you might want to set as your phone wallpaper. The reality is much less exciting. Raw photos are noisy, black and white, marred by airglow and cosmic rays and defective pixels. My assignment was to reduce these images, converting them into a form usable for scientific analysis.
Of course, I wasn’t going into this blind. I’d done my research, and I did similar work at a physics camp I attended last summer. I knew what type of program I’d have to write, what results I should expect. The task, I thought, should take a few days—a week, at most. Instead, it ended up taking almost a whole month.
That month started out well enough. I installed the software I needed, refamiliarized myself with the programming language, and set out, confident in my abilities. At camp, I’d used some pre-provided utilities for all our calibration needs, but now, I was determined to do it all myself. I reasoned that I knew all the steps and had all the skills, so how much more time could it really take?
The first sign that things wouldn’t go so smoothly was when my program failed to open all 50 or so of the first batch of images, yielding errors halfway through the process. The error messages revealed nothing useful, tracing the problem back to a line of code deep within the file-opening system, something I didn’t even write myself. I double-checked the documentation, wondering if I had made any syntax errors or included something I shouldn’t have. But for as long as I stared at my code (or had friends stare at it for me), I could not locate my error.
Despite this, I tried to make progress, throwing together a fix for the issue that would allow me to ignore it, at least for the time being. But one day, on a whim, I decided to check it again, running the problem code on various groups of images to see if it could open them. In all cases, it failed after opening 23, no matter what. The diagnosis? Memory issues.
Now, I haven’t actually confirmed this hypothesis. The error messages aren’t what you would expect if my computer had run out of memory. Programming experts may already be yelling at their screens, pointing out what I’ve done wrong. If I were really devoted, I could probably search the documentation for ways to circumvent the issue. But it’s difficult to justify spending four weeks on a task that really should have taken one, and it’s even more difficult to justify another week of chasing down an error
However, that’s not to say I didn’t gain anything from this experience. From a technical viewpoint, I certainly learned a lot, both about programming and about data processing. There’s also probably a lesson there about how you don’t need to reinvent the wheel, or that sometimes you just have to leave things where they are. But beyond that, perhaps most importantly, even with all the frustration, I had fun.
Laughing it off
by Logan, 11th grade research student
When I registered for research last year, I had a lot of expectations and most of them were accurate. One thing I did not expect, however, was the laughter in the research classroom. Research can be a very stressful undertaking. It requires you to be patient. You need to learn how to find and accept help from others when you need it, and figure things out on your own when you can. When doing research you are always questioning: questioning the work of others, your own work, your procedure and approach, your true purpose, and if it’s socially acceptable to wear your lab coat for fun.
When I joined the research program, I was expecting a serious, formal, and dedicated environment. That is true sometimes, but most of the time research is casual and full of laughs. The reason for this is the stress. All that stress has to be dealt with somehow, and the healthiest way for most people to deal with it is to laugh.
As an example, there are two groups of people in my class this semester growing living things in the research lab. Both groups managed to accidentally kill their living things only a few weeks after receiving them. In one situation it was likely due to the Minnesota winter temperatures while shipping. The other group accidentally suffocated their fruit flies. In both cases the students and my instructor simply laughed and got on with ordering more organisms. They could have been angry or frustrated, but instead they chose to laugh.
This applies to my project as well. I am working on developing an assistive bicycle stabilization system using the inertia of a rotationally opposed mass to help the rider remain upright. The goal of my project is to develop a system that could be added to existing bikes for users who struggle with balance or coordination. I have a strong biking background and absolutely love biking, so I wanted to be able to make that experience available to everyone.
Getting my proposal approved by the required safety board was a struggle. I submitted my proposal three times over the course of several months, and only after the third try was it accepted. I had to specify all sorts of details about my project: where I would ride it, when I would ride it, what I would be wearing when I was riding it, the traffic and weather conditions, the possible need for safety harnesses or pads on the floor, the potential self-confidence risks of getting seen falling off a bike, the list goes on. Instead of getting frustrated with the obscure rules of the safety board and how it was impeding my project from moving forward, my instructor laughed and told me what I had to add to my proposal so I could get it approved.
This positive and lighthearted attitude has been one of the most beneficial things I have learned from the research program. It has been a very good reminder of the necessity of laughter in life. You learn lots of very specialized things in research, like how to balance the pH level in a saltwater tank. But research is not just about your specific project, it is more about the experience as a whole. You learn things that are useful for your future work as a scientist, and useful for life in general. Things like how to keep a lab notebook, how to write a proposal, and most importantly, how to laugh.
Beyond the Glass 