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Diary of an Undergraduate Thesis

December 2, 2023

The Georgia Tech Research Option is available to all undergraduate students in the College of Sciences. It includes the completion of an undergraduate thesis. Students who choose to take on all this additional work are generally considered a bit sick in the head. Through these diary entries, I hope I can provide some insight into the joys and trials of completing this process. Particularly, for those who (for some reason) want to take on the same path.

August 24, 2023

Finally figured out the direction that I want my thesis to go in! This has been stressing me out quite a bit, so I’m glad I’m able to figure things out. I talked with my PI and we sort of figured out that I can do a project that combines the calcium sensors our lab has been developing and the dopamine recordings in freely moving mice that we’ve been doing. There’s still a lot of directions this project can go, but this sounds like a good place for me to start thinking (and just as importantly, looking at sources for the background section of my thesis). What I found super helpful is that my PI gave me a set of next steps if I want to pursue this project, which alleviated a lot of my uncertainty. Here they are:

  1. Get trained on stereotactic surgery (mouse brain surgery)
  2. Learning how to run and handle mice in our behavior rig
  3. Injecting mice with whichever thing we want to test (probably dopamine and the sensor at first)
  4. Running in vivo experiments

As you can see, running experiments is step 4, after having to learn a lot of other stuff. Hopefully, I’ll be able to start that step in October/November, but if not I should be able to do it in spring. 

We also discussed how there’s a huge gap in the literature that I honestly hadn’t really considered: we don’t really know how dopamine impacts the excitability of neuron populations. This seems like something really basic to the field, but we haven’t really had the tools to measure it until very recently. I don’t want to get too deep into the particulars of the field, but basically I’m glad that we’ve found something that I can reasonably say fills a need in this field of research. In addition to that being a required part of my thesis’ introduction, it makes me feel a lot more passionate about the work. I think a big challenge of this thesis will be staying motivated as the going gets tough, so this is good.

My next steps will be to get trained on the techniques I’m planning to use and look at some papers for background.

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October 6, 2023

I have been super busy this past month and change. I have been practicing stereotactic surgery, which has proven to be really hard. While I’ve been working on experimental techniques, I’ve also been reading a ton of articles.

Right now, I have around 25 articles in my Zotero (research sorting app), and I’ve read about 7. Although I’m improving in my ability to read research articles, it’s still taking such a long time. 

Now, my literature review is due in two days, and I haven’t read all the papers yet. However, since it’s just a draft, I’ll try to use the background section of my PURA proposal as a base for it. I’m going on a trip tomorrow, so I really don’t want to work on it during my trip.

I’m going to work on it now and just submit the draft. This thesis process has taught me to just turn something in, even if it isn’t perfect.

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November 4, 2023

Well–I think I’m at the point of the semester where it all feels like I’m fighting an uphill battle. Looking at my 4 step plan from August, I’m still working through step 1. My plan of conducting actual experiments in October was a little too rosy. One thing that’s slowed my progress is that although I’ve been practicing mouse surgery, I can only pretty much do one mouse per week. I share the surgery room with other people in the lab, and with scheduling around classes and other lab tasks, that’s all the time I have for practice. 

Still, I feel like I’m making progress, slow as it is. This week, I’m going to be doing my first survival surgery, which is one step closer to being able to put in implants and biosensors into mice.

On the writing side, it’s time for me to revise my lit review, introduction, and work plan and put them together. It’s also necessary for me to get all three (all together they’re called the proposal) signed off by my research advisor and second reader. Honestly, this part kind of scares me because I feel like I haven’t gone in depth enough for my lit review in particular. I’m meeting with my advisor later this week to show him my proposal, so I’ve got to get working on this today and tomorrow (the weekend). Currently feeling stressed out. But I keep telling myself that it’ll pass.

The thing is–I really like doing research, and I find reading articles and learning more information about the topic interesting. But deadlines and expectations always scare me. Even so, I’m trying to tell myself that I have all the tools I need to succeed. I just need to be patient with myself.

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December 1st, 2023

Well, I’ve basically done all my revisions. My readers gave me some really helpful feedback, and it turned out that my proposal was in better shape than I originally thought. I just need to check some of the formatting, and then I’ll wait for the approval form to come out so I can submit it. 

One thing I noticed–that I also talked to my advisor about–is the fact that when I’ve been working on my thesis, it’s made me think about why I am doing what I’m doing. Like it’s simple enough to say I’m working on a project that uses a biosensor, but when I started writing, I started thinking more about the details in a way that I never really did while just doing bench work. Why do we choose this type of biosensor? What gives our approach the advantage over another? In what way does our experimental setup even work?

I think as undergrads, a lot of stuff is technically really complex and hard to grasp. So the researchers who are mentoring us simplify things so we can get a general gist of what’s going on. But when you’re writing your own thesis, or even making a presentation on your research, you’re encouraged to delve deeper into the reasoning behind what you do. And in that way, I think I finally kind of understand why a thesis was put into the curriculum of the research option. 

As the semester is nearing its end, I’ve been thinking a lot about what I’ve done so far. And I feel like while I’m behind on my work plan, I still feel proud about what I’ve accomplished. It’s just an undergraduate thesis–I’m not really expected to produce groundbreaking. Still, I feel like the skills I’m learning (reading journal papers, scientific writing, study design, coordinating with my research advisor) are going to be really helpful in the future.

Or, maybe I just feel like this because the pressure is off, for now. I’m going to put the final touches on my proposal now–see you next semester!

Here is my followup to this article–the finale of my undergrad thesis journey!

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I'm a 3rd year neuroscience major interested in the intersection of science and art! I also like to share my experiences as someone studying an uncommon major.

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  Timothy Durham was convicted of rape when a test showed his DNA genotype matched the DNA recovered from the crime scene. Eye witnesses testified that Durham was in a different state at the time of the incident, but he wasn’t exonerated from his 3000 year sentence until follow up DNA analysis showed that the preliminary forensic analysis used in the trial was misinterpreted (Thomas et al.). DNA testing serves an invaluable part in our criminal justice system, but it comes with complications and bias that can lead to wrongful convictions and misinformed juries.  

Background:

Forensic genetics aims to identify the origin of a biological sample. It can be traced back to Karl Landsteiner who discovered human ABO blood groups. With blood groups, suspects could be eliminated based on their blood type. For example, if a suspect had type A blood and there was type B blood left at the scene by the perpetrator, the investigators could rule out the suspect. Unfortunately, the reverse didn’t work. If the suspect and perpetrator both had the same blood type, it can’t be concluded that the suspect was guilty. Blood identifiers evolved into 8 distinct categories which improved the ability to eliminate suspects, but could only conclude that (if the system matched) it might be the perpetrator or this person might be related to the perpetrator (Jobling and Gill). The field evolved in the 1980s with the discovery of Minisatellites, lines of repetitive DNA that don’t encode proteins. Minisatellite patterns in DNA create what we know today as the DNA fingerprint, and it has a much higher accuracy rate than previous methods (Augustyn et al.). Around the same time, a breakthrough for victims of sexual assault was discovered. In the case of assault, bodily fluids of both the victim and the assaulter can get mixed. A process called differential lysis was created which could selectively increase the concentration of sperm in a fluid sample thereby allowing for accurate DNA testing (Jobling and Gill). Forensics evolved to use single-locus probe testing after several years because of its ease of interpretation. It looked at specific minisatellites that had high variability between subjects. This was the first DNA-based method to be used in a criminal investigation. Two murder homicides from several years apart were connected using DNA evidence. The evidence was then used to exonerate an innocent man, and the guilty party was found when he tried to evade mandatory DNA testing for all men in the small town. His guilt was then reinforced when the DNA profiles matched, and he gave a confession (Jobling and Gill). Finding DNA at a crime scene doesn’t guarantee that you’ll find a murderer. There are issues with non-pure samples and limited samples that make DNA work difficult, and accreditation of facilities and new techniques and take time (Jobling and Gill).  

Subjectivity of DNA Interpretation:

In a 2009 publication, the National Academy of Science discusses the possibility for subjective influence in lab based forensics. The interpretation bias happens in complex cases where, for example, there could be a mixture of DNA. A study published in 2011 looked specifically at this issue. A gang rape happened in Georgia, and the mixture in DNA from the case was used to prosecute one suspect after another suspect took a plea bargain to testify against him. With DNA mixtures, there are three possible conclusions: suspect excluded, suspect cannot be excluded, and inconclusive. If the suspect is excluded, it means that there’s little to no possibility that his DNA is part of the sample. If the suspect cannot be excluded, it means that there’s a possibility that his DNA is part of the sample. In the trial, the DNA examiners who knew the context of the case concluded that the suspect being prosecuted could not be excluded. The 2011 study gave the DNA evidence from this case and the DNA profiles of the suspects to 17 forensic examiners. These examiners had no context of the case, and they all worked independently. Of the 17, only 1 came to the same conclusion (suspect cannot be excluded) as the examiners who knew the context of the case. Twelve of the 17 concluded that the suspect who was prosecuted and convicted had no relation to the DNA found in the sample. Not only does this show that subjectivity occurs due to the context of the case, but the 17 examiners came up with different findings based on their past experiences meaning that not all DNA analysis is objective. Some organizations like the Scientific Working Group on DNA Analysis Methods say that quantitative statistical evidence should be presented with every categorical conclusion, but the US doesn’t require this (Dror and Hampikian).

False Positives:

There are two categories that cause wrongful identification in a DNA report: coincidental matches and false positives. Coincidental matches are DNA matches between two unrelated people. The probability of these matches is about 1 to 500,000 for white individuals and about 1 to 350,000 for black individuals. This small probability of coincidental matches makes people feel confident in DNA evidence. False positives, on the other hand, are matches between DNA and test DNA that result from issues in the forensics lab. There have been multiple cases of forensics labs accidentally switching victim and suspected rapist DNA which lead to convictions that were later overturned when the lab realized the error. There are also cases of misreading or misunderstanding a sample. In a case from 1993, a man was convicted of rape because someone interpreted a mixed sample of victim and perpetrator DNA as an individual sample. The conviction was again overturned. To prevent false convictions, retesting DNA is allowed, but it’s not an efficient solution. Many people are pushing for statistical information on the probability of false positives, so that the jurors can make accurate judgements based on DNA evidence (Thomas et al.).  

Conclusion:

DNA analysis is a useful tool for the criminal justice system, but subjectivity can be an issue in forensic testing. To combat wrongful convictions, there are organizations like The Innocence Project who use DNA testing to free the innocent, but reformed forensic testing standards should be put in place to prevent subjectivity and to ensure juries are correctly informed during trials. https://www.innocenceproject.org/    

Citation:

Augustyn , Adam, et al. “DNA Finerprinting.” Encyclopedia Britannica , 26 Apr. 2018, www.britannica.com/science/DNA-fingerprinting#ref153186. Dror, Itiel E., and Greg Hampikian. “Subjectivity and Bias in Forensic DNA Mixture Interpretation.” Science & Justice, vol. 51, no. 4, 2011, pp. 204–208., doi:10.1016/j.scijus.2011.08.004. Jobling, Mark A., and Peter Gill. “Encoded Evidence: DNA in Forensic Analysis.” Nature Reviews: Genetics, vol. 5, no. 10, Oct. 2004, pp. 739–751., doi:10.1038/nrg1455. Thompson, William C, et al. “How the Probability of a False Positive Affects the Value of DNA Evidence.” Journal of Forensic Sciences, vol. 48, no. 1, Jan. 2003, pp. 1–8., doi:10.1520/jfs2001171.