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Diary of an Undergraduate Thesis: The Finale

April 24, 2024

This is a continuation of my first article from last semester where I started my undergraduate thesis writing process. You can find that here.

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January 24nd, 2024

Just submitted my methods and materials section. Honestly, at this point I’m a bit more stressed about actually finishing data collection than the actual writing. I’ve kind of reached a “well it’s just an undergraduate thesis and not the end of the world” mentality, which is helping a little. To be honest, I did have a couple stress dreams last week (one was where I was scrolling through an endless Excel sheet of data that I had to analyze), so just accepting that it’s not that deep is good to me. But we keep working. 

I also had to peer review one of my classmates’ methods section. We had this set up last semester too, where we had to peer review other people’s proposals. This semester, I’m paired with a group of other neuro students, so I feel like there’s a lot more back and forth I can actually have with them and their research. For this student, since we had similar experimental setups, I was able to see what she did well, and it also reminded me of things that I need to add to my section.

One thing I’m trying to do this semester is to work on my thesis stuff more consistently, rather than pushing it all to the few days before the deadline. For that reason, I’ve blocked off an hour every workday on my calendar as a reminder to work on my thesis, even if it’s just for 15-30 minutes. I’ll let you all know whether this is helpful or if it stresses me out more to have my thesis on my mind all the time.

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February 27, 2024

As always, problems come up right when you don’t want them to. The stereotaxic frame got broken, so we had to send it in for servicing. This means no surgery practice this month, which sets me back on my deadlines. Luckily, I’ve figured things out with my PI and my thesis class professor, but it’s still disappointing.

Still, the time will pass anyway, and I did practice with perfusions and drop fixing in the meantime. It turns out that I had gotten rusty with these basic skills, so the time spent on that still felt worthwhile.

While I’ve been waiting on unforeseen circumstances to clear up, I’ve continued working on my thesis results and discussion section. You might ask how I could write those parts without having data, but I did a method my professor calls “Mad Libs” writing, where you leave blanks where you don’t have the information yet. This has been helpful, since I have been able to get an outline of what my results and discussion sections will look like.

So, I’ll see you in a month, when I hopefully have some data I can cut my teeth on.

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March 30, 2024

Well, I’ve gotten pretty comfortable with surgeries, and next week I’m planning on doing my first optical implant. If all goes well, I can hopefully collect some data in two weeks. I’ve definitely been stressed about completing this thesis, and part of the process for me this semester is learning to deal with/live with the stress. This isn’t something I can finish in a weekend, after all, so I need to learn to work with this “unfinished task” bell dinging in my head until I turn this thing in. I really really want to have data collection done by the second week of April so we can do data analysis and I can submit the drafts to my readers. It feels like this semester has flown by faster than I thought, and I am worried about the deadline.

In terms of what else I can do on the writing side, I am working on the schematics that will take up part of my figures in my results section. This is something you never really think about when you think of writing a thesis, but working on making good figures is difficult and time intensive. However, it feels good to be able to make those to have in my paper for now.

There’s a lot going on outside of this thesis too–I’m getting ready for graduation, writing term papers, studying for tests, and looking at housing after graduation. It’s a lot to juggle, and I hope I’m doing okay. I’ve been reminding myself that I’m basically in the final lap of this process, and that I can do it.

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April 23, 2024

Finally got some data this month, and I was able to write it all up and make a complete thesis of it all. It was stressful surrounding the data collection, but actually doing it went pretty smoothly. I typed everything up today and sent it off to my first and second readers.

Really, I don’t know what to say here. After actually sending it off, I felt a little relief, but it wasn’t a super big change. That being said, I think I’m still focused on my work because I plan to continue it after graduation, and so my work doesn’t really feel finished. Still, I’m really happy that I was able to turn everything in with time to spare. By having it done about two weeks before I have to submit, this gives my readers enough time to give me feedback and turn in everything to UROP (undergraduate research office that approves undergrad theses).

Now, it’s time to focus on everything else I need to complete before the end of the semester: term papers, exams, and graduation. But tonight, instead of working on it all, I gave myself the evening off. It’s something I deserve after all this, I think.

Am I happy I did all this? Was it all worth it? I think it might be too early to tell, but I think it was well worth my time. I learned so much about research, working on a long term project, and scientific writing. But if I could go back in time and do one thing better, I would try not to stress as much about it. I think during this past year I’ve given myself so much unneeded pressure that never helped make my thesis better in the end. But I doubt that August 2023 me would have taken that advice to heart anyway. In any case, this is my last entry, because I consider this chapter of my life complete. I hope you enjoyed this mad little journal. I’m out.

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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.