So I fell really behind with my updates. April is always a really crazy month. And now somehow we are in May!
On Thursday April 28th the graduate students presented their final projects in class. David set it up like a meeting, complete with delicious goat cheese, brie, and fruit. He also invited members of his lab to come. Presentations were about 15 minutes long with time for questions. The undergraduates presented the following Monday. That was good news for me since my analysis finished on Thursday mid-morning.
On Friday morning Romina, Alexis, Alicia and I left for the Mid Atlantic States Mycology Conference. I was really terrified since I gave a talk , presenting the project I am working on (including work from this class). Romina and David told me the meeting was super small, but then I walked into a huge auditorium with a huge screen, podium and microphone. Even though the public speaking class helped me improve, I still panicked and blanked on some things I wanted to say. At least my talk was early in the day so I was able to get over my poor performance and enjoy the rest of the conference. Romina and Alicia also gave talks-Alicia won first place for best student talk, and Alexis presented a poster. Besides the talks and poster session, there were also tours of the U.S. National Fungus Collection. I really enjoyed the tour-It was amazing how old some of the specimens were. It was great to go to a smaller meeting- I was less overwhelmed and I was able to talk to lots of people. Everyone was very friendly and welcoming, and I received some advice on my research.
The following week was filled with finals. As a senior, I had mainly papers and presentations. The week before I presented a poster at Academic Spree Day. On Tuesday May 7, our final papers for this course were due. The papers were formatted like a scientific manuscript, which was helpful practice. After the course finished we all received detailed feedback from Romina and David on our papers. Now the semester is over! Alexis and I graduated on Sunday. We are continuing our work in the Hibbett lab as part of Clark’s Accelerated Master’s Degree Program. Things don’t feel that much different-we were back in the lab Monday morning. We did get new desk space in the graduate student office, and we had a chance to work with undergraduates beginning work in the lab.
I’m feeling really positive looking back on my time as an undergraduate and thinking about my future work. I really advise undergraduate science majors to get involved in lab work as soon as possible. My experience in the Hibbett lab was the highlight of my undergraduate education. The various courses I took complemented my lab work well, and in some cases, such as the Tree Thinking course, they were closely integrated.
Last week David gave a lecture on a method called ancestral state reconstruction and Romina gave us a tutorial on how to perform this method, which many of us will use for our projects. The homework assignments for the class have been completed, and now the focus has shifted to discussion of papers. We are still learning new methods and now we are working on applying these methods to our projects which are due in a month!
Yesterday we discussed a paper which used ancestral state reconstruction. As predicted in my last post, I was selected as discussion leader today. I remained calm and it seemed to go well. Alexis and I discuss the articles before each class and we usually manage to help each other better understand the research and come up with points for discussion. In phylogenetic studies incomplete taxon sampling is a constant problem. Spotting methodological problems can be more difficult. Yesterday was a little frustrating because we missed a few of the major problems David identified within the article. That is why discussing articles in class is so beneficial. I find that it is almost more important than lectures. Passively listening to someone lecture can give you an inflated sense of your understanding of a topic. Evaluating today’s paper required more than just knowing about the topic (ancestral state reconstruction). We needed to know how the method works and what assumptions it makes, how to apply the method appropriately, and how to interpret the results of such an analysis.
Yesterday’s discussion reminded me that I need to read more thoroughly and really think critically about each statement the authors make. This ability to critically evaluate articles is essential in science, but it is also a useful skill for life in general. I think we all have a tendency to be lazy or impatient readers and give statements made in published articles the benefit of the doubt without thoroughly evaluating the claims.
Spring Break is long over. Of course I had plans to catch up on work, but that never happened. Another week has flown by. Last week David gave a lecture on methods for dealing with large trees (with datasets much larger than the ones we are using for our projects). Romina explained how to partition and combine (concatenate) our data. On Thursday Romina gave us a tutorial on a program called SATé and then we discussed a paper comparing the program with other methods. It was our first paper discussion, so David brought out his basket filled with tubes containing our names. This method of sampling with replacement to pick the discussion leader filled me with dread last spring in the Biology of Symbiosis course I took with David, but a year later, I’m starting to feel more confident (watch me get picked next week!).
I thought I would mention the textbooks we are using in case anyone is curious. Getting new textbooks is my favorite part of starting a new semester. I’ve always been a book nerd and this part of my life has been completely accepted at Clark. I’ve even convinced a few friends to join goodreads!
So for this course we are using the textbook Tree Thinking: an Introduction to Phylogenetic Biology by David Baum and Stacey Smith. I’m really enjoying this textbook, the writing style is very clear and the examples and quizzes at the end of each chapter are useful. Of course the book can’t cover everything we are discussing in great detail, so supplementary books and articles are used.
The Phylogenetic Handbook provides great detail (often more than you ever wanted to know!) This is a good reference when you need a more comprehensive treatment of a particular topic. One problem is that it is impossible to keep up with rapid advances in the field, so many of the programs we are using are not included in this edition from 2009 and some programs the book mentions are no longer in use.
Phylogenetic Trees Made Easy: A How To Manual provides step by step instruction with screen shots. It doesn’t have much background information, but it is a good reference if you forget how to actually run something with the computer.
Evolutionary Pathways in Nature: A Phylogenetic Approach is an optional text recommended to the class. This is a book I wish I had read three or four years ago. Honestly when I started becoming interested in biology I hated phylogenetic trees. They were annoying to stare at and impossible to decipher. I knew they showed evolutionary relationships, but I had no idea the various applications and questions that could be answered using these methods. Now I can look at a tree without panicking. If you can’t this book would be a great place to start. A variety of topics (although disappointingly only one fungal example) illustrate the many applications of phylogenetic. Diverse examples include aposematic coloration in poison dart frogs, male pregnancy in seahorses, web building in spiders, and coral conservation.
This last book isn’t part of the class, but if you are looking for an introductory textbook on fungi I highly recommend The 21st Century Guidebook to Fungi by David Moore, Geoffrey D. Robson, and Anthony P. Trinci. Published in 2011, it covers a broad range of topics including fungal classification, development, cell biology, and genetics, the role of fungi in ecosystems, as symbionts and pathogens, and in biotechnology.
Before I proceed any further with this blog, I want to transition from referring to “Dr. Hibbett” and “Dr. Gazis” to referring to “David” and “Romina.” Of course when meeting a new professor or instructor it is important to respectfully refer to them using their professional title, and depending on the person, this may be the title you continue to use. However, both David and Romina prefer first names in the classroom, so I think for the purposes of this blog using their first names will be more natural.
Last week everyone met with either David or Romina to go over their project ideas. They suggested methods we could use to answer our research questions. Today our written proposals were due. We went around the room talking about our proposals for around five minutes each. Five minutes seems like nothing, but it was long enough to make me nervous. David wanted it to be more of a “casual conversation,” but I had a hard time looking away from my outline. Despite being nerve wracking, it was helpful to talk about our projects. David and Romina offered suggestions, and classmates were able to ask questions, so we got a sense if we were presenting the information clearly. It seemed to go well, and I was happy to go in the beginning of the class so I could actually listen to other people without being worried about my presentation. Those of us in David’s lab are doing projects about fungi, of course. These projects will examine many different fungal groups (more about my project to come!). Some of the other projects topics include: human influenza virus, MC1R (a gene involved in skin and hair color), Nitrate-reducing bacteria, and Banksia a genus of Australian flowering plants. These projects will utilize several different methods which we will discuss in upcoming classes.
Next week we have spring break! This will give me much needed time to catch up on my work and enjoy some time at home.
This semester I will be blogging about one of my courses, BIOL 254 Molecular and Evolutionary Systematics: Assembling the Tree of Life. This course is an upper level biology course co-taught by my faculty advisor Dr. David Hibbett and my other advisor, Dr. Romina Gazis, a Postdoctoral Researcher in the Hibbett lab. This class is part of the Open Tree of Life project which Dr. Gazis is working on and Dr. Hibbett is a Principal Investigator (PI) for. This project involves bringing together published phylogenetic trees into one large phylogeny of all life!
This is my second course taught by more than one instructor, and I’ve found that co-teaching has multiple benefits, including an opportunity for Dr. Gazis to gain teaching experience. There are 10 students in the class, so having two instructors enables each student to get a lot of attention. Very few people miss this class; an absence is immediately apparent at our small conference table. Both instructors are always available to meet with students, and often both read and comment on our homework assignments. The class is made up of graduate students from several biology labs, seniors, a junior, and a sophomore. Several of us are from the Hibbett lab, but we also have students interested in other organisms and applications including plants, animal behavior, microbiology, and bioinformatics.
This course has several exciting aspects which make it a LEEP course. The course has an interdisciplinary focus and emphasizes the diverse applications of phylogenetics. This is a broad field requiring knowledge of genetics, evolution, and even math! Phylogenetic trees are used to infer evolutionary relationships among organisms. The Tree of Life Web project is a great site to explore some of these relationships.
The homework assignments complement classroom lectures and focus on hands-on learning. The techniques we are learning will be applied to independent semester long research projects which will be presented at the end of the course. These topics will be elaborated on in future posts.