Why do it?
Last year many of you (those in phage lab) joined in on a research project to understand the variation in phage genomes. You were given the problem and the tools with which to solve it (though there was still room for creativity within this framework). In future bioinformatics courses (viz., BNFO301: Intro to Bioinformatics and BNFO420: Applications in Bioinformatics) you will define a bioinformatic problem yourself and find or make the appropriate tools. This semester you are offered the prospect of something in between: freedom in conceiving a research project without having to do it.

...but why research? There is a broad consensus that learning is deeper and more persistent when it is done with the whole mind engaged through active inquiry [1, 2]. Learned panels have concluded that research is the way to do this and should be a routine part of the undergraduate experience [3, 4]:

There is an additional benefit for those who choose to develop a research proposal (see below). Every February there's a competition amongst undergraduates for stipends given out by VCU and a separate competition for stipends from the Center for the Study of Biological Complexity. In both cases, undergraduates are asked to submit a proposal concerning the research they hope to do. You will have a proposal ready to go, critiqued and polished, should you wish to try for a stipend.

Even if you don't, you will have gotten a glimpse as to what you could do should you turn your hand to research during your time at VCU, and this is an effective method for achieving the goals of this course [5].

What is it?
Near the beginning of the semester, you will choose between two possibilities:

1. A research proposal
   A justification and presentation of an experiment that has never been performed that you believe will extend our knowledge of how some biological phenomenon works at the molecular level. It will present a phenomenon worthy of our attention and argue that we could make headway in understanding that phenomenon if we knew the answer to a specific bite-sized question amenable to experiment with the currently available tools of molecular biology. Then you will proceed to explain the workings of that experiment, the principles behind any method you propose to use, what results you might obtain (not just the result you want), and what are the implications of those possible results. Most will complete the proposal without ever having set foot in a lab. If you and your mentor strike up an association and you end up working in a lab -- wonderful! -- but that lies outside the scope of this course.
    
2. A translation of an existing research article A rewriting of a published research article into street English comprehensible to someone with a good high school science education. The article will focus on how some biological phenomenon works at the molecular level. Unlike popular science articles and science videos you may have run across, your translation will focus not on the personalities and bottom line conclusions but on the actual observations and experiments that led to them. You will no doubt have to remake figures and tables from the articles to make sense to your target audience and create new figures to explain the principles behind the experiments, but you will not oversimplify them. Here's a justification of the social need for article translations.
   

What topic?
Research is not done in a vacuum. You may have a wonderful idea for a new energy source for interstellar space travel, but if you're the only person who has ever thought about quantum self-annihilation, the chances of doing the crucial experiments are remote. In real life, you extend the boundary of what is known by just a bit, in an environment where others are exerting themselves in similar directions, in a group. Never mind the movies, this is how successful science is done. Science is a social activity.

With that in mind, you will choose a topic related to molecular biology that lies within the research interests of a faculty member, probably one at VCU. If you're sufficiently persuasive, this faculty member will serve as a mentor during the process of choosing the specific topic for your proposal or the specific article for your translation and bringing your project to fruition.

Click here to learn more of the process of finding a mentor and here to learn more of the process of writing the proposal.

What is the end result?
If you choose to make a proposal, you will end up with a written document that takes the reader from a big question to the small question you actually propose to answer, followed by a presentation of the method through which you will answer it. If you choose to translate an article, you will end up with a multipage web site that takes the reader through the motivation for the work, justifies each question asked, and presents each experiment in an intelligible fashion. At the end of the semester, a final version of your proposal or translation will be considered by a panel consisting of members of VCU's research community. You will present your work in a short presentation, and then they will have the opportunity to question you as they see fit.

How to get there?
There is no doubt that you will need a semester-long, major sustained effort to reach a successful conclusion. To have any chance of success, you will make multiple intermediate versions of your work, each subjected to scrutiny by your mentor, your colleagues, your TAs, and me. There will be several intermediary points along the way to help you find your way. Finding a mentor and learning how questions are addressed in your mentor's lab will be an important first step. You will also summarize one experiment from a research article, as preparation for your ultimate effort. You will also report on your progress at intermediate stages and give a presentation prior to the final presentation. Click here to learn more about the time course leading to the final proposal/translation.

It will be a lot of fun.

1. Michael J (2006). Where's the evidence that active learning works? Adv Physiol Educ 30:159-167
    
2. Freeman S, Eddy SL, McDonough M, Smith MK, Okoroafor N, Jordt H, Wenderoth MP (2014). Active learning increases student performance in science, engineering, and mathematics. Proc Natl Acad Sci USA 111:8410-8415.
    
3. Boyer Commission on Educating Undergraduates in the Research University (1998). Reinventing Undergraduate Education: A Blueprint for America's Research Universities. Stony Brook, NY.
    
4. American Association for the Advancement of Science (2011). Vision and Change in Undergraduate Biology Education: A Call to Action. (summary) (full report).
    
5. Wiegant F, Scager K, Boonstra J (2011). An undergraduate course to bridge the gap between textbooks and scientific research. CBE Life Sciences Educ 10:83-94.