CHEM 260: Concepts of Biochemistry

The research lifecycles has many ebbs and flows. A topic might gain a lot of scholarly attention for a time, fade out of popularity, then might be revived by a team of researchers several decades later.  This leaves us with an interesting twofold challenge: 

1. Discovering what research was conducted, either in the past or in the present
2. If limited (or no) research has been conducted, then how do modifications to the enzyme affect structures, generally speaking. 

In short, you will do your best to find relevant information sources, but it is okay to come up "empty handed." Not finding many (or any) sources still provides information about your topic-- namely where there is a gap in the literature. 

If this feels too abstract consider this allegorical example: Imagine searching for information like looking at an optical illusion. If you head into research expecting to see one thing, and one thing only, you might miss out on other potential revelations that are more subtle or hidden. For example, if you are told that this image is a rabbit, you will likely struggle to see the duck. Likewise, if you are only looking for scholarly, peer-reviewed sources, you might miss out on other helpful materials. 

We are going to use the PDF below to build a holistic research roadmap for the beginning stages of your research project. Writing things down on paper can go a long way in helping you to develop your research! 

In class, we are going to discuss the following. If you miss the in-class, librarian led workshop, see a peer for notes, or reach out to Prof. Shenk. She is happy to provide a 1-on-1 session for you. 

• Identifying your research topic 
• Different source types and their uses 
• Use reference sources to collect background information 
  • UniProt, BRENDA, etc.
• Take what you have learned from reference sources to conduct better database searches 
• Use the Libraries Databases to find relevant resources 
• Research is a reflective process, so continually update your strategy in order to receive the best results

As you read the scholarly literature and begin to make connections between authors (i.e. you enter the conversation more deeply), you will have to synthesize the literature. Which authors are important? What are the key concepts? Is this an outlying and/or unsubstantiated perspective? You will begin developing the themes present across time and across multiple authors. 

One tool to help you visualize this is Research Rabbit. Research rabbit can help you see how ideas have developed in regard to a particular topic. 

When you find one helpful article, this might provide other helpful leads. Look to an article's reference section to see if there are older articles that might be beneficial to you. You can search forward in time by limiting your database searches to a specific date range. 

Forward Citation Search: A search to find all of the articles (newer resources) that cite back to a specific article (older resource). This search looks forward in time to see how this article contributed to the scholarly conversation. Read: It's been in the room a long time! 

Backward Citation Search: A search to find all of the cited references in an article. This search looks backwards in time to see what informed the author's writing, at the moment in time that the research was being conducted. 

Middle Citation Search: A combination of forward and backwards searching. This is valuable when you are doing research that uses resources published in "middle years." For example, if you found a stellar paper from 2013, you will need to look backwards and forwards in time.

Author Citation Search: A search to find articles by an author or group of authors.  

For these types of searches, the Scopus database is a great option. In Scopus, you can customize your searches to be forward or backward in time. 

Finding information is fun, but it is also overwhelming. You might have fallen into a research rabbit hole if:

• You are not sure how the papers that you are finding are connected. Not even a little bit. 
• You have a lot of information and you don't know where to start. Or stop. 
• You feel that your searches are providing the same resources over and over again. 

These are all good signs to take a break from researching and to start evaluating the resources that you have collected. Start by reading the abstract for each article. If you feel that the abstract is helpful, keep the document for a more detailed review. If potentially helpful, set the document aside for a second read at another time. If the abstract makes no sense and you have no idea how it might be helpful, it likely needs to be deleted. Don't waste your time on unhelpful resources! Move on to more promising leads.

Annotated bibliographies are helpful research tools. Creating an annotated bibliography allows you to begin synthesizing your resources into a cogent narrative. As you read your articles consider the following: 

• Take notes while reading. Writing out a few lines at the bottom of each page will help you to stay active and engaged while reading dense scientific sources.
• Draw your ideas together at the end of each article. Gather your thoughts about the article, and write a few sentences summarizing the article's main themes and contributions. 
• Move beyond summary. After gathering the article's ideas, how can you see this fitting into YOUR research? Add your perspective to your overall summary. 

When it comes time to write up a longer research report, your annotated bibliography will provide the launch point for your work.