Lecture 07
Introduction editing
Date: Oct 9, 2024
Peer editing¶
As you read and review your peer’s introduction, focus on the following key areas. Provide constructive feedback aimed at helping your classmate improve their work. Use these questions and tips as a guide for your review.
Engaging Opening Statement¶
What to Look For:
- Does the introduction start with an engaging, clear statement that captures attention?
- Does it present a specific trend, challenge, or recent advancement that directly relates to the main topic of the paper?
Common Mistakes:
- Opening with broad or overly general statements like “Proteins are important for life.”
- Using vague language that doesn't engage the reader.
Example
Your opening statement is a little too broad. Try focusing on a recent breakthrough in your topic to make it more engaging. For example, you could highlight a new finding in molecular dynamics.
Background Funnel¶
What to Look For:
- Does the introduction flow logically from general information about the topic to a more specific focus?
- Is there enough context provided about the field to set the stage for the rest of the article?
- Does the background explain why the topic is important in the broader context of biology or drug discovery?
Common Mistakes:
- Jumping into specific details too quickly without providing enough background.
- Being overly vague and not explaining the significance of the topic.
Example
You need more context about why molecular docking is important in drug discovery before diving into specific limitations. Try adding a sentence that explains its role in finding potential drug targets.
Identifying Gaps¶
What to Look For:
- Does the introduction clearly identify gaps or challenges in current research?
- Are the gaps specific and relevant to the paper’s main argument?
Common Mistakes:
- Not clearly identifying gaps, or only vaguely mentioning that “there are limitations.”
- Failing to explain why these gaps are important.
Example
You mention that there are limitations in AlphaFold, but it’s not clear what they are. Try specifying exactly what AlphaFold struggles with, like disordered regions or large protein complexes.
Presenting the Thesis/Argument¶
What to Look For:
- Is the main thesis or argument of the paper clearly stated?
- Does the thesis provide a specific, debatable perspective that the paper will explore?
Common Mistakes:
- Having an unclear or vague thesis.
- Stating that the paper will “discuss” or “explain” the topic without providing an argument or perspective.
Example
Your thesis is a bit unclear. Instead of just saying ‘this paper will explore protein structure prediction methods,’ try something like ‘this paper argues that integrating deep learning with ab initio models offers a more accurate approach to protein structure prediction.'
Article Structure Outline¶
What to Look For:
- Does the introduction provide a brief outline of the article?
- Does the outline logically follow from the thesis and give the reader a clear sense of what’s coming next?
Common Mistakes:
- Missing the outline entirely or being vague about what the rest of the paper will cover.
Example
Your introduction could benefit from a brief outline of the structure. For example, mention that the paper will first explore AlphaFold, then compare it to ab initio methods, and finally propose a hybrid approach.
Clarity and Writing Style¶
What to Look For:
- Is the writing clear and easy to understand?
- Does the introduction avoid jargon or explain technical terms when necessary?
- Are sentences concise and to the point?
Common Mistakes:
- Overusing jargon or writing overly complex sentences.
- Having sentences that are too long or confusing.
Example
Some sentences are a bit hard to follow, especially the one about molecular dynamics. Try simplifying it by breaking it into two shorter sentences.
Use of Literature and Citations¶
What to Look For:
- Are relevant studies and seminal papers cited to provide background and support for the thesis?
- Are citations formatted correctly (APA style)?
Common Mistakes:
- Failing to include citations or using too few.
- Incorrect citation format (e.g., missing information, inconsistent formatting).
Example
You need more citations to support your background section. Try referencing a recent study that discusses the limitations of molecular docking.
Length¶
What to Look For:
- Is the introduction within the required length (around 500-750 words)?
- Does it avoid going into too much detail that should be saved for later sections of the paper?
Common Mistakes:
- Writing an introduction that is too long or too short.
- Including too many technical details that belong in the main body of the article.
Example
Your introduction is a bit too detailed in the discussion of MD simulations. Try saving some of this for later and keeping the introduction more focused on setting up the main argument.
General Improvements¶
What to Look For:
- Does the introduction as a whole flow logically and set up the rest of the paper?
- Are there any areas where the writing could be more concise or more clearly explained?
Common Mistakes:
- Disorganized flow between paragraphs or ideas.
- Being too wordy or using unclear explanations.
Example
I think the transition between your background section and your thesis could be smoother. Try revising the last sentence of the background to lead directly into your argument.
Additional Tips for Peer Review:¶
- Be constructive and respectful: Focus on how your feedback can help your peer improve. Avoid vague or negative comments like “This doesn’t make sense.” Instead, offer suggestions for improvement, like “This section could be clearer if you explained how molecular docking leads to faster drug discovery.”
- Give specific examples: Instead of saying “This is unclear,” explain why it’s unclear and suggest how to make it better.
- Balance praise with critique: Highlight what your peer has done well in addition to offering suggestions for improvement.
- Use track changes and comments: If you’re working digitally, use track changes to show edits and leave comments where something could be revised. If you’re working on paper, use clear markings and notes.
Alex's general feedback¶
Based on my review of the introductions submitted by the class, here is some general feedback that I believe will be helpful for everyone as they revise their drafts and engage in peer review:
Engagement with the Topic:
Many of you have done a good job introducing your topics and explaining the importance of your perspective within computational biology. However, several drafts could benefit from a more compelling opening statement that immediately engages the reader. Instead of broad or overly general statements, try to highlight a specific trend, challenge, or recent advancement in your field that directly connects to your main argument. This will set a strong tone for the rest of your paper.
Background Funnel:
The background section should smoothly transition from broader concepts to the specific focus of your paper. While most of you provide a good context, some drafts jump too quickly into specifics without adequately setting the stage. Make sure your background flows logically by introducing general concepts first, then gradually narrowing the focus to your particular area of interest.
Identifying Gaps:
One common area for improvement is the section identifying current gaps in research. This part of the introduction is crucial for justifying why your perspective is necessary. Some drafts touch on challenges but don't clearly articulate what key gaps your article will address. Focus on identifying one or two significant gaps in the literature or research landscape and briefly hint at how your perspective will contribute to filling them.
Introducing Your Perspective:
Several of you did well in introducing your main argument, but in some cases, the thesis statement could be clearer or more specific. Make sure to clearly state your unique perspective or the central argument of your paper. This statement should be debatable, setting the stage for the arguments you'll develop later. It’s not enough to merely summarize what’s known; instead, make sure to explain how your perspective adds to the conversation or offers a new take on the issue.
Use of Literature:
The literature cited in many drafts is generally relevant, but in some cases, it’s either too sparse or too dense. Try to strike a balance between citing foundational studies that set the stage for your argument and recent breakthroughs that are directly relevant to your perspective. Ensure that your citations are purposeful, helping to build the case for your perspective.
Writing Quality and Clarity:
Overall, the writing quality is strong, but some drafts could benefit from additional clarity and conciseness. Avoid overly technical jargon unless it is necessary and be mindful of your audience, which consists of your peers who may not be familiar with every detail of your topic. Keep your sentences clear and to the point.
Structure Outline:
In many drafts, the outline of the article structure is missing or only briefly mentioned. It’s important to provide a clear roadmap for your readers so they know what to expect. Spend 1–2 sentences briefly outlining the main sections of your article to help guide your reader through your argument.
Balance of Depth and Breadth:
Be cautious of going too in-depth in the introduction. The goal is to provide a snapshot of the key ideas without delving into the specifics of your argument or findings. The introduction should set the stage without overwhelming the reader with too much detail.
Clarity of Purpose and Opening Statements:
Many students introduced their topics clearly, but some drafts could benefit from a more engaging opening that immediately draws the reader into the significance of the topic. Rather than starting with broad statements, consider highlighting a recent trend or challenge to capture attention. For example, opening with a recent breakthrough in molecular dynamics or a key limitation in computational drug discovery can be more effective than a general introduction.
General Writing Tips
- Avoid long, complex sentences and unnecessary jargon unless needed. Aim for clarity.
- The introduction should not dive too deeply into technical details. Save those for the main body of the paper.
- Each paragraph should lead naturally to the next, maintaining a coherent structure from beginning to end.