Scientific Writing and Publication Processes

The Writing, Revision, and Submission Process

• Revision and Emotional Attachment:

  • Authors often develop a sentimental attachment to specific words and paragraphs crafted over long periods.
  • Revision often requires removing sections that do not contribute to the paper, even if they were difficult to write.
  • The T-Shirt Analogy: Removing sections of a paper is like putting a special t-shirt you have kept for sentimental reasons into a goodwill pile. Once it is gone, you might occasionally think of it, but generally, you do not miss it, and the final product is better as a result.
  • Draft Evolution: The final draft of a paper often bears very little resemblance to the first draft due to the extent of the revision process.

• Submitting to a Journal:

  • The Cover Letter: The primary purpose of the cover letter is to convince the editor that the paper should be sent to peer review.
  • Content of the Letter: It should act as a pitch, highlighting that the paper is original, important, and suitable for that specific journal. It should not be a simple copy-paste of the abstract.
  • Formatting and Guidelines: You must adhere to specific journal guidelines. Some journals are relaxing formatting for initial submissions, but others remain extremely strict.
  • Example of Strict Guidelines: The Journal of Wildlife Management maintains an author guideline document that is approximately $70$ pages long.

The Peer Review and Editorial Decision Process

• Editorial Outcomes:

  • Upon submission, an editor will either reject the paper without review or send it out for peer review.
  • Rejection without Review: Higher-impact journals are more likely to reject papers immediately. This is often preferable to a rejection after a long review period (e.g., four months), as an editorial rejection typically occurs within a week or two, allowing the author to move on quickly.

• Types of Review:

  • Single-blind Review: The reviewers know the names of the authors, but the authors do not known the names of the reviewers. This is the convention in the wildlife field.
  • Double-blind Review: Both the reviewers and authors remain anonymous to each other.
  • Rationales for Single-blind: Some argue it is hard to maintain anonymity because specific labs research specific topics. Others suggest it allows reviewers to verify if the research was already published or to check the author's previous work, though these rationales are often debated.

• Decision Levels:

  • Decisions generally come after several months.
  • Options include: Rejection, Major Revisions, or Minor Revisions.
  • Reject with Invitation to Resubmit: This is often equivalent to a "major revisions" decision but is used by journals to "game" their response time metrics. By rejecting and asking for a resubmission, the journal resets the clock, allowing them to advertise a faster total time from official submission to publication.

• Finalization Steps:

  • Point-by-Point Response: When resubmitting, authors must provide a letter addressing every single comment from the reviewers. Satisfying the reviewers in this letter is crucial for acceptance.
  • Post-Acceptance: The manuscript goes through copy editing and proofs. Authors must review the proofs carefully.
  • Fees: Publication fees vary. Open access fees can be $3,000$ or more. Some universities, such as the University of Washington (UW), have agreements to cover these fees for their researchers.

Philosophical Outlook on Rejection

• The Skiing Analogy: Rejection is a standard part of being a scientist. Just as a skier who never falls may not be pushing themselves hard enough, a scientist who is never rejected may be aiming for journals that are too low in impact.
• Targeting High Impact: Aiming for high-impact journals is encouraged because it ensures the research reaches a wider audience.

Questions & Discussion

• Quiz: Most Dangerous Animals:
  • Question: Which of these animals (dogs, snakes, crocodiles, hippos) kills the most humans annually?
  • Snakes: The correct answer. They kill approximately $50,000$ people per year worldwide. Most of these deaths occur in the tropics. In the Eastern US, notable species include diamondbacks and water moccasins. In Washington, the only venomous species is the rattlesnake.
  • Dogs: Kill approximately $25,000$ people per year.
  • Crocodiles: Kill approximately $1,000$ people per year.
  • Hippos: Kill approximately $500$ people per year.
  • US Context: Deer are likely the most dangerous wildlife in the US if vehicle collisions are counted.

General Format of a Scientific Paper (IMRAD)

• Standard Components: Most journals use the IMRAD format: Introduction, Methods, Results, and Discussion.
• Short Formats: High-impact journals like Science, Nature, and PNAS use a condensed format where sections are not explicitly broken up, and methods may be placed at the end or in supplementary materials.
• Paper Length and Citations: Research indicates a negative correlation between paper/title length and citation frequency—shorter papers with shorter titles tend to be cited more often.
• The Abstract: A summary of the entire paper, typically limited to a specific word count (e.g., $200$ words for certain assignments).
• Acknowledgments: Used for people who helped but do not qualify as co-authors, such as paid field technicians.
• Co-authorship Ethics: To be a co-author, an individual must typically contribute more than one thing (e.g., they cannot just provide funding or just collect data; they must also help with writing, editing, or conceptualizing).
• Visuals: While traditional printing required separate figure legends and tables at the end of the draft, modern online publishing allows (and reviewers prefer) tables and figures to be embedded within the text at appropriate places.
• Supplemental Materials: Authors can provide raw data (e.g., Excel files or R Markdown files) as appendices to aid in future research.

Strategy for the Introduction Section

• The Funnel Shape: The introduction should start broad and move toward a narrow focus. It should not fluctuate between broad and narrow topics.
• Content Sequence:
  1. General Question: Address broad dynamics (e.g., predator-prey relationships, urbanization impacts).
  2. State of Knowledge: Summarize what is currently known in the field.
  3. Knowledge Gap: Identify the specific justification for why the study was needed.
  4. Objective: State the specific goal of the study (integrated into the text, no separate heading).
  5. Study System/Approach: Briefly describe the study species and general methods (e.g., camera trapping, echolocation detectors).
  6. Hypotheses and Predictions: These must follow logically from the provided background information.
• Length: For a 10-page paper, the introduction might only be $3$ to $4$ paragraphs.

Strategy for the Discussion Section

• Interpretation Over Restatement: A common mistake is to simply repeat the results. The discussion must interpret what the results mean and how they advance the field.
• The First Paragraph: Should focus strictly on the "main take-home message."
• Citations: A good rule of thumb is that every paragraph in the discussion should have at least one citation to relate findings to existing literature, except for the paragraph discussing study limitations.
• Addressing Limitations: Authors should anticipate criticisms and address source bias. It is effective to justify why the findings are still valid despite limitations (e.g., explaining that a bias makes the result "conservative").

Case Study Example: Moonlight and Kangaroo Rats

• Introduction Example:
  • Broad Point: Mammalian nocturnality and the fact that illumination is $3$ orders of magnitude higher on full moon nights than new moon nights.
  • Background: Most studies find small mammals avoid moonlight, but some report increased activity.
  • The Gap: Contradictory results highlight a poor understanding of factors affecting the direction of moonlight effects.
  • Objective: Examining the giant kangaroo rat (Dipodomys ingens), which is endemic to California and federally endangered.
  • Approach: Multi-season, multi-year dataset on trapping success and foraging activity.
  • Prediction: Foraging efficiency and trapping success would decline as moonlight increased, especially in areas with high kit fox abundance.