This page lists relevant papers and links that I feel offer interesting or insightful tips, critiques, or thoughts on various aspects of scientific endeavor. Some of the links will take you to additional pages that I have created to address common questions or to offer thoughts on various matters. Where I have provided a link highlighting a paper, the link will sometimes take you to a paper hosted at someone else's site. If you notice that a link has broken or that someone no longer hosts the paper I have linked to, please notify me by email so that I can update the list.
- Finding the Right Advisor [internal link]
- Some Modest Advice for Graduate Students [link to external PDF] - This manuscript written by Stearns provides invaluable (but perhaps cynical) advice for graduate students. It is recommended that you read this before entering graduate school AND after entering.
- Some Acynical Advice for Graduate Students [link to external PDF] - A response to the above manuscript. This one, written by Ray Huey, offers additional practical advice to graduate students from a different perspective.
- So Long and Thanks for the PhD! [external link] - A webpage with information written by a recent computer science PhD listing everything he wished he knew before he started graduate school. He also touches on the post-graduation job search.
- Feeling Awkward at National Conferences [external link] - Regardless of what any accomplished scientists tells you, this is an experience that most people have been through.
- How to Be a Good Graduate Student [external link] - Originally prompted by thoughts on how to encourage and retain women students in graduate programs, this author provides overall advice on how to thrive in graduate school.
- Professional Tips for PhD Students [external link] - A list of many helpful links.
- Online PhD [external link] - A site with lots of information about what is involved in completing a PhD.
- I did a PhD and did NOT go mad [external link] - Another great webpage with additional information for graduate students.
- Additional resources [external link] - A webpage that contains links to much additional information for graduate students.
- Chaos in the Brickyard [link to external PDF] - A somewhat antiquated allegory about the perils of "modern science". Originally published in Science in 1963, it is probably still true today. It was clearly written by a pessimist.
- Why Ecology Lags Behind Biology [link to external PDF] - This author implores ecologists to think more deeply about the questions we ask, why we ask them, and how we should try to answer them in their research.
- One Hundred Questions of Importance to the Conservation of Global Biological Diversity [link to external PDF] - This recent publication (2009) in the journal Conservation Biology is a worthy read for any conservation biologist. A diverse group of scientists and practicioners assembled a very comprehensive list of questions that if answered should have a tremendous impact on conservation practice and policy.
- Strong Inference [link to external PDF] - This manuscript by Platt was published in Science in 1964. It has become an important classic and offers useful insights and perspectives about the nature of science and how we perform research and test hypotheses. This manuscript could also be listed below in the section about "hypothesis testing".
- The Ecologist as Zen Master [internally hosted PDF] - An interesting manuscript from 1973 that offers thoughts on the inherent "nonduality" of ecology. Perhaps a little philosophical, but certainly a valid read for anyone interested in environmental issues or ecology. Considering the year in which this was published, I have to wonder if the author wasn't trying to capitalize on the popular book Zen and the Art of Motorcycle Maintenence by Robert Pirsig.
- The Conservation Biologist as Zen Student [internally hosted PDF] - A recent followup to the above manuscript. This article published in Conservation Biology in 1997 extends the earlier manuscript to remind us how interconnected we are to our natural resources.
"Writing is easy; all you do is stare at a blank page until drops of blood come out of your forehead." - Anonymous
"It's not science until it's published." - Anonymous
- Who Belongs on the Author Line? [internal link] - Criteria to ease the process of determining who should be included as a coauthor on a scientific manuscript.
- Scientific Writing and Publishing Results [external link to PDF] - A very comprehensive guide to writing and publishing scientific research. Written and hosted by the Tropical Biology Association.
- Sounder Thinking Through Clearer Writing [internally hosted PDF] - Yet another classic publication from Science in the 1960s. This article by Woodford in 1967 provides one of the earliest and most broadly applicable critiques of science writing. Most of the points are still valid today.
- A Plea For Scholarly Writing [internally hosted PDF] - A 2008 paper by the editor of Integrative and Comparative Biology. This article offers additional suggestions to improve manuscript clarity.
- Where to Publish [external link to PDF] - This informative guide was originally written by Kareiva and Yuan-Farrell in 2005. It provides a very comprehensive look at the status, scope, and impressions of conservation journals at the time of the writing. Although it could be updated to reflect the rapid growth in the impact of many conservation journals, it still provides a valuable look at them as scientists think about where to publish their conservation and ecology research.
- Link to Many Additional Sources [external link] - A page with many, many resources on writing and presenting scientific research.
- How To Write a Scientific Paper [internally hosted PDF] - A humorous look at the sad reality of how most articles are written today.
"Biology should dictate the use of statistics; the use of statistics should never dictate the biology." - Anonymous
Traditional hypothesis testing in many science disciplines follows a standard model of formulating and testing an alternative hypothesis compared against its null hypothesis counterpart. With the development of advanced processors in the past 20 years (i.e. modern computers), many scientists have seized the opportunity to use information theoretic approaches and/or Akaike's Information Criterion to evaluate support among multiple competing hypotheses. What follows is a list of several editorial and theory papers offering insights into the advantages and drawbacks of various hypothesis-testing approaches, as well as potential statistical issues that must be kept in mind in traditional hypothesis testing analyses. I also list a few entreaties from various editors and scientists suggesting to end our fascination with statistics in favor of paying more attention to the biology or ecology we are attempting to quantify.
- Pseudoreplication and the Design of Ecological Field Experiments [external link to PDF] - This classic paper by Hurlbert from 1984 provides the first real criticism of a recurring problem in the design and analysis of field experiments using frequentist statistical methods. This paper alone is probably most responsible for coining the term "pseudoreplication" as well as "demonic intrusion" (a word used far too infrequently). Sadly, most journal editors have ignored Hurlbert's point that they should "be liberal in accepting good papers that refrain from using inferential statistics when they cannot be validly applied." For more on this theme, see "Are We Sacrificing Biology for Statistics" below.
- Pseudoreplication: A Sine Qua Non for Regional Ecology [external link to PDF] - This important followup paper from 1992 offers a rebuttal of sorts to Hurlbert's classic manuscript above. Hargrove and Pickering point out the value of many field experiments despite difficulties and often the absence of true landscape-level replication.
- Are We Sacrificing Biology for Statistics [link to journal] - Michael Chamberlain, the general editor of Journal of Wildlife Management in 2008, makes the case for a greater emphasis on good biology and sound management research rather than a cult-like over-fascination with statistics and whether or not P-values are small enough. I wish more people acknowledged this problem and heeded his advice when considering manuscripts for publication in scientific journals.
- Statistical Confusion Among Graduate Students: Sickness or Symptom [link to journal] - A short read describing a frequent problem in many graduate programs.
- Suggestions for Presenting the Results of Data Analyses [external link to PDF] - These authors, including Anderson and Burnham, provide useful guidelines for how and when to report P-values and other statistical results in manuscripts.
- Null Hypothesis Testing: Problems, Prevalence, and an Alternative [external link to PDF] - Another of several worthwhile papers from Anderson, Burnham, and others that gives invaluable insights on the use of information theoretic approaches based on likelihood theory and its application to the evaluation of competing hypotheses in science.
- Avoiding Pitfalls When Using Information-Theoretic Methods [external link to PDF] - More from Anderson and Burnham.
- Concerns About Finding Effects That Are Actually Spurious [external link to PDF] - You guessed it: another from Anderson, Burnham and others.
- On the overreliance on statistics in wildlife studies [external link to PDF]
- The Need to Get Basics Right in Wildlife Field Studies [external link to PDF]
- Rigourous Science: Suggestions on How to Raise the Bar [external link to PDF]