Scientific literature needs discipline – an example from a killer whale life expectancy study

If you let a puppy piddle on the carpet without discipline, it will keep doing it. It will grow into a big dog that destroys your carpeting and rugs and makes your whole house stink.

So it is with scientific literature.


We all know bad papers are out there. When you read them, you’re left scratching your head and wondering, “How on earth did these pass peer-review?” Worse still, there are “ugly” science articles, where the scientific method goes by the wayside and data are cherry-picked, misinterpreted or manipulated to justify a political or ideological agenda or to undermine science that interferes with that agenda.

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This Paper Should Not Have Been Retracted: #HandofGod highlights the worst aspects of science twitter

I really didn’t want to care about this paper, at all.

When news broke Wednesday afternoon that a paper in PLOS One referenced the “Creator” in the abstract, introduction, and discussion, I took a look, read through the methodology and results, asked a few colleagues in that field if there were any methodological problems that would indicate that the actual science was unsound, and concluded it was… fine. Not phenomenal, earth-shattering, or paradigm shifting, but methodologically sound.

Incidentally, publishing based on the soundness of the methodology rather than the ground-breakingness of the research, is one of PLOS ONE’s mandates.

But the paper was awkwardly framed around a few phrases referencing the role of the Creator. This framework didn’t bleed into the methods or results but it was there, and the scientific community noticed. I noted, under the assumption that the authors were inserting creationist language into their paper, that there are numerous papers that try to hang their studies on tenuous frameworks and draw not entirely supportable conclusions, and not just in PLOS. Then I chatted with a few colleagues about it and called it a day.

Here’s the weird thing about Twitter: sometimes even your apathy is newsworthy. Continue reading

How I prepare a peer review

Over the last couple of months the question of how to write a peer review came up quite a few times, and a couple of my colleagues even asked me directly to help them prepare for their first  peer reviews. Preparing solid, critical peer review is an essential component of being a good citizen in the scientific community. I generally do about two for every paper I submit. I thought it might be helpful to provide a brief overview of how I personally prepare a peer review, primarily for marine science and conservation journals geared towards population genetic studies. I’d like to think that this advice is broadly applicable to any scientific peer review.

Step 1.  Read the paper. It might seem silly to start with this but a lot of people dive into their peer reviews before they’ve even read the submitted paper in its entirety. You start thinking about how you’ll review it as soon as you get a request from the editor with the title and authors. When you get a paper to review, you immediately start reading it with a critical eye. Think about when you  read a paper for pleasure or because you are interested in the content. You’re generally not looking for the fine details or nitpicking word choice, you’re looking for the ideas in the paper. You’re trying to understand what the paper is about and you’re trying to understand what the authors concluded with paper. So before you even begin with your peer review just read the paper as if it were any of a dozen other scientific papers that slide across your desk every week..

Step 2. Write down what you think the paper is about. Do this in broad terms, not so much focused on the methodology but rather the ideas behind the methodology, the motivation for the study, the questions the authors want to answer. Use this as a framework to hang the rest of your review on because you’re not just looking for technical precision but to make sure that the study itself is relevant to the broader themes of the paper. Continue reading

Is peer-review best left to academic journals?

If you have ever dealt with scientific data, you’ve probably encountered one of the shadier sides of science: academic publishing. While they’ve stood, in some cases, for centuries, as the official record of scientific advancement safeguarded under the watchful eye of peers, modern journals live in a modern world. Millions of words have already been spilled on the subject, so that’s not what this article is about. Instead, I’m left asking whether academic publishing is the only means of getting the stamp of peer-review these days?

The reasons leading me to ask this question are many, but primarily through working in a management arena lately. One example, in particular, highlighted many of the disconnects between the need for verified scientific data and the incentives of journals. This moment was at a Chesapeake Bay Program Sustainable Fisheries Goal Implementation Team meeting (for those of you not in the Chesapeake region, that’s a consortium of regional fisheries managers), where a room full of decision-makers needed a verified stock assessment of blue crabs to move forward with their management planning. Peer-review is the time-tested, well-understood, and arguably easiest means of verifying data. Continue reading

How to write and publish a scientific paper in the field of marine ecology and conservation

Author’s note: The following blog post is an adaptation of a professional development training workshop that I gave to our lab’s interns. It is intended to serve as an introductory guide for advanced undergraduate and beginning graduate students who have never published a scientific paper before. It’s a combination of advice I’ve received from teachers, colleagues, and training workshops. This advice has worked well for me personally in the fields of marine ecology and conservation; as of this writing I have 14 published papers and have served as a peer reviewer for 26 different journals. However, there are lots of other strategies out there, and you should seek them out and figure out what works best for you, particularly if you’re in a radically different academic discipline. 

Part 1: What is a scientific paper?

The process of writing and publishing peer-reviewed scientific papers can be confusing and intimidating to beginning students, who may know that these papers are professionally important but not how to create their own. Different in scope, style, and significance from a class term paper or thesis, these papers are formal, technical writeups of a scientific research project or idea. They are written by scientists or technical experts, and peer-reviewed by other scientists or technical experts who (ideally) provide constructive criticism.

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