peer review | Southern Fried Science

Boaty McBoatface triumphs, Narluga ascends, Sharks decline, too many bro-authors, and more! Monday Morning Salvage: June 24, 2019

Posted on June 24, 2019 by Andrew Thaler

Foghorn (A Call to Action!)

In every issue of the Monday Morning Salvage, we try to highlight 2 to 5 papers from the scientific literature. In doing so, we attempt to provide a broad and diverse cross-section of the diversity of people conducting scientific research. However, our priority is in highlighting papers of particular interest to ocean science, and occasionally that means that we end up recommending papers that are exclusively authored by men. A new paper by Salerno and friends highlights the extreme extent to which papers led by men excludes women co-authors.

To do our small part to push back against this phenomenon, we are adopting a new style guide for paper citations. Conventionally, at Southern Fried Science, we use the colloquial “and friends” instead of “et al.” to make paper citations more approachable and less jargon-y. Going forward, in cases where a paper contains only male co-authors, we will instead replace “et al.” with “and some other dudes“.

Flotsam (what we’re obsessed with right now)

It is the hero we deserve. Boaty McBoatface Just Helped Solve a Deep-Sea Mystery.

Boaty McBoatface, fresh off of doing science. Photo: NOC

Shark populations in NC coastal waters are down, despite uninformed opinions based on absolutely nothing.
It may be formed from rock and plastic, but ‘plasticrust’ is by far the most Metal name they could have come up with. A Strange New Blend of Rock and Plastic Is Forming on a Portuguese Island.

“Plasticrust” sticking to rocks on the shores of Madeira. Photo: Ignacio Gestoso

How goats got the bends, a new ship for VIMS, a new deep-sea submersible for all of us, our looming destruction, and more! Monday Morning Salvage: October 15, 2018.

Posted on October 15, 2018 by Andrew Thaler

Foghorn (A Call to Action!)

It ain’t going to be easy, but it isn’t over yet and none of us have earned the right to quit. What genuine, no-bullshit ambition on climate change would look like.

Flotsam (what we’re obsessed with right now)

Goats are magnificent. We don’t deserve goats. The Dark Story of How Scientists Used Goats to Solve the Bends.

Bends in the foreleg of a goat after experiments performed by physiologist John S. Haldane, published in the Journal of Hygiene Vol. 8, 1908.

There’s a new full-ocean capable submarine in town, and for $50 million, you could buy it! Discovery and Science Channel to Document the Five Deeps Expedition in Limited Series.

Photo courtesy Discovery.

Frisky Anglerfish, Persistent Aquatic Living Sensors, Make for the Planet Borneo, Sea Cucumber Mafia, and more! Monday Morning Salvage: March 26, 2018

Posted on March 26, 2018 by Andrew Thaler

Foghorn (A Call to Action!)

Sign up for Make for the Planet Borneo and help push forward the next generation of conservation technology!
Announcing the Con X Tech Prize for Hacking Extinction! Apply for funding to create a working hardware prototype and win up to $20,000 in awards.

Flotsam (what we’re obsessed with right now)

This is a totally ordinary, not at all alarming, call for government bidders on a contract to build “new systems that employ natural or engineered marine organisms as sensor elements to amplify signals related to the presence, movement, and classification of manned or unmanned underwater vehicles.” They even adorably call these Persistent Aquatic Living Sensors PALS. Normal!
Here’s a video of anglerfish mating, because anglerfish are beauty.

This week in science and conservation slowly, awkwardly coming to terms with their racist history: For Decades, Our Coverage Was Racist. To Rise Above Our Past, We Must Acknowledge It and Environmentalism’s Racist History.
Scientists in Survival Mode: After a disastrous hurricane season, scientists in the storms’ pathways struggle to return to work.

The Levee (A featured project that emerged from Oceandotcomm)

Marine lab has ‘front row seat’ to Louisiana coastal loss.

Photo by Melissa Miller

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

Posted on August 23, 2016 by Chris Parsons

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.

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

Posted on March 5, 2016 by Andrew Thaler

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. Read More

How I prepare a peer review

Posted on February 11, 2016 by Andrew Thaler

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. Read More

Is peer-review best left to academic journals?

Posted on July 21, 2015 by Amy Freitag

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. Read More

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

Posted on March 6, 2015 by David Shiffman

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.

Shades of Gray: Gray literature, peer-review, and the struggle for data in fisheries management

Posted on November 15, 2010 by Andrew Thaler

The dissemination of science follows the conventional route of rigorous peer-review followed by publication in an accredited scientific journal. This process has been the standard foundation from which the general public can trust that the science is, at the very least, valid and honest. Of course this system is not without its flaws. Scientific papers of questionable authority, dishonest methodology, or simply flawed design frequently make it through the gates of peer-review. Politically charged papers possess strong biases and many high impact journals favor sexy or controversial topics.

Beyond the conventional route of peer-review, there exist a vast accumulation of gray literature – conference reports, technical notes, institutional papers, various articles written for specific entities that enter into general circulation without the filter of peer-review. Much of gray literature is valid, robust science, but much of it is not. The challenge is that sometimes gray literature is the only science available.

Scientia Pro Publica #30

Posted on May 17, 2010 by David Shiffman

I am proud to host the latest edition of Scientia Pro Publica, a blog carnival that celebrates that best science, medicine, and nature writing aimed at the general public.

Biology/Evolution/Conservation

Melissa from Out Walking the Dog invites you to celebrate Bird Neck Appreciation Day. Learn how and why bird necks are so flexible and diverse.

Wendy from Bio Loser explains how fish react to their own reflection.

Sarah from Surprising Science shows us how we can find live online video of bird nests. It’s almost as cute as Puppy Cam.

Jeremy from Agricultural Diversity Weblog talks about genetically modified crops and how many people misunderstand them.

Madhu from Reconciliation Ecology tells an amusing story about how birds can be elitist. Certain bird species prefer to spend their time in more affluent parts of cities.

Medicine

Dr. Shock summarizes everything you always wanted to know about body piercings and psychopathology. Find out if your kid’s new piercing is indicative of other high risk behaviors.

Christie helps us to understand the role of insulin at Nutrition Wonderland.

Akshat from Contemplation asks if fish oil supplements are any good for children.

Science and Society

Warren from Generally Thinking reminds us all to be skeptical of how science is reported by the news media. A careless fact-checker or a changed word can alter the entire meaning of a scientific study.

Mike from Theoretically Speaking believes that involving non-specialists will improve the peer review process. As more and more science becomes interdisciplinary, I hope his idea catches on.

That’s all for now.

The next edition will be hosted by Andrew at 360 Degree Skeptic. To submit a blog post, use this handy online form.

~WhySharksMatter