Academic life – Page 4 – Southern Fried Science

This Paper Should Not Have Been Retracted: #HandofGod highlights the worst aspects of science twitter

March 5, 2016March 5, 2016 Andrew Thaler 6 Comments

Academic life

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.

How I prepare a peer review

February 11, 2016February 10, 2016 Andrew Thaler

Academic life

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.

The power of coffee … a comfy sofa and a bit of a chinwag

December 31, 2015 Chris Parsons

Academic life

When I was an undergraduate I walked into the coffee area of our zoology building and was informed that “some of the most important papers on animal behavior were written here”. It was a somewhat ugly coffee area in an ugly concrete building, with vinyl covered plywood tables and bright orange upholstered bucket chairs that looked like they had escaped from Austin Power’s 1960s love pad. The coffee wasn’t even good, in fact the zoologists were highly envious of the botany department who had a tea trolley with excellent tea and chocolate covered cookies, but I digress… The coffee area was the place to be as that was where everyone in the department congregated, talked about what they were reading or working on, and most importantly, brain-stormed ideas. Sure there was a certain amount of procrastination going on, with faculty avoiding having to go back to grading, hiding from sheets of data that had to be entered onto excel spread sheets, or balking at yet another hundred samples to analyze back in the labs. But the collegiality that there was in that coffee area: with undergrads chatting to the “silverbacks” of the zoology faculty, sharing their innovative ideas, and getting mentoring advice in return; or scientists from different disciplines advising on different or new techniques to colleagues that had encountered a brick wall in their research progress; was quite frankly more valuable than many lectures, and worth the price of a disgusting cup of instant coffee. Our department was not alone. At the famous big science facility CERN, home of the large hadron collider, there are whiteboards in the lunchrooms because when the scientists there get together they can’t but help brainstorm ideas, and this is encouraged as some of these lunch time collaborations have yielded important scientific fruit.

It’s a truth universally acknowledged that conferences are a necessity for the growth of an academic. They give you a chance to share your ideas with other academics to receive support, or possibly criticism, so that you can strengthen and refine your analysis and your interpretation of your data. They are important events to find out the methods and results of peers in your field, information that could be incorporated into your own studies. Informal places where you can get advice, share ideas and develop research and writing partnerships. Rare is the conference where I don’t come home with a note book full of contacts to email, studies to cite and methods to try out. You can travel around the world to find a venue to discuss and debate with your peers. But isn’t it ironic that there are often few of such places within a university?

Scientific Stockholm Syndrome

December 11, 2015December 11, 2015 Chris Parsons 1 Comment

Academic life

In response to unprofessional behavior by another scientist, a marine science colleague recently stated that they were so used to bad behavior in their area of research that they just accepted it as normal, and that they basically had “Stockholm syndrome”. Sadly this all too common, that unprofessional behavior in some fields and areas is so common (whether it be academic bullying and hazing, plagiarizing and stealing ideas and data, or sexism and harassment see The Dark Side of Academia) that it becomes the accepted norm. This is particularly prevalent in fields that are small and insular.

Stockholm, despite its associated syndrome, is really quite lovely

The Yellow Admirals of Academia

October 31, 2015October 31, 2015 Chris Parsons 1 Comment

Academic life

As a fan of nautical writers CS Forester and Patrick O’Brian* I do like reading the rollocking adventures of the intrepid Captains of His Majesty’s Navy avasting their mainsails and hoisting their topgallants against the scourge of Emperor Napoleon’s forces. In these books I discovered a new nautical term, a “Yellow Admiral”.

When naval captains of the 18^th/19^th Century achieved seniority they were promoted to the ranks of admiral. There was no promotion on merit, it was simply a case of surviving until a position opened up. There were three ranks of Admiral (rear Admiral, Vice Admiral and Full Admiral) for each of the main naval forced: the Red, White and Blue squadrons, which were patrolling key strategic areas of the world’s oceans. However, there were some captains that you really did not want to be in charge of a single ship, let alone a naval battle group. These individuals were dubbed “Yellow Admirals” and were given administrative positions on land. As a result, a lot of naval logistics in the Napoleonic wars was mired by incompetence, ego-driven power plays, and financial irregularities. We have something similar in academia: instead we don’t call them Yellow Admirals, we call them Associate Deans.