How I prepare a peer review

Academic lifeFebruary 11, 20160

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. (more…)

Ocean Kickstarter of the Month: Whale Science Double Feature

Natural Science, ScienceFebruary 10, 20160

whale1Comprehensive Conservation of Southern Resident Killer Whales in the Modern Ocean

Southern Resident Killer Whales are endangered; only 85 remain. In today’s modern ocean they face many threats simultaneously. A holistic approach to addressing the cumulative impacts of all threats is needed. However, data are sparse, making it difficult to identify which threat(s) is causing the most harm. We are developing a new, comprehensive way to assess threats by having experts fill data gaps. With your help, we can pinpoint which protective actions will help Southern Residents recover.

blowWhale snot and blubber: Tools used to better understand basic physiology in free ranging cetaceans

Baseline indices for steroid hormone levels in humpback whales do not exist, and current monitoring techniques are invasive. Hormones can advise in management, and help in understanding climate change related population shifts. We want to test if whale snot is reliable in collecting sufficient data without disturbing them. By analyzing hormone levels in both blubber and snot, we can establish hormone level baselines from blubber, and see whether less invasive snot-collecting is just as telling.

We haven’t featured Experiment yet in this Ocean Kickstarter series. Experiment is a crowdfunding platform exclusively for scientific research. It helps practicing scientists connect with a community funding base. Because of its narrow focus, Experiment is a little bit different. There are no rewards, instead you get access to updates about the project as it progresses. There is an elevated focus on budget, and, because it’s more akin to a philanthropic donation, rather than an investment, there is often fund-matching from NGOs and larger foundations.

Since last month’s recommendation won’t launch for another 25 years, this month I’ve picked two excellent projects to support.  (more…)

What is it about mercury? Thinking about chemicals in the public discourse

Education, Science, Social ScienceFebruary 9, 20160

All of the revelations about the lead in the water system of Flint, Michigan have made residents and curious neighbors alike  wonder ‘haven’t we solved the lead problem’? There are thousands of well-established scientific studies; the sources and even many of the solutions are well-understood and frequently implemented. Not to say the problem’s gone, but we’ve wrapped are heads around it. So how is it possible that a new lead problem has surprisingly reared its ugly head? And more importantly, what does that mean for exposure to chemicals for which we’ve barely scratched the scientific surface?

The world of fisheries has its analog – mercury. We’ve all heard the recommendations for pregnant women and small children to avoid tilefish, swordfish, mackerel, and shark. We understand that it bioaccumulates in the food chain – and that as humans not exactly at the bottom, we’re susceptible. The dynamics of methylmercury (the poison variety) and elemental mercury are fairly well mapped out and we can identify areas of potential hazard where more methylmercury is likely to be naturally created. We’ve also stopped doing things like spraying mercury-based pesticides and covering our landscape and foodscape with the toxin. Kids have even stopped playing with ‘quicksilver’, it’s been removed from dental fillings and vaccines, and you should get rid of that mercury-based thermometer. Yet, if you scanned most people’s hair (the way we measure these things), there would be mercury present. And there’s still a host of ways they might have been exposed. But the better question is – if there’s still mercury in your body, what else is floating around in your system? And why do we focus on only the best-understood pathway of chemical exposure?

Modern Mercury Exposures (more…)

Playing against the slaughter rule

#OceanOptimism, Blogging, Personal StoriesFebruary 8, 20161

My middle school baseball team was bad. Really bad. Ball droppingly, bat throwingly, pitch ditchingly bad. It was a good inning if four of our batters made it to the plate. A great inning if the other team didn’t rotate through it’s entire line-up, twice. Our MVP was the kid who caught a ball. And if you think this is going to be one of those articles about how one tough player (me?) turned a bunch of scrappy underdogs into winners, it’s not. I played right field, and not particularly well. We lost, often.

In peewee sports, at least in the US, there’s something called a “slaughter rule”. The slaughter rule ends the game if a team is losing by more than a certain number of points. In our case, it took something like a 20 run difference to trigger a slaughter. The slaughter rule exists so that outmatched teams don’t have to slog through 7 innings of a brutal losing streak, racking up demoralizing 112 to zero defeats. Once, we got slaughtered in the first inning.

Were it not for the slaughter rule, I would probably still be out somewhere in right field, wondering if maybe I should sign up for the Latin team next year.

(more…)

Fun Science FRIEDay – Bionic Eye

Fun Science Friday, Science, UncategorizedFebruary 5, 20160

Every year modern medicine brings more and more surprises. It really does seem that the limitations of man’s achievements are solely limited to our creative ability to dream what is possible. This week we bring you the bionic eye. As part of an ongoing trial at Oxford’s John Radcliffe Hospital surgeons implanted a micro electric chip into a patients eye restoring part of her sight.

Human eye.

Human eye.

(more…)

Making your scientific outreach go further

UncategorizedFebruary 3, 20160

1009103_10151717293838265_589812446_oCatherine Macdonald is the Executive Director of Field School, an interdisciplinary field science training programShe is also a fifth year PhD student at the Abess Center for Ecosystem Science and Policy at the University of Miami, and the Intern Coordinator for the Shark Research and Conservation Program (SRC).

Like a lot of the scientists I know, teaching (outside the classroom) and outreach are a key part of the work I do, and one of the things I love most about my job. This isn’t because scientists accrue big rewards for prioritizing outreach (in the academic tenure system, we can actually pay a pretty high price for spending time on anything other than research/required teaching/publication) but because we want to get people excited about science and care a lot about the subjects we study.

Unfortunately, we aren’t always maximizing our positive impacts on students or citizen scientists who engage with our research—maybe because we aren’t familiar enough with the vast and labyrinthine social science literature on what works in education.* (I wish I had a dollar for every time a natural scientist, in talking to me about education or outreach, has said “if only someone would study this…” without being aware that education researchers have been studying it, in some cases for decades.)

This list is in no way comprehensive, but distills some key points I’ve come across that have influenced the way I teach and interact with students. My thinking here is geared towards programs like those I work with, which take students into the field and involve them in science or outreach in a direct, hands-on way. Although I think it’s great for scientists to go into classrooms and give talks, this advice is only partially applicable to that kind of outreach, and is really geared towards out-of-classroom folks.

Let’s also note that a variety of good potential outcomes have been shown to result from experiential education programs, including increased academic success, improved self-esteem and “self-concept” (i.e., how kids see themselves), increased personal and social responsibility, and better attitudes towards and relationships with adults. There’s no question that those of us who work with students above and beyond what is required or expected of us are doing a good thing. The question becomes: how do we do that good thing better?

* In this list, I am not attempting to differentiate between environmental education, experiential education, service education, scientific outreach, adventure education or any of the other various terms which can be used to describe similar programs. Although there can be important differences in approaches and goals among these categories, it is key elements that the most effective programs have in common that I am interested in.

(more…)

On spending a month publishing science fiction from our Ocean Future.

Blogging, Field Notes from the FutureFebruary 2, 20161

January 2016 was different.

We blocked off an entire month, primed it with some of the best speculative fiction from our ocean’s future, wrapped it in a narrative to connect seemingly disparate topics, and launched Field Notes from the Future, 41 blog post imagining the issues we would face in 2041, 25 years in the future. This was the first time in the blog’s almost 8-year run that we dedicated an entire month to a single concept. It was also the first time that the authors collaborated and coordinated our content.

I am incredibly happy with the results. Field Notes from the Future gave us a chance to flex our creative muscles in new and exciting ways. It gave us an outlet to express our hopes and fears, to expand on our concerns, and to look beyond the horizon and imagine the conflicts that have yet to emerge.

Science and Science Fiction have always been deeply connected. For all the great work of the “heroes of science communication”, the STEM-advocates, the science outreach professionals, it was Clarke, Verne, Shelley, Wells, and Le Guin who inspired me to pursue a career in science. Science shows us the world as it is, Science Fiction imagines the world as it could be.

(more…)

The final server update: All systems normal.

Field Notes from the FutureJanuary 31, 20160

He showed me exactly what we needed to see.

He? I, me, we. The me that is yet to be.

The Nautilus is not of the future. Only data flow backwards. That much, I understand.

_20151230_213505

At least I think I understand. He that is, well, me, eventually, understood. Will understand.

The message was a code. Is a code. Will be many codes.

One was the Nautilus. An icon of past futures. A cipher meant only for me. The symbol of a promise made to myself. A totem that whispers “I know you.”

Two was a command, in plaintext, delivered to the 3D Hubprint this, write this, flash this, send these.

Three was the bootloader, flashed to a microSD, hidden within the Nautilus. He showed me… (I showed myself?) the future we needed to see. He knew. It was not enough to know that he is me… will be me. I needed to understand what we become. I needed to trust myself.

Four was the genome. A machine language written in base pairs that cannot be read yet none-the-less must be spread. Will spread. Has spread. It will percolate through our networks, permeate our systems. When the first transcriptors come online, it will march down the new central dogma: Source Code -> DNA -> RNA -> Protein and transcribe the vaccine to a virus that has not yet been written.

The final piece of the puzzle: a temporal anomaly, a glitch buried in Facebook. Or meant to appear that way. An artifact of the moment that drove Southern Fried Science into the future, that uploaded the future to my server. Tracks in the sand.

The tide has risen, the tide has fallen. All is washed away.

This is where our paths diverge. There is nothing here but the present. No one here but me. Though a million questions remain, they cannot be answered. Though a thousand stories hang, half-formed, they cannot be told.

They must be lived.

Happy New Years, old me

Field Notes from the FutureJanuary 30, 20160

I really hope this old twitter embed code works, otherwise this whole thing is going to fall apart.

Hey Dr. Thaler circa 2016, did you get my package?

theend

Check the infill.


On January 1, 2016, the Southern Fried Science central server began uploading blog posts apparently circa 2041. Due to a related corruption of the contemporary database, we are, at this time, unable to remove these Field Notes from the Future or prevent the uploading of additional posts. Please enjoy this glimpse into the ocean future while we attempt to rectify the situation.

How to fight invasive software: the cure to the cyborg crisis.

Field Notes from the FutureJanuary 29, 20160

On January 1, 2016, the Southern Fried Science central server began uploading blog posts apparently circa 2041. Due to a related corruption of the contemporary database, we are, at this time, unable to remove these Field Notes from the Future or prevent the uploading of additional posts. Please enjoy this glimpse into the ocean future while we attempt to rectify the situation.


It came from the deep.

The heart of Zero Cloner is a snippet of cunningly concealed genetic code isolated from shrimp on the Mid-Cayman Spreading Center, retro-edited to create an easy to edit gene region to which other Cloner derivatives can latch.  Zero Cloner pave the way for Omega Cloner. Omega Cloner spread across the world, locking augmented humans out of society. The Standard Deviants launched a series of attacks early Monday morning, destroying essential digital architecture needed to maintain a fully integrated world.

Entire nations are grinding to a halt. We needed a cure, and we needed it fast.

It also came from the deep.  (more…)

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