Recommended reads #42


I’ve mentioned this before, but it bears re-mentioning. NSF’s Division of Environmental Biology has a superb and informative blog, DEBrief. The latest post is called: How to win over panels and influence program officers: advice for effective written reviews. If you’ve ever wondered what NSF wants to know when you’re writing a review and the best way to write one, this is what to read.

There is a useful and detailed “mentoring” section on the lab page of Anna Dornhaus, of the University of Arizona. These pages include a lot of links to other resources, separated for undergrads, grad students, and postdocs.

An open letter to parents of college students, from Hope Jahren.

Preparing students for class: How to get 80% of students reading the textbook before class. This is a peer-reviewed paper in a physics journal. But the abstract says it works just as well for biology courses. So there.

From Veritasium, so frickin’ good, a 7-minute video: This Will Revolutionize Education. It explains the history of dumb technological fads in education. The best line, of many, in this video: “The fundamental role of a teachers is to guide the social process of learning.” Totally worth your while, and worth even more the time of your administrators. If you can dupe your adminfolk to watch this, even better.

The invasive hippos of Colombia are getting fixed. Fixed, as in, “take Rover to the vet to get fixed.” This is not a small task. You knew about the invasive hippos, right? It turns out that druglord Pablo Escobar had two hippos in his private zoo. A boy and a girl. And then in the aftermath of the Escobar empire, they just sort of made their way beyond the Escobar estate. So far, these hippos have only suffocated one cow, to our knowledge.

Jeremy Fox had a post at Dynamic Ecology reviewing the various tools that we can use to detect plagiarism, in addition to the widely used Turnitin service. The comments on the post are also useful. (On my campus we use Turnitin, which is integrated with our online course management system. And it gets lots of exercise in our department.)

Scientists are not that smart. Science is about effort and creativity.

This is hilarious. A pair of annoying pundits were doing their annoying punditry on C-SPAN, and their mom called into the show. To scold them for being so annoying. The first thirty seconds are hilarious, just to see the looks on their faces.

How far do you go with collaborative coding? Simon Goring makes the point that when you’re the collaborator dude on a project, it matters that other people in the project can understand what you’re doing. On the other hand, the reason people collaborate with coders is because they provide specialized skills, but working to avoid being needlessly inaccessible is still important.

I apparently missed this great piece in TREE two years ago by Fischer, Ritchie & Hanspach: about the important of Quality of science over Quantity of science in publishing. Box 1 in the paper has a very specific “roadmap” to get academia beyond quantity. The road looks as navigable as the road to Mordor or the route in the Phantom Tollbooth, but that doesn’t mean it’s not worth the trip. Euan Ritchie puts this paper in perspective on his site.

What do obscenely inexpensive oil prices mean for the future of oil exploitation? To keep this place from becoming a furnace, massive amounts of oil reserves must stay in the ground, resulting in lost profit for people making money off of greenhouse gas emissions. It’s a dilemma that as we become more fuel efficient and ramp up use of alternative energy sources, the demand for oil will drop relative to supply, resulting in cheap oil prices. Which’ll in turn make people want to use oil. Here’s a piece where we hear what Al Gore has to say about it.

There’s a new tree for birds, with a lot of interesting finds.The Avian Phylogenomics Project site, which manages to be both slick and useful. Among the key results are that what we’ve called raptors are, for sure, not a monophyletic group. And a lot, lot more.

This new field station built by the University of Chicago is a gorgeous structure. So purty that it was written up with a bunch of photos in the New York Times Home and Garden section.

One year ago (back when people would leave comments with additional recommended reads, boy that was great, hint hint), Wendy recommended the book The Evolution of Calpurnia Tate. Well, I finally read it. It was really good. If there’s an aspiring naturalist in your life, especially though not necessarily a tweenish girl, this could be a nice present. And I just saw while preparing this link that next year a followup is due! That will be a nice read, I bet.

I recently put in my preorder for Rob Dunn’s next book, The Man Who Touched His Own HeartI imagine it’ll be at least as half good as his last two, which makes it a must-read.

Please list comments with other great reads over the last couple weeks! For links, thanks to Kelle Cruz and Emilio Bruna. Note that posts will more sporadic over the holidays and beyond, in part because I’m away on fieldwork for half of January.

Students say the darndest things!


Oftentimes, professors make sport of sharing humorously incorrect exam answers. I’ve seen a bunch of these during this end-of-semester grading season.

When students don’t know the answer, they sometimes entertain us with witty, technically correct answers that don’t answer the intended question. (There’s a well-selling book about this. And at least one website, too). But that’s not what I’m talking about.

More often, students flat out just write things on exams that go counter to everything we’ve been teaching. Often these trespasses are laced with poor spelling and grammatical errors. In these cases, it’s evidence of failure (of our students and ourselves as teachers). Sometimes our students are just so mistaken and messed up that what they write is tragically funny. It’s gallows humor.

What’s the harm in sharing the errors that our students make as long as we do it anonymously?

I sent the question to the ether of social media. Here’s how students responded, which reflects the overall discussion on twitter:

Among folks I know on Facebook, the prevailing opinion was different.

As for myself, I’m trying to apply the Golden Rule. Thinking back to when I was an undergrad, I would have been really pissed off if my professors if I knew that my professors were using my errors for giggles. And some of them probably were.

Does it matter whether or not the students are aware of it? If you disrespect someone privately does it matter if they are unaware? I try my best to not share opinions or information about someone that I wouldn’t regret if they found out about it. I’ve been critical of certain people and actions at times, but when I do this, I am prepared for the notion that they’d hear about it.

I wouldn’t ever want my students to think that I’m making fun of their mistakes. The way I go about it is to not make fun of their mistakes.

I know my opinion isn’t unique. Here’s Dezene Huber’s opinion that happens to encapsulate mine pretty well:

And if you’re more practical about it, then there is this to consider:

A couple people have pointed out that if students effectively do the same to us, but more publicly and without anonymizing us, with Rate My Professors. So it’s not wrong if we do it anonymously? I like Kenneth Fortino’s response:

Yeah, some students treat us horribly. But I’ll be the first to unilaterally disarm and show respect even when it isn’t merited. I am the professional educator. People can talk smack about their doctors and their lawyers, but doctors and lawyers don’t post insulting things about their clients on Facebook. (Some do in private gatherings, I imagine.) I don’t partake in this reverie because I want to act professionally, and in my opinion, sharing student screwups as entertainment on Facebook isn’t suited to the profession of professoring.

I realize I just shared a judgey opinion. I confess to harboring other opinions too, and I do my best to not let this get in the way of normal interactions with people who disagree with me. (For example, I think it’s immoral to eat factory-raised vertebrates. But nearly everybody around me does it all of the time, and yes, I find this behavior to be wrong. But I get along with folks just fine. So, I’m hoping that this opinion about faculty-student relations doesn’t get me in hot water with colleagues and friends.)

As far as I have seen, this genre of humor only happens at the university level among grad students and professors in the United States. I’ve had a variety of Australian and Canadian colleagues express that this ranges from unprofessional to disrespectful to unethical, whereas many of my US colleagues seem to be fine with it. Based on the number of people involved from various places, I don’t think it’s a result of poor sample size. This thing is okay with US scientists but not so much outside the US. Why the distinction?

Here’s a working hypothesis: education isn’t taken seriously as a profession in the United States compared to other places. Heck, even the US Department of Education recognizes that teachers aren’t recognized as professionals and sees this as a problem. This problem extends into higher education, in which undergrads are no longer the raison d’etre of a university, but merely are the source of funding. As undergraduate learning has evolved to be the by-product of a university, then the respect that is required for effective teaching is now optional.

UndergradsAreI visited google and searched “undergrads are.” Go ahead and try it for “professors are.” We’ve got a major deficit of respect on both sides.

One US professor shared, “As long as it remains anonymous, they really don’t care where it gets posted… I don’t post things to be mean. I post things because being an educator is a ridiculously hard job and we all need to stay amused.”

It’s so smarmy-jargony when professorly people say, “Let’s unpack that statement.” So I won’t say it, without putting it in quotation marks. But I’ll spend this long paragraph trying to make sense of that previous quote. Many professors, including me, see that a lot of students don’t take their education seriously. Some student don’t try as hard as they should, and some who do try don’t have adequate skills for studying, communicating, or thinking critically. So, it’s no surprise that a bunch of dumb stuff appears on exams, some of which are genuinely funny. Likewise, a bunch of students disrespect faculty in a grand variety of ways. The university provides the same rewards to the faculty who teach barely adequately and to those who teach really well. Investing time into high quality teaching typically creates more professional difficulties than opportunities, as long as most of the students are pleased then you should be good to go. And nobody at all bothers to spend any time or money to actually evaluate whether a professor is teaching effectively. Teaching in a US in a university is not only ridiculously hard, but also — outside the classroom — a thankless task which isn’t valued by our peers, bosses, or society. (Okay, I think I’m done “unpacking.”)

If teaching isn’t considered to be a professional activity, then sharing stupid things that students write can’t be considered unprofessional.

Because we have so many students who don’t learn what we intend for them to learn during the semester, when the exam produces tragically comical evidence of this fact, then sharing these failures on social media can seem like a reasonable outlet.

In my opinion (founded on my experiences and observations), the biggest thing that gets in the way of effective university teaching is a lack of respect for students on the part of the instructors. When I’ve had a not-so-good semester, it has been caused by my failure to respect students on account annoying behavior and entitlement. When I’ve had a really good semester, it’s when I respect the students, and my respect for them shows in both my effort and my demeanor.

When students that I am advising volunteer gripes about other classes, they typically start with, “He doesn’t even like us,” or “You can tell that she doesn’t want to be there,” or “He doesn’t even care if I do well.” Students can tell when you don’t respect them. And they’re a lot less likely to care about learning as a result. Maybe college shouldn’t be that way, maybe people should be that way, but that’s the way it is. The first ingredient in getting our students to learn is to show them respect and do what we can to earn it. Even when they sometimes deceive us with dead relatives, academic misconduct and a lack of effort.

I have the fortune of working in a university that is (relatively) inexpensive, with most of the student body that is under-entitled. This presents different teaching challenges than over-entitled attitudes that prevail in expensive private universities, but also makes it really easy to respect the students. I’m not in a position to evaluate their choices. I only am evaluating how well they’ve met the expected learning outcomes. I wouldn’t want my profs to share my screwups behind my back, so I’m doing the same courtesy for my students.

I don’t eat meat, and I don’t share exam outtakes. It’s still okay to eat a ham sandwich in front of me and it’s still okay to share exam funnies around me too.

Be a gracious winner and not a sore loser (or don’t be a jerk)


There are a bunch of life skills that come in handy in academia. Some are obvious and discussed a lot like time management, setting goals, getting stuff completed, etc. Others fly under the radar but maybe shouldn’t. One of those things is how you handle competition. Academia is one of those careers where competition is constantly part of the gig. As much as collaboration can be an essential part of success, there are also winners and losers throughout. The competitions vary but all of us fall on both sides of the line at least some of the time.

It starts even before grad school with who gets in, on what scholarship (or not) and where. Continue reading

Recommended reads #41


45 things I’ve learned about science since I was a student, by Rob Dunn. Knowing these things matters. Staying conscious of these things when it matters is even more important. Pretty much the best set of advice for science and life as a scientist I can recall ever reading.

American universities are experiencing a brain drain, especially the University of Texas.

Next year I’ll be able to wear this awesome women-in-STEM shirt designed by Elly Zupko. You can still order your own! The kickstarter was fully funded within a day, and there’s still almost a month left. Get in on it, and share this widely! I’m loving this constructive response to the sexist incident that interfered with the successes of the comet robot mission. It’s lot better than dudes using shrill insults.

Here is a particularly cogent argument against traditional grading systems. It’s in Robert Talbert’s blog on the Chronicle of Higher Ed site. The whole blog itself looks pretty good, actually.

A paper just came out in PNAS explaining that triclosan, the widespread antimicrobial compound that people like to put in soap and a whole other bunch of stuff, promotes liver tumors.

So, the story about how the Secretary Bird got its name might be apocryphal? The latest from Frontiers in Ecology and the Environment.

“It’s quite striking how a small number of “elite” labs function as gateways to the professoriate. We found that about 10% of all faculty members are members of the National Academy of Sciences, but about 60% of new faculty members did a postdoc with a member of the National Academy.”

The British Ecological Society just published the handiest, informative, and most useful Guide to Data Management in Ecology and Evolution. This goes looks like to be a good partner to another BES document, a so-excellent-it-might-be-perfect guide to peer review. Kudos and thanks to the good folks of the BES.

One down, hundreds to go. The University of Alabama at Birmingham is shutting down its football program. But it’s not a principled stand about the exploitation of student labor, the corruption in the NCAA or the fact that American Football directly causes severe brain injury and dementia. It’s just about saving money.

You might be wondering how a 25 g mouse can take down a 9 kg albatross chick, but I can assure you that a) it does happen, and b) it’s a big problem.

That and a lot more from bird guy Alex Bond, who has been chronicling extended fieldwork in Tristan de Cunha, the most remote group of islands inhabited by humans anywhere in the universe. This is a seriously underbiologized location. He’s been writing about his work there on his site, The Lab and Field, with a series of posts. Prologue; Part 1; Part 2; Part 3; Part 4; Part 5. The only reason to not read this is that you’ll get jealous at the adventure cool natural history.

Do you want the Charles Darwin Research Station in the Galapagos Islands to shut down? Me neither! You can help prevent this from happening – which might be imminent – by contributing. And if you click through there’s a great image of Darwin-as-Santa. Is individual philanthropy of non-wealthy academics a reliable funding model for an important research station? Of course not. But as a stopgap measure to allow them to find their feet, it’s not a reasonable thing to request at the moment.

My great-great-aunt discovered Francium. And it killed her.

A nice obituary for Chespirito, the comic genius.

BioMed Central discovered at least 50 papers with fake peer review in several of their journals, in which authors recommended reviewers with email addresses that point back at themselves.

Bring back the dead with old ecology photos. While long-term ecological data are valuable, old photos can often provide things that you won’t get in a spreadsheet.

An organization that advocates vegetarianism did a big survey about who, how and why some Americans are vegetarian. The results are really interesting. As one of the 2% of veg people in this country, I’ve always been curious about the numbers of people who adopt – and typically drop – the veg habit, and their motivations and challenges.

Meg Duffy flipped her intro Bio classroom. And it worked out well. Find out why she’s reluctant to recommend it to others. (How’s that for clickbait?)

NSF has a three-month pilot forum to discuss graduate education. Want NSF to know about priorities and challenges that might shape future funding guidelines? It would be a good idea to participate!

My Vassar College faculty ID makes everything ok.

The Chronicle of Higher Edcuation has “created a booklet full of tips, trends, and ideas collected from news articles and first-person accounts” about How to Be a Dean.

The community of Imperial College London suffered a tragic loss with the death of Stefan Grimm. Why would an academic kill himself over the prospect of a looming performance review? I recommend we listen, very carefully, to Kate Bowles.

This is what happens if you buy a scam dissertation. It’s a long read that I heard was funny.

Conferencing with a kid, on Tenure, She Wrote. A great prescription in this post: “Treat graduate students like the adults they are.”

The campus alcohol problem that nobody (except Rebecca Schuman) talks about.

The site Biodiverse Perspectives publishes Flump every Friday. That’s not so much an insult, but just a fact. If you’re looking for even more links on Friday, try Flump. And, of course, Dynamic Ecology’s friday links.

What ideas or discoveries have had the greatest impact on the science of ecology?


We’re celebrating the 100th birthday of the Ecological Society of America. Ecology has come a long way over this short period of time. The ESA is asking us (via #ESA100) to answer the question:

What ideas or discoveries have had the greatest impact on ecological science over the last century?

Here are our responses: Continue reading

What reference manager is the best option?


Managing references can be a major pain in the butt. It’s one of the more annoying parts assembling a manuscript, especially when you have to reformat after a rejection.

So, what’s the most efficient way of managing references for a manuscript?

Some of the options people use are BibTeXEndnote, Mendeley, PapersReference ManagerZotero. Or you could just keep a big list of references in a word processing file.

  Continue reading

Why I don’t use my campus email address


What good things does an institutional email address do for you? Here is a list:

  • It gives you legitimacy. If you’re working at Important University, then people know this from your email address.

And that’s the end of the list.

What not-so-good things come with your institutional email address*?

  • It is ephemeral. If you are a student or postdoc, then you know there will be a day, not that far away, that emails to you at this address will bounce back to the sender.
  • It is subject to the changing tides of university IT office policies, support, and archiving practices.
  • In theory, and perhaps in practice, it can be read others in your university, (whereas all of your email can be read by big corporations even if you use your university account).

Continue reading

Recommended reads #40


A peer-reviewed paper in a computational biology journal called “Ten simple rules for better figures.”

Lisa Buckley explains “Why I will always give new students scut-work.” Sounds mostly right to me, at least in that experimental system.

Jon Christensen, a historian at UCLA, wants us to abandon the legacy of John Muir. “‘Muir’s a dead end,’ he said. ‘It’s time to bury his legacy and move on’.” Or maybe Christensen wants some press. Which is a more parsimonious explanation?

As species decline, so does research funding, writes Terrie Williams. A powerful and on-point op-ed piece.

The University of British Columbia is opening a big fancy new college. Which is not open to Canadians, and designed primarily for high-spending international students, primarily from China.

In my opinion, a lot of ecology is a mess right now because we lack a clear vocabulary to discuss how processes vary with spatial scale. What does it mean that a phenomenon or a process is “scale-dependent?” You’ll get a different answer depending on who you ask as well as the context. Brody Sandel writes in Ecography in an attempt to clean this mess up, seeking a “taxonomy of spatial scale-depenence.”

Have you heard of The Knowledge? It’s the supremely difficult evaluation required to become a licensed London taxi driver, requiring years of study. If you’re not familiar, then this is a fascinating article about The Knowledge and whether or not it’s required in the era of GPS and uberlyft. If you are familiar with it, the article might be even more fascinating.

As far as I’m concerned, the science policy news of the decade or the century might be that the US and China have agreed to some mighty substantial cuts in carbon emission rates. It’s a helluva a lot better than what any of us have been expecting, and I bow deeply to Barack Obama, John Kerry, and their team for some incredible diplomacy.

“University sued after firing creationist fossil hunter.” Excerpt: “In recent years, a schoolteacher, academic and NASA employee who were creationists have claimed that they were fired unjustly for their religious beliefs. (None were reinstated.) But what makes this case different is that Armitage managed to survive for years in a mainstream academic institution and to publish research in a respected peer-reviewed journal.”

The BBC reports: It’s hard to get an academic job at an elite university in the UK. Duh.

Amanda Graves, a senior at a public high school in New Jersey writes in the Washington Post, “Dear elite colleges, please stop recruiting students like me if you know we won’t get in.

Jon Wilkins asks: “Is EO Wilson senile, narcissistic, or just an asshole?” I imagine that some are now asking the same question about Wilkins. (As for myself, I’m not trying to figure that out about either of them.)

Meanwhile, let’s consider the notion that Wilson floated that invoked the ire of Wilkins. Wilson called Richard Dawkins a “journalist.” Should be we thinking of Dawkins as scientist or a journalist? When I’m asked to assess someone’s science credentials, one of the first places I’ll go are their lab website and google scholar pages. Let’s go look at Dawkins’ page on Google Scholar. Oh, wait, he hasn’t created one. Let’s look at his lab page. Oh, he doesn’t have one that I can tell. I can just find a website for the Richard Dawkins Foundation. But here’s the result of a search for Richard Dawkins in google scholar. You can decide for yourself whether or not he’s more of a journalist than a scientist. Is Dawkins narcissistic? That’s an easier question to answer.

It’s not your kids holding your career back. It’s your husband. This about CEOs and other exec-types, but I think it applies just as well to scientists.

Eighty-nine percent of all fathers took some time off after their baby’s birth, but almost two-thirds of them took one week or less” and a lot more interesting stuff about paternity leaves.

Simon Leather explains that he’s been using social media for work for the last two years, and is still digging on it.

NASA creates a lava lampesque video showing CO2 emissions of the planet over a year.

A wikipedia page that lists the titles of deleted Wikipedia articles with “freaky” titles. Including: “Bring your Pez dispenser to work day,” “Chesterfield Snapdragon McFisticuffs,” “CNBC anchors who have never held even a moderately high position in the financial field,” and “Debated questions regarding the procreation and existence of certain Narnian creatures.” However, the majority appear to have been written by prepubescent boys.

As more academics use twitter, more people are live-tweeting talks from conferences. Is this okay, and if so, under which conditions? Here are a few pieces about the topic: “Let’s have a conversation about life-tweeting academic conferences” and “We need a clear policy on tweeting from academic conferences” and “Live-tweeting at academic conferences.” Tweeting is banned from the Neuroscience meeting. That should cover the bases. (Next time I talk, I encourage it!)

A few years ago, six scientists were convicted of killing civilians by inadequately predicting an earthquake. The good news is that they were just cleared of manslaughter charges by an appeals court. The bad news is, well, that scientists were convicted of manslaughter by failing to predict an earthquake.

If you’re Australian, probably know who Tim Winton is. If not, then it might be a good idea to pick up a book or two of his for a read. For a short taste, here is an account of Winton’s relationship with hospitals.

What does macroecology say about economic diversity?

Here is the entire abstract of a new paper by David Colquhoun:

If you use p=0.05 to suggest that you have made a discovery, you will be wrong at least 30% of the time. If, as is often the case, experiments are underpowered, you will be wrong most of the time. This conclusion is demonstrated from several points of view. First, tree diagrams which show the close analogy with the screening test problem. Similar conclusions are drawn by repeated simulations of t-tests. These mimic what is done in real life, which makes the results more persuasive. The simulation method is used also to evaluate the extent to which effect sizes are over-estimated, especially in underpowered experiments. A script is supplied to allow the reader to do simulations themselves, with numbers appropriate for their own work. It is concluded that if you wish to keep your false discovery rate below 5%, you need to use a three-sigma rule, or to insist on p≤0.001. And never use the word ‘significant’.

There’s been a lot about That Shirt. Here are two good ones: That Shirt and Science isn’t the problem; Scientists are. If anybody still thinks that That Shirt was okay, then I recommend “A guide for science guys trying to understand the fuss about that shirt” as well as “Slurstorm, and the flaws in “Shirtstorm” arguments.”

About that comet. It has organic molecules on it.

How the changes in the media environment alters the perception of public work:

These days, being attacked isn’t just the result of saying something badly, it’s the result of saying anything at all… 

But a funny thing has happened since the rise of professionalism. The tenets it embraced—that some people are more qualified than others, that training and apprenticeship have value, that not everyone can or should (or needs to) gain admission into the club—have become unfashionable. And that is because haterade is not exclusive to the media world. It’s not merely an occupational hazard of being a bigmouth. It affects just about anyone who tries to do anything that is subject to public (which is to say online) discussion. It affects the business owner who’s at the mercy of random, nameless Yelp reviewers who might well be his competitors in disguise. It affects the physician for whom the few patients who post reviews on medical-ratings sites are inevitably the disgruntled ones. It affects the educator who can’t give a poor grade without risking retribution via the websites Rate My Teachers or Rate My Professors. It takes the very essence of what it means to be a professional—training, experience, sheer chops—and reduces it to a stage act to be evaluated with an applause-o-meter.

You might have seen this make the rounds, and it’s a good one. The makers of Barbie wrote a really sexist book, showing how Barbie needs boys to code for her. And Casey Fiesler, a computer science PhD student, went ahead and fixed the book for all of us.


For links, thanks to those shared by Kate Bowles, Kate Clancy, Susan Letcher, Amy Parachnowitsch, Timotheé Poisot, Nate Sanders, John Thomlinson, Ed Yong, and Carly Ziter.