Citation Software Automates the Wrong Step

Yesterday I read with interest an article on the Chronicle’s blog Lingua Franca about citation software. In it, the author argues for the importance of consistency in citation style and notes that most academics try to accomplish that through the use of citation management software. However, because the software is misused, the quality and consistency of citations is degenerating. The proposed solution is better training, especially of current students, who will one day be the major manuscript contributors and copy editors. I argue that the problem is with the tools themselves, in this case both the citation management software and writing environment, and that there are two potential solutions.

At first blush, citation management seems like a problem just begging for a software solution: citation information is highly structured and its insertion into a working manuscript should follow a set of rules. Various software solutions have done a good job at data entry and management. Programs like Papers, Sente, and Zotero are my favorites in this regard. I’ve been a Papers user almost since its release due to its lovely and highly useable interface. All of these programs (and many others) are very good at managing references.

But the second part of the equation is inserting a citation into a manuscript, and I still find this process entirely too fragile. As pointed out in the comments at the original article, much of this frailty is because of the thousands of citation styles, many of which are not even internally consistent. When I choose a particular journal from the list of 1400 supported formats in Papers, though (if my journal is on the list, which it usually is not), I expect the citations and bibliographic information inserted to be perfect. It is almost never perfect, so I argue that the existence of the named journal in the style list sets up a false expectation: automatic = perfect.

One solution to this problem is to focus so much on the details that the software is capable of every possible rule and permutation, which is the direction this seems to be going (did I mention there are 1400 named styles in Papers?). But if these styles don’t produce a picture perfect citation, with not a comma out of place and the correct abbreviations and colons and bolds and italics, you’re in for trouble. What I have found is that, at least for the volume of writing I do, I can format my citations by hand as fast as I can correct that misplaced comma, as long as the program spits out a citation that is close enough. This is getting better, largely because of concerted efforts to standardize the definition files that make the rules (CSL files). With online tools that make editing CSL files easy, this is getting better and better. But it still seems so fragile. The focus in this system is still confounding display and content, so we’ve automated at the wrong step in the process.

I guess I’ve taken all these words to say that I think we’re doing it wrong. I wonder why we haven’t greatly simplified the display of citations, relying completely on DOIs and endowing our display software to present human-readable citations based on a lookup of the record associated with the DOI? At least this would move the complexity of styles out of the users’ hands and onto the network. I’m thinking here about doing for citations what the combination of HTML and CSS does for web pages: it separates the display style from and content, which is really what we mean when we talk about citations and their style. We want to display certain information from a citation in a context-dependent way. Why not build that into our reading software?

Scientific Stupidity

From a great essay on scientific stupidity:

The crucial lesson was that the scope of things I didn’t know wasn’t merely vast; it was, for all practical purposes, infinite.

While the essay specifically addresses the change in perspective required to successfully complete a Ph.D., I couldn’t help but to think about the same idea from the standpoint of an undergraduate institution. So much of the focus at this level is on establishing the foundations of modern biology, getting students prepared so that they can begin identifying questions at the frontiers of biology for themselves some day. The ways in which we go about helping to lay those foundations will have a tremendous impact on how easily they make the transition from student to discoverer. If we show them that the things we know today were unknown yesterday, that somebody took a chance and waded into the infinite sea of possible explanations and began rejecting some, then I think we have done our students a service.

Using Poll Everywhere for Classroom Clicker Questions

A couple years ago, we combined 2 of our 3 intro biology courses into a single organismal course, providing me the opportunity to start teaching our introductory cell biology class. When I began working on my prep for the different class, I was interested in introducing more teaching methods that have proven to be so effective in science education over the past decade, but because all of the material was new for me to teach, I defaulted to the more familiar lecture-driven approach. Now that I have been through the course twice, I felt more comfortable trying some of these new approaches this fall.

So what are these “new approaches” I keep alluding to? I mean, for example, things like Just-in-Time teaching, pioneered as a means to teach college physics; clicker questions to test and challenge students during class; more activities during class that enable students to really think and develop understanding of the material, rather than act like scribes and copy down everything I say. I’ll try to write more about my implementation of the first and third approaches later, but I want to focus on my incorporation of clicker questions for now.

My first problem with implementing clicker questions was, I don’t have any clickers. And neither do my students. Instead of asking them to buy one on top of their $169 textbook, I did some research about asking clicker questions without clickers. Most of the options involve the web, as I expected, but one of them, Poll Everywhere, also includes the option for respondents to use text messaging as a means of response. I figured most of my students would be able to get on the web in class, but all of them would at least have their cell phones, so this is the path I chose. Plus, this way maybe they or their parents could deduct the cost of their SMS plan as an educational expense, right?

Poll Everywhere is designed with a number of use cases in mind, including everything from taking a live poll of an anonymous audience to classroom use. Because I wanted to use the response data as part of my students’ grade, I needed to sign up for a paid plan. This allows me to see a list of participants and associate a response with a given student. The registration process for my students went smoothly, I emailed them a special link that took them to an account creation page and automatically associated them with my class. Those students using text messaging to respond had to text a unique code that linked their cell phone to their account.

Now that all of those logistics are settled, it works like a charm. I can pose a question in class and the results show up in real time, just like the purpose-built clickers would but with one big advantage. I can ask open-ended questions in addition to multiple-choice ones, and students can text in their free responses. This works great for big picture kinds of brainstorming, then I can collect all of the responses and, for instance, make a word cloud of them. I have used this to have the class identify the “unifying themes” in biology, and to add a few that they overlooked.

That brings me to my last point, which is the usefulness of this tool. Only two weeks in to the semester, I have seen it uncover 3 misconceptions that I could help the students correct on the spot. The first is the one I mentioned above regarding some themes in biology that students overlooked. The second was a point of confusion between electron orbitals and energy levels (see above). The third was confusion about what an isomer actually is. I am admittedly a novice at constructing sound questions for this kind of assessment, but if I have already found these misconceptions, I’m hopeful that this approach will bear even more fruit as I improve at it.

Inkling Updates Worth Talking About

I have written previously about my impressions of two electronic textbook platforms, CourseSmart and Inkling. Most of my impressions of each platform still stand: CourseSmart has a larger catalog, faithful preservation of the printed page, and lousy legibility; Inkling has better navigation through their ‘card’ metaphor that breaks each chapter into sections, excellent typography and graphics, and a small catalog of titles. I wanted to return to this issue again because, as with all things tech, the picture is evolving quickly.

Inkling just released version 2.0 of their platform just as classes are resuming here on campus, and they are touting the enhanced sharing capabilities as one of the major new features. I suppose if I were a better instructor, I would annotate my copy and share those notes with the world, but I tend to use the book much more as a reference, as I suspect do most of my students, so I’m not sure how critical this feature will prove to be in the sciences. But in playing with the sharing feature even a little bit, it seems too clunky for most of my students to bother with. It isn’t integrated with any existing social networks, instead offering an apparently random collection of users for you to follow, presumably because they have the same text. Alternatively, I could type in an email address to find a specific person, but this seems like reinventing the wheel when I’ve already done that elsewhere.

The big news to me is that, somewhere along the way, Inkling introduced the ability for instructors to request a free copy of one of their titles, which was one of the weaknesses I mentioned in my previous entry. Their hope is that by getting their product in front of instructors, they will gain a recommendation. This is no different than the rest of the textbook publishers providing free desk copies of textbooks for review. In truth, I placed links to all electronic versions of the textbook on my syllabus page this year, but Inkling was the only one I specifically called out on the first day of class, demonstrating some of its nicer features for the class. Why? It offers a great user experience, and it doesn’t expire.

Push Pop Press Acquired by Facebook

Ugh, what a bummer — Push Pop Press, the software designers behind Our Choice for iOS, has been acquired:

With millions of people publishing to Facebook each day, we think it’s going to be a great home for Push Pop Press. […]
There are no plans to continue publishing new titles or building out our publishing platform that was in private beta.

I really thought the tools they were building, and the vision they described for electronic publishing, would have been a great fit for academe. I guess that’s one of the problems with being so good — you’re too good for a big fish to overlook.

An Update on the BRCA1 Story

First, the setup:

In an opinion issued in March 2010, United States District Judge Robert W. Sweet in Manhattan ruled the patents were invalid. The importance of DNA, he said, was the information content it carried in terms of how proteins should be made. In that aspect, he said, the isolated DNA was not really different from the DNA in the body. The argument that isolating the DNA made it different, he said, was just “a lawyer’s trick.”


But the appellate decision Friday rejected Judge Sweet’s reasoning, saying that since DNA is a chemical, the chemical structure is what matters and that “informational content is irrelevant to that fact.”

I think my mind just exploded. I guess I better revise my notes on DNA for next semester, since a judge just ruled that its informational content is irrelevant to its chemical nature.

via Gene Patent in Cancer Test Upheld by Appeals Panel –

iPads outsell Macs

But last quarter we sold more iPads in K-12 than we did Macs. And to do that after just five quarters is absolutely shocking. We would have never predicted this. And so we feel very, very good about the different areas that iPad is being sold into. It’s clear that it has a universal appeal in many different markets, from consumer to business to government, and on and on.

–Tim Cook

Thoughts on the Current State of Electronic Textbooks

Over the past 9 months, I have been using electronic versions of the textbooks I have adopted for my classes. My main motivation was to avoid the need to carry a text back and forth between office and home, a nuisance that I resolved in the past by asking the publisher for an additional copy, the cost of which, no doubt, was passed along to students in the form of higher prices. Occasionally, I could borrow a copy from a colleague to keep at home, assuming we used the same text and we were not teaching from it in the same semester.

The two main vendors I have experience with so far are CourseSmart and Inkling. CourseSmart has the far greater number of titles available as of now, but Inkling just announced more support from publishers recently as well, so we’re clearly very early in this game.

Leasing Leads to Lousy Legibility?

Plenty of people have complained about the lack of imagination represented by the CourseSmart approach, essentially shoe-horning all of the trappings of a printed book into a digital form. I agree with many of these complaints, but it is also safe and low-risk, so I don’t fault them for starting here. Where I do have a complaint with the CourseSmart titles, however, is the poor typographical quality. And I don’t mean just in some esoteric, fancy-font-picking sense, I mean the characters in these titles are borderline illegible. It appears that they run each page image through some kind of machine that crappifies the text and introduce a not-so-secret watermark on the page at the same time. Hoping that the version rendered through the iPad app would not suffer from the same crappification, I logged in to my account from there, only to find the same lousy typography. They seem to have found a way to make the iPad look bad, which I didn’t even think was possible when it comes to typography. I’ve copied some sample screen captures from the iPad below for reference.

I’m guessing that this DRM layer, and the resulting reduction in quality, is due in part to their business model. Rather than selling a digital copy of the book to a person, they are leasing access to the information on a temporary basis. When a student “buys” a CourseSmart title, they have access to it for 180 or 360 days. The upside of this arrangement is a lower cost than the printed-and-bound version bought new, and the ability to access the book anywhere over the web, including on the iPad and other mobile devices. In most cases, I could most likely find a used copy of the book for the same cost or cheaper and either keep it forever or resell it at the end of the semester. If I knew in advance I didn’t want to keep the book, I could rent it from Chegg or some other textbook rental site for even less. I would have given up the ability to access the electronic book from anywhere, but given the poor legibility of the CourseSmart copy as it stands, so what?

While I have been disappointed with CourseSmart books in terms of legibility, their selection is awesome, and their tight integration with textbook publishers pays off. My textbook publisher representative can simply grant access to ‘exam copies’ within CourseSmart and I can look them over wherever I am. This saves an awful lot on receiving unwanted, unrequested textbooks. This pays off for the textbook companies in another way, I’m sure, which is that they can track how thoroughly I’ve reviewed one of their titles. I don’t know for sure whether CourseSmart is providing tracking data back to the publisher, but I’m sure they will soon. It just makes sense to collect this information and use it to improve your sales approach and/or to improve the textbook.

The First Inklings of a Better Book

Rather than take the static textbook and copy it over into the digital realm, the folks behind Inkling are trying to re-imagine what a textbook could be. The first improvement over a CourseSmart version to mention is that the text is not degraded, it’s nice and crisp, with selectable sizing and copy-and-paste functionality. This is because it’s real text and not a hyper-processed image of a page. Another huge advantage is the navigation tools for getting around the book. It’s like they’re assuming you might actually want to jump from section to section quickly, say, to refer back to that section about organic functional groups while reading about cell metabolism. This issue of scanning and discovery is always a problem in an electronic document because I always feel like any “page” not visible has disappeared from reality until I summon it back open. I think the navigation tools in an Inkling book do a lot to circumvent this problem for the reader. Add to that the more interactive nature of an Inkling title (at least the Biology volume I’ve used), including definitions for new terms and expandable figures, and it’s clear this publisher has taken an earnest step into the new medium.

I think there are at least two reasons why Inkling can provide a higher-quality reading experience. First, they aren’t playing games with their sales. When you buy an Inkling chapter, it’s yours. It lives on your iPad and it doesn’t expire. Chapters cost $2.99, and buying a whole book typically gives a discount over buying the chapters individually. So this is more expensive, but it’s yours. Can you tell I’m not crazy about the rental model? I feel like the Inkling model is a more honest way to sell a book. Secondly, Inkling is providing real text and real graphics that are high-quality, resizable, real. How can they do this? Because an Inkling book is actually something like a book “browser” or reading platform that assembles these parts into a complete experience in real-time. The only place it can live is on an iPad (for now), so the risk of piracy is effectively nil.

The major downside so far with Inkling is the dearth of titles and the lack of integration with publishers. By integration, I’m referring to access to complementary exam copies. I’ve personally paid for the Inkling chapters I’ve used so far, which is something I’m not altogether opposed to, but it would be nice to see something more like the CourseSmart model described above. The recent announcement by Inkling (mentioned above) of support from more publishers holds the hope that both of these weaknesses are being addressed. Who knows though, maybe the exam copy issue is not resolvable given the constraints of the Apple app store and the purchase process therein. It may not matter though, because if the quality is good enough, it’s worth paying for.

Our Article Got the Cover!

The last article I wrote here was about my experiences publishing in science at a liberal arts college. Since getting the article accepted, I’ve completed a couple of rounds of revisions, with a final acceptance in early December. Now I’ve learned that one of our images was selected for the cover of the April 2011 issue! More than anything, I just wanted to note it here for posterity. I’m so grateful I get to work with students I love on interesting research questions.

Publishing in Science with Undergraduates at a Liberal Arts College

I just submitted the revisions on a manuscript that was (tentatively) accepted in Physiologia Plantarum in mid-September. I’m hopeful the changes I made will make it acceptable to the reviewers and editor. I’m writing this summary today to remind myself what it takes to see a project through from conception to publication here at OWU. I’m publishing it on my blog in case this narrative might be helpful for other biology faculty members at undergraduate institutions. I don’t expect that my experience is normal, or even comparable, but it might nonetheless be helpful to have another data point. As of today, I am a tenured Associate Professor, in my ninth year at OWU. I have not received extramural funding for my research (to be honest, I haven’t even attempted it yet), but I have benefitted from 2 ASPB SURF awards to students.


Now that it’s close to complete, it’s a good time to look back at the project and take stock. I started this project in the spring semester of 2006 with my honors tutorial students, Alex Paya and Natalie Janney. I had been thinking about it for several years before then, but we got to work screening for starchless mutant roots (pgm-1) carrying the DR5-GFP reporter gene during that semester. Alex stayed in my lab that summer, along with Liz Calhoun, and he worked almost exclusively on the starchless mutant project throughout the summer. He also returned to the lab several times over the next three years for independent studies, continuing the work he started as a freshman characterizing the growth and gravitropic response of the mutant. During that time, Jonida Toska joined the lab and worked hard on collecting more auxin flux data using the confocal microscope and our DR5-GFP/pgm-1 plants. Both Alex and Jonida are co-authors, along with me, on the paper.

To be fair, this is not the only project I have been investing in over the last 4 years. I have had a number of other summer and independent study students over this time, and have been driving 2 other projects unrelated to this one. Hopefully I’ll be able to write about those in the same light as I am this one at some point in the not-too-distant future!

Time to write

We first submitted the manuscript to a journal last summer/fall, and it was not accepted. The general sense of the reviewers was that it needed more data, and one experiment in particular, to be accepted at that journal. We tried to complete the suggested experiment, which involved the creation of a new double mutant, but couldn’t identify a successful cross when we screened the putative offspring last winter. So I decided to rewrite the paper and submit it to a different journal. During that process, I used the first set of reviews to identify weaknesses, and I felt the paper was much better by the time I completed the rewrite, a sense that was confirmed upon receiving the favorable editorial decision in mid-September.

Over the last 3 weeks, I made a lot of small-ish changes and improvements in the revision stage, many of which were suggested by the three reviewers. I have to say, the feedback from reviewers was some of the best I’ve ever received on a paper — very balanced, helpful, insightful, and generally positive. They also pointed out some weaknesses that I was able to address in the revision, including the addition of new data I’ve collected over the last 3 weeks.


In an attempt to put this publication into the context of the rest of my professional life cheap jerseys from China here at OWU, here is an abridged accounting of the inputs into this project:

  • 1 freshman honors tutorial project
  • 1 summer science research student
  • 4 independent study credits (2 for Alex, 2 for Jonida)
  • 1 sabbatical leave (partial)
  • 3 years of data collection and analysis
  • 4 years to publication

Here is an accounting of my teaching load over this period:

For comparison, our accounting of teaching load in the sciences at OWU is based on ‘contact hours,’ which includes time spent in lectures and labs. We’re asked to maintain an average of 10-12 contact hours. I should note that I taught a new (to me) class and lab in Fall 09, and 2 new classes in Spring 10. I have also been pretty busy with committee work and university service over this time period, but I don’t want to try to account for that!
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