Herbicide Tolerance in the Fields

I’ve had a chance to drive I-71 through southwestern Ohio a few times this fall, and I can’t help but notice the explosion of weeds in the soybean fields this year. I’m guessing almost all larger growers are using Roundup-Ready soybeans, a genetically-engineered cultivar that allows growers to control weeds with the potent herbicide, Roundup. This herbicide is actually an enzyme inhibitor which, when present, prohibits the plant from making aromatic amino acids, killing them. Roundup-Ready crops have a gene originating from bacteria that encodes the target enzyme. This variant of the enzyme is less inhibited by Roundup, allowing the crop to survive even in the presence of Roundup.

Because of its combination of specificity and relatively short half-life in the soil, Roundup has been considered a once-in-a-lifetime herbicide, not likely to be matched anytime soon. And now, because of misapplication and overuse, we are seeing the artificial selection of plants with tolerance for Roundup, rendering it an ineffective herbicide in certain locations. The implications of losing Roundup are huge, as it has been a key enabler for no-till agriculture practice, which helps improve soil structure and reduce soil erosion.

Steve Jobs quote

I think one of the things that really separates us from the high primates is that we’re tool builders. I read a study that measured the efficiency of locomotion for various species on the planet. The condor used the least energy to move a kilometer. And humans came in with a rather unimpressive showing about a third of the way down the list. It was not too proud of a showing for the crown of creation. That didn’t look so good, but then somebody at Scientific American had the insight to test the efficiency of locomotion for a man on a bicycle. And a human on a bicycle blew the condor away, completely off the top of the charts. And that’s what a computer is to me, what a computer is to me is, it’s the most remarkable tool that we’ve ever come up with. It’s the equivalent of a bicycle for our minds.

–Steve Jobs

RNA in Food Alters Metabolism

In what I would consider a bombshell finding, researchers have demonstrated a new way that food can influence our metabolism. For the first time, researchers have identified microRNAs that originated in grains of rice circulating in the blood serum of research subjects. MicroRNAs are short sequences of RNA that can bind to messenger RNA sequences and cause their degradation, thus influencing gene expression. From the article:

Like vitamins, minerals and other essential nutrients derived from food sources, plant miRNAs may serve as a novel functional component of food and make a critical contribution to maintaining and shaping animal body structure and function.

Not only did the researchers simply identify miRNAs from plants in human blood plasma and serum, they also demonstrated a physiological effect in a mouse. Using bioinformatics, they identified a number of candidate targets that the specific miRNA may interact with. One of the candidates is involved in cholesterol metabolism, and by feeding the rice to mice, they were able to observe a change in cholesterol processing within 3 hours of feeding.

There are so many implications to this finding, I’m not sure where to start. One of the first thoughts that came to mind was the ongoing discussion surrounding organic foods. I have always been of the opinion that there could be only slight advantages, if any at all, to eating organic fruits and vegetables in terms of the actual food quality itself, assuming any potentially harmful substances had been removed from conventionally grown produce. But wouldn’t it stand to reason that there could be significant differences between the microRNAs actively expressed in organic crops compared to conventional ones? And if that’s the case, their influence on human health could be dramatically different.

I guess this same research group had shown several years ago that microRNAs that are secreted from cells can circulate in blood and influence expression elsewhere in the body, so in some ways this work is following on the same idea. Depending on where this work goes from here, and how wide-ranging the implications turn out to be, this seems like the kind of research that can attract serious attention from the Nobel folks. Makes me wonder why it’s in Cell Research and not the flagship of the same publisher, Nature.

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 – NYTimes.com.

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