A writing project that bridges two worlds

For the last several months I’ve been working on a manuscript to be included in an edited volume tentatively called Plant Gravitropism: Methods and Protocols. It is part of a series called Methods in Molecular Biology, published by Springer.

rotating stage and camera systemMy contribution focuses on ROTATO, the image analysis and feedback system we use routinely in my lab to measure root gravity responses. The objective of the series is to allow “a competent scientist who is unfamiliar with the method to carry out the technique successfully at the first attempt,” which seems pretty unlikely to me. I can’t think of a single experiment that I’ve every carried out successfully on the first try, but that’s another matter. I’ve been surprised by how hard it’s been to write this, so I thought I’d do some thinking out loud to try to gain a little insight into my struggle.

I think some of my struggle has come from being too close to the method to see it with “beginner’s eyes.” I’ve been working with ROTATO since it was a pile of parts stripped from IBM PCs (we used the computer power supply for 5 V DC and the stepper motor from the floppy drive). I watched over my friend Jack’s shoulder as he wrote the software to make it work. I know the ins and outs of how it works and what makes for a good experiment. Through the years I’ve had a tough time teaching my students how to get good data with it, and I think that’s in part due to the hidden assumptions I make about it. Dragging those assumptions out into the light has been an ongoing process, and writing this paper has been helpful.

Another aspect of the struggle is with how to handle the software part of the method. I am not releasing the code (it’s not mine), and even if I could it wouldn’t do much good because of its dependence on an obsolete frame grabber card. So I’m trying to include enough detail about how it works to allow a scientist/programmer to reimplement the method. But I’m a biologist, not an engineer, so I’m struggling with how much to say and how to say it. I think this is the heart of the issue, that I’m trying to bridge the worlds of biology and engineering.

This is, in fact, what ROTATO is about, and what makes it so important. It takes pictures of a biological response and uses them to control the position of the organ doing the response. It is clever, naive in certain ways, clunky, finicky, crashy, and it works. It has allowed us to learn new things about how roots respond to gravity. So that’s what I’m trying to convey in this methods paper, how to make a ROTATO that works well enough to learn new things, of which there are plenty, I am sure.

Nutrients in vegetables vary according to the clock

You may not realize this, but most fruits and vegetables are still living when you eat them — this is what keeps them from turning mushy and limp. In a new study, researchers from Rice University have shown that these plants are not only living, but their metabolism continues to cycle in response to light/dark periods, influencing their nutritional quality:

“Vegetables and fruits don’t die the moment they are harvested,” said Rice biologist Janet Braam, the lead researcher on a new study this week in Current Biology. “They respond to their environment for days, and we found we could use light to coax them to make more cancer-fighting antioxidants at certain times of day.”

Evidence planted in an Oregon wheat field?

Several weeks ago, the USDA announced it had confirmed the presence of Roundup-Ready wheat in an Oregon field. Roundup-Ready wheat underwent field trials in the late 90’s and early 00’s, but trials were suspended before final approval was granted. The wheat is a match to the exact strain tested by Monsanto. Now it appears somebody may have planted evidence (sorry, couldn’t resist at least one bad pun):

“None of standard farming practices are consistent with, or can explain, a smattering in only one percent of a field or in patches or clumps,” he said. “In our view the finding is suspicious.”

The strain of wheat has never been shown to be harmful, and it carries the same genetic construct as several Roundup-Ready crops that have been approved. But the wheat has not completed the approval process, so the finding caused considerable concern.

Supreme Court ruling denies patent to DNA sequence

The Supreme Court ruled today in the case involving Myriad Genetics’ patent on the BRCA1 and BRCA2 genes. Thankfully, they found that DNA sequences are not patentable because they are a product of nature. The Myriad lawyers had argued that the acts of isolation and sequencing make DNA “inventions” rather than natural discoveries, but the court wasn’t buying that argument.

As I’ve noted previously, not only do I find Myriad’s argument wrong in theory, I also find it misleading in practice. They did not bear any of the costs or risks in actually discovering the sequences in the first place. These two genes were identified in an academic lab at the University of Utah. The original paper describing BRCA1 and BRCA2 acknowledges numerous NIH grants as the source of funding.

Most comments I’ve seen on Twitter seem excited or relieved about the ruling, including one by the NIH Director himself, Francis Collins:

Science writer Carl Zimmer linked to a blog post pointing out some factual errors in the ruling:

Comments on the blog post point out not only factual mistakes, but also an inherent contradiction in the reasoning of the ruling, which is more disturbing still. Details matter, and I’m not impressed by the way the law is (mis)interpreting molecular biology.

A gene that helps roots find water

I’ve been reading on plant water sensing to get some better background for projects we’re starting in the lab this summer. I came across the photo below in a paper describing the identification of a gene involved in sensing water gradients, called miz1, short for MIZU-KUSSEI1, the words for “water” and “tropism” in Japanese.

miz1 mutant roots failing to respond to water gradientThe photo shows an elegant experiment the researchers designed to pick out mutants in water sensing. They allowed the roots to grow in a Petri dish along a block of agar (seen in the upper left part of each panel) and into an opening. Normally, an open space in a closed Petri dish would have very high humidity, but they added a solution that soaks up water vapor, so the air was very dry.

The two photos across the top (D1 and D2) show the response of a wild-type root when it grows into the dry chamber — it immediately turns back toward the agar surface, where the water is. The two photos across the bottom (E1 and E2) show the mutant failing to curve back toward the agar. They found this mutant like a needle in a haystack, by looking at 20,000 mutant lines for ones like this, that fail to respond to the water vapor gradient.

The researchers have gone on to study this gene in great detail, and have made a number of exciting discoveries about how plants sense water.

Citation: Kobayashi, A., A. Takahashi, Y. Kakimoto, Y. Miyazawa, N. Fujii, A. Higashitani, and H. Takahashi. 2007. A gene essential for hydrotropism in roots. Proceedings of the National Academy of Sciences of the United States of America 104: 4724–4729.

Comparing research citations with web links

graph of recent page views on this site
Recent page views on this site
Everybody likes it when their work is recognized, especially when the recognition is coming from leaders in the field. Over the course of the past week, your humble correspondent has had work noted in two very different realms. One of my posts here on Gravitropic was linked by several people, most visibly by Dave Winer, the developer of the software I was discussing, resulting in a big (for this site) spike in traffic. At the same time, an article was published in Current Biology that cited our recent paper on lateral root patterning. Both events represent the same principle and illustrate the power of the citation. At the same time, there seem to be significant differences between online links and scholarly citations that may be worth considering. I wonder whether scholarly writing could take some lessons from online linking.

When I link to an article or blog post on the web, or when I cite an article as a building block in an argument, I am assigning credibility to that source. I am usually saying I agree with the point being made, and in the case of a scientific article, I am likely proposing to build on top of that finding. Sure, sometimes we link to outlandish articles online just to point and mock, or we cite findings that are refuted by the results at hand, but those are the exception. By and large, to cite or link is to endorse.

It follows from this that I judge the work I am citing to be of high quality or in some way noteworthy, and the act of citing it helps it grow in status. In the case of online articles, more links from quality sources leads to greater status and higher ranking in search results. But for scientific articles, the surfacing of high impact papers is not an automatic process. It seems to rely more on a researcher noticing a particular work cited by multiple sources rather than an algorithm returning a work closer to the top of the search results. I would posit that the process of identifying important work and incorporating it is part of the art of practicing science. Of course you can set a database like Web of Science to sort by number of times cited, but that tends not to be all that useful. I wonder if the identification of important papers in a field is done algorithmically by any scholarly databases in a way similar to PageRank?

Links and citations also differ when it comes to which side of the link has the most value. In the case of research and scholarship, articles that become highly cited earn their authors an increasing level of influence within a field. While this is true up to a point with online links, much of the value in this field seems to lie with those entities — individuals or companies — that do the linking. One example of this is Google itself, which created value by “organizing the world’s information“. They drive so much of the traffic on the web by acting as an index and arbiter of quality for a given keyword or topic. In a similar way, sites like Daring Fireball that link to important articles in a particular field have become extremely valuable, in part for their original writing, but also due to the web traffic they drive.

I wonder why there are not such drivers of traffic in specific, narrow fields of research, experts that both express an opinion and drive viewers to particular articles worth reading. In a certain sense this is what review articles do, but on a timescale of years. Is this ‘middleman’ missing because of the time and caution required to puzzle together a research mystery? Is it missing because nobody has the time? Maybe the missing element in scholarly work is the ‘pageview’ metric? Will the incorporation of page views for more progressive online publishers like the PLoS journals change any of this?

Defining success in summer research

Yesterday marked the first day of the summer research season. One of the things I really like about my job is the cycles of the academic year: the excitement and anticipation of the new school year every fall, the sense of exhaustion just before the break, autumn on campus (you can almost picture the tweed, I know), intermission between semesters, etc. Summer research with students is one of my favorite times.

I was at the dentist yesterday morning, and he was asking what projects I was working on in the lab for the summer. I told him a few of the new directions we were heading and he commented that he hoped everything went well and that we had a successful summer. That exchange started me thinking about what defines a successful summer for me, and it may not be exactly what you would think.

Of course the highest form of success for summer research is to generate publishable data, and I make this the clear goal for the students. In an ideal world, they would work on an important question, carry out carefully controlled experiments in a systematic way, and find a clear difference between their control and experimental treatments. Although the first 3 of these factors are under their control, there is no way to know the outcome of an experiment and its significance in advance, so I try not to think of success in terms of the outcomes of experiments and whether or not they represent publishable results. If I were at a research university, I’m sure I would have a different perspective, but I’m not, and the nature of working with undergraduates doesn’t permit this definition of success.

If the publishability of the results doesn’t determine the success of a summer research experience, what does? For me, I think summer research has been successful when a student has done real research. That means they grasped a question (see below for more on this), conceived of an experiment to test a hypothesis, performed the experiment, analyzed the data, and evaluated the results in light of their original hypothesis. Sometimes (hopefully) their work forms a unit on or around which other units can be built into a paper.

‘Grasping a question’ is not to say they get free reign to choose any topic they want. In my lab, students have to focus on an area that supports the direction of the lab as a whole. I think it’s important that they own the project to some degree, but the only way to ensure the importance of their project is to limit it to something in my area of expertise.

Studying gravitropism in lateral roots

Arabidopsis seedlings showing lateral rootsQuick, what’s the first thing you think of when you think about plants? A tree? Leaves? A flower? Chances are slim that you thought first of a root, yet roots make up nearly half of the typical plant’s body. They are the hidden side of the plant, feeling their way in the dark, around stones and through soil, in search of the water and minerals needed for survival. They sense things like moisture gradients, solid objects like rocks and pebbles, and can tell up from down, using these cues in ways that remain largely unknown to guide their growth. Considering that we humans are completely dependent upon our photosynthetic, green cousins for the food we eat and the air we breathe, and considering the vulnerability of plants to drought, we would do well to learn more about how roots do what they do.

Despite making up the vast majority of the root system, how lateral roots choose their path remains uncharted territory. For example, lateral roots are content to grow sideways for long periods, a situation that is anathema to primary roots, which react swiftly with a course correction when they find themselves growing sideways. It isn’t like lateral roots are unable, however, to mount such a course correction. When displaced from their route, they will return to it, whatever it was. But when the course was not-quite-vertical, how do they know where to go? Are they using the same cellular tools as the primary root to detect gravity? Are the same circuits that activate curvature in the primary root activated in lateral roots? Given their role in nutrient uptake, do lateral roots change their course when nutrient conditions change? In our most recent paper, we set out to address some of these questions about lateral root growth. Over the coming weeks, I’ll be posting more on how we carried out our experiments and what we found out.