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.

AirPlay Display coming to the next version of OS X

It looks like the next version of OS X will improve on AirPlay, turning an AppleTV display into a full-on display for the Mac and overcoming some of the severe limitations I’ve experienced and written about previously.

Here’s what Apple says about the new feature, called AirPlay Display:

With AirPlay and Apple TV, your HDTV works as a fully functional display. So while you’re using your TV to present a slideshow or stream a video lecture, you can take notes on your Mac or chat using Messages.

I’ll revisit this issue when the next version of the OS ships, later this fall.

I’m also reasonably excited about iBooks for Mac, as this will bring the iBooks store into closer feature parity with the Kindle store. As it stands, I can read my Kindle books anywhere, but my iBooks are restricted to the iPad and iPhone/iPod touch. The demo looked good, and the big advantage of interactive, high-quality artwork and feature-rich note-taking could potentially tip the balance in favor of iBooks for me.

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.

Evernote in the lab

EVERNOTE logoThis summer the lab is using Evernote again as an organizing tool for our work. I upgraded to a premium account on a month-by-month plan to test and see how well it would work, and so far it’s exceeding expectations. We just have a single account for all five research students, with each student maintaining their own notebook within the one account. I like this approach for a community space like a lab because I can keep each computer logged in to the one account and everything’s already there. If they each had their own account, I could imagine students accidentally saving to another user’s account if they sat down at a computer where somebody else had been working.

Each student has a slightly different approach to using it, but they all post their daily activities, experimental plans, timelines, and observations. A couple are collecting primary data in their notebooks. Some attach spreadsheet files with results. Some have uploaded images that they are analyzing. All use it to take notes on the articles they are reading.

Speaking of readings, I also created a notebook for journal articles related to all of the various projects going on. That is the main reason I upgraded, so we could upload and store many PDFs without running into the upload limit. A few of them have found articles on their own and uploaded them, but I’m mostly the one collecting the literature.

Whenever I would come across an important paper in my Papers library, I would hop over the Evernote on the web, create a new note, make an attachment, open the PDF in Finder, and drag it in — a tedious process, to say the least. This would be easier if I logged in to the lab account in the Evernote client on my Mac, but I like to stay logged in to my personal account with that.

Papers application dialog boxAs I was looking over the options in Papers, I remembered I could email notes to Evernote through a private address. I created a contact on my Mac called Lab Evernote, pasted in the private email address for the lab Evernote account, and tried it out — BOOM! it worked. I can even specify the ‘papers’ notebook by adding @papers to the subject line. The PDF becomes fully searchable, too, which makes it easier to find later.

I’ve tried lots of different tools for managing lab groups, including blogs, wikis, Dropbox, and network shared folders. I have to say, Evernote is the best tool I’ve found. I can’t think of any way to do it better.

A new view on Twitter with Twitterific

I’m not a huge Twitter user, but it has largely replaced reading RSS feeds in daily use for me. My primary interface for it is my phone or iPad, and I chose Tweetbot as my client a long time ago. I was pleased with it, especially once it could sync my position in my timeline. But over the last few weeks its sync began failing for me, and none of the troubleshooting I tried revived it.

After poking around a bit, Twitterific seemed like the closest competitor in terms of features and polish, so I took the plunge. Sync via Tweet Marker has worked perfectly for me so far, and there are several features that are implemented better in Twitterific than in Tweetbot, in my opinion.

For example, I love how I can set it up to save links to either Instapaper or Pinboard at the same time. It never made sense to me why Tweetbot made me choose between these two services — there isn’t much overlap in the way I use them, yet it lumped these and others into the “Read Later” services. I tend to save lots of links to Pinboard that I think I might want to access later, but Instapaper is only for long articles I know I want to read later, most likely offline. Everything I post to Instapaper I want in my Pinboard account, but I don’t want random links cluttering up my Instapaper reading list. I never found a comfortable configuration in Tweetbot, even resorting to emailing links to my Instapaper account as a workaround.

I also like the implementation of “muffling” better in Twitterific than “muting” in Tweetbot. When I muffle a user in Twitterific, the program displays a single line indicating that the muffled user has posted something, a reminder that I’m still following them and can check back in any time. In Tweetbot, if I “mute” a user, I don’t see anything in my timeline from them.

Reading notes on Objective-C Programming book


I just finished chapter 14 of the Objective-C book and realized I haven’t written about it again since my first post. That is partly because I fell out of rhythm during the first week of teaching summer session, and when I returned to it, I had to back up and repeat a few chapters. But I found my groove again over the weekend and am hoping to keep it up as class resumes tomorrow.

It has been exciting learning (again, in some ways) how to do something new. I feel like I learn about new things fairly regularly with my job, but I don’t have that many opportunities to learn a new skill. The doing aspect really started to become apparent around chapters 7 (loops) and 8 (addresses and pointers); in both of these cases, the challenges were surprisingly satisfying to solve. I also spent a good bit of time wrestling with structs and typedefs in chapter 10.

Crossing into the Objective-C part of the book was a welcome change, as I feel more affinity for the syntax and wealth of tools compared to straight C. The challenges feel more like puzzles in part because of this, like all the pieces are there and I just have to learn how to put them together.

The discussion forum for the book is also helpful as a reference and to see how others have solved the challenge problems. I was stuck on how to convert a BOOL type return into the word ‘Yes’ or ‘No’, and someone had posted their syntax for doing so:

BOOL dst = [tz isDaylightSavingTime];
NSLog(@"Is it daylight saving time? %s", dst ? "Yes" : "No");

I continue to appreciate the Kindle version. When I’m working in my office, I can have a browser open to the Kindle Cloud Reader on one side of the screen and Xcode on the other; at home, I can command-tab between them. I’ve read this book on my iPad far less than I anticipated due to the need to practice the exercises while reading. I did find myself doing some review and re-reading on my phone while away from my computer for a few days, which was nice.

Printing lab equipment

3d printed LED holderThis summer is shaping up to be a very productive one in the lab, with great students and a variety of projects already underway. One of the side projects I hoped to work on was to get familiar with our new 3D printer, a Makerbot Replicator 2, and possibly figure out how to design and print some lab parts to make certain experiments more reliable.

As it turns out, all I had to do was to throw the idea out to the research students and they took over. They’ve figured out how to use Google Sketchup to design parts, then import it into the Makerware software to drive the printer. One of the students has already designed and printed a small part to hold an LED in a position that induces a phototropic response (see above). If we find it doesn’t quite work when we test it out, we can modify it slightly to reposition the LED and reprint it.

The other object I’m interested in printing is a tray that would hold a digital camera in exactly the right position to take photos of roots on a Petri dish. We use stock cameras running the CHDK hack to take time-lapse photos for growth analysis, as I’ve described previously. The quality of the images can vary widely depending on very slight differences in camera positioning, so having a way to fix everything in place will really help us.

There is a lot of hyperbole about 3D printing these days, but there is also the occasional gem of a story about how the technology can be used to do something that was impossible just a few years ago, like printing a tracheal splint for a baby. Holding Petri dishes in place is completely insignificant compared to saving a life, but I am convinced that putting a tool like this in the hands of students to solve problems they weren’t even aware of teaches them something significant. Plus we can hold our Petri dishes better.

Embedding a Fargo outline in Canvas

Today was the first day of summer session here at OWU, and I’m teaching my summer class on food. It’s an effective way to teach some basic plant science concepts through a relatively familiar subject for students. I’m teaching from an outline in Fargo, so I thought I would take advantage of the Reader feature to share it with my class. That way, when I fall behind (as I inevitably will) I can juggle topics on the fly and the changes will automatically show in the students’ outline.

I’m using the Canvas learning management system, which supports embedding via iframes. I created a new page, toggled the view to plain text mode, and inserted the code for an iframe, using the link to my outline in the Reader. The code looks like this:

<iframe src="http://reader.smallpicture.com/?opmlurl=https://dl.dropboxusercontent.com/s/fk7y3u63ndhre50/foodClassSimple.opml" width="575" height="500" style="overflow: hidden;"></iframe>

Here is how the embedded Reader looks in Canvas:

screen shot of a Fargo outline embedded in Canvas LMS

I can expand a topic for the day in the original outline within Fargo and collapse the rest as a cue for students to know what we’ll be discussing. Of course, they can also expand and collapse levels on their own, but at least when they navigate to it, it will be cued up for them.

I also took the opportunity to introduce them to Fargo and pretty much told them they were crazy not to use it.

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.