Measuring the pH of plant cell walls

New work out of Wolfgang Busch’s lab in Vienna, lead by Elke Barbez, describes a new and relatively simple method for measuring the pH of plant cell walls:

Here, we present a fluorescent dye that allows for the correlation of cell size and apoplastic pH at a cellular resolution in Arabidopsis thaliana.

I already ordered the dye, can’t wait to try it on some mutants!

I’m really pulling for the SpaceX launch scheduled for this week, as my colleague and friend John Kiss’s experiment is launching on it:

Our experiment uses the same hardware and facilities on flight as John’s, so I’m also really hoping everything goes well up there, otherwise we’ll have problems getting approved to launch.

UPDATE 2017-06-01: Today’s launch was scrubbed due to lightning in the area; they’re going to try again on Saturday.

Faculty governance and technology

I’ve been trying for many (like, 7?) years to help our faculty governance system to recognize the importance of the Campus Technology Council, to little avail. In the last couple years I’d pretty much quit asking for it to be considered as an ‘official’ committee, even though it’s just as active and engaged in new projects as ever. This piece by Jonathan Rees and Jonathan Poritz in Academe spells it out clearly:

Faculty must educate themselves about the possibilities and dangers of IT in order to maintain their prerogatives. Information technology might seem like merely an instrumental aspect of institutional operations that might be left entirely in the hands of administrations, like landscaping or decisions about which model of copiers to put in department offices. But when IT is a fundamental part of the creation and dissemination of new truths, and when it can be used to monitor and to control all aspects of research and teaching, it necessarily becomes one of those areas where the faculty should exercise its primary responsibility.

Since I know for a fact that faculty at my university have actively “engaged” (thrown down) with the administration over decisions about both copiers AND landscaping, it seems like I ought to be able to rouse some interest in academic technology. Anyway, I’ve ordered a copy of Poritz and Rees’s book, maybe I’ll pass it along to the appropriate committee chair when I’ve finished it.

Chipotle’s GMO- (and evidence-) free marketing strategy

In a (not very) bold move, the restaurant chain Chipotle has announced that they are moving to a completely GMO-free menu. Reading the NYTimes article, there is a startling lack of explanation for why the chain is spending the effort and additional cost to source certified GMO-free ingredients:

Chipotle’s chefs preferred sunflower oil but finding enough was tricky. Chipotle found a farmer willing to increase his production of sunflower, but the company needed more oil than he could produce.

So instead of using one oil for the majority of its needs, Chipotle now uses sunflower to fry its chips and tortillas, while a non-G.M.O. rice bran oil will be mixed into rice and used to fry fajita vegetables.

Given that there has never been a single reputable article to support the claims of the anti-GMO crowd that GMOs are harmful, and given the 20-plus years of crops with genetically-engineered traits raised and eaten, the reason for a major chain to do this seems baffling. Then, this:

So Chipotle’s flour tortillas are now made with a non-G.M.O. canola oil, which costs more, and the company said last week that it might have to raise prices slightly this year.

So, given the lack of scientific evidence indicating a difference, why are they doing it? Marketing, I think. It’s brilliant, really. They have chosen a marketing strategy that pays for itself by justifying higher prices, borrowing a page from the Whole Foods playbook. Never mind that there is nothing wrong with GMO foods, there doesn’t have to be. Just by marketing the fact that their food is not GMO, they are able to set up a (false) dichotomy in consumers’ minds, planting the idea that perhaps GMO foods are not as healthy. And they don’t even have to make a case, really, because just to suggest a difference is enough. It doesn’t matter that they are playing a game of ‘cooties’ or ‘cheese touch‘, as long as it works to devalue the other options.

Here is Chipotle’s page explaining the decision. It comes down to 2 reasons (their 3rd is just preference): 1) GMOs need to be studied more, which is really the precautionary principle — prove no harm — which is quite difficult to do; and 2) GMOs harm the environment. These are the planks of the anti-GMO party platform, and both have been roundly refuted. Perhaps the fact that we now have definitive evidence that the exact same process of genetic engineering has been occurring in the wild for millions of years will help to convince some that there is no inherent risk in the technology itself?

Anyway, go ahead and enjoy a 1200-calorie GMO-free burrito. Whatever you do, though, don’t even think about washing it down with a Coke. That stuff is LOADED with sugar from GMOs! I wonder why they’re still selling that?

Looking forward

Launch of SpaceX Dragon on a Falcon 9 rocket, 14 April 2015, Cape Canaveral, FL. Image credit: NASA

I’m looking forward to the day that my seeds are transported to the ISS on one of these babies! There’s still a long way to go before my project is even ready to apply for a flight position, but I’ve started working with support scientists to schedule all the tests that need to be done. It’s going to be a very busy summer around my lab!

Read more about today’s launch, known as the CRS-6, at NASA’s page about the mission.

Seeds can change their coats for the season

Whenever I teach on seeds, either in my non-majors Food class or my Plant Physiology class for majors, I can’t help describing them as the children of the mother plant. I know, not exactly creative, but it helps to paint a picture of the roles of the parent plant and the seed. I like to talk about how the endosperm or other food reserve is like a packed lunch, put there by the caring mother to feed the baby plant as it germinates and becomes able to feed itself. And what kind of parent sends its babies out without a coat? It usually gets a few chuckles, at least, to put this all in human terms.

That coat on the seed? Sometimes it’s a jacket, and other times it’s more like a down coat, and the mother plant chooses based on the temperature. I’m not making this up. In a study published this week, plant scientists link the toughness/thickness of the seed coat to the temperature endured by the mother plant. If the mother experienced warmer temperatures, it will make more of a protein that limits the production of tannins in the fruit. Less tannin makes for a thinner seed coat and faster germination. On the other hand lower temperatures cause the mother plant to make more tannins, leading to a thicker coat. Simple, yet remarkable.

See a news article on this research, or go check out the paper itself.

Virtual progress

Although I’ve been on sabbatical this semester, it appears that our experiment using Chromebooks in our introductory biology courses has been going well. From what I’ve heard, only a few students have been burned by the extra layer of abstraction of running Windows in a web browser, occasionally closing the Chrome tab instead of just the program running in the virtual Windows environment. All told, I’d say that’s pretty impressive for an idea I dreamed up last winter, made possible by the excellent support from our IT department.

I can only imagine this is the early days of a growing trend, both within and beyond academic settings. I noticed a few days ago that Adobe has been working with Google to make their flagship application, Photoshop, available in a “virtual” environment. It sounds like an unholy combination of virtualization, VNC, and JavaScript, but it might work well enough to be worth it. Interesting, too, that Google is investing engineering resources to make this happen, as this clearly increases the value of Chromebooks if it can provide an adequate user experience.

While this is an example of making a particular program run virtually, Amazon continues to push forward with their more general solution, called AppStream. They’ve just announced the ability to run almost any Windows application on their virtualization platform, removing the need to manage a server on site. It costs $0.85 per hour, billing only for the time used. I’m not sure it would make sense for every app or student or teacher, but for certain programs that need to be run only occasionally, it seems like a great idea.

Google Scholar’s creator

From a nice article by Steven Levy on Anurag Acharya, the man behind Google Scholar:

I can do problems that seem very interesting me — but the biggest impact I can possible make is helping people who are solving the world’s problems to be more efficient. If I can make the world’s researchers ten percent more efficient, consider the cumulative impact of that.

What a great motive to guide your work.

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.