32,000 year-old plants

New Life, From an Arctic Flower That Died 32,000 Years Ago

By taking advantage of a property of most plant cells, a Russian research group may have revived a 32,000 year-old plant:

They then took cells from the placenta, the organ in the fruit that produces the seeds. They thawed out the cells and grew them in culture dishes into whole plants.

As the article goes on to point out, if this can be confirmed this represents a unique opportunity to study recent evolution in this species. But just think about this for a second: these cells that were revived were in a squirrel hole for 32,000 years. Whoa.

Plant Defense uses the Clock

Plants Use Body Clocks to Prepare for Battle

Lest I gave the impression that the animal immune system was using the circadian clock but the plant defense system was not, we have this:

Some of the circadian-regulated genes are linked to wounding or healing responses, meaning that they can anticipate an attack from insects just as they anticipate the sunrise.

This is really cool work, showing that plants use circadian regulation of defense compounds to provide maximum protection at the most likely time of insect feeding.

E-books can’t be burned

I love this article about ebooks and the nature of literature by Tim Parks:

The literary experience does not lie in any one moment of perception, or any physical contact with a material object (even less in the “possession” of handsome masterpieces lined up on our bookshelves), but in the movement of the mind through a sequence of words from beginning to end. More than any other art form it is pure mental material, as close as one can get to thought itself.

I continue to grow less and less inhibited about buying ebooks, I know that much.

Why study plants?

A few years ago, I put together a talk to give to a science club here at OWU offering my answer to the question, “Why study plants?” I organized my ideas around the concepts of plants being beautiful, interesting, important, and useful. I still think these are useful categories to address the original question. But over the last several years, I have become increasingly convinced that the latter two reasons have grown in stature in my thinking at least, if not in actual stature with respect to the problems facing humanity.

My conviction on this point has crystallized recently as I read two separate, totally unrelated articles. I’ll discuss one of them today, and the other some other day.

In his annual letter on the activities of his foundation, Bill Gates articulates the need for more investment in crop research:

Over time, governments in both developed and developing countries focused less on agriculture. Agricultural aid fell from 17 percent of all aid from rich countries in 1987 to just 4 percent in 2006. In the past 10 years, the demand for food has gone up because of population growth and economic development—as people get richer, they tend to eat more meat, which indirectly raises demand for grain. Supply growth has not kept up, leading to higher prices.

He goes on to argue, among other things, that we place ourselves at risk by ignoring the need for agricultural improvement. Plants are sitting ducks for pathogens, and Gates points out the nasty wheat rust known as Ug99 as an example of the kind of threat posed to crops grown in monoculture. With this fungal pathogen, it is not a matter of if it will affect North American wheat production, just when.

In a place like the U.S., we’ve enjoyed the luxury of taking food for granted for so long, we can hardly imagine the impact that a crop failure would have on our economy. We assume that the yearly corn harvest, the crop that undergirds most of our food economy, will maintain low prices at the grocery — Gates points out that a mere 15% of our consumer spending goes toward food — and allow us to spend our paychecks on more scintillating purchases like iPads XBoxes (sorry Mr. Gates). Without sustained efforts to outrun pests and pathogens that attack crop plants, we are almost guaranteeing a major crop failure some day.

But there is another wrinkle to funding as it currently stands, and that is that by leaving half ($1.2 of $3.0 bil) of agricultural spending on the most important crops up to the private sector, we almost guarantee that crop improvements will be directed at wealthy, developed nations and pass over the poor, developing nations. Individuals and families will remain in poverty, scraping out subsistence yields with no surplus for the market, and no opportunity to join the global economy, largely because they lack the stability of predictable crop yields that only comes from research investment. In other words, this discussion quickly incorporates issues of social justice and the fight to end extreme poverty.

So this is one prong of an argument to invest in plant science research, either financially (if you are a billionaire) or with your time and talent. If you are interested in a career in research and have a desire to do good in the world, becoming a plant scientist is a path worth exploring. But this is not the only reason, there are several other great reasons to explore this field that I’ll talk about some other day.

Infinite possibilities

Interesting bit of research picked up by the mainstream press (albeit with no link to the article) in this week’s US News. In this case it’s a review article on the state of engineering plant secondary metabolism to create novel or high-value compounds:

Møller envisions a future where plants’ internal systems are re-engineered to create rare chemicals, such as artemisinin, a powerful anti-malarial drug that is found in trace amounts in only one plant worldwide. The plant would be rewired so that instead of making trace amounts of the drug, it would make lots of it.

Now that all the molecular tools are in place to even propose such an undertaking, the possibilities start to seem infinite.

Making interactive diagrams with Hype

I’ve been dabbling again with making my own animations to use as teaching aids. I say ‘again’ because I remember how excited I was to create a crude, two-dimensional animation of photosynthetic electron transport in my first year at OWU. I used Flash for that, when it was still produced by Macromedia (before Adobe bought them).

Instead of Flash or some other complicated authoring tool, I’ve been using Tumult Hype, which does its magic with only HTML5 and Javascript. The web has changed a lot since the early 2000’s, including the introduction of greater support for animation in the browser with HTML5, making it possible to bypass the plugins altogether. I’m still learning my way around the software, but I’ve managed to realize a couple of simple animations already — one demonstrating osmosis, one on meristem-driven growth, and one on cell expansion. They are, admittedly, not much to look at, but I think I spent all of 15 minutes on each. The design goal (if you could call it that) was to create the equivalent of a chalkboard sequence of drawings, and I think they accomplish that much.

In my opinion, even though Hype seems to be designed with web professionals in mind, it is perfect for this kind of activity. It has a mode in which you can ‘record’ an animation by simply dragging objects around and advancing the timeline. Alternatively, you can also control each object and animation sequence with manual controls, which I used for the cell division and growth example to obtain pixel-precise layout of each new cell. I’ve barely scratched the surface of the interaction capabilities thus far, only creating buttons on my examples for replaying or jumping to a new scene, but there is massive potential here for allowing students to explore the impact of changing different variables, for example.

One of the great benefits of the output format is that I can embed the animations on web pages and, using the same output, bundle them into a widget and insert them into iBooks Author projects, where they can become fully interactive diagrams. As I’ve written recently, I’m interested in exploring the creation of interactive books with iBooks Author, and having a simple tool for creating animations is an important complement to that process. I’m looking forward to tinkering with Hype more, and I’ve set my sights on remaking my old photosynthetic electron transport animation, which promises to be a bit more involved than growing squares.

Why iBooks Author is Interesting to Me

Today Apple announced a number of new initiatives relating to textbooks, including a new version of their iOS app iBooks, a new authoring tool to create iBooks, and a new iOS app for iTunes U. None of these announcements was an utter surprise, as rumors had been swirling for several weeks before announcements were even delivered to the press for the event. And while I think the new initiative to sell textbooks for iBooks is important, I want to focus on the authoring tool and its implications for higher ed in this post.

This semester I am teaching an upper-level course in my main area of specialty, plant physiology. Since I began teaching the class 10 years ago, and even when I took the class as an undergrad, I have used the standard-bearer text, Plant Physiology by Taiz and Zeiger. It is an excellent book with an encyclopedic coverage of the topic — it’s great. In fact, it is too great, going into detail at a level more appropriate for advanced courses. I have tended to assign readings from the text as a supplement and a reference for the students, and in almost no topic do we exhaust the coverage of the book. I provide the students with an outline for each topic so they know which details I want them to focus their attention on. For some time, I have felt like they aren’t getting their money’s worth out of the book using it in this way, but they are much more comfortable having an “official” textbook than going without (I’ve tried that experiment). The only alternative seemed to be to write my own, but the fact that the textbook in a field is too good did not seem like strong motivation to write something else. I have no interest in writing a real textbook and trying to get it published, as it seems to me like a monumental task, and I’d frankly rather be in the lab.

But if there were a way to “publish” a book only targeting my class, by converting those outlines I’ve made into short chapters on each topic, well… Why not? I have no intentions of any other students wanting or needing my vastly inferior collection of topic overviews, but it would be fine if they wanted them. The iBooks Author app seems like just the kind of tool to create such a book — I can take words I already have lying around (or write new ones), package them up, and push a button. I can export a PDF for students without iOS devices. I can publish them to the web for still others to find them. I can use something like pandoc to shape them into a file in ePub format.

And all this makes me wonder, how many other faculty members out there are like me, having a collection of notes and points of emphasis for a topic that they know something about, but had no interest in producing a textbook through a traditional publisher? Or perhaps they wrote their own “book” and published it through the campus copy shop? I think having an authoring tool and distribution system all wrapped up together has tremendous potential for these situations. Having the freedom and flexibility to put together a little book to accompany a specialty course is an attractive idea to me, one that I plan to experiment with.

If I end up doing the work to turn those outlines into book chapters and distribute them to my class, I will likely do so without cost to the students (despite the objections of my wife!). I have felt for a long time that textbooks are far too expensive, especially those that are used only as a secondary reference like I described above. I would love to save my students the cost of the textbook yet still provide them with something that serves as a reference for them as they study. I haven’t even begun investigating the new iTunes U app as a distribution means, but I understand it could work in conjunction with iBooks to provide all manner of resources to our students. Makes me wonder which will be more disrupted, textbook publishers or LMS vendors?

Academic Publishers Enemies of Science

The academic publishing system has bothered me for some time, seems like it’s only getting worse:

The Research Works Act, introduced in the US Congress on 16 December, amounts to a declaration of war by the publishers.

Sounds like the act is basically an end-run around the NIH rules requiring open access. Nice. I’m pleased to see my society is not part of the Association of American Publishers, which fully supports the legislation.

The $1000 genome

Last summer:

We have demonstrated the ability to produce and use a disposable integrated circuit fabricated in standard CMOS foundries to perform, for the first time, ‘post-light’ genome sequencing of bacterial and human genomes.

This week at CES (of all places), Ion Torrent announced they have achieved the $1000 genome, a full year ahead of their 2013 goal. Hitching their prospects to integrated circuit technology looks like it was a good bet, as it’s hard to imagine the gene sequencing technologies that rely on the detection of light to scale in this way. I think it’s an exciting time to be in biology.

Dangerous RNA in Food?

[Update Jan 13: The original article has been edited and extensively modified in response to reader feedback. The author has acknowledged several mistakes in the original and generally improved the clarity of his argument. However, the main point I make in response remains despite the changes to the original. —cw]

As I wrote about previously, a research group has shown that miRNA from rice is present in human blood and can influence gene expression in the liver. In response to this work, Ari Levaux (@arilevaux) has published a somewhat sensationalistic opinion for The Atlantic that concludes:

The news that we’re ingesting information as well as physical material should force the biotech industry to confront the possibility that new DNA can have dangerous implications far beyond the products it codes for.

Most of the article takes aim at the purported implications of this research for GMO foods. Specifically, he believes this finding contradicts the long-standing policy of “substantial equivalence” claimed by the pro-GMO producers. If I were an author of this study, I would be disappointed to have my work so badly misconstrued for the general public.

Clearly, LeVaux has an axe to grind with the large, multi-national agribusiness industry (who doesn’t, besides incumbent politicians?). And I don’t necessarily even support the concept of substantial equivalence, but I must point out that there is a major hole in the evidence between “the food we eat can regulate gene expression in a new way” (the new research) and “GMOs are dangerous to human diet because they contain new DNA” (LeVaux’s claim).

If the uptake of miRNA from food is widespread (which is not known yet), then potentially every food we eat of biological origin could have previously unknown effects on the cells of our body. Think about that for a moment and I think you will agree that to focus on GMO foods is to miss the potential scope of this finding. If widespread (again, a big if), then wouldn’t every food need to be reevaluated as a precaution? This is nothing short of the kind of shift in thinking that humanity underwent upon discovering the need for essential vitamins, maybe bigger.

The other big problem I have with LeVaux’s piece is that there is no reason to think that the miRNAs in GMO corn would be any different than those in nonGMO corn. Most GMO corn carries one of the Cry1 genes from soil bacteria, encoding a protein that is toxic to insect larvae. What is the proposed connection between the expression of this gene and any miRNA expression? None, as far as I know and as far as LeVaux informs me. Back to the quote above from his article, there is nothing new or known to be harmful in ‘ingesting information’, we have been doing it as long as we’ve been eating, apparently.