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.

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.

Bringing biological insights to solar cells

Converting the energy from sunlight into a useful electric potential in order to charge a battery or power a lightbulb is almost always carried out by silicon solar panels. There are a lot of good reasons why silicon is used for light collection, but there is no reason this process must rely on this material. In fact, one reason to look at other possible materials is that nature itself has a number of materials that convert light energy into electrochemical gradients.

The capacity to harvest light energy and use it for powering the cell is ancient, having evolved on Earth at least 1 billion years ago. We find the results of this in all of the true plants today, as well as numerous algae and phytoplankton. But it’s also found in many more primitive organisms, and they may have some tricks for collecting light efficiently that could prove useful as a model to follow for solar technology. That’s exactly what a research group has been working on at the Photosynthetic Antenna Research Center at Washington University.

Taking a page out of the way primitive photosynthetic cells harvest light, they have found a way to assemble the pigments needed to harvest light by studying a structure called the chlorosome, found in photosynthetic green bacteria. Unlike the high degree of structural specialization found in land plant chloroplasts, these bacteria lack any such specialization, instead relying on the chlorosome region to harvest light. It is the self-assembling nature of the pigments into the chlorosome that the researchers find to have potential application in the development of alternative solar technology. Seems obvious to look throughout nature to solve difficult problems like these, and to provide the funds in basic research to do so.

Lytro cameras and research imaging

All of the tech blogs are abuzz over a new kind of camera by a company called Lytro. Rather than focus on a plane in space to form an image, the Lytro captures an entire light field in front of the camera, allowing you to focus on any plane in the field after capture. To get an idea how it works, go play with their photo gallery and come back.

As someone who uses images as data to understand how plants grow and respond to stimuli, I’m very intrigued by this concept. One of the obvious weaknesses of our current methodology is that we usually limit our growth analysis to a 2-D plane because it’s tough to capture 3-D data. To get an idea of how this problem has been overcome in the past, see the article by Randy Clark and others from June 2011 in Plant Physiology (see Figure 1 in particular). If I understand this technology correctly, it could overcome that limitation in an elegant way and allow us to collect full 3-D data sets with a single, inexpensive camera. I’ll be curious to get ahold of one and try it out when they ship early next year.

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.

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.”

Then:

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.

Our Article Got the Cover!


The last article I wrote here was about my experiences publishing in science at a liberal arts college. Since getting the article accepted, I’ve completed a couple of rounds of revisions, with a final acceptance in early December. Now I’ve learned that one of our images was selected for the cover of the April 2011 issue! More than anything, I just wanted to note it here for posterity. I’m so grateful I get to work with students I love on interesting research questions.