Posts Tagged ‘technology’

Anthers pollenEscape of the Transgenes?

Last week, I was a bit startled as I listened to a podcast of NPR’s Science Friday program.

In this episode (2/18/2011), host Ira Flatow was interviewing the new president of the American Association for the Advancement of Science (AAAS) Dr. Nina Fedoroff (a distinguished plant molecular biologist, by the way).

She shocked me (and, apparently, Ira Flatow) by flatly denying that there were any cases of transgenes “leaking” into the environment from genetically-engineered (GE) crop plants.

To Ira’s credit, he challenged her on this somewhat preposterous statement. (See below why it was indeed such a surprising remark.)

Because this episode elicited a “storm” of letters and e-mails, Ira Flatow did a follow-up interview (which you can listen to here) with Fedoroff and plant ecologist Dr. Allison Snow.

Briefly, Dr. Snow provided several examples of transgenes being acquired by wild relatives of genetically engineered crop plants, particularly canola. Dr. Fedoroff seemed to dismiss these examples as merely “management” problems.

It’s Hard To Corral A Transgene In The Wild.

Contrary to Dr. Fedoroff’s statement on Science Friday, there is ample evidence that transgenes have “leaked” from GE crops to other plants.

Escape plantFor example, in a previous post regarding the herbicide Roundup® (glyphosate), I noted how a transgene conferring resistance to Roundup® had escaped from a test plot of genetically-engineered turfgrass to adjacent populations of a related native grass.

There certainly are other published examples (see ref. 1, e.g.) of gene flow from GE crops to other non-GE crops and to weedy or wild relatives. And, as genetically-engineered organisms (GEOs), such as crop plants, proliferate, there will likely be more.

It’s not hard to imagine the ecological and agricultural implications if so-called “weedy” plants acquire transgenes conferring herbicide tolerance and pest resistance, for example, from related GE crop species.

But, although gene flow from GE plants to wild relatives has been well documented, the ecological significance of these occurrences is much less well understood.

Overall, there are relatively few data available with which to evaluate the potential for increased weediness or invasiveness in a crop species with fitness-enhancing abiotic and biotic GM traits. A better understanding is needed of the factors that presently control population size and range limits of either the crop volunteers or wild recipient populations, and the degree that survival or reproduction in the field is presently affected by the relevant biotic or abiotic stress-tolerance trait.” – from Ref. 1 below.

In a sense, Dr. Fedoroff is correct in stating that this is a “management” issue. But perhaps such management of GE crops should be conducted primarily by plant ecologists, such as Dr. Snow (see ref. 2, e.g.), rather than by plant genetic engineers.

Re. DIY Biotechnologists: This is certainly one of the serious drawbacks of GEOs that all of you DIY genetic engineers must seriously consider before releasing your creations into the wild.


1. Warwick, S.I., H.J. Beckie and L.M. Hall (2009) “Gene Flow, Invasiveness, and Ecological Impact of Genetically Modified Crops”, Annals of the New York Academy of Sciences, Vol. 1168, pp. 72–99. (PDF)

2. Snow, Allison A. (2010) “Risks of Environmental Releases of Synthetic GEOs”, Invited Presentation for the Presidential Commission for the Study of Bioethical Issues, July 8, 2010 (PDF) The agenda and video of this meeting are available here.

HowPlantsWork © 2008-2011 All Rights Reserved.


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DIYbio.jpgBiotech in Your Garage.

Is it possible that the kids across the street could someday soon be creating genetically engineered plants in their garage or greenhouse? (Now there’s a scary thought.)

This may be more feasible than you think.

An article called Garage Biology in a recent issue of Nature magazine (see ref. 1 below) attracted my attention to the burgeoning field of “do-it-yourself” (DIY) biotech.

For relatively modest amount of money, a person can set up a reasonably functional molecular biology lab, in part, by acquiring used lab equipment in places such as eBay. See, for example, this garage biology lab in Silicon Valley.

The above article is mainly about Dr. Rob Carlson, a pioneer in the field of “garage biotech” (see refs. 2 & 3 below). He has recently published a book called Biology Is Technology: The Promise, Peril, and New Business of Engineering Life. According to one prominent reviewer: “Since Rob Carlson is THE authoritative tracker of progress in biotech, this book is the most complete – and exciting – chronicle of the technological revolution that promises to dominate this century.” –Stewart Brand, Author of Whole Earth Discipline: An Ecopragmatist Manifesto.

fruit_helix.jpgInformation regarding “biohackers” can, of course, be found online (e.g., see ref 4 below).

But even if you don’t have the money or knowledge to do such science yourself, there may actually be community biotechnology labs in your city (e.g., see ref. 5 below) that provide the training and equipment. A DIY Biotech hacker space has recently opened in NYC.

So, similar to open source computer software, does there exist a growing field of “open source biotechnology”. Some say yes, but others say no.

Regardless, the recombinant DNA genie is out of the bottle (so to speak), and the knowledge and equipment required to perform gene splicing can easily be acquired (or built).

And getting such recombinant DNA (artificial genes) transferred into plants is relatively easy (compared to animals).


See here and/or here, for example.

But for a sobering look at the current limitations of so-called “synthetic biology“, please see reference 6 below.

Here’s a new book on the subject: Biopunk: DIY Scientists Hack the Software of Life


1. Ledford, Heidi (2010) “Life Hackers.” Nature Vol. 467, pp. 650-652. (PDF)

2. Carlson, Rob (2005) “Splice It Yourself: Who needs a geneticist? Build your own DNA lab.” Wired, Issue 13:05. Splice It Yourself

3. Rob Carlson’s Blog

4. DIYbio.org WebsiteDIYbio.org is an organization dedicated to making biology an accessible pursuit for citizen scientists, amateur biologists and biological engineers who value openness and safety.

5. GenSpace – New York City’s Community Lab GenSpace is a nonprofit organization dedicated to promoting education in molecular biology for both children and adults. We work inside and outside of traditional settings, providing a safe, supportive environment for training and mentoring in biotechnology.

6. Kwok, Roberta (2010) “Five hard truths for synthetic biology.” Nature Vol. 463, pp. 288-290. (HTML) (PDF) “Can engineering approaches tame the complexity of living systems? Roberta Kwok explores five challenges for the field and how they might be resolved.

HowPlantsWork © 2008-2011 All Rights Reserved.

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Ava_Scenery.jpgiPlants: An Introduction

From movies and video games to landscape design to education to scientific research, we are increasingly encountering plants in silico (that is, computer-simulated plants).

Virtual plants fall into three categories: (1) computer-generated images, (2) outputs from computer algorithms, and (3) computer-searchable plant gene and protein databases.

What follows is a summary of my experiences with virtual plants, mainly online. (However, I don’t claim this is a comprehensive review – please let me know via comments what I’ve missed.)

The Botany of Pandora

The alien planet Pandora in the movie Avatar (and also the video game based on the movie) is swathed in a bioluminescent tropical landscape, populated with truly “out of this world” plants and fungi. As a consultant, plant physiologist Professor Jodie S. Holt helped create this computer-generated imaginary world as well-described here.

Virtual Landscaping

Landscape designers have been using cad programs for years. But thanks to web-based apps such as Second Life® and Google Sketchup anyone so-inclined can landscape in silico.

For example, some fantastic examples of such landscapes in Second Life® are presented here. And Google Sketchup has a 3D warehouse full of virtual plants for your virtual landscape.

Virtual Plants For Education

For years I’ve referred students to Virtual Plant Cell to help visualize plants at the cellular level.

At a more macro scale, one can learn some plant anatomy, for example, at The Virtual Plant.

Botany for Computer Geeks

Way back in the day, when I first taught a class in plant development, I introduced the class to the computer modeling of plant growth.

The example I chose was the so-called L-system or Lindenmayer system of the computer modeling of plants. An example of such modeling can be found at Algorithmic Botany, the website of the Biological Modeling and Visualization research group in the Department of Computer Science at the University of Calgary.

As head of this program, Professor Przemyslaw Prusinkiewicz has greatly refined and expanded this system. An illustrated list of their publications can be found here.

Is Plant Research Going To Be Like Shopping On Amazon.com?

One aspect of iPlant-related research involves functional genomics (putting the genetic puzzle pieces together), exemplified by MetNet at Iowa State University.

The VirtualPlant is another web-based software platform to support systems biology research. According to a recent report: “VirtualPlant helps biologists who are not trained in computer science to mine lists of genes, microarray experiments, and gene networks to address questions in plant biology,..”

As shown in this figure, “VirtualPlant follows the e-commerce site logic…users browse and query the database and add products of interest to their shopping cart”, analogous to Amazon.com. (Thanks, by the way, to the journal Plant Physiology for public access to this paper.)

“Big-Ass Science”

The ultimate “iPlant”, however, may be The iPlant Collaborative Project or, in other words, a $50,000,000 US-taxpayer-funded project to do plant research by committee. An excellent summary of this giant project can be found here.

Years ago a colleague referred to such endeavors as “big-ass science”. Personally, I feel that giving 200 young (under 40) plant scientists (profs or post-docs, by the way) $250,000 each to pursue her/his personal research interests would yield much more creative and innovative outcomes. But that’s a discussion for another day….

HowPlantsWork © 2008-2011 All Rights Reserved.

Inorganic Flora
A couple of weeks after editing the original post, I discovered some amazingly beautiful images of flowers by botanical CG artist Macoto Murayama.

More about Murayama can be found here and here.

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Roundup.jpgThe Last Roundup?

The herbicide that most Americans are likely familiar with is Roundup®.

Unlike the auxin-based herbicides I discussed in the previous post, Roundup® is not a selective herbicide. That is, it usually kills all green plants (except if the plant is Roundup Ready® or if the plant is a naturally Roundup®-resistant “superweed” – see below for more).

Roundup® is the Monsanto brand of the artificial chemical glyphosate, which was first synthesized in the 1970’s by Monsanto as a so-called “broad-spectrum” herbicide (i.e., kills all plants).

Glyphosate kills plants by specifically blocking the action of a key enzyme (5-enolpyruvylshikimate-3-phosphate synthase or EPSPS) that plants use to synthesize three amino acids (tyrosine, tryptophan and phenylalanine) that are essential components of all proteins. Without the ability to synthesize these amino acids, the plants will die.

Why doesn’t glyphosate similarly affect animals?

Humans and most other animals don’t have this enzyme, so glyphosate has no specific target as it does in plants*. (Since they do not have this enzyme, animals do not synthesize these three essential amino acids. They get them from their food.)

*Please note: This is NOT to say, however, that glyphosate is totally non-toxic to animals – more below.

Roundup may be losing its effectiveness, however, due to several factors.

Are Your Plants “Roundup Ready®”?

During the 1980’s there was a revolution going on in the plant sciences. Scientists discovered how to insert genes into the genome of some plants by using the bacterium Agrobacterium tumefaciens (At) as a genetic vector. Here’s how:

Scientists were able to use recombinant DNA technology to load genes into the Agrobacterium. And the bacteria were then able to “infect” susceptible plant tissue and deliver the genes straight into the plant cell’s genome. These foreign genes were actually “hard-wired” (stably inserted) into the plant’s genome. Moreover, these genes were able to be passed along to the plant’s offspring.

Simply put, Agrobacterium was like a taxicab, and the DNA was the passenger.

Using such technology, Monsanto scientists discovered a bacterial version of the enzyme EPSPS (see above) that was not affected by glyphosate, isolated the gene coding for it from the bacteria, and then inserted this bacterial gene into soybeans.

Roundup Ready® soybeans were born. Followed by Roundup Ready® cotton and canola. And when scientists learned how to genetically engineer grasses (Agrobacterium doesn’t work so well on grasses) using the so-called gene gun, along came Roundup Ready® corn. And maybe even Roundup Ready® turfgrass for lawns!


Roundup® Ready crops have certainly contributed to the extensive use of glyphosate, making it the most widely used herbicide in the U.S. This has likely increased the evolutionary selective pressure on “weeds”, leading to the generation of naturally glyphosate-resistant plants, a.k.a., “superweeds”. (Figs. 1 & 2 from Ref. 1 below)

Here Come the Superweeds.

Recent articles, such as this one in, of all places, Business Week have discussed implications of the appearance of so-called “superweeds”.


Examples of more recent reports of Roundup®-resistant weeds can be found here, here, and here. The increase in the number of such glyphosate resistant plant species has elicited warnings from environmental groups such as the Union of Concerned Scientists, as well as the international press.

In addition to naturally occurring gylphosate-tolerant weeds, there also is the risk of the spread of the genes conferring herbicide tolerance from GM (genetically modified) plants to native plants. Such events have recently been reported to have occurred in test plots of Roundup Ready® turfgrass in Oregon.

Briefly, the artificial gene conferring gylphosate-tolerance was discovered to be present in some native grass species growing adjacent to the test plots. (The genes presumably traveled via pollen from the GM plants to pollenate the native grasses.)

Thus, the possibility of the creation of superweeds via the escape of herbicide-resistance-conferring gene constructs is a very real possibility indeed.

May Increased Use of Glyphosate Also Be Toxic to Animals?

Though glyphosate has been considered one of the more benign pesticides, its environmental impacts are being reconsidered in light of some recent evidence to the contrary.

1. Boerboom, C. and M. Owen (2006) “Facts About Glyphosate Resistant Weeds”, Purdue University Extension, publ. GWC-1. (PDF)

Bottom Line: Though glyphosate kills plants by targeting an enzyme not present in animals, its overuse – due in part to GM Roundup Ready® crops – may be harmful to agriculture, to the environment, and, ultimately, to human health.

HowPlantsWork © 2008-2011 All Rights Reserved.

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