The windowless room, dank an dark, was not an obvious place for inspiration. I took notes, wondering if I would be able to glean anything meaningful from Professor Helen Stafford's (1922-2011) meandering lecture. I was skeptical. After all, this was the same teacher who, annoyed with our choice of vegetarianism, had told us that "plants have feelings, too".

But what I learned that day, 33 years ago, would trigger a grand curiosity about the natural world and draw me into the greatest scientific puzzle of my career.

Helen informed us that human language is not the only way that species communicate. Plants form intimate associations with fungi and bacteria, which allow them to thrive in stressful environments. Establishment and maintenance of the relationship depends on the passing and receiving of coded information between partners. She also told us that plants can only defend themselves against microbes that they can sense.

This interspecies communication is not restricted to plants and microbes. The human intestine is home to diverse bacteria, allowing us to harvest nutrients that would otherwise be inaccessible. The human immunodeficiency virus chooses for its target only those of us that carry a specific receptor, decorated in a particular way.

All these interactions dramatically affect human health and farm productivity.

I was hooked.

Listen to the NPR interview with enthusiastic Professor Emeritus Murray Gardener.

He describes recent UCDavis symposium with 2011 Nobel Laureates Bruce Beutler and Jules Hoffman

"Evolution of Common Molecular Pathways Underlying Innate Immunity" will feature the 2011 Nobel Laureates in Physiology or Medicine, Jules Hoffmann of the University of Strasbourg, France, and Bruce Beutler of the University of Texas Southwestern Medical Center, Dallas. Luke O'Neill, professor of biochemistry and immunology at Trinity College, Dublin and I will also give lectures.

The symposium is scheduled from 1 to 5 p.m. Wednesday, Jan. 25, in the UC Davis Conference Center. Admission is free, with preregistration required online.

It will be the first symposium at UC Davis to highlight the remarkable similarities between the plant and animal immune systems. The discovery of a role for fly Toll and mouse TLR4 in immunity provided a structural link between receptors utilized by animals and those used by plants (eg. Rice XA21, flax L6 and tobacco N) to detect infection.


[Bruce and I share more than an interest in science; my father (Robert Rosenthal) and Bruce's father (Ernst Beutler) were young cousins in Berlin in the 1920 and early 1930s. Their families fled the Nazi's and reunited in the US after the war. Listen to Bruce discuss XA21/Ax21 and our shared family history during his Nobel lecture last month (starts at 40:45)]

More on the Nobel discoveries, the history of plant and animal immunity and the XA21 cypher-breaking detection system can be found on my recent blog posts here and here.

Here it is. Happy reading.

Ring out, wild bells, to the wild sky,
The flying cloud, the frosty light:
The year is dying in the night;
Ring out, wild bells, and let him die.

Ring out the old, ring in the new,
Ring, happy bells, across the snow:
The year is going, let him go;
Ring out the false, ring in the true.

Ring out the grief that saps the mind
For those that here we see no more;
Ring out the feud of rich and poor,
Ring in redress to all mankind.

Ring out a slowly dying cause,
And ancient forms of party strife;
Ring in the nobler modes of life,
With sweeter manners, purer laws.

Ring out the want, the care, the sin,
The faithless coldness of the times;
Ring out, ring out my mournful rhymes
But ring the fuller minstrel in.

Ring out false pride in place and blood,
The civic slander and the spite;
Ring in the love of truth and right,
Ring in the common love of good.

Ring out old shapes of foul disease;
Ring out the narrowing lust of gold;
Ring out the thousand wars of old,
Ring in the thousand years of peace.

Ring in the valiant man and free,
The larger heart, the kindlier hand;
Ring out the darkness of the land,
Ring in the love that is to be.

Like the German military strategists, single-celled bacteria communicate with each other using coded messages to coordinate attacks on their targets. For bacteria these targets are plants and animals that provide the nutrients needed for growth. Until now, the diversity of codes employed by invading bacteria was thought to be extremely limited. However, our new research shows that bacteria communicate with a previously unknown signal. The research is described in two articles published today in the Public Library of Science and Discovery Medicine.

In a feat worthy of the Turing cryptographers, some plants have evolved a cypher-breaking detection system, called the XA21 receptor, that intercept the bacterial code and use this information to trigger a robust immune response, preventing disease.

in the coming issue of PNAS, we describe a genome-scale model for predicting the functions of genes and gene networks in rice, an important staple food. Called RiceNet, this systems-level model of rice gene interactions allows us to effectively predict gene function. This information can be used to help boost the production and improve the quality of one of the world's most important food staples.

With RiceNet, instead of working on one gene at a time based on data from a single experimental set, we can predict the function of entire networks of genes, as well as entire genetic pathways that regulate a particular biological process. RiceNet represents a systems biology approach that draws from diverse and large datasets for rice and other organisms.

Rice is a staple food for half the world's population and a model for monocotyledonous species - one of the two major groups of flowering plants. Rice is also an excellent model for the perennial grasses, such as Miscanthus and switchgrass, that have emerged as prime feedstock candidates for the production of renewable cellulosic biofuels.

Given the worldwide importance of rice, a network modeling platform that can predict the function of rice genes has been sorely needed. However, until now the high number of rice genes- in excess of 41,000 compared to about 27,000 for Arabidopsis, a model for the other major group of flowering plants - along with several other important factors, has proven to be too great a challenge.

Our Joint BioEnergy Institute and the University of California at Davis teams were very fortunate to collaborate on this project with stellar researchers at the University of Texas in Austin and Yonsei University in Seoul, Korea. The paper is titled "Genetic dissection of the biotic stress response using a genome-scale gene network for rice." The article is open access.

RiceNet builds upon 24 publicly available data sets from five species as well as a mid-sized network of 100 rice stress response proteins that my group constructed previously through protein interaction mapping. We have conducted experiments that validated RiceNet's predictive power for genes involved in the rice innate immune response regulated by the XA21 pattern recognition receptor.

We also showed that RiceNet can accurately predict gene functions in another important monocotyledonous crop species, maize.

Insuk's team generated a user-interactive web tool for RiceNet-based selection of candidate genes, which is publicly available.

The ability to identify key genes that control simple or complex traits in rice has important biological, agricultural, and economic consequences. RiceNet offers an attractive and potentially rapid route for focusing crop engineering efforts on the small sets of genes that are deemed most likely to affect the traits of interest.

My co-authors are Insuk Lee, Young-Su Seo, Dusica Coltrane, Sohyun Hwang, Taeyun Oh and Edward Marcotte.

This research was supported in part by JBEI through the DOE Office of Science.This work was also supported by the National Research Foundation of Korea funded by the Korean government Ministry of Education, Science, and Technology Grants 2010-
0017649 and 2010-0001818 and POSCO TJ Park Science fellowship (to I.L.);
the National Science Foundation, National Institutes of Health (NIH), Welch
Foundation Grant F1515, and Packard Foundation (to E.M.M.); and NIH
Grant GM 55962 (to P.C.R.).

All of the challenges and issues facing the agriculture industry are very complex and multifaceted. The issue of using biotech seeds and traits is no different. U.S. Farmers & Ranchers Alliance (USFRA) has encouraged farmers and ranchers to share their experiences and provide some insight into why they choose - or choose not - to use biotech seeds.

They have set up the "food dialogs" on their website and tomorrow have invited myself and Michael Dimock, President, Roots of Change, to hold a conversation streamed live from U.C. Davis in northern California on November 2 at 9:30 a.m. Pacific Time / 12: 30 p.m. Eastern Time. During this approximately 60-minute conversation, we will share our knowledge in and address the questions people have about genetic engineering and what that means for the future of our food.

Click here for more information.

Click here to watch the live video discussion.

Neither Michael or myself represent USFRA or its affiliates

Michael Dimock is president of Roots of Change Fund. ROC Fund develops and provides resources to a network of leaders and institutions in California collaborating in pursuit of a sustainable food system. It has invested nearly $6.3 million directly and attracted nearly $5 million in match for its programs and projects since 2004.

Dimock was a marketing executive in Europe for agribusiness, farmed organically for three years in Sonoma County, and in 1992 founded Ag Innovations Network, where he began his work on community consensus building and strategic planning to create healthier food and agriculture. From 2002 to 2007, he was Chairman of Slow Food USA and a member of Slow Food International's board of directors.

Last week the U.S. Department of Agriculture concluded that a new variety of rose, genetically engineered to be an unusual shade of blue, does not pose a risk to the economy or ecosystems. This decision paves the way for the company, Florigene, to sell cut roses in the US. The mauve creation is based on the discovery by Davis-based biotech pioneer Calgene Inc, which isolated the "blue gene" from Petunia.

Is genetic engineering for entertainment what it takes for biotechnology to be accepted by consumers?

Physicist and philosopher Freeman Dyson thinks so.

In a provocative lecture on TED.com, Dyson says that proliferation of glow-in-the-dark zebra fish, fruit cocktail trees (7 species on one tree -already very popular with backyard gardeners) or even a grow your own dog kit is exactly what it will take before biotechnology becomes accepted as part of the human condition.

"We should follow the model that has been so successful with the electronic industry." Dyson said. "What really turned computers into a great success in the world as a whole, was toys. As soon as computers became toys, when the kids could come home and play with them, then the industry took off. That has to happen with biotech."

We may believe this or even recognize that it is true, but if so, doesn't this vision condemn us to a kind of self-centeredness? Isn't it a declaration that most of our behavior is governed by an emotional response to pleasure and an acknowledgement that pursuit of entertainment is what truly drives us to action?

I would like to believe that most wealthy world citizens have more compassion, more imagination and more humanity than that. That we will soon wake up and applaud applications of biotechnology that have reduced the amount of insecticides in the environment or those that have the potential to save the lives of thousands of malnourished children.

Will such humanistic inventive applications of biotechnology ever appear as essential to consumers in the developed world as a lego set that self-assembles into a live cat? Are more glofish and strangely colored roses needed before we accept biotechnological advances in agriculture?

Tragically, Dr. Ralph M. Steinman of Rockefeller University, who discovered a new class of cell, known as dendritic cells, which are key activators of the adaptive immune system dies a few days ago. It is unclear if his family will be able to share the prize because Nobel Prizes are not awarded posthumously.

Hoffman's group showed that Drosophila Toll, originally known for its function in development, is also important for the response to fungal and Gram-positive bacterial infection. Read the 1996 Cell paper for which he received the Nobel Prize here.

In mammals, the groundwork for receptor discovery was laid as early as the 1890s, when heat-stable molecules of microbial origin were shown to induce fever and shock in the mammalian host. Foremost among the inducers was endotoxin (LPS), represented in most Gram-negative bacteria. Widely known for its ability to induce septic shock, LPS is perhaps the most powerful elicitor of inflammation known in mammals. The identification of the receptors for these molecules was the central challenge in the field of animal innate immunity. Bruce studied two spontaneous mouse mutations that affected the response to Lps. Both mutations rendered mice insensitive to LPS and highly susceptible to Gram-negative infection. These results suggested the existence of a LPS receptor. Bruce's lab isolated the genes corresponding to these mutations by positionally cloning in 1998. Read the paper here.

Like rice XA21, the protein that my laboratory studies, Toll and TLR4 carry a leucine rich repeat protein motif in the predicted extracellular domain and signal through a subclass of kinases called non-RD (arginine-aspartate) kinases. TLR4 and TOLL also shares the Toll /interleukin-1 (IL-1) receptor (TIR) domain with several plant proteins involved in immune signaling. Thus, the discovery of a role for Toll and TLR4 in the innate immune response provided a structural link between sensors used by plants and animals to detect infection.

Is it a surprise that Jules and Bruce won the Nobel Prize? No. The importance of their discoveries has long been known. Both Bruce and Jules have won one many well-deserved prestigious prizes for their work during their careers. Still, until the prize is awarded, you never know if the research will be recognized by the Nobel committee. I am ecstatic that it was.

Not only am I a great admirer of Bruce's work but I am going to boast RIGHT HERE that he is my third cousin. I knew his multi-talented, lovely grandmother Kathe, a physician, who told me stories about our family during their escape from Nazi Germany. So I take special pride in this award. Here is a story about our shared ancestry.

I also had the great honor to coauthor with Bruce a review last year in Science magazine about the plant and animal immune responses.
Science-2010-Ronald-1061-4.pdf
Ronald_SOM.pdf
We dedicated the review to our great-great grandparents, Julius Rothstein (1830-1899)
and his wife, Fanny Rothstein née Frank (1834-1911), our last common ancestors.

To control these pests, more than 9.5 million pounds of pesticides, including over 3 million pounds of methyl bromide, a toxic ozone-depleting chemical is applied each year. Methyl bromide is also associated with an increased risk of prostate cancer in farm workers.

We all like strawberries, but this pesticide use seems excessive: more pounds of pesticides were applied to 28,000 acres of strawberries than to 780,000 acres of cotton (and cotton is one of the world's most pesticide intensive crops).

To avoid contributing to the use of methyl bromide, I have long purchased locally grown, certified organic strawberries. The organic approach is to rotate strawberries with other crops such as broccoli or a cover crop. Although yields in organic strawberries are only 65% to 89% that of conventional production, organic strawberries sell for 50% to 100% more than conventional berries, so the organic grower still does quite well.

Problem solved? Not so says an article in yesterday's New York Times.

It turns out that even certified organic strawberries are fumigated with chemicals, including methyl bromide, at the early stages of their lifecycle.

"Before they begin bearing fruit, virtually all plants -- whether they will go on to produce conventional berries or organic ones -- are treated with fumigants and other synthetic pesticides." In 2011, more than a million pounds of methyl bromide was applied around the world to young strawberry plants grown in nurseries. Most of the world's nursery plants are produced here in California.

Why is this practice acceptable to organic growers?

The NYT reports that many organic strawberry growers say that using organic stock amounts to taking a big financial risk with little chance of reward. "You bring sick plants from the nursery, I mean, you might as well keep your money in the bank," said Carlos Vasquez, who grows 24 acres of organic strawberries in Monterey for Driscoll Strawberry Associates, the largest berry distributor in the world.

Some growers may not know that they are purchasing fumigated stock; others growers don't see it as a big issue anyway.

"Once the plants bear fruit, they are not treated with synthetic chemicals, so the berries themselves can logically be considered pesticide-free."

But if you follow this line of argument, then many conventionally grown strawberries can also be considered pesticide-free. Methyl bromide is a soil fumigant and is not sprayed on the fruit. There is no evidence that methyl bromide or any of the other very low levels of pesticide residues on conventionally grown produce cause harm to human health. These residues are usually well below the tolerance levels set by the United States Environmental Protection Agency. In other words, most pesticides sprayed on crops are not harmful to consumers.

Many consumers therefore may conclude that if they are not harmed and their children are not harmed by a particular pesticide, then the application is acceptable. But most farmers and environmentalists would disagree. The toxicity of the pesticide does matter. That is because when it comes to methyl bromide and most other pesticides, farm worker safety and environmental health are key concerns. For this reason, an important goal of sustainable agriculture is to reduce the use of the most toxic substances.

Where do we go from here? Clearly new and improved methods of disease control are needed for organic and conventional growers of strawberries. This includes development of alternative, less toxic compounds that can control serious diseases such as Verticillium wilt. This disease is especially destructive in semi-arid areas where soils are irrigated such as the farmlands of California. Another approach is the development of genetically engineered strawberries with robust resistance to soil-borne pathogens. Because organic farmers are prohibited from growing genetically engineered crops, they would not be able to use such new varieties if they were ever to become available. But they may still be able to use methyl bromide.

Right now Secretary Vilsack is speaking with host Claire Shipman. He says "diversity makes sense..we need all kinds of agriculture (big, small, conventional, organic) to drive the rural economy. We need to try to figure out how to help all aspects of agriculture because agriculture helps all of us."

In an hour the NYC panel will answer questions about consumer issues.

Tune in to ask questions here

http://www.fooddialogues.com/

The twitter hash tag is #FoodD