Untold Stories, Beyond Methyl Bromide

January 17, 2018

“THE IDEA TO write this book came to me after I retired in 2005 and was cleaning out, re-reading, and reorganizing 40 years of files…in spite of three books and more than 200 journal publications and book chapters, my files filled with history and unpublished data were headed for the trash bin…the greater my urge to somehow pull the stories together into a single read-through description of my career…unique, it is the approach I took and the philosophy behind my approach to do hypothesis-driven research starting in the field, followed by the laboratory,” writes R. James Cook in the “Preface” to his book, Untold Stories (APS Press, 2017).

In 1974, Cook and Kenneth F. Baker co-authored a landmark book, Biological Control of Plant Pathogens. That book, which in some ways is a precursor to Untold Stories, summarized scientific evidence relevant to creating ecological balances favoring beneficial organisms (e.g. biocontrol agents, antagonists, competitors) as pesticide alternatives to control pathogens capable of weakening and destroying plants, including major food crops such as potato and wheat. Human medicine has at various times in various places employed a similar biological approach, such as using bacteriophages to fight diseases such as cholera, but for an array of reasons biological control has found more fertile ground in agriculture. Ecological balances can be tilted or nudged from pathogens to beneficial organisms in various ways, including via soil pH adjustments, tillage systems, cropping sequences, fallows, composts, amendments, nutrients, etc. The specifics can vary widely among crops, individual fields, regions, soil types, etc. Dr. Cook, as the Untold Stories subtitle, “Forty Years of Field Research on Root Diseases of Wheat,” hints, found wheat a fertile microcosm for exploring the phenomena of naturally disease suppressive soils for producing healthy crops.

Cook’s job when he joined the USDA Agricultural Research Service included soil diseases afflicting wheat, one of humanity’s most ancient crops and a worldwide dietary staple. The USA grew 45.7 million acres of wheat in 2017, most of it winter planted varieties, the lowest acreage since record keeping began in 1919. USA farmers grow twice as much corn and soybean, roughly 90 million acres of each. Wheat exports earn the USA roughly $6 billion a year, out of $140 billion in total agricultural exports. Though wheat helps the USA balance of trade, family farms growing wheat are not sustainable or economically viable if soil pesticides are used. Dr. Cook’s challenge was curing wheat soil diseases without costly pesticides. In the 1970s, the mainstream view was that solving pest problems without pesticides was drug-induced organic hippie crazy talk, a near impossible task with low probability of success.

Fortunately Dr. Cook possessed sound inner instincts complemented by scientific understanding of ecology and microbiology, with an emphasis on biological control of plant diseases absorbed working alongside Kenneth Baker and others at the University of California, Berkeley where biological control was still honored and respected despite falling from its early 20th century heights during the synthetic pesticide era. Cook briefly acknowledges Louis Pasteur, the famous French freelance microbiologist, chemist and entomologist who developed modern medical germ theory and laid the foundations for modern epidemiology while alleviating a mysterious silkworm colony collapse (disease epidemic) depressing the mid-19th century French economy.

On page 236 of Untold Stories, Cook quotes Pasteur: “In the field of observation, chance favors the prepared mind.” I would go back one step more to Pasteur’s mentor, chemist Jean Baptiste Dumas, who according to French-borne microbiologist René Dubos, persuaded a reluctant Pasteur to tackle the silkworm problem despite an insect ignorance for which he was widely ridiculed: “To Pasteur’s remark that he was totally unfamiliar with the subject, Dumas had replied one day: ‘So much the better! For ideas, you will have only those which shall come to you as a result of your observations!’” Microbiologist Alexander Fleming, famous for the fungal antibiotic penicillin, noted another important factor: “Louis Pasteur in his youth and throughout his life believed in hard work. He lived for his work and put his whole heart and soul into it. His was not a 40-hour week. He worked so constantly in his laboratory that it was inevitable that he became a beautiful technician…”

Another message embedded in Cook’s Untold Stories: Successfully tackle hard problems that appear insoluble to everyone else, and the probability of job security and life success increase. Cook developed an expertise in finding cooperative wheat farmers and locating fields where natural biological controls seemed to be working on their own. Then did a laboratory form of reverse ecological process engineering to find out why these fields developed a disease immunity or natural suppression of wheat soil pathogens. When you can replicate or duplicate the phenomena experimentally, then a degree of understanding can be claimed.


Untold Stories feels like the real nitty-gritty, with behind-the-scenes stories about how research projects are accomplished. The type of details typically omitted from science journals, by design. If anyone dared put into their journal article the details of how they obtained funding, navigated the bureaucracy to win support, or cleverly acquired a piece of new equipment, it would no doubt get edited out. This is a reason Roald Hoffmann in his book, The Philosophy, Art, and Science of Chemistry (Oxford University Press, 2012), suggested a new kind of science journal allowing first person “voice” and personal experience. Actually, it would only be “new” in the “retro” sense that “everything old is new again.” In the early days of modern science, personal autobiographical expression, musings and miscellany were common. These early science articles could be confusingly messy and hard to decipher, perhaps harking back to the deliberately obscure days of alchemy. However, personal observation and experience was handled well by agricultural researchers in the early 20th century. Which is not meant to denigrate the utility and immense value of standardized journal formats with introduction, methodology, results, discussion, etc. There is room in the world for both.

Untold Stories embeds science in a wider human context, beyond what is possible in the modern journal format, which necessarily excludes the human dimension, but leaves behind an unintended residue, a subjective impression of a science rendered lifeless by the invisibility of its practitioners. Cook family members pitched in to write the forward, edit, design and deliver their father’s book ready for printing by the American Phytopathological Society (APS) Press. Cook’s attitude towards public service is refreshing, and clearly extended into his so-called retirement. Judging from the 2005 start date and the 2017 book publication date, Dr. Cook put over a decade into this “Magnum Opus” book project. Wife and family were promised this would absolutely be his last book. One might lament, but I have to believe Dr. Cook mined his past experiences so thoroughly as to be able to rest on his laurels and not feel that much was left out that could not be remedied in a few journal articles.

A mathematical ratio of untold stories to published stories would be interesting, and Dr. Cook is in a position to be the expert. Let’s say the Untold Stories:Published Stories ratio was 1:1 and had a certain “volume.” Then the “volume” (e.g. measured in pages, articles/books, person-years of work, or whatever) of untold stories could be multiplied by the number of scientists or the amount published in a given time period to yield an estimate of how much scientific research ends up in the proverbial trash bin.

The Untold Stories photo caption on page 52 brought to mind a much maligned molecule, methyl bromide, a research tool and experimental control integral to scientific investigation of naturally disease suppressive wheat soils. Salt marsh microbes naturally produce methyl bromide as an antibiotic type weapon in waging ecological warfare for survival against competitors and antagonists. The caption: “A discussion session in progress at a Pacific Coast Research Conference on Soil Fungi with Professor S.D. Garrett, Cambridge University, as the discussion leader…Steve Wilhelm from UC Berkeley, credited with the introduction of soil fumigation to the California strawberry industry, is in the front row…”

Dr. Wilhelm, who I knew to also be interested in promising methyl bromide alternatives such as steam, marigold cover crops and green manures, crops up again on page 186 of Cook’s book: “it was not until the middle of the twentieth century that soil fumigation was used on a large scale…Steve Wilhelm at UC Berkeley…together with Albert Paulus at UC Riverside, did the pioneering work on the use of mixtures of chloropicrin and methyl bromide to control soil-borne pathogens and weeds before planting strawberries in California starting in the late 1950s. Strawberry yields were roughly 5 tons per acre in fields not fumigated and up to 25 tons per acre in fields that were fumigated.”

Soil fumigation with methyl bromide and chloropicrin worked so well that California had near zero untreated strawberry fields available to investigate for naturally suppressive soils, which is unfortunate, as methyl bromide use is being phased out under the Montreal Protocol as an ozone depleting substance. Something I learned about in more depth working with the late Jamie Liebman, a plant pathologist at BIRC (Bio-Integral Research Center), where as subcontractors we helped develop a Montreal Protocol methyl bromide alternative research agenda for funding by the U.S. EPA and United Nations. I wrote a short chapter on this period in history titled “Rowland’s Recipe for Climate Treaty Success” in an ABC-CLIO book titled Science and Political Controversy, edited by David E. Newton in 2014. In 2015, attending agricultural, soil and entomological science meetings in Minneapolis, not far from APS headquarters, I was pleased to find that research agenda still extant and going deeper. Funny what a mere photo caption can trigger in human memory. No doubt Untold Stories will have similar effects on readers whose interests and paths intersected with those of Dr. Cook.

California’s $2 billion strawberry industry, which produces about 90% of the USA crop, an awesome 1.7 billion pounds on about 40,000 acres (43,000 pounds of strawberries per acre), was for all practical purposes birthed into existence by injecting chloropicrin and methyl bromide into soils under plastic tarps. California’s hyper-productive strawberry growers, like Florida tomato and inland Pacific Northwest potato growers, can earn back methyl bromide soil fumigation costs. Family wheat farms would be bankrupted and abandoned to tumbleweed and erosion by soil fumigation costs. Scientifically, the less prosperous economics of wheat growing were fortuitous, as Dr. Cook was precluded from earning a living testing and recommending soil pesticides. Instead, as Dr. Cook’s book rigorously details, applied science became indistinguishable from pure science (much as it did for Pasteur) as it delved into the microbiology, ecology and non-chemical remedies for soil pathogens causing unhealthy plants and crop failures.

A key scientific discovery was that growing wheat in the same field again and again, year after year without interruption or rotation, can result in soils becoming naturally suppressive or functionally immune to disease pathogens. But this goes against centuries of accumulated wisdom arguing that toxic root secretions (allelopathy) poison the soil, and are best alleviated by crop rotations. Cook’s objection on page 227: “this makes no mention of a role for root diseases and ignores one of the most fundamental principles of plant pathology taught to beginning students in plant pathology, that growing the same crop in the same soil increases the populations of pathogens of the roots of that crop…It takes a long time to replace the first explanation with the correct explanation for almost any phenomenon in nature.” It also takes time, as those who have studied ecology know, for pathogen, prey or pest populations to build up to peaks before predator and natural enemy populations reduce or crash them down to low levels. Dr. Cook’s mission was to shorten that time.

One set of wheat experiments described in the “Take-All Decline” chapter 7, owed inspiration to 1950s’ potato scab disease research in Washington State, where small amounts (10%) of suppressive soil (presumably containing beneficial microbes) were added to disease-susceptible soils. Within 2-3 years, wheat soils were growing healthy plants. “Although I never repeated this experiment (nor did it need to be repeated), it would turn out to be the most influential experiment of my career,” wrote Dr. Cook on page 144. “It led to my award of a Guggenheim Fellowship…to my first competitive grant awarded by the USDA Competitive Grants Research Office (CARGO) in 1978…to the USDA ARS approving the formation of the Root Disease and Biological Control Research Unit in 1984; and to the USDA ARS providing permanent funds for me to hire…”

This only scratches the surface of a truly remarkable book likely to become a classic of science.


Ozone Oxygen (O3) Fumigation for Organics

June 29, 2010

OZONE, A NATURAL OXYGEN (O3; 3 oxygen atoms) molecule that can also be synthesized, is among many other things an alternative to fumigants such as chlorine, methyl bromide, phosphine, and sulfuryl fluoride. Modern day humans have an almost schizophrenic, Jekyll-and-Hyde relationship with ozone, alternately and simultaneously seeking to eliminate and preserve ozone in the environment.

At stratospheric heights 12-15 miles (20-25 km) above the Earth’s surface, in what is called the ozone layer, 90% of the planetary ozone swirls and drifts about in molecular clouds, protectively absorbing mutation-inducing ultraviolet solar radiation wavelengths (also linked to immune disorders, cataracts, skin cancer, crop damage). For that reason an international treaty, the Montreal Protocol, was enacted in the mid-1980s to protect the ozone layer against known and unknown (to be discovered in the future) molecules destructive to ozone. That’s the good Dr Jekyll aspect of ozone (with apologies to Strange Case of Dr Jekyll and Mr Hyde author Robert Louis Stevenson).

Closer to Earth’s surface, where the 10% of planetary ozone not in the upper atmosphere resides, metropolitan areas such as Los Angeles and Phoenix suffer from ozone pollution and come under regulatory fire from the U.S. Environmental Protection Agency (EPA) because what is good 12 miles high is harmful at ground level. In “America’s Most Polluted Cities,” Forbes.com’s (04.28.10) Tim Kiladze calls it “harmful ozone, a ground level gas that contributes to urban smog and inflames the lungs, causing shortness of breath, wheezing and throat irritation.” The American Lung Association State of the Air 2010 report web site formulates EPA ozone and particle pollution data for American cities and counties into searchable form.

So, will ozone gas as an alternative to ozone-destroying fumigants like methyl bromide create more ground level ozone pollution or help replenish and preserve the protective stratospheric ozone layer?

“Chemicals can have their seasons, just like fashions. What one age admires as fine, another will reject as folly, and a good example of this is ozone,” writes John Emsley in his 1998 book, Molecules at an Exhibition. “A century ago ozone was also something to worry about, and for exactly the opposite reason: it was thought there was not enough of it around. Ozone was deemed to be natural, wholesome and invigorating, and the very locations where its levels were highest proved this: up in the mountains and along the coasts…Such was the esteem in which the Victorians held ozone that they had generators pumping it into churches, hospitals, theatres and even their underground railways.”

At the 2009 Entomological Society of America (ESA) annual meeting in Indianapolis, ground-level ozone was back in fashion as an environmentally-friendly fumigant molecule (unstable; decomposes quickly). Methyl bromide (another natural molecule) faces demise as a fumigant under the Montreal Protocol for destroying ozone. And stored grain insect pests are becoming resistant to phosphine. Carbon dioxide, a waste gas exhaled by humans and a feedstock of sorts for green plants, has some fumigant potential but is too slow-acting and unfashionable as a warming greenhouse gas.

Though it is easy to pump ozone through hoses into grain bins, ozone does not penetrate the dense grain well and fumigations can last 3-10 days. Purdue University’s Marissa McDonough noted that the grain is more quickly disinfested of red flour beetles (Tribolium castaneum), maize weevils (Sitophilus zeamais) and other pests by physically moving the grain in layers exposed to ozone sprays in passing.

Potency, ease of use, and low cost make for a good fumigant, said Kansas State University’s Mahbub Hasan, who noted that phosphine, sulfuryl fluoride and ozone are all potential alternatives to methyl bromide fumigation for dry-cured hams attacked by red-legged ham beetles (Necrobia rufipes), ham mites (Tyrophagus putrescentiae), cheese skipper flies (Piophila casei) and carpet beetles (Dermestidae). Carbon dioxide was too slow, said Hasan, taking six days to knock out ham mites. An integrated (IPM) approach combining biological controls, cooling, pheromone traps, ozone and botanical fumigants may ultimately be devised for protecting stored foodstuffs.

However, ozone remains out-of-favor in the plant world. “Tomato plants may be more susceptible to wounding by caterpillar pests in ozone than in ambient air,” Western Illinois University’s Sue Hum-Musser told the ESA meeting in Indianapolis. “Several genes play important roles in plant defenses against the combined stress of ozone and insect herbivory. Increasing ozone levels cause damaging effects on the plant community, and insect pests cost billions of dollars to agriculture.”

Fashion is a fickle thing, and future ozone fashions will likely remain a twenty-first century Jekyll and Hyde muddle.