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spite of three books and more than 200 journal publications and book chapters, my files filled with history and unpublished data were headed for the trash bin…the greater my urge to somehow pull the stories together into a single read-through description of my career…unique, it is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.


Sunflower Power & Health

October 10, 2016

WITH PERHAPS 25 MILLION ha (62 million acres) of sunflowers grown for seed oil worldwide, sunflower diseases and pests and their remedies have a global impact. “Sunflower oil can be used as an alternative or additive to diesel fuel to create biodiesel, a clean-burning alternative fuel produced from a renewable resource,” wrote G.J. Seiler, one of many worldwide contributing authors to the Compendium of Sunflower Diseases and Pests, a book produced by the American Phytopathological Society (APS), a scientific group whose essence includes plant doctoring, discerning what makes for healthy versus diseased plants. “Use of the product may decrease farmers’ dependence on petroleum fuels by substituting ‘farm-grown’ fuel for use in diesel engines. For use in diesel engines, sunflower oil requires more extensive purification, including removal of waxes and gums. Minor engine modifications, such as improved fuel filters, are also necessary to burn any vegetable oil. Since the energy content of sunflower oil is less than that of diesel fuel, consumption is greater and power output is less.” However, the high-protein residues leftover from sunflower oil extraction have the right amino acid balance to mix with soybean meal to grow healthy chickens and livestock, a virtuous ecological cycling of sunflower plants.

Indeed, in Argentina’s southern Pampas, if you get the planting times right, sunflower and soybean are compatible as intercrops. Working in agriculture, I observed sunflower border rows or perimeters around conventional crop fields attracting pollinators and natural enemies providing biological control of pests. However, sunflowers are so attractive to beneficial insects that they do not want to leave. Thus, sunflower stalks need vigorous shaking to get green lacewings and natural enemies of aphids and other pests to take flight into adjacent crops needing protection. At the moment, fields of GMO canola producing high quality cooking oil are displacing sunflower fields in many areas. But the APS sunflower Compendium awakened my love for sunflowers, as even the diseases afflicting the plants have a certain beauty under the microscope. So, I can see the APS sunflower Compendium serving as an outstanding library reference for biology teachers and students looking for projects in sunflower-growing areas.

R.M. Harveson opens the APS sunflower Compendium with a brilliantly concise narrative chronicling the journey of sunflower seeds from their native North America to Russia, where innovative plant breeders painstakingly created the first modern sunflower seeds high in oils, providing the platform for today’s worldwide sunflower industry. The Mennonites, an anti-violence religious group migrating from Germany (Prussia) and a war-plagued Europe to Russia in the 1780s for free farm land promised by Catharine the Great, pioneered commercial sunflower oilseed farming in a harsh landscape long thought unsuitable for even subsistence farming. Their descendants were lured to Saskatchewan and Manitoba, Canada to create North America’s sunflower industry. During World War II, when “securing the fields of Ukraine was a major objective of Adolf Hitler’s war on Russia,” sunflower oil was a superior antifreeze, lubricating World War II weapons that froze with conventional gun oils. Joe Pappalardo’s excellent and entertaining book, Sunflowers: The Secret History: The Unauthorized Biography of the World’s Most Beloved Weed (Overlook Press) adds color and specifics, and is cited in Harveson’s “Selected References” in the APS Compendium.

Personally, I love the feel on my head and hair of a shampoo blending organic sunflower oil, citrus oils and herbs; and organic sunflower seeds at breakfast supply trace minerals like zinc, which is often deficient in produce grown in local California soils. Sunflower sap, which occasionally has been used medicinally, contains terpenoid compounds that show potential as alternative botanical pesticides. As ingredients in traditional medicines, wild sunflowers have been used for everything from wound healing and rattlesnake bites to combating infection and pain relief. Modern medical uses include topical oil formulations with sunflower oil to improve skin health, fight fungal infections, relieve inflammation and itchy, dry skin, and in dentistry to improve the gums.

Seed hulls of certain sunflower varieties are traditional sources of yellow, ruby red, purple, and black dyes or colorants (e.g. anthocyanins) useful in body painting, cosmetics, foods and textiles. Indeed, some plant breeders are working on a sunflower seed that would be high in oil and have a ruby red husk or hull that could be extracted to replace commercial synthetic red food dyes. Other researchers see the hulls as useful absorbents for wastewater reclamation. But by far, sunflower seed oils (e.g. NuSun for cooking) are the main sunflower item of commerce, and even trade on the commodities futures markets. Sunflowers seeds like Mammoth Russian for eating and snacking or adding to birdseed blends are important crops, but minor compared to the large acreages of sunflower oilseeds grown worldwide.

For various reasons, sunflowers have not become commercialized as a biotech GMO (Genetically Modified Organism) crop, which makes life easier for organic growers. Though perhaps better known from Van Gogh canvases, sunflowers were experimental subjects on the USA’s Apollo space missions. And “sunflowers have been successfully used as vehicles for the phyto-remediation of soil contaminated with heavy metals and radioactive materials (e.g. following the Chernobyl disaster),” wrote Harveson. In March 2011 after the Great East Japan Earthquake and Fukushima Daiichi Nuclear Power Plant accident, sunflowers and sunchokes were among the “alternative technology” plantings to concentrate and remove from soils radioactive cesium, which emits gamma rays and has a 30-year half life.

Sunchokes or Jerusalem artichokes, perennial sunflowers grown for edible tubers high in inulins, are sometimes recommended for diabetes and cardiovascular diseases, being associated with lowering blood sugar and cholesterol. Indeed, Jerusalem artichoke chips have been tested as a snack food alternative to potato chips for diabetics, being almost devoid of starch and fats. Several dozen other sunflower species are known, including one that is 92% pure natural rubber. Most likely sunchokes and other sunflower species including backyard ornamentals are subject to pests and diseases similar to those described in the APS Compendium.

To prevent pests and diseases, as a kind of insurance, perhaps 95% of commercial sunflower seeds are coated with neonicotinoid pesticides (e.g. thiamethoxam, clothianidin) at planting time, according to Michael Bredeson of South Dakota State University in Brookings at the 2015 joint meeting in Minneapolis of the Entomological Society of America (ESA), the American Society of Agronomy, the Crop Science Society of America, and the Soil Science Society of America. Bredeson studied 11 commercial sunflower fields, and found that “the seed treatment failed to improve yield or decrease herbivores.” In other words, quite apart from whatever effects on honey bees and beneficial organisms higher in the food chain, the neonicotinoid seed treatments are mostly a waste of resources and money. Though perhaps they do buy peace of mind for commercial sunflower growers, much like any insurance policy.

But the peace of mind bought by unnecessary early-season pesticide seed treatments may bring ecological food chain effects that cost sunflower growers more money and crop loss later in the season. The neonicotinoid pesticides may enter the food chain via plant nectar, plant tissues and predator consumption of tainted prey. Indeed, Pablo Gontijo and colleagues (2015) reported that sunflower seeds treated with thiamethoxam poisoned minute pirate bugs (Orius insidiosus), which are major predators of aphids, caterpillars, spider mites and other pests. Part of the problem is that the beneficial bugs, besides eating pests, also suck moisture directly from plants and thereby become poisoned by systemic pesticides used as sunflower seed treatments.

Likely the poisoned pirate bugs are only the tip of the proverbial iceberg. At the 2015 ESA meeting, Sirilak Lankaew from RYFCRC in Rayong, Thailand reported that cassava cuttings treated preventively with thiamethoxam provided 1-2 months cassava mealybug protection at the cost of food chain effects on beneficial insects via poisoned cassava nectar. Specifically the wasp Anagyrus lopezi, a cassava mealybug natural enemy, feed on the poisoned cassava nectar and “experience acute mortality for up to 21 days after treatment, and have significantly reduced lifespan for at least 42 days after treatment.” With 8 million farming households in Thailand growing cassava and 70% of Thailand’s small-scale farmers using neonicotinoid pesticides, there is a need for alternative technologies “fully compatible with (naturally-occurring and cost-free) biological control.” In sunflower, something like the APS Compendium to identify the potential problems is a good first step towards minimizing unnecessary pesticide treatments and developing alternative technologies.

One approach to developing sunflower soils that are disease-free and avoiding seed treatments is the opposite of crop rotation. Namely growing the crop repeatedly in the same soil so that disease organisms build up and then are destroyed by natural biological agents. It is like the predator and prey cycle, where pests buildup to high levels and even cause some damage before being opportunistically exploited and knocked down by their natural enemies. This approach, known as building a disease suppressive soil, can take a few years; and is perhaps best suited to patient organic growers with the wherewithal to weather those tough early years, and possessed of a confidence, hope or faith that the natural cycles will eventually play out. Likely the Mennonites whose experiences Joe Pappalardo recounts in his book took this route in turning the barren Ukraine, Russian and Canadian lands into productive agricultural fields in the era predating intensive chemical agriculture.

Another interesting alternative technology with ancient roots is interplanting, the idea of mixing different crops in the same fields. In Pakistan, sunflowers are being considered as a healthful alternative for local cooking oil shortages via interplanting sunflowers with the staple mungbean crop. In Florida, sunflower strips have been proven to attract honey bees and a variety of predators and parasitoids supplying natural biological pest control to adjacent organic vegetables. In China, parts of Asia and Africa, and even the Americas, sunflowers are viewed as an alternative technology to reduce herbicide use. Sunflowers provide natural weed control via shading the ground and natural herbicidal compounds (allelochemicals) toxic to some of the world’s worst weeds, such as dodder and barnyard grass. Multiple benefits if you can get rid of a weed patch, produce beneficial insects and pollinators, and harvest some seeds at the same time.

The health benefits of sunflowers will likely be a key driver for this crop in the future, though medicinal sunflower benefits are far from the cutting edge of agriculture and medical research in the genomic era. Broader medical applications may involve anti-inflammatory and cardiovascular benefits, bone health, detoxification, skin protection (e.g. from light & anti-aging) and anti-cancer effects. Applied to the skin, sunflower oil formulations may reduce bacterial and fungal infections, and are touted by some for premature newborns. In Cuba a product called Oleozon, sunflower oil treated with ozone gas, was registered in 1999 to treat fungal skin diseases (tinea pedis); and can stop bacteria and viruses resistant to multiple drugs.

Interestingly, researchers in Iran writing in the Journal of Food Science and Technology like the idea of infusing highly unsaturated oils like sunflower seed oil with raspberry or related Rubus species (e.g. blackberries) as a GRAS (Generally Recognized As Safe) alternative to preservatives like BHA and BHT. Rubus leaves add other medicinal properties to sunflower oil, “including as astringent, hypoglycemic, anti-diarrhea, anti-inflammatory agents for mucous membrane of oral cavity (mouth) and throat.” Many other oils and herbs may have medicinal value when combined with high linoleic acid sunflower oil. Time will tell.

The whole idea of plant medicines may yet return to modern medical practices for a variety of reasons. “Extended life expectancy is accompanied with an increase in age-related pathologies that include cardiovascular and neurological diseases, obesity, and cancer, conditions that are inflicting an immense pressure on health care costs and quality of life,” write researchers Andrea Doseff and Erich Grotewold at The Ohio State University and Arti Parihar in Ujjain, India, in the book, Pigments in Fruits and Vegetables (Springer, 2015). “Thus, there has been an increased interest in recognizing and understanding the mechanisms of action of active nutritional compounds with health benefits, or nutraceuticals, for the prevention and treatment of various diseases.”

The researchers in India and Ohio note that over 8,000 flavonoid chemicals beyond vitamins have been identified, including a range of anthocyanins like those in sunflowers, “which are responsible for providing colors to fruits and vegetables, and have dietary value as color additives with potential health benefits.” Over 10,000 tons per year of anthocyanins from black grapes alone are consumed every year, and this whole general category of plant pigment compounds has “uses in the prevention and treatment of inflammatory diseases including cardiovascular diseases, obesity, and cancers.” Who knows what concentrated research into sunflowers would reveal?

Coffee Grounds for Mosquito Control

August 2, 2009

RECYCLE BIODEGRADABLE coffee grounds and simultaneously knockdown mosquitoes vectoring dengue, yellow fever, West Nile virus, malaria and other diseases. Hermione Bicudo at Universidade Estadual Paulista in Sao Paulo, Brazil, has been working towards that goal since the early 1980s. Mosquito control alternatives are needed, as mosquitoes are rapid, prolific breeders that rapidly develop resistance to pyrethroid, organophosphate and other types of insecticides.

Bicudo’s lab began studying caffeine effects on Drosophila fruit flies in the early 1980s. Drosophila fruit flies are a model insect widely used from the early twentieth century to unravel the mysteries of inheritance and genetics. Caffeine has been used relatively safely for centuries, and is found in medicines, cosmetics and food and beverages like coffee, tea, guarana and chocolate. Used coffee grounds are a ubiquitous waste product in modern caffeinated societies.

A resurgence of yellow fever mosquito, Aedes aegypti, in Brazil prompted Bicudo’s lab to test whether deleterious caffeine effects on Drosophila fruit flies (e.g. less frequent mating, less egg laying capacity, shorter life spans) might also slow mosquito population growth. Approximately four full soup spoons of used coffee grounds in a 250 mL glass of water killed 100% of aquatic mosquito larvae. This translated into fewer adult mosquitoes (the biting, blood-sucking stage) and less new mosquito egg laying (thus, lower mosquito populations over time). Used coffee grounds also have fertilizer value for plants, and can be dusted onto Bromeliads and other garden plants (possibly also puddles, ponds, tree holes, used tire breeding sites, etc.) where accumulated water forms potential mosquito breeding sites.

In contrast to other researchers, Bicuda’s lab found that caffeine solutions became more effective against mosquitoes with age. Day-old caffeine solutions took 20 days to kill 100% of mosquito larave; 25-day old caffeine solutions killed 100% of mosquito larvae in 1 day. Combined with elimination of mosquito breeding sites, used coffee grounds or caffeine solutions could prove very useful in IPM (integrated pest management) programs to slow pesticide resistance and reduce mosquito breeding.