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spite of three books and more than 200 journal publications and book chapters, my files filled with history and unpublished data were headed for the trash bin…the greater my urge to somehow pull the stories together into a single read-through description of my career…unique, it is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


Medicinal Caterpillar Fungus High in Nepal’s Himalayan Mountains

December 27, 2012

CATERPILLAR FUNGI ARE not everybody’s finger food, though their beautifully-sculpted medicinal mushrooms are rich in fiber, amino acids, minerals and vitamins. The caterpillar fungus of commerce, Cordyceps sinensis, grows high in the Himalayan Mountains in the larvae (caterpillars) of equally high-altitude Asian ghost moths (genus Hepialus). An ancient medicine or tonic, caterpillar fungus is in reality part insect (mummified caterpillar) and part fungus; and perhaps a conundrum for vegetarians, who might have to take a pass on its medical benefits because of its animal kingdom (insect) component.

Cordyceps is an abundant resource of useful natural products with various biological activity, and it has been used extensively as a tonic and health supplement for subhealth patients, especially seniors, in China and other Asian countries,” write Kai Yue and colleagues at Sichuan Agricultural University in an article pre-published online in October 2012 in the Royal Pharmaceutical Society’s Journal of Pharmacy and Pharmacology.

For perhaps thousands of years (at least several hundred) in China and other Asian countries, “Cordyceps sinensis (Caterpillar fungus) has been used as a tonic for longevity, endurance, and vitality,” write Chinese Academy of Sciences researchers Zhenquan Liu et al. in an Open Access journal, Behavioral and Brain Functions. “Many studies have shown that Cordyceps sinensis modulates immune responses, inhibits tumor cell proliferation, enhances hepatic function, regulates insulin sensitivity” and modulates steroid production.

“Although Cordyceps sinensis is extensively used in Chinese medicine, it lacks scientific grounds for its efficacy,” write Liu et al. In other words, it has worked like magic for centuries; providing practical benefits, though the exact mechanisms of how it works are unknown or speculative. The Chinese researchers argue that even proponents of modern medicine objecting to traditional natural or folkloric medical treatments could benefit from studying the caterpillar fungus. Their argument is that the research results from studying the mechanisms of how the caterpillar fungus works to heal or prevent disease could also be used to develop more conventional medical or drug treatments.

Caterpillar fungus could be particularly useful for certain brain strokes, where modern medicine lacks effective drugs and treatments. ”The lack of effective and widely applicable pharmacological treatments for ischemic stroke patients may explain a growing interest in traditional medicines,” wrote Liu et al. An example is “self-medication or preventive medicine” to prevent cerebral ischemia. In this type of stroke, brain oxygen levels are too low; which can trigger a cascade of biological events leading to brain damage and death. Caterpillar fungus prevents or protects against this type of brain stroke (“ischemia-induced brain infarction”), presumably by inducing or modulating production of a steroid, 17beta-estradiol.

Cordyceps sinensis mushrooms growing out of golden caterpillar bodies are sometimes artfully and decoratively displayed in high-end Chinese herbal shops. Caterpillar fungus achieved some notoriety when it was revealed to be a dietary supplement for Chinese athletes bringing home gold and silver medals at the 2008 Beijing Olympics.

“In China, this fungus is usually called ‘Dong Chong Xia Cao,’ which means ‘Worm in winter and grass in summer,’” write Kai Yue and colleagues at Sichuan Agricultural University. “This insect parasitizing fungus lives primarily on the head of the larva of one particular species of moth, Hepialus armoricanus Oberthur (Lepidoptera), but is occasionally found growing on other moth species. Cordyceps was first introduced to Western society during the 17th century. In 1878 Saccardo, an Italian scholar, named Cordyceps derived from China officially as Cordyceps sinensis (Berk.) Sacc., and this nomenclature has been adopted up to the present day.”

At a Nepal Overseas Entomologists members symposium at the Entomological Society of America (ESA) annual meeting in Nov. 2012, at the Convention Center in Knoxville, Tennessee, Bhishma Subedi of the Asia Network for Sustainable Agriculture and Bioresources (ANSAB) screened a 20-30 minute documentary film as part of a talk titled, “Cordyceps sinensis a natural viagara(sic) from the mountains of Nepal.” Even the other Nepali entomologists in attendance learned something new, as the caterpillar fungus is found only in remote Himalayan Mountain locales; and it is not common knowledge, even in Nepal.

Known in Nepal by its Tibetan name, yarsagumba, caterpillar fungus is well-hidden; blending like a camouflaged black joss stick into black soils and grasses on slightly north-facing (5-10 degrees) Himalayan slopes 3,200 to 4,500 meters (10,500 to 14,800 ft) high. Yarsagumba lands are several days trek from anyplace where people normally live, and the ground is covered in snow 6 months of the year. But this is where temporary high-mountain camps must be set up for hunting the difficult-to-find caterpillar fungus.

Searching for the camouflaged black and debris-covered yarsagumba means crawling on hands and knees or bending over among short grasses and melted snow. Men search for yarsagumba and other medicinal herbs in the vicinity, while women stay behind and maintain the base camps. A certain Buddhist purity is maintained in yarsagumba lands; there is no alcohol, no tobacco and no shouting, loud voices or arguing. People pray, and the first yarsagumba found is offered to the Gods.

The beauty of the mountains belie the harshness of the climate and the difficulty of the life in search of yarsagumba; it’s a tough way to earn money in these remote mountains where economic opportunities are few. Storms can come at any time, and it is easy to fall down a steep cliff when climbing in the snow. A fall near a cliff edge can mean loss of limbs and frequently death. There are no second chances, no safety nets to catch you up here. Medical treatment is do-it-yourself, by necessity. Conventional medicine and doctors are many days distant. Widows are commonplace at all ages; and many subsistence families in Nepal have lost husbands, fathers, brothers and sons during the search for yarsagumba and medicinal herbs that may help others prevail against brain strokes and other maladies.

It takes seven cleanings with a toothbrush to remove all the debris and black soil, and make the black yarsagumba look like a proper insect, namely a golden caterpillar. The going price from the middlemen is 80,000 rupees per kilo; with 3,500 to 4,000 pieces of clean golden caterpillars per kilo. It takes five people a month to find a kilo. People are doing well to come out of the season with 60,000 rupees, before the expenses of the trek and weeks or months of camp costs. Recently, the Nepal government imposed a 20,000 rupee per kilo tax or royalty on the trade.

After being steamed and packaged, most of the yarsagumba eventually is exported and finds its way to the Chinese market. The yarsagumba trade is estimated at 2 tons annually. But in Nepal, since the government-imposed 20,000 rupee/kilo royalty or tax went into effect, it was like the yarsagumba harvest had become illegal for Nepal’s subsistence mountain people. Royalties were paid on only 3 kilos in a recent year. Perhaps there is a free market and tax lesson in all this. Or perhaps it is just part of the great wheel of life.