Archive | The Study – Deconstructed

Sourcing the Menu: Background on GMO

By Lewis Perdue on July 24, 2019 in The Study – Deconstructed

NOTE: This is an edited version of portions of Appendices 3 of the “Revised Stealth Syndromes Study Protocol as approved by the University of California San Francisco Medical School Committee on Human Research. We will avoid products known to have GMO ingredients. While the debate on potential negative effects has not reached a scientific consensus, […]

Sourcing the menu: Sugar and sweeteners

By Lewis Perdue on July 24, 2019 in The Study – Deconstructed

NOTE: This is an edited version of portions of Appendices 3 of the “Revised Stealth Syndromes Study Protocol as approved by the University of California San Francisco Medical School Committee on Human Research. No refined sugar or sugar substitutes will be allowed in this diet. Sugar undergoes extensive processing from harvest to store and has […]

Sourcing the Menu: Fish

By Lewis Perdue on July 24, 2019 in The Study – Deconstructed

NOTE: This is an edited version of portions of Appendices 2 & 3 of the “Revised Stealth Syndromes Study Protocol as approved by the University of California San Francisco Medical School Committee on Human Research. Standards and Sourcing (From Appendix 2) Fish not allowed. Water pollution and microplastics also prohibit its inclusion. Rationale (From Appendix […]

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Supplemental Information – Best Practices Index

Basic scientific lab standards — Best practices for a replicable dietary intervention

NOTES: All of the best practices described below have been developed and hands-on tested in an actual dietary intervention study as feasible and minimally disruptive in a commercial-standard kitchen. The kitchen must be treated as a laboratory; a recipe is a protocol; foods are reagents; every item used in preparation and cooking is equipment and instrumentation; detailed notes must be captured on every item, step, and procedure. CARDINAL COROLLARY#1: You must know, and disclose: the exact composition and source of every ingredient, item, and piece of equipment. CARDINAL COROLLARY #2: The exact ingredients, items, and pieces of equipment must be readily available to the broadest geographical spectrum of investigators. CARDINAL COROLLARY #3: The preparation environment must be precisely and completely described in a manner that it can be duplicated by other investigators. CARDINAL COROLLARY #4: Rely only on data that you have observed and collected. Do not use self-reported or memory-based information or rely on un-monitored test subject compliance. Accuracy and replicability depend upon using precise methods under identical conditions using identical materials, reagents, apparatus, and test subjects. Unfortunately, human dietary intervention studies located in a search of the scientific literature are fatally confounded by the failure to employ basic scientific methods that are standard in bench experiments. In addition to these shortcomings, dietary intervention studies treat the kitchen as a black box to be provided by caterers, institutional kitchens, or even test subject memories. (Black Box meals: A look at five dietary intervention studies. ) Most studies involving BPA and phthalates have given general instructions to food preparers to use only “fresh” ingredients and to avoid any plastic contact. However, specific food sources and the details of their production are not available. Neither are specific cooking protocols nor the identities of the utensils, pots, pans, cleaning regimen (surfactants an issue), recipes, or ingredients (processing & methyl contributors an issue). Data regarding those conditions cannot account for the wide variability of contamination in the growing, processing, and sourcing stages. As a result, instructions in previous dietary studies account only for contamination transfer from food packaging materials and preparation. No studies have been found that succeed in quantitatively parsing the growing, production, and processing contamination from that of food contact materials and preparation. Unlike clinical blood panels and mass spectrometer tests which have accepted standards, meals — even those using the same recipes — are rife with confounding factors to which no laboratory-quality standards have ever been addressed. Few chefs, other than bakers, adhere to the precise requirements of recipes. And even bakers can be confounded by variations in measurements, sourced materials, timing, and baking temperatures. This is a first effort at applying the basic principals of laboratory bench science protocols and practices to a kitchen responsible for dietary intervention meals. Best bench science practices in the kitchen developed in a study of the effects of Bisphenol A and Inflammation. Non-food exposures Numerous non-food sources of BPA are present in the environment and likely pose significant “background” contamination which will vary depending upon the test subjects’ lifestyles and environments. This is particularly critical because major health effects including estrogen/testosterone disruptions, inflammation, and metabolic events such as insulin resistance and lipid imbalance, can be affected by low doses of scores of chemicals. For more on this see: Reducing Non-Food Exposures. Sanitation/Hygiene As with all appropriate bench science work, preparation surfaces should be non-reactive, non-porous, resistant to chemicals, heat, and easy to clean. Stone or ceramic tiles can accumulate contaminants in grout. Sealants will contain polymers. Polymer-based surfaces cannot be used. Dietary interventions also require that preparation surfaces must be efficient to maintain hygiene in the event that food makes incidental contact. Stainless steel offers all of those characteristics which is why professional and health-department approved kitchens are almost totally stainless steel. Environment – Floor, walls, ventilation PM2.5 Constant ventilation of HEPA-filtered air is vital to prevent contamination of food with polymer-based particles which can confound results. Air should be constantly monitored throughout the trial and records kept. The type and age of the HVAC system should be noted as well as the type of filter used and the ducting materials (metal versus plastic). Immediately after dusting, the HVAC filter should be changed and the system fan run continuously for four hours to collect as much dust as possible which has been stirred up from cleaning. A fresh filter should then be installed. HEPA-class air purifier use should report the make, model, capacity, and whether it is portable or installed with the HVAC system. If portable, the location should be noted along with the distance from the HVAC air return. PurpleAir is an accurate and cost-effective solution for monitoring. Other than the cost of the sensor ($179), monitoring is free and historical data can be downloaded and saved. Cleaning Protocol – Floors Polymer-based materials are universally found in professional and institutional kitchens given to their durability and ease of cleaning. However, friction against the floor caused by shoes and rolling carts inevitably creates ultra-fine particles many of which qualify as PM2.5 which — regardless of chemical composition — cause inflammation when inhaled. Significantly, many of the polymers from which flooring is made (such as polyvinyl chloride) have known health effects and can contaminate food destined for test subjects. For this and standard hygiene reasons, floors should be wet-mopped with at the end of every food preparation day. The cleaner for this task and food preparation surfaces should be hypochlorite-based and free of surfactants such as ethoxylates that have been shown to cause health effects. Spills and other unanticipated incidents should be cleaned with water — minus cleaning agents — when possible. Exceptions should be noted in the list of materials. Cleaning Protocol – Preparation Surfaces The same cleaning agents and protocols should be employed. No paper towels. Towels – Sourcing and Washing Only 100% cotton towels should be used. The source should be noted in the list of materials. Before first use, study towels should be washed and dried twice to remove […]
Why a Dormitory Setting is Needed for replication and valid causal conclusions in Dietary Intervention Studies

Non-food-exposures (NFEs) — including environmental conditions — are so numerous and variable that a precise replication of those is impractical and, perhaps, impossible. See: Reducing Non-Food Exposures in dietary intervention studies. Plastic contamination is inescapable. Plastic micro-and nanoparticles — as well as the chemical compounds used to produce the polymers — are ubiquitous in the environment and present formidable confounding factors that make it impossible to establish causal relationships between a single chemical and measured human health outcomes. Expense and Practicality Issues As we proceeded to implement our original study protocol, we were continually confronted with a self-reinforcing cascade of confounding factors. Among these confounding factors we discovered were: Extreme variations among published studies that measured BPA and phthalate concentrations in many common food items.[i],[ii],[iii],[iv],[v],[vi],[vii] Evidence of inherent contamination in production and processing and not solely from food contact materials.[viii],[ix],[x],[xi],[xii],[xiii],[xiv] Ubiquitous contamination of all commonly available foods. See Appendix 3. The necessity to test every food ingredient for nutrition and contamination levels. Substantial controls that needed to be imposed on non-food contamination sources. Lengthy testing regime a barrier to subject compliance. Those chemicals exist in, and are mostly inseparable from: the air, food, dishes, non-stick coatings, water, clothing, surroundings (floors, walls, draperies, fabric coverings etc.), polymer gloves, thermal cash register receipts and an unknowable number of other sources. What’s more, the consistency of those contaminants change over time and place and will vary from person to person. Given the vast nature of confounding factors, it is not surprising that dietary intervention studies studying the effects of Bisphenol A (BPA) are inconsistent, not replicable and, on the whole, incapable of supporting a causal relationship. Without a valid, causal relationship, it is not possible for a clinician or other health professional to make fact-based recommendations to their patients and clients. Likewise, regulatory decisions based upon those are not based on solid science and subject to endless arguments among scientists. What factors need to be considered? Within the bounds of the possible, a proper dormitory environment will will minimize confounding factors by providing the same environment — air, water, food — for all study participants. Minimize the use of, and contact with plastic. Towels, napkins and all other cloth material will be 100% cotton. All cotton fabric will be sourced from that which is grown organically, without pesticides. All items will be laboratory tested for pesticide and plastic residues. Bedding will be 100% cotton. Multiple layers will be installed to minimize migration of plastic from sanitary mattress covers which are expected to block migration from mattress materials. Subjects will be provided with a choice of all-cotton under-garments (possibly scrubs). All cotton outerwear will be provided. All garments will be pre-washed multiple (TBD) times to reduce/remove sizing or possible plastics contamination. All garments will be changed daily. Study-issued socks and slippers will be issued. Exercise shoes and cotton socks to be allowed in the ventilated exercise area only. Shoes must not be worn outside that area. Rooms will be identically equipped and all surfaces cleaned with an acceptable detergent and implements. If dormitory flooring is vinyl or polymer based, all chair legs will be covered with a sock-like cotton covering to reduce microplastic contamination. No chairs with rolling wheels will be permitted. Air monitoring for PM 2.5 New HVAC air filters will be installed. Portable HEPA air filters will be employed. Number TBD Access to the dormitory will be restricted to study-related personnel Tub bathing will be allowed every 2 days. No showers will be allowed due to aerosolization of plastic chemicals and nanoparticles. Opportunities for exercise must be investigated, but remain problematic because of the use of plastics in exercise equipment. This may be possible by the use of proper ventilation to remove plastic contamination from leaching and frictional shedding of micro/nanoplastics. Psychological factors must be considered and resolved including need for privacy, minimum stress (to reduce cortisol levels), possible conflicts among study participants. This will be particularly important for sleeping arrangements unless it’s possible to provide a private room for each participant. Creative partitioning in multiple-occupant rooms might provide a solution. In addition to other screening requirements for potential participants, should study subjects be screened psychologically for their suitability to comply with the protocol and to interface appropriately with other subjects. Broadband internet access [i] Fasano, E., Bono-Blay, F., Cirillo, T., Montuori, P., and Lacorte, S. 2012. Migration of phthalates, alkylphenols, bisphenol A and di(2-ethylhexyl)adipate from food packaging. Food Control 27(1): 132-138. [ii] Serrano, S.E., Braun, J., Trasande, L., Dills, R., and Sathyanarayana, S. 2014. Phthalates and diet: a review of the food monitoring and epidemiology data. Environmental Health 13: 43. [iii] Guart, A., Bono-Blay, F., Borrell, A., and Lacorte, S. 2011. Migration of plasticizers phthalates, bisphenol A and alkylphenols from plastic containers and evaluation of risk. Food Additives & Contaminants Part A: Chemistry, Analysis, Control, Exposure & Risk Assessment 25(5): 676-685. [iv] Bhunia, K., Sablani, S.S., Tang, J., and Rasco, B. 2013. Migration of chemical compounds from packaging polymers during microwave, conventional heat treatment, and storage. Comprehensive Reviews in Food Science and Food Safety 12(5): 523-545. [v] Bang, D.Y., Kyung, M., Kim, M.J., Jung, B.Y., Cho, M.C., Choi, S.M., Kim, Y.W., Lim, S.K., Lim, D.S., Won, A.J., Kwack, S.J., Lee, Y., Kim, H.S., and Lee, B.M. 2012. Human risk assessment of endocrine-disrupting chemicals derived from plastic food containers. Comprehensive Reviews in Food Science and Food Safety 11(5): 453-470. [vi] Groh, K.J., Geuke, B., and Muncke, J. 2017. Food contact materials and gut health: Implications for toxicity assessment and relevance of high molecular weight migrants. Food and Chemical Toxicology 109(1): 1-18. [vii] Bittner, G.D., Denison, M.S., Yang, C.Z., Stoner, M.A., and He, G. 2014. Chemicals having estrogenic activity can be released from some bisphenol a-free hard and clear, thermoplastic resins. Environmental Health 13: 103. [viii] Schecter, A., Lorber, M., Guo, Y., Wu, Q., Yun, S.H., Kannan, K., Hommel, M., Imran, N., Hynan, L.S., Cheng, D., Colacino, J.A., and Birnbaum, L.S. 2013. Phthalate concentrations and dietary exposure from food purchased in New […]
Indexing in progress and regularly updated

Please be patient. A massive amount of information and photos on apparatus, food sourcing, preparation and other protocol-related data are being uploaded as swifty as possible given limited resources. Basic scientific principles designed to establish causality. Scientific standards and food-related laboratory best practices Black Box meals Controlling non-food exposures, Co-confounding factors and micro-nutrients. The problem with animal models. How food processing adds plastic-derived chemical contamination Best practices — Herbs and Spices: Powerful in small amounts, precise measurement needed Best Practices Backgrounder: Micro- and Nanoplastics Best practices: Herbs and Spices – avoiding contamination Best practices – Spices: Make your own baking powder Best practices: Scale calibration Prepping bacon and lunch meat ham to minimize plastic packaging contamination. Avoiding plastic contamination when storing food. Best practices: De-waxing apples Best practices — Sourcing Dairy: Milk, Cheese, Yogurt, Butter methods and barriers Best practices: Sourcing cheese & butter and minimizing plastic contamination from packaging.

Supplemental Information – Apparatus, Formulae (Recipes), Reagents (Food)

Professional-grade Kitchen – Wood, Glass & Stainless Steel

We removed the flowers and other non-investigation materials.
How Strict Rules on Sourcing Dairy Proved impossible — and Would Have Hurt Reproducibility As Well

Dairy has many opportunities for plastic contamination For dairy products, we created an ultra-strict sourcing protocol that assumed that the introduction of plastic chemicals into the dairy food chain begins with the milking process. That strict protocol had to be drastically altered will be described below. To consumers, the most obvious connection between plastic and dairy products comes in packaging — shrink wrap, plastic bottles (“paper” bottles have plastic coatings), plastic yogurt containers, butter in plastic tubs or wrapped in paper impregnated with chemicals. Additionally, previous studies — including dietary interventions — have focused primarily on packaging materials as sources of contamination. H0wever, the dairy chain’s many contamination sources from plastic-derived chemicals (BPA and phthalates involves numerouds additional contacts with plastic and other chemicals before it reaches the consumer. Some of those contacts include: include “teat washes” to clean and disinfect cow udders, as well: polymer filters to screen out dairy and other foreign matter, hoses to transfer raw milk from the milking machine to holding tanks, hoses to transfer milk from holding tanks to transport tankers whose stainless steel tanks may have polymer liners and potentially traces of chemicals used for disinfection. More hoses are used to transfer milk from tanker trucks to the creamery which uses a variety of plastic and stainless steel components to process the milk and get it ready for sale to tee consumer. In addition, once at the creamery, there are polymer-based components used for the movement of milk through filtering, pasteurization, cream separation, homogenization, and finished packaging. Dairy contamination begins with what the cow eats While there are few studies studying the presence of plastic chemicals in milk produced by American dairy cows, work in Europe <citations to be added here and elsewhere in final version> indicates that milk produced in warmer weather when cows are eating in pastures seems to have fewer contaminants than when they are fed manufactured (processed) feed in colder weather. Because of the extensive contamination from feed to consumption our original approved protocol for sourcing milk demanded that we start as low as possible on the processing chain. That approved protocol required us to obtain certified organic raw milk from cows raised in pastures that were not irrigated. Especially, not irrigated with recycled municipal wastewater which contains scores of pharmaceutical byproducts, illegal drug metabolites, and toxic chemicals. Our plan for the raw milk was to obtain the milk directly from the milking machine. While milking machines use many plastic components, we were prepared to pay for replacing the most common plastic parts with ones that were known not to leach BPA and phthalates. Processing, transparency, source traceability and reproducibility The most reproducible results for our study meant we had to start with the least-contaminated dairy products.The logic dictated that, if we knew where the raw milk came from, we could trace the source for the cheese (for cheeseburgers and sandwiches), the butter (to be used as the only oil for cooking), and the milk products for consumption. That also meant that we would rely on those resulting dairy products were to use in preparing other foods. Because of that, dairy became a foundational role for the study’s entire menu. For more on that, see Menu: Dairy – Milk, Cheese, Yogurt, Butter. In addition, the wide variety of possible materials and used by individual dairies and creameries, plastic contamination levels are likely to vary significantly from one operation to the next. That, we reasoned, would mean that other investigators wishing to replicate our study might could might up with substantially different conclusions unless they obtained raw milk from our source and used the same methods and materials we did to process raw milk. That requirement meant that processing our own raw milk and resulting foods could make our study more reproducible. Because reproducibility is a key foundation of a well-conducted investigation, we were ready to exert the extra effort. Based on this set of assumptions, we hypothesized that the minimum contamination and the best chances of replicability of the study protocol demanded a “back to the future” effort that required us to acquire raw milk — milked by hand (with conditions). Once we had obtained the raw milk, the protocol required that we: Filter the raw milk to remove physical contaminants such as hair. Pasteurize the milk. Separate the cream from the milk. Use the cream to make butter which we would use as our basic fat/oil for cooking. Make yogurt Use the lower-butterfat (approximately 4%) milk from the separation for cooking and direct consumption. Make cheese. By taking on so many basic processing steps, we could minimize plastic contamination by making sure that only glass and stainless steel came in contact with the milk once we had obtained it from the milking machine. Based on our study protocol revision approved by the Committee on Human Research at the University of California San Francisco Medical School, in latye 2018, we began to contact Sonoma and Marin County dairies, creameries, farm organizations, and agriculture-related educational institutions. Unexpectedly, we ran into a stonewall of silence and lack of cooperation from the dairy industry. Over a period of eight months least 43 phone calls and emails to dairies, creameries, went un-returned. We failed to get even a reply from dairies, creameries, farm organizations, ag-oriented educational institutions — even — cheese and yogurt makers — anyone who might know a dairy farm who would cooperate. When that produced no results, we resorted to personal visits and “milk driving” around Sonoma and Marin County looking for any dairy or cheesemaker who might be willing to help direct us to a source of milk. Every door we knocked on remained shut. That included Cooperative Extension and the Farm Bureau. The the dairy industry’s refusal/inability to cooperate set the study back by at least nine months and required a one-year extension by the UCSF Committee on Human Research. That frustrating effort is told in more detail in this DRAFT post “No milk for research!” […]
The Cream Separator From Hell = No Cheese & Butter As Originally Planned. (And Reflected Flawed Logic and Impossible Logistics)

Even if we had solved the reproducibility conflicts with our “close to source, minimum contamination” plans for milk, the final problem was the fact that the only small-production cream separator we could find was full of plastic parts and “stainless steel” that was actually aluminum. That despite the fact that the seller said it contained all food grade stainless steel and contained no plastic So after spending far too much time and effort — eight months — trying to source raw milk, there we were in July 2019 with four major problems to solve for a study that was way behind on time: It was proving to be impossible to obtain raw milk to pasteurize and use in the study <<link>> The cream separator was vital to producing all our dairy products: milk, cheese & butter. More importantly, obtaining raw milk from with the same precise composition as we had secured from the single small producer we had located in Sonoma County would have been practically impossible for another lab to obtain and replicate. Furthermore, that milk was dependent on the plant composition of its specific pasture location — something that would change day to day and season to season. The metal parts — supposedly stainless steel — were highly attracted to magnets. That indicated inferior “stainless” construction.
Oil for cutting boards

For treating wooden cutting boards, in our dietary intervention lab/kitchen, we used olive oil packaged in glass from a local supplier who has minimal plastic components in their oil-making mill. While some food sources suggest that vegetable-based oils will somehow turn rancid in contact with water, we found no evidence of this. We washed and scrubbed the boards frequently — and in hot water when meat was in contact — let them dry thoroughly and applied a modest coating of olive oil. No flavor transfer to food was observed. Avoiding mineral oil We avoided food-grade mineral oil for several reasons: First because many plastic-based chemicals contaminate liquids of all sorts when they leach out into the contents. Plastic contact occurs in both the production and packaging stages. Second, because mineral oils are a products of crude oil production, the origin of the oil is undetermined as it its precise chemical composition given unknown and variable production and packaging. Both of those reasons violate our protocol to eliminate both known and unknown sources of contamination.
Milk Samples: Making aluminum foil barriers to avoid contamination by migration of plastic bottle caps

To avoid possible plastic contamination in the milk samples we sent for Mass Spec testing, we used glass bottles and aluminum foil to prevent sample contact with the plastic cap. This technique also works well in the kitchen when glass storage containers have plastic lids.
Home-made pasta — as UNprocessed as possible.
Pepper – Use a mill and avoid plastic

Like most ground spices, pepper experiences significant plastic contact during processing and packaging. Use whole spices and grind your own.
Cutting boards: Wood=Yes; Plastic=No; Bamboo=questionable

Remember that every abrasion, every knife cut on a plastic cutting board will produce microplastic particles. Tight-grain maple avoids plastic + the fewer glue joints the better. Bamboo has many glue joints, plus the raw material undergoes extensive processing.
Pasta, Plastic Fail!
Pasta, No Plastic
Replacing plastic wrap and bags for bread and pastries
Menu Development, Part 1: Assessing the serious faults in an NIH study to avoid repeating them

In early July 2019, we were brainstorming our final menu planning and decided to see if we could replicate the results of a major NIH study focused on ultra processes foods: “Ultra-processed diets cause excess calorie intake and weight gain: An inpatient randomized controlled trial of ad libitum food intake.” A supplement to that NIH study included the menus they used for theiur study, so we decided to see if we could base our menu on theirs. Because the NIH study was two weeks and ours was six days (focused on plastic derived chemicals which are always found in ultra-processed foods) we decided to choose items from the ultra-processed leg of the NIH study and adapt them for days 1-3 of our study menu. Those same recipes would be used for the second leg of our study using items where ingredients were as free as possible from plastic contaminants. For the reduced plastic chemical leg of our study, we undertook to reverse engineer the items in the first three-days using the least-possible contaminated foods from known replicable sources. We then developed methods and recipes that used extraordinary methods we developed to further reduce possible plastic contamination. Those techniques are described in the “Best Practices” articles on this site. Extensive work underpinning those Best Practices can be found at this link. NIH errors made menu replication impossible Our attempts to replicate the NIH study menu were abandoned in large part because a large number of the supposedly UN-processed food in the NIH menu were contaminated both with plastic-derived chemicals and with food processing additives and processes. The NIH study used pre-prepared foods — many highly processed — and did not have an accurate (or even knowable) food composition. This was obviously as prime reason the NIH investigators never responded to our requests for recipes. They had no recipes and were unaware of the actual composition — or contamination level — of the foods in either leg of their study. This is the same as a chemist working with compounds of unknown composition. And that a major violation of accepted fundamentals of experimental design and practice. Initial menu brainstorming The formal text in the illustrations below are taken from the menu supplement to the NIH study. The hand-written notes are a first pass of brain storming about the recipes we would create for both legs of our study.
Instant Cookers acceptable

Instant cookers with one-pot recipes are popular because they offer convenience and minimal cleanup. Regardless of manufacturer, make sure all interior cooking surfaces are stainless steel. In this case, the seal between the top and the rest of the pot is silicone, but the exposure surface is minimal when the lid is locked down.

Reagents: Consumables and Food

How Strict Rules on Sourcing Dairy Proved impossible — and Would Have Hurt Reproducibility As Well

Dairy has many opportunities for plastic contamination For dairy products, we created an ultra-strict sourcing protocol that assumed that the introduction of plastic chemicals into the dairy food chain begins with the milking process. That strict protocol had to be drastically altered will be described below. To consumers, the most obvious connection between plastic and dairy products comes in packaging — shrink wrap, plastic bottles (“paper” bottles have plastic coatings), plastic yogurt containers, butter in plastic tubs or wrapped in paper impregnated with chemicals. Additionally, previous studies — including dietary interventions — have focused primarily on packaging materials as sources of contamination. H0wever, the dairy chain’s many contamination sources from plastic-derived chemicals (BPA and phthalates involves numerouds additional contacts with plastic and other chemicals before it reaches the consumer. Some of those contacts include: include “teat washes” to clean and disinfect cow udders, as well: polymer filters to screen out dairy and other foreign matter, hoses to transfer raw milk from the milking machine to holding tanks, hoses to transfer milk from holding tanks to transport tankers whose stainless steel tanks may have polymer liners and potentially traces of chemicals used for disinfection. More hoses are used to transfer milk from tanker trucks to the creamery which uses a variety of plastic and stainless steel components to process the milk and get it ready for sale to tee consumer. In addition, once at the creamery, there are polymer-based components used for the movement of milk through filtering, pasteurization, cream separation, homogenization, and finished packaging. Dairy contamination begins with what the cow eats While there are few studies studying the presence of plastic chemicals in milk produced by American dairy cows, work in Europe <citations to be added here and elsewhere in final version> indicates that milk produced in warmer weather when cows are eating in pastures seems to have fewer contaminants than when they are fed manufactured (processed) feed in colder weather. Because of the extensive contamination from feed to consumption our original approved protocol for sourcing milk demanded that we start as low as possible on the processing chain. That approved protocol required us to obtain certified organic raw milk from cows raised in pastures that were not irrigated. Especially, not irrigated with recycled municipal wastewater which contains scores of pharmaceutical byproducts, illegal drug metabolites, and toxic chemicals. Our plan for the raw milk was to obtain the milk directly from the milking machine. While milking machines use many plastic components, we were prepared to pay for replacing the most common plastic parts with ones that were known not to leach BPA and phthalates. Processing, transparency, source traceability and reproducibility The most reproducible results for our study meant we had to start with the least-contaminated dairy products.The logic dictated that, if we knew where the raw milk came from, we could trace the source for the cheese (for cheeseburgers and sandwiches), the butter (to be used as the only oil for cooking), and the milk products for consumption. That also meant that we would rely on those resulting dairy products were to use in preparing other foods. Because of that, dairy became a foundational role for the study’s entire menu. For more on that, see Menu: Dairy – Milk, Cheese, Yogurt, Butter. In addition, the wide variety of possible materials and used by individual dairies and creameries, plastic contamination levels are likely to vary significantly from one operation to the next. That, we reasoned, would mean that other investigators wishing to replicate our study might could might up with substantially different conclusions unless they obtained raw milk from our source and used the same methods and materials we did to process raw milk. That requirement meant that processing our own raw milk and resulting foods could make our study more reproducible. Because reproducibility is a key foundation of a well-conducted investigation, we were ready to exert the extra effort. Based on this set of assumptions, we hypothesized that the minimum contamination and the best chances of replicability of the study protocol demanded a “back to the future” effort that required us to acquire raw milk — milked by hand (with conditions). Once we had obtained the raw milk, the protocol required that we: Filter the raw milk to remove physical contaminants such as hair. Pasteurize the milk. Separate the cream from the milk. Use the cream to make butter which we would use as our basic fat/oil for cooking. Make yogurt Use the lower-butterfat (approximately 4%) milk from the separation for cooking and direct consumption. Make cheese. By taking on so many basic processing steps, we could minimize plastic contamination by making sure that only glass and stainless steel came in contact with the milk once we had obtained it from the milking machine. Based on our study protocol revision approved by the Committee on Human Research at the University of California San Francisco Medical School, in latye 2018, we began to contact Sonoma and Marin County dairies, creameries, farm organizations, and agriculture-related educational institutions. Unexpectedly, we ran into a stonewall of silence and lack of cooperation from the dairy industry. Over a period of eight months least 43 phone calls and emails to dairies, creameries, went un-returned. We failed to get even a reply from dairies, creameries, farm organizations, ag-oriented educational institutions — even — cheese and yogurt makers — anyone who might know a dairy farm who would cooperate. When that produced no results, we resorted to personal visits and “milk driving” around Sonoma and Marin County looking for any dairy or cheesemaker who might be willing to help direct us to a source of milk. Every door we knocked on remained shut. That included Cooperative Extension and the Farm Bureau. The the dairy industry’s refusal/inability to cooperate set the study back by at least nine months and required a one-year extension by the UCSF Committee on Human Research. That frustrating effort is told in more detail in this DRAFT post “No milk for research!” […]
Oil for cutting boards

For treating wooden cutting boards, in our dietary intervention lab/kitchen, we used olive oil packaged in glass from a local supplier who has minimal plastic components in their oil-making mill. While some food sources suggest that vegetable-based oils will somehow turn rancid in contact with water, we found no evidence of this. We washed and scrubbed the boards frequently — and in hot water when meat was in contact — let them dry thoroughly and applied a modest coating of olive oil. No flavor transfer to food was observed. Avoiding mineral oil We avoided food-grade mineral oil for several reasons: First because many plastic-based chemicals contaminate liquids of all sorts when they leach out into the contents. Plastic contact occurs in both the production and packaging stages. Second, because mineral oils are a products of crude oil production, the origin of the oil is undetermined as it its precise chemical composition given unknown and variable production and packaging. Both of those reasons violate our protocol to eliminate both known and unknown sources of contamination.
Study Recipes

Perdue Study Recipes 2019 Kate’s Pasta Dough Ingredients: 280g 00 flour 25g for dusting surfaces 168g whole eggs 32g egg yolks 1.45g salt 7g Baking Olive Oil Directions: Measure ingredients. Make a well on a clean workspace with the flour Make sure the sides are high enough to accommodate liquid ingredients Mix eggs, olive oil, and salt in a separate mixing bowl Pour eggs into well and slowly incorporate flour until it becomes a thick dough Knead dough for 3-5 minutes until elastic Dough should spring back when poked Dust with extra flour if dough remains sticky Let rest at room temperature for 45 minutes Roll out dough into desired shape Cook for 3-4 minutes or until pasta floats Classic Maple Waffles Ingredients: 263g flour 42g honey 6.51g baking powder 3.31g salt 220g whole milk 106g eggs 26g oil Directions: Mix flour, sugar, baking powder and salt in a large bowl Whisk eggs, milk and oil in a separate bowl Gradually incorporate wet mixture into dry ingredients until fully incorporated Let batter sit for 25 minutes at room temperature Pre-heat waffle iron Pour batter on to waffle iron at the center Cook 2 minutes per side Homemade Mayonnaise Ingredients: 50 whole egg 32g lemon juice 154g canola oil 8.37g salt Directions: In bowl of blender or food processor add egg, salt, and lemon juice Turn on to medium-high speed and slowly incorporate oil until combined Continue to beat mixture until it thickens in texture and holds shape Yeastless Focaccia Ingredients: 238g water (room temperature) 250g flour 7g baking powder 5g salt 13g olive oil 2g black peppers 5g crushed garlic 1g dried basil 34g grated Reggiano parmesan cheese Directions: Preheat oven to 425F (220C) Pour water and garlic into bowl of an electric mixer fitted with a dough hook Soft together flour, baking powder, and salt to previous bowl Mix on medium speed until dough forms into a ball Put dough into baking pan Using oiled fingers, spread dough to ½ inch thickness. Make sure there are no holes in the dough Rub top and sides of dough with olive oil. Season with black pepper and basil Bake in preheated oven for 20 minutes Remove from oven and sprinkle with cheese and return to oven Bake for an additional 8 minutes or until golden brown Oven Fries Ingredients: 311g potatoes 22g olive oil Additional 11g to brush baking tray 6g salt 1.25g pepper Directions: Preheat oven to 375F Wash potatoes leaving skin on and cut into desired size Soak potatoes in cold water in sink or bowl for 30 minutes then remove and dry well Toss in oil and seasonings Place on greased tray and bake for 20 minutes, then turn the oven up to 425F and cook 15 minutes or until fries are golden. “Boring” Baked Chicken Ingredients: 662g boneless chicken breasts w/ skin 22g olive oil Directions: Preheat oven to 450F Brush making sheet with 11g olive oil Baste chicken with 11g olive oil Cook for 10 minutes and flip Baste with oil already in pan Cook another 15-20 minutes or until internal temperature is at least 165F at the thickest part Put on platter and cover loosely with tin foil to cool Olive Oil Roasted Almonds Ingredients: 469g whole raw almonds 26g olive oil 12g salt Directions: Preheat oven to 350F In a medium bowl toss all ingredients together until evenly coated Spread onto a single layer in baking tray Roast for 10 minutes, stir, and continue to roast for 5-8 minutes or until lightly browned Watch carefully as they can burn easily Cool completely on baking sheet until storing in an airtight container Basic Quick Bread Ingredients: 286g flour 15g baking powder 2g salt 160g eggs, room temperature 373g whole milk 77g canola oil Directions: Preheat oven to 350F (177C) and prepare a 9” x 5” (23cm x 13cm) loaf pan with light butter In a large mixing bowl whisk together flour, baking powder and salt. In a separate mixing bowl combine eggs, milk and oil. Pour liquid ingredients into dry ingredients and using a spoon stir the two together until combined Do not over mix the dough. The more you mix the tougher the bread becomes Pour batter into loaf pan and bake for 40-45 minutes or until a toothpick inserted in the center comes out with moist crumb Baked Macaroni and Cheese Ingredients: 105g pasta 15g butter 14g bread crumbs 70g minced onion 5g flour 1.75g salt 1g pepper 355g whole milk 227g shredded cheddar cheese Directions: Prepare pasta in boiling water (about 2 minutes) Preheat oven to 350F and grease 2 quart casserole dish with 3g butter In a saucepan, melt 12g butter, add onion until tender (aprox 3 min) Stir in flour, salt and pepper until blended gradually stir in milk and cheese until smooth Place pasta in casserole dish and pour cheese sauce over pasta, mixing lightly. Sprinkle breadcrumbs over top Bake 18-20 minutes or until bubbly and golden brown Greek Olive Oil Cinnamon Cookies Ingredients: 100g canola oil 100g honey 6.5g butter 66g maple syrup 77g orange juice 278g flour 5.46g baking powder 2.55g baking soda 1g cinnamon Directions: Preheat oven to 350F (180C) In a large bowl mix oil, honey, syrup and orange juice In a smaller bowl mix together flour, baking powder, baking soda, and. Cinnamon Gradually add dry mixture to wet mixture until a soft dough is formed Cover dough and let it sit for 10 minutes Grease a pan with 6.5g of butter Bake 15-17 minutes Beef Stock Ingredients: 2.75 lbs beef stock bones (plenty of marrow) 10g olive oil (per pan) 295g yellow onion, peeled and quartered 106g carrot cut into 1 inch segments 50g celery 27g parsley 8g garlic 1g bay leaves .42g […]
Best Practices: Spices/Black pepper

Best practices for spices and pepper mills.

Appendices to the study

Revised Stealth Syndromes Human Study Protocol- APPENDIX 1 – Reproducibility

REPRODUCIBILITY – THE SCIENTIFIC PROBLEM THAT DEMANDED ENHANCED SOURCING OF THE STUDY DIET Reproducibility + Confounding factors drive changes, increase complexity, & costs Reproducibility is the acid test of properly done studies that produce valid data. In the past couple of years, the “reproducibility crisis” has been the subject of numerous scholarly articles and comments. The most data-based is this one from Nature (1,500 scientists lift the lid on reproducibility Survey sheds light on the ‘crisis’ rocking research.). That article found that: “More than 70% of researchers have tried and failed to reproduce another scientist’s experiments, and more than half have failed to reproduce their own experiments.” While data do not indicate a substantial rise in irreproducible results, the persistence of non-replicable studies is unacceptable. We should not add to that phenomenon. See also: When Quality Beats Quantity: Decision Theory, Drug Discovery, and the Reproducibility Crisis Opinion: Is science really facing a reproducibility crisis, and do we need it to?
Revised Stealth Syndromes Human Study Protocol – APPENDIX 2 – Detailed parameters of intervention diet selections

PLEASE NOTE: Extensive photographs and study documenting the following items will be added as time allows after the main study text is finished. Those photos to be added are of apparatus, supplies, utensils, and will demonstrate methods used to further decrease plastic contamination in intervention foods whose surfaces were potentially contaminated by contact with plastic packaging. Water All water consumed and/or used for cooking, washing, drinking or used to irrigate self-grown plants will be obtained from a commercial device using a solid-block carbon filter and certified by NSF for reduction of BPA and phthalates. One such device is the Aquaversa filter from Multipure which uses a carbon block filter that lists BPA among its contaminant reduction list. The list does not mention phthalates. However, the list does cover many chemical with similar phenolic structures. If study funds are available, it would be valuable to determine BPA and phthalate levels in the water water before the filter and afterwards. In addition, independently published research indicates that other types of carbon filters are effective in reducing many harmful compounds including organic chemicals. Effects of activated carbon types and service life on removal of endocrine disrupting chemicals: amitrol, nonylphenol, and bisphenol-A. Adsorption characteristics of selected pharmaceuticals and an endocrine disrupting compound—Naproxen, carbamazepine and nonylphenol—on activated carbon Bisphenol A Removal from Water by Activated Carbon. Effects of Carbon Characteristics and Solution Chemistry, Environmental Science and Technology, 39 (16) (2005), pp. 6246-6250 Beverages Coffee Only locally roasted and ground beans will be used. Provider will be selected on the smallest amount of plastic involved. Beans and grounds will be handled with metal or glass only and packed in glass jars. Beans will be ground in a mill with no plastic components. The beans will be prepared using either an all glass and stainless steel French press or a stainless steel percolator with all metal parts. Also acceptable is the Moka pot-style espresso maker or a pour-over, glass and metal coffee maker with water from an all metal tea kettle. All metal wire basket for grounds must be used, no filter paper. If an automatic drip system can be located with no plastic ever touching the water or coffee stream, that will be obtained and used. The weakest links in drip coffee makers that appear to be all glass and/or metal usually lies in plastic tubing that connects the heating element to the water reservoir, the hot water application tube, and the filter basket. Tea No tea will be allowed. Like spices, the extensive harvest, curing, processing, and packaging offers many contamination routes. Also like spices, the tiny fragments that compose tea increase the surface area capable of acquiring chemical contamination. Soft drinks Highly processed. Not allowed in the study diet. Fruit juice No commercial juices allowed. Highly processed. Not allowed in the study diet. Freshly prepares using no plastic contact. In general, whole fruits are a healthier alternative to juices. Beer and wine No commercial products allowed. All are extensively processed using plastic. Sourcing ingredients All food items will be sourced from the provider. All provider locations will be personally visited and inspections made of their premises, equipment and processes. Beef, lamb, chicken, pork, fish Minimum standards: Organic certification, no plastic in growing, harvesting, handling, or packaging. All animals must be free-range. Even if allowed by exceptions to organic regulations: No commercial fertilizers, pesticides, or recycled wastewater irrigation are allowed in this study. No irrigation of pasture and feeding areas is preferred. Drinking water from well or municipal water only. No PVC or other plastics. Beef and lamb must be grass-fed and comply with AGA Statement of Best Practices. Preference given to non-irrigated pasturing. For welfare of animals, supplemental hay is allowed but must come from non-irrigated pasture. Possible source: Crowd Cow Slaughter standards Must be humane. Solid cuts of meat only. No sausage or ground meat. Slaughter to avoid all plastic contact unless absolutely vital for health and hygiene. Nitrile gloves. Finished cuts to be placed in glass containers covered with aluminum foil (not in contact with meat) and finally sealed with a plastic lid. Beef, lamb & goat Lean cuts (minimum marbling) on beef and lamb. Lower fat content helps minimize lipophilic content. Visible fat to be removed before cooking to minimize lipophilic concentration. Chicken Skin to remain on chicken, to be removed before cooking to minimize lipophilic concentration. Breasts only for chicken. Pork, fish Not included in the study diet. Diet and subsequent flesh contamination are extremely hard to control or monitor. Study note: An exception was made for organic, un-smoked bacon because the intervention diet needed to include a version of the all-American bacon cheeseburger. An exception was also made to use organic sliced ham (minimal water, no preservatives) in a ham and cheese sandwich. Dairy Same water, feed, and pasturing requirements as beef, lamb, and goat. Udder and teat cleaning and treatments for animal welfare and human hygiene must be examined for plastic exposures and contamination minimized. Milking must be done preferably by hand or using milk machines certified as BPA and phthalate-free. Nitrile gloves to be used. All collected milk must be in stainless steel vessels. Filtering stages cannot use polymer filters. Separation, homogenization (if any) and pasteurization must be plastic free. Glass containers must be used for bottling of milk. Cream gathered during the separation process will either be used for cheese or discarded to minimize lipophilic contaminate concentration. Cheese will be made using milk prepared as described above. Preference will be given to low- or moderate-butterfat cheeses. The cheese process will use stainless steel in the initial heating processes. Curds will be gathered and drained in stainless-steel wire baskets. The whey will be discarded. Drained curds will be pressed in stainless steel molds. Finished cheese will be packed in aluminum foil then placed in Ziploc-type airtight containers. Note: Ziploc claims to be BPA free but has not addressed phthalates. It is also unknown whether “BPA free” means a switch to a Bisphenol analog such as BPS. […]
Revised Stealth Syndromes Human Study Protocol – APPENDIX 4 – Additional references: Non-food contamination sources

Xenobiotic Organic Compounds in Greywater and Environmental Health Impacts Phthalates in Indoor Dust and Their Association with Building Characteristics Green Chemistry and the Search for New Plasticizers Overview of air pollution and endocrine disorders Neurotoxicity of fragrance compounds: A review Poly(Vinyl Chloride) Green Chemistry in Textiles Formaldehyde in your fabrics Toxic Free Supply Chain for Textiles and Clothing Bisphenols, Benzophenones, and Bisphenol A Diglycidyl Ethers in Textiles and Infant Clothing Eco-testing of textiles By K. Amutha, K. Saranya Phthalates in cosmetic and personal care products: Concentrations and possible dermal exposure Hazardous substances in plastics: – ways to increase recycling Green Chemistry and the Search for New Plasticizers Characterization of phthalates exposure and risk for cosmetics and perfume sales clerks Risk assessment to human health: Consumer exposure to ingredients in air fresheners Xenobiotic Organic Compounds in Greywater and Environmental Health Impacts Overview of air pollution and endocrine disorders Personal care product use as a predictor of urinary concentrations of certain phthalates, parabens, and phenols in the HERMOSA study Possible endocrine disrupting effects of parabens and their metabolites Phthalates in Indoor Dust and Their Association with Building Characteristics Fragrance compounds: The wolves in sheep’s clothings Development of an Endocrine Disrupting Compounds Footprint Calculator Determination of phthalate esters in cleaning and personal care products by dispersive liquid–liquid microextraction and liquid chromatography–tandem mass spectrometry Characterization of phthalates exposure and risk for cosmetics and perfume sales clerks Risk assessment to human health: Consumer exposure to ingredients in air fresheners *PDF: FINAL REPORT — Study on the Link Between Allergic Reactions and Chemicals in Textile Products Principal European Commission, DG Enterprise and Industry *PDF: Phthalates and Their Alternatives: Health and Environmental Concerns – VALUABLE FOR LIST Can That New Car Smell Harm You? Or Someone Else? Reprinted by permission from the Feb. 9, 2014 issue of Nano Active By Lewis Perdue Driving with the windows down when you are tired may keep you awake in more ways than just the sounds and tactile effects of air currents. It could also keep you from being poisoned and, perhaps, prevent you from killing someone. Take, for instance, Navindra Kumar Jain, a 63-year-old retired Silicon Valley tech executive who told police that the intense new car smell of his Tesla S made him drowsy enough to fall asleep at the wheel. When Jain lost control of the Tesla on Nov. 2, 2013, he killed 40-year-old librarian Joshua Alper who had been riding a bicycle in a wide shoulder lane on Highway 1 north of Santa Cruz. Most public reactions to Jain’s claim have been met with derision and disbelief. But scientific evidence, including a major one by Australia’s CSIRO14, indicate that many of the chemicals given off by automotive dashboards, upholstery, wiring, adhesives and interior trim can offer the same consciousness-impairing and mind-altering effects as sniffing glue. The CSIRO study and others have found that — in addition to toluene, xylene, benzene and other Volatile Organic Counpounds (VOCs)(1-4) , there are phthalates (5-7), flame-retardants(11,12) and other Endocrine Disrupting Compounds that are outgassed from car interior materials and form the scummy film on windshields and windows.(5-7). And, in a contra-Darwinian sense, people love the fragrance of these VOCs so much that they support an entire industry of sprays and air fresheners containing many of the same petrochemicals and EDCs. (See: shop on Google for new car smell) The National Highway Traffic Safety Administration considers toluene (a key compound in “sniffing glue”) to be a Central Nervous System depressant(8) with symptoms that include: “Dizziness, euphoria, grandiosity, floating sensation, drowsiness, reduced ability to concentrate, slowed reaction time, distorted perception of time and distance, confusion, weakness, fatigue, memory loss, delusions, and hallucinations.” The California Department of Public Health says in an official statement that, “Toluene, like most organic solvents, can affect your brain the same way drinking alcohol does.” Significantly, in addition to VOCs like toluene, xylene, and benzene — all of which can cause leukemia(10) — we found studies that detected more than 100 compounds — many of which are petrochemicals and fit into the California Department of Public Health’s definition of “organic solvents.” The CSIRO study stated that, “Controlled exposures of human subjects to a 22-compound mixture at TVOC [Total VOC] concentrations of 7,000–33,000 µg/m3 have observed effects within minutes, such as subjective reactions (odour, discomfort, drowsiness, fatigue/confusion), eye/nose/throat irritation, headache, and (in symptomatic subjects) neurobehavioural impairment” Further, the CSIRO study noted conditions which suggest that it is altogether possible that Tesla driver Jain had been impaired, as he has stated, by the sedan’s new car smell. “Investigation into VOCs in new cars has been limited. Bauhof and Wensing (1999) described a standardised test procedure used in Germany in which VOC concentrations were measured at car interior temperatures of 23–65°C and an unspecified ventilation rate. “TVOC concentrations of 35,000–120,000 µg/m3 were reported for six new cars (test temperature not specified), these concentrations decreasing exponentially over a 40-day period to about 10,000–30,000 µg/m3. VOCs consisted of aromatics, glycol ethers and esters, aldehydes, ketones and amines. “Grabbs et al. (1999) screened four new cars in the USA, all after being closed for one hour and without temperature control. Three exhibited initial TVOC concentrations of 300–600 µg/m3 and the fourth 7500 µg/m3. The latter decreased exponentially by about 90% within three weeks.” Click here for a chart of chemicals from Grabbs, et. al. Click here for a chart of chemicals from Faber, et. al. A sampling of the top 10 petrochemicals found were: Methylcyclohexane is also used in perfumes for its minty fragrance. This compound is closely related to 4-Methylcyclohexanemethanol, MCHM, spilled in the vast West Virginia chemical spill in January 2014. Ironically, MCHM has been patented for use in air fresheners. (13) Undecane, the National Toxicological Program says, is an organic solvent and Central Nervous System depressant. Ethylbenzene, is classified by the EPA as the same sort of organic solvent with Central Nervous System effects. Used as a perfuming agent in cosmetics. As time allows, we’ll work our way through those lists […]

Collaborator Biographies

Lewis Perdue, Project Co-Founder, Co-principal Investigator

William Lewis Perdue IIICo-Principal Investigator, Stealth Syndromes Study Education B.S., Communications & Biology (Ecology, Evolution & Systematics), With Distinction, Cornell University, 1972 A.S., Math & Science, (1st in class, 1st ever 4.0 graduation GPA), State University of New York (SUNY)/Corning Community College, 1970 Fellowship, Aerospace Engineering, Mississippi State University, summer 1966 Internship, Westinghouse Electric (Nuclear Reactor and Special Purpose Tube Divisions), summer 1967 Independent Study, Multiple collaborators & mentors including: Dr. Arthur C. Guyton, Dean of the University of Mississippi Medical School, NASA, Oak Ridge National Laboratory, 1960-1967 Publications Perdue, L., & Yeamans-Irwin, R.L. “Low-Dose BPA Paper in Toxicological Sciences is Contaminated by Massive Errors & Should Be Retracted.” Uploaded February 2014. (Please click this link for a .pdf version.) Perdue, L., “Heat Shock Protein Hsp27 points to causal link between BPA and cancer & chemotherapy resistance.” Uploaded May 12, 2016 Perdue, L., “Precision evaluation of environmental chemical risk assessment: Using existing pharmaceutical evaluation results as a more accurate paradigm,” Uploaded May 12, 2016 Research & Teaching Experience Cornell University – 1970-72 Teaching Assistant, Organic Chemistry Lab, specializing in assisting students with the use of gas chromatography and mass spectrometry equipment in lab experiments. Received the only A+ awarded in an organic chemistry class of 150. Also only student to accurately answer final exam extra credit question to diagram the quantum resonance bonding orbitals of ozone. As a first semester junior, offered a scholarship to change biology major to chemistry after I alerted the department to 27 errors (many in quantum bonding orbital diagrams) in the new text book for organic chemistry. Added communications as an unsanctioned double major. Cornell did not formally support double majors at the time. Because of that, I changed my major to communications at the end of my junior year during which I completed all required courses in just two semesters. Financially self-supporting since age 18: paid for college and living expenses by working as a journalist and photographer. Financial considerations — which included substantial student loan debt — mandated that I interrupt my lifelong passion for science and technology to follow a temporary vocational path in communications instead. Honors program: allowed to take courses at Cornell Law School. Teaching Assistant, Mass Communications Law. State University of New York (SUNY)/Corning Community College – 1968-1970 Independent research: Conducted abiogenesis experiments including complete replication of Miller-Urey experiment confirming that complex organic compounds including vital amino acids, could have been created from simple inorganic compounds during the by postulated primitive environmental conditions which mat have been present on Earth more than 4 billion years ago. Teaching Assistant & Faculty-Appointed Tutor, Calculus, Physics, & Biology Westinghouse Electric Internship — Summer 1967 Course work in the theory and practice of nuclear fission, reactor design, and mechanics of neutron cross sections, capture, fission moderation. Responsible for calibrating neutron sensors used in civilian and military reactors. Created custom calibration curves unique for each neutron counter. Responsible for construction of, and suggesting design changes for, solar flux measurement sensor tubes for NASA’s 1969 Mariner 6 Mars flyby. Course work in theory of electron guns used in color cathode ray tubes. Hands on experience with efforts to reduce corner landing misplacement of electron beams in color picture tubes. Course work in the theory of quantum-based spectral output of specific pure elements, primarily metals. Hands on work in the utilization and calibration of the Westinghouse Hollow Cathode spectral output tubes. Independent Study — 1966-67 Research focus: Magnetohydrodynamics, plasma physics, ultra-high-vacuum physics. Designed and built a magnetohydrodynamic thrust accelerator for space propulsion. The ionized particle stream was provided by a plasma jet. The thruster used sequential electromagnetic field compression to provide thrust. A variation of this is currently used in NASA’s deep space probes such as dawn. Mississippi State University – Summer 1966 Coursework and lab experience in plasma physics, fluid flow instrumentation, mechanical resonance. Collaborated with faculty in further exploring ion thruster linear accelerator. Independent Study, 1965-66 Mentors: Werner Von Braun, NASA scientists at Redstone Arsenal (George C. Marshall Space Flight Center) and the Oak Ridge National Laboratory. Research focus: high-energy particle physics, plasma physics, ultra-high-vacuum physics, interplanetary and interstellar particle flux density, ultra-high-vacuum technology With a suggestion from NASA that they would welcome a way to increase the relatively small thrust of the ion engine as it currently existed, I designed and built a two-stage thruster. And a vacuum chamber capable of 10-12 Torr to simulate the vacuum of outer space. The first stage was an improved version of my previous ion engine design coupled with a linear particle accelerator for the second stage. This thruster was designed to use the interplanetary particle flux as fuel. This required an electromagnetic collector to attract and compress a simulated solar plasma (He and H ions). The particles from the collector were then separated using mass spectrometer principles to provide a uniform He+ stream to the particle accelerator. Dubbed “The Cosmic Engine” by the media, the entire system won a number of awards at the International Science and Engineering Fair. I became a Westinghouse Science Talent Search Finalist and received a fellowship from the Aerospace Engineering Department of Mississippi State University where I attended classes and continued to explore the capabilities of my system. Independent Study — 1964-65 Research focus: plasma physics, fluidics of ionized gases Completed design and construction of electromagnetic ion space thruster and vacuum chamber required for operation. Exhibited and demonstrated ion space thruster and modulated laser combined under the title, “Space Communications and Propulsion.” Won First Class overall Bay State science fair along with numerous awards from NASA, AAAS and other entities. Independent Study — 1963-64 Research focus: optical and electromagnetic radiation and high-energy particle physics. Completed construction of a visible spectrum Ne/He ion laser approximately 18 months after the first one was developed by Bell Labs in 1962. Further research into removal of trace contaminants from the Ne/He plasma along with precision optical adjustment of mirrors and interface windows resulted in a functional laser. Work began on possible methods for analog […]
Becca L. Yeamans-Irwin, Collaborator, Project Co-Founder

Becca’s CV is at this link (pdf).
Victor Reus, Co-Principal Investigator

Victor Reus biography can be found at this link

The Study

UCSF IRB/CHR Approves study extension

2019-UCSF-CHR-IRB-study-Extension-to-102720 Human Research Protection Program Institutional Review Board (IRB) Expedited Review Approval Principal Investigator Victor I. Reus, MD Co-Principal Investigator Lewis Perdue Type of Submission: Continuing Review Submission Form Study Title: Clinical blood profile assays as biomarkers to directly assess potential health effects resulting from the controlled elimination of suspected dietary and environmental chemical toxins. IRB #: 15-17703 Reference #: 265715 Committee of Record: San Francisco General Hospital Panel Study Risk Assignment: Minimal Approval Date: 10/27/2019 Expiration Date: 10/26/2020
SSHS – Early study results, thoughts and anomalies

Note: There is an inconsistency in the literature on reporting high sensitivity C-Reactive Protein levels. The actual protein is properly abbreviated CRP. The test procedure for measuring quantities below 10 mg/L is hsCRP. However, published papers most often refer to the protein as hsCRP which is, technically, incorrect because that is the test, not the protein. Because most papers use hsCRP consistently to refer to the protein, Investigators have followed the inaccurate terminology and done that as well even though it seems like a foolish consistency. Stealth Syndromes Human Study – Follow-up thoughts and questions The hsCRP readings at the end of the trial were not what was expected. On the other hand, real science often starts when the results are not as anticipated. The following is a quick summary of findings and possible considerations and roots of the unexpected results. Citations are available. Note that the analysis of concentrations of BPA and other chemicals in the panel are not yet available. Initial expectations Investigators expected hsCRP to increase over baseline after the “typical diet” leg of the trial. Investigators also expected hsCRP to decrease substantially after the “minimum plastic/processing” intervention leg. Investigator expectations were that final hsCRP mg/L concentration would be substantially lower than baseline. EXPECTED FOR STEALTH SYNDROMES HUMAN STUDY (SSHS) SSHS AS MEASURED UNEXPECTED RESULTS ALSO IN NIH/HALL DIETARY INTERVENTION STUDY Interestingly, a major NIH funded study (Hall et al., 2019, Cell Metabolism 30, 67–77, July 2, 2019 (https://doi.org/10.1016/j.cmet.2019.05.008) also showed a similar anomaly after the ultra-processed menu phase, but then showed a further decrease after intervention. NIH/HALL vs SSHS – CONCENTRATIONS, DELTAS Both studies showed a net decrease in hsCRP at the end of the trial, with the NIH/Hall study showing a decrease almost double that of the SSHS. The NIH/Hall study began with a baseline almost twice that of the SSHS. In addition, investigators expected that SSHS would show a larger decrease in hsCRP following the intervention. This is because the SSHS study protocol was stricter than NIH/Hall because it eliminated commercial food processing contamination and, in addition, employed the most extreme measures to reduce BPA and plastic chemical exposure in sourcing and food storage and preparation. One unknown data point in the comparison is the margin or error on the hsCRP measurements conducted by UCSF labs. The NIH/Hal study cited a +/- 0.3 mg/L margin of error. Assuming UCSF labs have a similar margin of error, that is more relevant given the low concentrations involved. However, doesn’t change the overall relative behavior of the amounts in either study. The difference might possibly be explained by the length of the studies. Our study ran for a week. The NIH/Hall study ran for four weeks which may have offered more time for hsCRP to reach equilibrium. The NIH/Hall study The NIH/Hall study was designed to investigate a possible connection between ultra-processed foods and excess intake of calories. As such, it was an ad libitum trial which allowed subjects to eat as much (or little) of the foods in each leg. The 28-day trial included 20 adults (10 male, 10 females) and was conducted at the NIH Metabolic Clinical Research Unit. The NIH study is noted not only because of the apparent anomaly in the first leg results, but also because it is the only dietary intervention in my literature searches with an extensive blood panel for the subjects and the only one in which hsCRP was measured. Accordingly, the hsCRP level decrease after the ultra-processed leg in the Hall study — like that in the SSHS — would seem to run counter to expectations. The Hall study is also significant because it measured so-called “appetite” compounds: leptin, ghrelin, and adiponectin as well as insulin. This is important because: BPA and phthalates exercise effects on those proteins in a similar manner as illustrated in the Hall study. Ultra-processed foods are also higher in BPA and phthalates due to the extensive use of plastics in processing and packaging. An expanded discussion of this study as related to ours is in order, given that the investigators of that study made numerous protocol errors that render the study incapable of being replicated. Some of those fundamental errors include: Failure to provide recipes (formula), sourcing of materials, preparation, description of equipment, materials including relevant food contact materials. Failure to note whether food preferences of test subjects were taken into account. Failure to take into account that ad libitum food consumption will depend on food preferences (or aversions) as well as seasoning, preparation method or time. What’s going on? A look at the baseline versus “unhealthy” trial leg hsCRP anomaly Unhealthy pre-baseline diet? The anomalous results in both the NIH/Hall study and the SSHS could indicate that the processed/plastic contaminated legs were actually healthier than baseline. In my case, the initial efforts to begin the actual study were urgent and rushed in order to try to complete the trial before the CHR expiration date. As a result, my baseline diet relied heavily on pre-prepared supermarket meals and fast food. Thus, my baseline could have been less healthy than the plastic contamination leg of the trial. The same “unhealthier baseline” diet, may have influenced the NIH/Hall anomaly with hsCRP levels dropping after the end of the ultra-processed leg of the study. Air pollution confounding factors The Kincade Fire in northern Sonoma County started on October 23, 2019, was contained on Nov. 6 but continued to burn and affect the test location during and after the SSHS study was finished. Because PM 2.5 is a potent inflammatory agent, a monitoring device was purchased to track indoor air quality and activated the day before the first (baseline) blood draw. In retrospect, activities probably should have been restricted before the baseline draw. However, a literature search has not found a reference dealing with the pharmacokinetics of PM 2.5. It is, at this point, unknown how long a pre-baseline isolation period would need to be for an unconfounded valid baseline. Accordingly, outdoor activity was limited during […]
UCSF IRB/CHR Approves Revised Study Protocol

Right-click images to view a much larger version. The full revised protocol and appendices are at this PDF document Summary Revised Protocol: UCSF IRB/CHR Number: 15-17703 Approved by IRB/CHR Co-Principal Investigators: W. Lewis Perdue, Dr. Victor I. Reus MD Study Title: Clinical blood profile assays as biomarkers to directly assess potential health effects resulting from the controlled elimination of suspected dietary and environmental chemical toxins. This study is the first of its kind to go beyond simply measuring serum and urine concentrations of the subject chemicals. Instead, this study will measure clinically useful outcomes using widely accepted diagnostic tests available at most medical facilities. The investigators of this study recommend a revised protocol to increase reproducibility and decrease costs. This revision is based on 2-1/2 years of intensive research that has determined that the original protocol would be impractical, too expensive for allocated resources, and could not be replicated by other investigators. These revisions did not result from a single incident of sudden enlightenment. Instead, they are the result of a steady accumulation of insight built upon the closer scrutiny of previously published diet intervention studies. Underpinning that was the accumulated discovery of confounding basic science factors never before considered in these previous studies. which rendered them irreproducible. Chief among the non-replicability of is the fact that the food supply chain is ubiquitously contaminated with widely varying and uncontrolled levels of Bisphenol A, phthalates and other environmental chemicals. The investigators believe they have developed a reliable method of preparing and sourcing foods that will allow consistent results across other investigations. The full revised protocol and appendices are at this PDF document
The Study & Protocol As Approved in 2015

A PDF of the complete study as approved by UCSF/IRB in 2015 can be found at this link. The revised study protocol available here was approved by UCSF-IRB/CHR on Nov. 14, 2018. The Committee on Human Research (CHR) at the University of San Francisco Medical School has approved the Stealth Syndromes experimental protocol. This study approval allows Stealth Syndromes co-founder Lewis Perdue to become the test subject for a “proof of concept” study to determine if standard clinical blood tests can be used to detect physiological changes that may be caused by the absorption of environmental chemicals, including endocrine disrupting compounds. The CHR gave its go-ahead for the study on on Nov. 11, 2015. The Stealth Syndromes Project is very fortunate (and grateful) to have had the guidance and institutional mentorship of UCSF Professor Victor Reus, M.D. Dr. Reus is an internationally renowned, and widely published biomedical scientist whose interests include neurobiology and behavior as well as the genetic origins of psychiatric disorders. In the coming days, I will be writing numerous posts that describe the various facets of the study and examine them in more detail. Those will look at the value of a first “proof of concept study,” and what makes this study different from the hundreds of others dealing with environmental chemicals. iRIS – Let a Thousand Computer Forms Blossom Study submissions at UCSF are entirely electronic. Everything is submitted through the secure, web-based iRIS system which provides scores of forms in a relatively intuitive framework. iRIS centralizes all aspects of study, makes sure that all the relevant parts of a study are included, assures compliance with human research protections, and makes all that available to the university compliance process without needing paper versions. The complexity of the iRIS system lies somewhere between IRS income tax forms and the paperwork associated with buying and mortgaging a new house. The following is from the iRIS FAQs: iRIS is a web-based system that enables online application submission, real-time submission tracking, review, post-approval compliance activities, and data management. The system also functions as a document repository, providing investigators with easy access to submission records and study documents. The committees that will conduct their reviews using the iRIS system include the: Committee on Human Research (CHR), the CTSI Clinical Research Services (CRS) Advisory Committees, and the Human Gamete, Embryo, and Stem Cell Research Committee (GESCR committee). Investigators can use the system anywhere they have Internet access, helping to connect faculty, researchers, students and partners around the world. The iRIS system also has expedited the CHR review and approval process. In addition, prior to the implmenetation of iRIS, the CHR received about 5 million pieces of paper each year. The electronic system has helped us eliminate this waste and supports UCSF’s efforts to incorporate environmentally-friendly practices across campus. Summarizing the study submission The text below is taken directly from the UCSF iRIS system. I have included ALL of the sections relevant to the study and omitted only those sections associated with administrative details and the online human research protection training courses I needed to pass in order to qualify as a study co-principal investigator. Correct section numbers from iRIS are used to designate each portion. 10.0 STUDY DESIGN This is an interventional dietary study to determine the usefulness of carefully selected tests from standard medical blood profiles to indicate health effects resulting from the reduction of specific foods and substances known to contain certain environmental chemicals. This study is the first to use easily accessed and medically accepted laboratory methods to directly measure health effects of dietary intervention on the reduction of persistent and ubiquitous environmental chemicals. While this is an n=1, proof-of-concept study using co-Principal Investigator Lewis Perdue as the test subject, it expands upon previous studies with a longer observation period, and by designating specific substances (packaged in glass vs plastic or cans, elimination of dermal contact) for intervention instead of general parameters (fresh versus prepared foods). 11.1 HYPOTHESIS 11.2 LIST THE SPECIFIC AIMS: The primary aim of this study is to determine whether a positive correlation exists between CEC intervention, test subject blood profiles, and CEC levels in serum and urine. Because the significance of CEC urine and serum levels is controversial, the primary aim of this study is to provide a measurement of direct CEC health effects (or lack thereof) using widely available laboratory blood profile indicators. A secondary aim of this study is to provide a method to correlate potential health effects of CECs with their observed human levels as previously measured by NHANES and other investigations. 12.1 BACKGROUND INTRODUCTION The human health effects of low-level concentrations of certain Chemicals of Emerging Concern (CECs) has stirred immense controversy between traditional toxicologists and a more recent, emerging body of scientists grounded in epigenetics and molecular-level effects. Traditional toxicologists insist that current risk evaluations at high concentration levels can be monotonically extrapolated to low concentrations and that a firm No Observed Adverse Effects Level (NOAEL) of safety can be established. On the other hand, a more recent and growing body of peer-reviewed, published data indicates that many CECs exhibit non-monotonic behavior and present risks to humans at low concentrations. That controversy continues partly because of the lack of controlled human studies and the almost complete absence of investigations into effects of combinations of CECs. BACKGROUND Exposure to environmental chemicals in the U.S. is widespread20. More than 84,000 chemicals are approved for use in the United States today1, and at least 4,000 of those are present in food contact materials2,3,4. The health effects of most of those chemicals is unknown and/or incomplete5.. While controversial by some, many of these chemicals in low-level concentrations are increasingly classified as endocrine disruptors22,23. Among chemicals of emerging concern (CEC) are Bisphenol A (BPA) and phthalates, both of which are present in approximately 97% of the U.S. population.6,8 Public concern over the risks from these chemicals have resulted in the reduction of concentrations of some7, but also increases in concentrations of substitutes which are also […]

This study supported by the Center for Research on Environmental Chemicals in Humans

The Center for Research on Environmental Chemicals in Humans, is a 501(c)(3), tax-exempt nonprofit organization

Please visit the Center for Research on Environmental Chemicals in Humans to learn more about our tax-exempt research. Our Mission: The Center’s mission is to enable individuals and health professionals to take medically valid actions to avoid the risks of Endocrine and Epigenetic Disrupting Chemicals (EEDCs). The CDC says that EEDCs are found in most Americans. To do this, our first-ever human research is designed to establish a scientific cause-and-effect connection between EEDCs and their effects on clinically proven health indicators such as standard hospital blood tests. Read more

Why Is This Study Important?

The Importance of Addressing the Previously Unaddressable

The outcome of this study may make a substantial contribution by definitively and credibly evaluating the human effects of endocrine disruptors and other environmental chemicals. Regardless of whether the thesis of this study is proven or not, it will add vital data that can help scientists, health professionals, and the general public to understand risks that may be caused by the small levels of chemicals that federal regulators have decided are “safe” to consume but which hundreds of university studies say are harmful. If the study does provide support for its thesis, it will help resolve the current regulatory and scientific stalemate caused by: (a) arguments about correlation and causation, (b) flaws with animal models, and (c) the dismissal of low-dose, non-monotonic effects by many traditional toxicologists. Missing Links There are missing links in environmental chemical risk assessment including: Moving beyond “associated with” to “causes.” (Correlation does not equal causation). The absence of controlled trials on humans. (Unethical to deliberately expose humans to harmful substances). Research conducted on rats, mice and other lab animals is no guarantee the same effects will be seen in humans. How does this study address the missing links? Epidemiology is the science of using data to find correlations — connections or links — between substances, behaviors or environmental factors and diseases or other harms. But while links, associations, and connections can save lives, such statistical correlations are not scientific conclusions or proofs of cause. This study moves conclusions about cause and effect closer than epidemiology can by past “associated with.” If the results provide support for the thesis, this study will advance knowledge that the chemicals in question cause changes in clinical blood tests, double-stranded DNA breaks and epigenetic profiles already established as valid markers of health and illness by the medical and scientific community. The ethical considerations are resolved by this study by using a controlled protocol to systematically remove specific environmental chemicals from the test population rather than adding them. This is possible because very, very few people are without measurable levels of environmental chemicals in their bodies. For example, Bisphenol A, which this study focuses on, is already ubiquitous in the environment and, according to the Centers for Disease Control, is present in 95 % of Americans. Removing potentially harmful chemicals already present in test subjects from environmental exposure is not unethical. It is worth noting hat deliberate exposure of an unwitting population to potentially harmful chemicals is an ethical quandary that neither governments, nor companies, nor universities has addressed. What are the benefits to society? Society can benefit because: This study can offer new, outcomes-based diagnostic and recommendation tools for doctors and other health professionals. This study can give individuals additional of clear, credible, fact-based, steps that are actionable and convenient to adapt to everyday lives. Food, beverage, chemical manufacturers and government agencies will — for the first time — have credible, cause-and-effect data for solid, evidence-based decision making. Cause-and-effect data for solid, evidence-based decision making can allow members of the general public and their health professionals to leapfrog regulatory inertia and special interests in order to take direct healthy personal actions.

The Science

Air pollution: Confounding factors for study

Air pollution confounding factors The Kincade Fire in northern Sonoma County started on October 23, 2019, was contained on Nov. 6 but continued to burn and affect the test location during and after the SSHS study was finished. Because PM 2.5 is a potent inflammatory agent, a monitoring device was purchased to track indoor air quality and activated the day before the first (baseline) blood draw. PM2.5 is used to make health recommendations AIR QUALITY INDEX (AQI)The following text and Figure 3, from the California Department of Public Health (PDF) “The US EPA created the Air Quality Index (AQI) to communicate information about air quality to the public.10 The AQI communicates the health impacts of air pollutant concentration using a 6-level color system (Green, Yellow, Orange, Red, Purple and Maroon). “Each color-coded level has an associated descriptive term, progressing from “Good” to “Hazardous.” For each pollutant, the AQI scale value of 100 corresponds to the 24-hour primary health standard. The AQI is most often displayed for two pollutants, PM2.5 and ozone. For PM2.5, the 24-hour health standard of 35 μg/m3 corresponds to the AQI value of 100; AQI values greater than 100 indicate increasing levels of health risk, beginning with “Sensitive Groups” in the Orange category and progressing to “Everyone” in the Red, Purple, and Maroon categories. See Table 3 below.” In retrospect, activities probably should have been restricted before the baseline draw. However, a literature search has not found a reference dealing with the pharmacokinetics of PM 2.5. It is, at this point, unknown how long a pre-baseline isolation period would need to be for an un-confounded valid baseline. Accordingly, outdoor activity was limited during the trial because of wildfire smoke pollution. In addition, a new HVAC filter was installed and two stand-alone HEPA air purifiers employed at the trial location to keep indoor air in the range of healthy as defined by Because outdoor activities were not restricted before the trial, the baseline hsCRP was probably affected, contributing to an unhealthy baseline measurement. Indoor air quality at the test site was constantly monitored. Multiple HEPA air purifiers assured that indoor quality was maintained at a healthy level which was most often below 5 ppb. In addition, the air was extremely unhealthy on the North coast on Nov. 8: the date of the first blood draw and the first day of the “Typical” diet. Significant to the PM 2.5 exposure is that the blood sample for BPA and other toxics testing needed to be delivered to the lab at UCSF Mt. Zion within four hours of the draw. Because the test subject and investigator were the same person, that means that the scientist/lab rat had to be exposed to extremely unhealthy PM 2.5 for at least 3 hours including the commute into San Francisco and the deliveries of blood samples to the lab and the hsCRP sample to the lab at the Parnassus campus. More air quality snapshots are available at: Air quality exposure may have confounded results. Restriction of outdoor exercise meant forgoing regular exercise such as jogging. The lack of that exercise and the effect of being “trapped” had a noticeable effect on SSHS subject psychological stress. Unhealthy environmental pre-baseline stress? Many environmental factors affect hsCRP levels and inflammation via psychological and physical factors including: Noise — traffic, neighbors, housemates, barking dogs. Psychological stress (increases in cortisol production) — work, co-workers, work and domestic interpersonal interactions, commuting, driving in traffic. Air quality (especially PM2.5) Home, & Office — cooking, vinyl flooring, wall coverings, upholstery, and other plastic-based products, pet dander, printer toner. External – Smog, wildfires. Adequate regular exercise Physical exercise has been shown to decrease cortisol levels and reduce inflammation.
Inflammation, PM2.5 and serious health effects

Particulate pollution, especially those of 2.5 microns or smaller — has been demonstrated to cause, promote, or aggravate numerous serious health effects including inflammation and specific syndromes involving the immune system, diabetes, insulin resistance, metabolic syndrome, cardiovascular disease as well as neurological and psychological maladies. Reid CE, Brauer M, Johnston FH, Jerrett M, Balmes JR, Elliott CT. Critical Review of Health Impacts of Wildfire Smoke Exposure. Environ Health Perspect. 2016;124(9):1334-1343. doi:10.1289/ehp.1409277 Feng S, Gao D, Liao F, Zhou F, Wang X. The health effects of ambient PM2.5 and potential mechanisms. Ecotoxicol Environ Saf. 2016;128:67-74. doi:10.1016/j.ecoenv.2016.01.030 Ohlwein S, Kappeler R, Kutlar Joss M, Künzli N, Hoffmann B. Health effects of ultrafine particles: a systematic literature review update of epidemiological evidence. Int J Public Health. 2019;64(4):547-559. doi:10.1007/s00038-019-01202-7 Wei T, Tang M. Biological effects of airborne fine particulate matter (PM2.5) exposure on pulmonary immune system. Environ Toxicol Pharmacol. 2018;60:195-201. doi:10.1016/j.etap.2018.04.004 Miller MR. Oxidative stress and the cardiovascular effects of air pollution. Free Radic Biol Med. 2020;151:69-87. doi:10.1016/j.freeradbiomed.2020.01.004 Wolf K, Popp A, Schneider A, et al. Association Between Long-term Exposure to Air Pollution and Biomarkers Related to Insulin Resistance, Subclinical Inflammation, and Adipokines [published correction appears in Diabetes. 2017 Oct;66(10 ):2725]. Diabetes. 2016;65(11):3314-3326. doi:10.2337/db15-1567 Esposito K, Petrizzo M, Maiorino MI, Bellastella G, Giugliano D. Particulate matter pollutants and risk of type 2 diabetes: a time for concern?. Endocrine. 2016;51(1):32-37. doi:10.1007/s12020-015-0638-2 Pope CA 3rd, Turner MC, Burnett RT, et al. Relationships between fine particulate air pollution, cardiometabolic disorders, and cardiovascular mortality. Circ Res. 2015;116(1):108-115. doi:10.1161/CIRCRESAHA.116.305060 Xu MX, Ge CX, Qin YT, et al. Prolonged PM2.5 exposure elevates risk of oxidative stress-driven nonalcoholic fatty liver disease by triggering increase of dyslipidemia. Free Radic Biol Med. 2019;130:542-556. doi:10.1016/j.freeradbiomed.2018.11.016 ======== Health effects of ultrafine particles: a systematic literature review update of epidemiological evidence Exposure to airborne fine particulate matter is associated with impaired endothelial function and biomarkers of oxidative stress and inflammation Ambient particulate air pollution and circulating C-reactive protein level: A systematic review and meta-analysis Oxidative stress and the cardiovascular effects of air pollution Ambient particulate air pollution and circulating C-reactive protein level: A systematic review and meta-analysis Particulate Matter Exposure and Stress Hormone Levels ” Shou Y, Huang Y, Zhu X, Liu C, Hu Y, Wang H. A review of the possible associations between ambient PM2.5 exposures and the development of Alzheimer’s disease. Ecotoxicol Environ Saf. 2019;174:344-352. doi:10.1016/j.ecoenv.2019.02.086 Jia Z, Wei Y, Li X, et al. Exposure to Ambient Air Particles Increases the Risk of Mental Disorder: Findings from a Natural Experiment in Beijing. Int J Environ Res Public Health. 2018;15(1):160. Published 2018 Jan 19. doi:10.3390/ijerph15010160 OTHER Air pollution and inflammation in type 2 diabetes: a mechanism for susceptibility Inflammatory and oxidative stress responses of healthy young adults to changes in air quality during the Beijing Olympics Particulate Matter Air Pollution and Cardiovascular Disease Associations of Short-Term and Long-Term Exposure to Ambient Air Pollutants With Hypertension Associations between ambient air pollution and blood markers of inflammation and coagulation/fibrinolysis in susceptible populations Fine Particulate Air Pollution (PM2.5) and the Risk of Acute Ischemic Stroke
Biomedical science and pharmaceutical research embrace n-of-1 trials

The use and scientific acceptance of “n-of-1″ trials have accelerated in recent years, especially in connection with personalized medicine and drug discovery. This increase in interest and acceptance is reflected in the number of studies on the field. A Google Scholar search (July 26, 2020) for “n-of-1 trial validity” for all date ranges, yielded 3,430 results. By contrast, the same search string for the period 2019-2020, yielded 527 results. That search found 221 results in the first seven months of 2020. Those studies reflect a broad acceptance with major studies comparing n-of-1 trials to Randomized Control Studies and other long-accepted research methods [1,2,3,4,5] In addition, established standards organizations such as SPIRIT [6] and CONSORT [7] have embraced n-of-1 trials and offer structures for reporting on most major forms of biomedical studies. This article from the British Medical Journal [8] notes: “Well conducted, randomised clinical trials create the evidence base that informs modern medical practice, guidelines, and regulatory decisions. However, these trials estimate average treatment effects, providing little information about heterogeneity and no information about individual treatment effects. “Randomised clinical trials are not always feasible, are rarely conducted on rare diseases, and often exclude individuals with comorbid conditions or concurrent treatments even though these individuals constitute the majority of patients. “Based on the methodology of randomised clinical trials, n-of-1 trials can rigorously measure intervention effects for individuals, either singly or in a series.” ======== [1] Single-case experimental design yielded an effect estimate corresponding to a randomized controlled trial [2] Making the switch: From case studies to N – of – 1 trials [3] Practice-Based Research in Complementary Medicine: Could N-of-1 Trials Become the New Gold Standard? [4] Comparison of Aggregated N-of-1 Trials with Parallel and Crossover Randomized Controlled Trials Using Simulation Studies [5] To meta-analyze or not to meta-analyze? A combined meta-analysis of N-of-1 trial data with RCT data [6] SPIRIT – Standard Protocol Items: Recommendations for Interventional Trials [7] CONSORT – Consolidated Standards of Reporting Trials [8] SPIRIT extension and elaboration for n-of-1 trials: SPENT 2019 checklist More references N-of-1 Trials Take on Challenges in Health Care Understanding and misunderstanding randomized controlled trials
Additional posts incorporated in or used as references in primary articles

Primary articles Results of Proof-of-concept study indicate that hsCRP may be valid indicator of Bisphenol A contamination, but finds that ubiquitous co-confounding factors may invalidate most dietary interventions Significant changes necessary in order for dietary intervention studies to be causal and replicable Supplementary/ reference articles How food processing adds plastic-derived chemical contamination How does the food chain get contaminated with plastic-derived chemicals? Micro- and Nanoplastics: Health Implications Sourcing the Menu: Avoiding Microplastics, biosolids and nano particles Recent dietary interventions relevant to Plastic-Derived Chemicals Reducing Non-Food Exposures in dietary intervention Basic scientific lab standards — Best practices for a replicable dietary intervention Accounting for unknown interactions of co-confounding factors prohibit valid causality conclusions Dosing of a single compound to establish causality in dietary interventions & enable clinically valid health decisions.

The Study – Deconstructed

Methods: Food preparation and serving

Note: The complete set of exhaustively detailed standards developed for this trial, can be accessed at this link: Basic scientific lab standards — Best practices for a replicable dietary intervention. That link is an ongoing work. To facilitate replicability the kitchen was operated in much the same manner as a bench lab. Food preparation took place in a 400-square-foot professional kitchen with stainless steel countertops and carbon-filtered water. A 1,200 cubic-feet/minute, four-centrifugal-fan exhaust hood was used over an eight-burner natural gas stove. Central air with HEPA filters ventilated the kitchen which was also equipped with two auxiliary standalone HEPA filter machines. Two electric ovens were used for baking. Additional efforts were also made to reduce other non-food exposures and confounding factors. PM2.5 levels were monitored via sensors from PurpleAir.Com, one which monitored the kitchen air quality, as wel as numerous other outdoor sensors in a roughly five-mile radius. All unacceptable materials were removed from the kitchen, including plastic and polymer items utensils, containers, and cookware with non-stick coatings. Only glass, stainless steel, aluminum foil, and tight grain maple cutting boards were allowed. Vinyl gloves were used in food preparation for sanitary control in both legs of the trial, but actual food contact with the gloves was minimal and incidental. 100% cotton dish towels were allowed, but paper towels could only be used for cleanup. All measurements were by metric weight, and none by volume. This facilitated the kitchen’s staff’s accommodation from English to metric measurement because they could dispense with volumetric measurements which are problematic because of packing and granular particle size in solid items, and meniscus errors for liquid. In converting recipes with English measurements, initial measurements for liquids was done in measuring cups with dual English/Metric gradations. Then, with a glass mixing bowl with dry ingredients already on a metric measuring scale, the liquid was added to the bowl and the metric weight recorded for the investigation data. All main ingredients were measured to the nearest gram, but small-weight items such as spices, herbs and other seasonings and other items were measured to the nearest tenth of a gram. This is vital because those ingredients often have metabolic and other health effects in amounts out of proportion to their weight. For the same reasons, Investigators used spices they had grown for the purpose. Black pepper was obtained from an organic source. Peppercorns were rinsed, dried and ground with a grinder without plastic components. These measures were necessary because store-bought spices are among the most contaminated. Items with known plastic contamination (such as micro-plastic contamination of table salt) were replaced where possible with reagents from Sigma-Aldrich. Small kitchen-ready scales were obtained and calibrated using brass gram weights. Culinary assistants were briefed on the measurement procedures and adapted very quickly. All recipes and menus and a calendar of their serving dates and times were posted on a kitchen whiteboard directly above a dedicated counter surface on which recipes were places, and data recorded. Hand-written data was transferred to two master Excel spreadsheets for the Baseline and Intervention legs.
Moving toward the trial: Some final thoughts on procedures, methods, food acquisition, and best practices

Developing a scientifically sound set of methods for a dietary intervention that could result in replicable, causally valid results took investigators five years of intensive effort. That was a necessary first step because no such standards, protocols, methods or best practices existed. That absence required investigators to develop those standards and protocols de novo in order to move dietary intervention studies closer to replicability and credible conclusions of causality. Establishing principles for replicability The University of California, San Francisco IRB/Commitee on Human Research approved the n=20 study & on Nov. 14, 2014. Once approved, the investigators began an intense effort to scrutinize every aspect of the study. That resulted in the recognition that no such effort at using basic laboratory practices and data recording had ever been made. This realization came from an examination of five dietary intervention studies. A sixth study, which was published in 2019, should be add to that list: At that point, investigators determined the following principle: A kitchen must be subject to the same established practices as a laboratory. Consequently, the following three implementation strategies were created: Food, water, spices and all consumables must be treated as reagents whose sources, provenance, treatment, handling, measurement, and usage must be fully disclosed. Cookware, dishes, appliances, utensils and all other items involved in the preparation, cooking, serving and consumption must be treated as laboratory devices and apparatus. Recipes must be treated as protocols with scientifically accurate and complete conditions, materials, procedures, and timing recorded. Researching and developing specific implementations of the revised protocols took four years, As a result, the UCSF-IRB/CHR Approved a revised study protocol and a one-year extension on Nov. 14 2018. A further extension was granted due to delays — including planned and actual power outages — caused by wildfires in the San Francisco Bay area. The PM2.5 particles in wildfire smoke can cause many adverse health effects including inflammation. (See also). This situation was a serious concern because our study’s primary indicator was hsCRP — a potent measure of inflammation. Sourcing the Menu – Sources & Provenance The primary goal of this strategy was to define Plastic-Derived Chemical contamination sources for specific menu items. This work — described in a lengthy appendix to the revised protocol — determined the principles of which foods could be used for the uncontaminated intervention leg and which PDC-contaminated analogs would be used for the initial leg. The following guiding principles would later cause numerous difficult decisions as investigators applied the principles to the acquisition and treatment of specific foods from specific sources. Decisions were made on the basis of whether the foods were typical of An American diet (according to the USDA) and which could be readily obtained in the United States by investigators who wished to replicate the study. Sourcing the Menu: Water & Beverages Sourcing the Menu: Dairy – Milk, Cheese, Yogurt, Butter Sourcing the Menu: Fish Sourcing the menu: Sugar and sweeteners Sourcing the Menu: Background on GMO Sourcing the Menu: Background on Lipophilia – Prime contamination problem for cooking and food processing. Sourcing the Menu: Snacks Sourcing the Menu: The spice lipo-paradox Sourcing the Menu: Water & fertilizers: Ubiquitous contamination sources. Sourcing the Menu: Avoiding Microplastics, biosolids and nano particles Sourcing the Menu: Oils Sourcing the Menu: Going against the grain: Bread and cereal Sourcing the Menu: Fruit & veggies Sourcing the Menu: Dairy – Milk, Cheese, Yogurt, Butter Sourcing the Menu: Meat & Poultry Sourcing the menu: Pork Accommodating the ideal with the realistic As the trial grew near in 2019, investigators refined and tightened strategies 2 and 3/ They also reconciled their ideal measures of menu item purity with the practical need need to execute of a trial which could be conducted without going to hysterical lengths which were proving to be un-necessary, expensive and time-consuming. Items in progress Actual selection choices, their rationale, and concordance with the revised protocol will be noted as an update at the top each of the sourcing links, above. Choices will also be described in a detailed list of final ingredients that is analogous to a list of reagents and their sources. A separate methods section will detail preparation and all recipes. Best Practices Following the UCSF/CHR approval of the revised study protocol, investigators also began developing a set of best laboratory practices to implement the study. Note that the following is a partial presentation of a much larger number of links. Basic scientific lab standards — Best practices for a replicable dietary intervention Best practices — Herbs and Spices: Powerful in small amounts, precise measurement needed Best Practices Backgrounder: Micro- and Nanoplastics Best practices: Herbs and Spices – avoiding contamination Best practices – Spices: Make your own baking powder Best practices: Scale calibration Prepping bacon and lunch meat ham to minimize plastic packaging contamination. Avoiding plastic contamination when storing food. Best practices: De-waxing apples Best practices — Sourcing Dairy: Milk, Cheese, Yogurt, Butter methods and barriers Best practices: Sourcing cheese & butter and minimizing plastic contamination from packaging. Best practices – Precise measurements NOTE: there are approximately 30 more food specific “Best practices” yet to be written Reducing Non-Food Exposures in dietary intervention Micro- and Nanoplastics: Health Implications How Food Processing Adds Plastic-Derived Chemical Contamination
Accounting for unknown interactions of co-coexisting factors that confounded causality conclusions in two studies

Dietary interventions as now conducted are incapable of rendering valid causal conclusions about specific substances, compounds, or chemicals. This is because the near-infinite variations in foods produce unknown and unknowable co-contamination errors that are further confounded by preparation inconsistencies. This can be illustrated by comparing two recent dietary intervention studies — one studying Plastic-Derived Chemicals (Reus, Perdue) and the second of Ultra-Processed Foods (NIH/Hall). While the two studies were quite different in scope, size, and duration, they arrived at very similar results in the behavior of the high-sensitivity C-Reactive Protein (hsCRP) test as a clinical measure of intervention inflammation changes. The NIH/Hall study, “Ultra-Processed Diets Cause Excess Calorie Intake and Weight Gain,” was a 28-day trial published in the May 16, 2019 issue of Cell Metabolism and represented the most thoroughly documented dietary intervention published so far. In addition to documenting the association between Ultra-Processed Foods (UPFs) and weight gain from over-eating, the study was conducted in a dormitory setting to compensate for non-food environmental exposures, test subject compliance and differences in exercise, and metabolism. In addition, the study conducted an expensive battery of clinical tests (op. cit. Table 3) including hsCRP, insulin, and the appetite peptides leptin, ghrelin, and adiponectin. The Reus, Perdue six-day trial was far more limited in scope and sought primarily to determine whether hsCRP levels could be affected by Bisphenol A and other commonly associated Plastic-Derived Chemicals (PDCs). Extensive efforts conducted by investigators over a period of more than three years to determine which foods, sources, packaging, and preparation methods were least — and most — contaminated by PDCs. That work included efforts to: develop a set of protocols and best practices to avoid PDC contamination in sourcing and preparation, determine how the food chain gets contaminated with PFCs, and ascertain how food processing adds PDC contamination. Among the data and methods developed by the Reus, Perdue investigators in that pre-trial effort was the determination that fast, convenient, ready-to eat, and pre-prepared — Ultra-Processed — foods were the most contaminated by PDCs. For that reason, UPFs were often chosen for the “contamination” leg of the study. Intervention leg meals were “reverse engineered” to match the composition of the UPFs in order to make the”before and after” legs as identical as possible save for PDC contamination. Within days of the publication of the NIH/Hall study, Reus, Perdue investigators initially considered replicating the “before and after” selections of that extensive study and requested recipes. No response was ever made. A thorough examination of supplemental material from NIH/Hall failed to find recipes or any food sourcing and preparation details. In the interim, a closer examination by the Reus, Perdue investigators revealed that the NIH/Hall intervention meals included foods that the Reus, Perdue investigators had previously determined had been processed more than minimally and likely contained higher PDC levels than desired. Similar results and an anomaly indicate unavoidable mutual co-contaminants that confounded both dietary interventions and negated causal conclusions Levels of hsCRP decreased 21.4% from baseline to end of the minimally contaminated leg: 1.1 mg/L from 1.4 mg/L. In addition, our study results demonstrated a final reduction in hsCRP that was approximately half of that reposted by a major NIH-funded dietary intervention by Hall, et. al. published in 2019 approximately four months prior to our trial. The lower overall decrease in hsCRP in the Reus, Perdue study was reasonably attributable to: The shorter duration of our trial (six days rather than 28), and The Northern California wildfires of November/December 2019, whose smoke pollution dramatically increased PM2.5 particulate which is a notorious promoter of inflammation. Further discussion is available in the Reus, Perdue study. Investigating An Unexpected Anomaly of the Intervention Legs Despite expectations that inflammation would increase with foods projected to contain higher levels of BPA, hsCRP actually declined at the end of the “typical/contaminated” diet leg. Significantly, NIH/Hall independently exhibited this same anomaly. Efforts to explain this anomaly led investigators to consider possible causes. NIH/Hall’s primary outcome focused on obesity and investigated weight gain from the ad libitum consumption of UPFs versus less processed foods. The results confirmed weight gain from the contaminated UPF leg of the study. In looking for a possible cause of the anomaly of how BPA, hsCRP counterintuitively declined at the end of the “typical/contaminated” diet, Reus, Perdue study investigators had long recognized that Bisphenol A has been widely accepted as an “obesegen<Google Scholar cite>” and associated with obesity, diabetes, insulin dependence, as well as cancer and cardiovascular disease. Further, chronic inflammation is associated with all of those syndromes and non-communicable diseases. That was a primary reason Reus, Perdue study investigators had chosen hsCRP as a marker for PDC concentrations. The NIH/Hall study included the “appetite peptides” ghrelin, leptin, and adiponectin which we previously knew were associated with eating behavior. Because of that, the Reus, Perdue investigators searched the literature for relevant BPA clinical markers of health outcome associations. Data revealed that Bisphenol A affected ghrelin, leptin, and adiponectin affected in the ways as the NIH/Hall study recorded for Ultra-Processed Foods. In addition, the metabolic peptide behavior in the NIH/Hall study is the same as those caused by BPA exposure A further search for disease/syndromes and clinical indicator similarities between Plastic-Derived Chemicals and Ultra-Processed Foods (table below) further confirms that both show nearly identical activity. From this, the only conclusion that can be reached is that neither trial can delineate a specific causal action of PDC’s or UPFs because both are present in study foods, exert almost identical effects and are, therefore, mutually confounding factors. Click this link to download Excel spreadsheet with full-sized text The path to a revised protocol: Confounding factors lead to greater complexity and expense This study’s investigators, from the beginning, recognized that basic nutritional levels — protein, fat, and sugar/carbohydrates would need to be the same at each level of the study. While unnecessary in previous dietary intervention studies that measured only BPA levels, the present study also measures health effects which can be affected by nutritional composition. […]
Summary: What’s the Stealth Syndromes Human Study About?

NOTE: This is a summary of the current amended menu selection, rationale, and other information. The full study, including revised scientific protocol and the expanded nutritional and food selection process as approved by the University of San Francisco Medical School Committee on Human Research can be accessed at this link (pdf). A previously approved (UCSF-IRB/CHR) version that includes numerous footnoted references describing the scientific and health needs for the study can be found at this link. Internal web footnotes do not work as well in this web summary version. They can be found in the full 66-page pdf. PHASE 1: Exposure, Typical American Diet During this three-day period, study subjects will consume a diet designed to emulate a “typical” American diet. To create that diet, investigators will rely, in part, upon the U.S. Department of Agriculture’s 2016 study: Americans’ Eating Patterns and Time Spent on Food: The 2014 Eating & Health Module Data[xv]. A more recent edition will be relied upon if available. The search will begin in the frozen foods section of a supermarket. Ultimately, the retailer may be Walmart because they are located in all American states making specific brands easily accessible to other investigators. Our assumption for this strategy is that a branded frozen food is likely to be consistent in content, nutrition and contaminant exposure regardless of the location of purchase. This is not a certainty because processing may have taken place at different facilities depending upon distribution and location of sale. We will make an effort to determine the processing facility for all goods. Because data from numerous sources indicate that chicken, beef and pork are the most popular meats, we will reflect this by using each for one of the evening dinner menus during the 3-day exposure phase. In cases where a suitable complete meal is not available, we will select multiple items and combine as a meal. Items will be prepared as indicated on their labels. This will, inevitably mean microwaving frozen foods in plastic containers or in paper containers with plastic liners. To best reflect “typical American” meal and to assure widespread availability and reproducibility, we will select best-selling brands. PHASE 2 – Reduced contamination, commercial Once a menu has been established for the typical exposure phase, the components of this diet phase will be structured to emulate the typical exposure phase meals as closely as possible using less-contaminated food choices. This phase, which has been missing from all other diet intervention studies of BPA and phthalates, offers study participants a “standard dose” of BPA and phthalates. This phase is intended not only to assess the effects of a typical American diet, but also to “standardize” food-exposure levels for each participant. Standardized food exposure levels, combined with the final phase (minimum non-food exposure – NFE) may be useful in establishing estimates of overall individual NFE. Foods and beverages will be obtained from Organic Certified sources, selected for minimum processing and plastic food contact materials. Currently, Whole Foods is the only national chain that prohibits biosolid use in its foods and may be a primary source because its availability facilitates reproducibility by other investigators. Other widely available sources will be sought, especially from among direct-shipping vendors who adhere to the enhanced organic rules developed by this study’s investigators. No plastic contact. Exceptions are not preferred, but may include BPA and phthalate-free nitrile gloves and tubing such as Tygon S3 B-44-3 Beverage Tubing or other manufacturer’s equivalent. Any plastic product used must be tested to assure manufacturer claims because studies have shown that some manufacturer claims are false.[xvi],[xvii],[xviii] Preparation & cooking The following are forbidden: Sous vide non-stick pans most cooking oils plastic utensils plastic prep bowls synthetic gloves plastic bags plastic wrap drip coffee makers Sodastream Keurig and other “pod” beverage makers Beverages in cans, plastic bottles or glass. PHASE 3: Enhanced organic This diet will work to provide identical menu items served in previous phases but will follow a set of guidelines developed by this study’s investigators for sourcing local food and beverage products. Those guidelines eliminate many sources of endocrine disruptors — such as recycled wastewater irrigation — that are allowable under USDA organic regulations. Adherence to these rules should facilitate reproducibility. The guiding principals are summarized below. More details are available in Appendix 2 of this document. Commercially processed foods are unacceptable. All food will be obtained directly from local Certified USDA Organic sources whose premises have been voluntarily inspected for compliance with those and the following enhanced requirements. Do not consume any ingredient whose composition cannot be traced to, and inspected at its origin. No recycled wastewater is allowed in irrigation or other on-premises uses. No biosolids are allowed in irrigation or other on-premises uses. No food contact with plastics or recycled paper or cardboard. Minimum or incidental contact may be approved depending upon the plastic composition. Irrigation water must not be transported via plastic pipes. Drip irrigation is discouraged, but if used must not contact edible surfaces. Harvest and food transport must be in metal containers. PHASE 4 – Enhanced, local sourced, reduced contamination diet, minimum Non-Food Exposure The unknown — and possibly unknowable — variabilities in this class of exposures offers the greatest set of hazards to reproducibility. Numerous non-food sources of BPA are present in the environment and likely pose significant “background” contamination which will vary depending upon the test subjects’ lifestyles and environments. This is particularly critical because the major health effects being measured in this study; estrogen/testosterone disruptions, inflammation, and metabolic events such as insulin resistance and lipid imbalance, can also be affected by a wide variety of chemicals other than BPA and phthalates. This is why this final phase of the protocol has been added to reduce non-food exposures of all harmful chemicals as much as possible. In addition, the personal environments of participants (personal care products, medications, etc.) must be noted for the record and reduced in a manner that can be illuminated by comparison with measured BPA, phthalate, and […]