Biobeef Blog

Thoughts of public sector animal geneticist - all views are my own

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Unnatural Selection

I binge watched Unnatural Selection on NetFlix last night, because it is of dual interest to me – both from the perspective of my research, but also because of my interest in science communication. I had also spent a couple of days with the directors, Leeor Kaufman and Joe Egender, at UC Davis in late 2017 and early 2018 as they filmed some of our discussions with the public over the use of genome-editing to produce the “hornless” dairy animals we have been researching.

Ultimately the miniseries ended up not including any of the agricultural applications of genome editing, as the directors wrote to me in an Email earlier this month, “we were not able to open the discussion about food engineering within the scope of 4 episodes.” They rather focused the show on the biomedical and gene drive applications for pest control noting that “other stories – especially of the patients – became larger than we anticipated, making it very difficult to introduce such a broad subject in between.”

I can certainly understand the emotional appeal of treating genetic conditions, and that such framing lends itself to narrative storytelling. However I believe it unfortunate because the many researchers I know working in this area are addressing very real and pressing problems in food production, and we have not had much success at effective science communication on the need for these genetic innovations in agricultural production systems.

One of the more bizarre characters featured on the miniseries was a dog breeder called David Ishee located in Mississippi who was apparently trying to create a green fluorescent mastiff puppies by adding Green Fluorescent Protein (GFP)-expressing E. coli to dog sperm. I just watched dumbfounded, knowing all of the animal use authorizations and regulatory hurdles we have to go though to perform any animal research on campus. And also  because that is not how genetic engineering works, that is not how any of this works. If it was that simple, my laboratory would not have spent the last three years trying to get a CRISPR knock-in cow.


It is possible to get fluorescent animals, like the GloFish. But they are expressing a transgenic fluorescent gene under the control of a eukaryotic muscle promoter, and this recombinant DNA gene construct was integrated into the genome though genetic engineering in developing eggs. The reason you can see fluorescence clearly in Glofish is that they are somewhat translucent. Mastiff puppies are not. Even if it green fluorescent protein (GFP) did somehow find itself expressing in these puppies, it would not express or be visible in their dark hair. It is similarly lacking in the plumage of the GFP-chick in the featured image made by the Roslin Institute.

A fluorescent rabbit was made 20 years ago,  in the bizarre case of Alba the GFP-bunny. In 2000, Eduardo Kac, a professor of art and technology at the Chicago School of Art Institute produced a picture of a green fluorescent protein (GFP) transgenic bunny called “Alba”. “GFP Bunny” was realized in 2000 and first presented publicly in Avignon, France. The artist proposed that “transgenic art” is a new art form based on the use of genetic engineering to transfer natural or synthetic genes to an organism, to create unique living beings.

Alba Image

The artist came under considerable criticism for the picture which some consider to have been fabricated. According to a 2002 Wired article “The picture itself is a construction,” said Reinhard Nestelbacher, a molecular biologist at the University of Salzburg.  “The rabbit could never look like that,” he said. “The main reason is that the GFP gene is expressed, for example, in the skin and cannot be expressed in the hair.” Stuart Newman, a member of the Council for Responsible Genetics and a cell biologist at New York Medical College, said “Art misrepresents reality all the time — and he’s an artist, not a scientist, but I think people are beholden to tell the truth.”

Which raises an interesting question, are artists beholden to tell the truth about genetic engineering?

And that is I think what frustrated me most about the miniseries. This was potentially an opportunity to have a fresh look at this technology of genome editing, and how it does and does not differ from the older technology of genetic engineering. The two technologies were rapidly conflated in the miniseries, along with other issues such as the cost of medicine in the US healthcare system. And while these tensions were thoughtfully addressed, I would argue the tensions around food production are equally important and were not addressed.

There is a very real reason that the public fears the use of genetic engineering in food production, and it is not the science or decades of safe use. It is a deliberate misinformation campaign that has been waged by competing-business interests and special-interest group for decades. That topic warrants its own examination.

It was therefore somewhat ironic to see Dana Perls from “Friends of the Earth” as one of the interviewees in Unnatural Selection. She was unchallenged when allowed to repeat the same unsubstantiated talking points around genome editing and food safety risks that have been parroted for decades to demonize genetic engineering,   This to me was opening a discussion around food engineering, but in the absence of any mention of the 30 years of safe use, or the overwhelming weight-of-evidence.

Just as there is money to be made in commercializing pharmaceutics, there is money to be made in fermenting fear, uncertainty and doubt, especially against your competitors. If those same special interests again direct their well-funded coffers towards a campaign against the use of genome editing in food production, then I fear that as a society we will lose. We will forgo the benefits that could result from bringing in useful genetic variation like disease-resistance into our food species using genome editing.

One of the most powerful stories in Unnatural Selection was that of a young boy who had a genetic condition that threatened his sight. And the $850,000 treatment that might help save him from blindness. It is very moving part of the series, as we see his parents grapple with their frustration at his deteriorating sight.

There is a non-genetic condition that results in between 250,000 and 500,000 children going blind every year, Vitamin A deficiency. And yet the war that special interest groups like Greenpeace and Friends of the Earth have waged against GMOs for the past 30 years, in concert with the retarding force of government regulations on GMO crop development, has slowed the release of vitamin-A enriched crops as detailed in this recent book, Golden Rice: the imperiled birth of a GMO superfood.

The 2019 Wolf-prize for Agriculture laureate Prof. David Zilberman from University of California at Berkeley, estimated in 2014 that if Golden Rice had not be delayed in India alone it would have  “prevented 600,000 to 1.2 million cases of blindness, and about 180,000 deaths of children.” Likewise 129 nobel-laureates “have joined in a campaign to convince the Green Parties and the public that they should support the use of GMOs, especially for the sake of the developing world”,

Fortunately, after millions of dollars and years of effort, the United States, Canada, Australia, and New Zealand have all recently approved golden rice as safe for consumption. Golden rice is in now front of regulators in the Philippines and in Bangladesh, where it is expected to be approved by the end of 2019. There it will have the opportunity to benefit many poor children, each of whom have parents who I am confident are equally anxious and concerned about addressing  the preventable blindness of their children. Perhaps emerging developments in food engineering with such profound beneficial health implications are worthy of their own miniseries!


Harmonize US gene-edited food regulations

I have been fairly consistent about my concern that the 2017 FDA’s draft guidance to regulate “intentional genomic alterations” in food animals as new animal drugs will preclude the use of this technology in livestock breeding programs in the United States. The webinar that was held today by the FDA Center for Veterinary Medicine (CVM) did little to assuage my concern. For two hours, various speakers from the FDA CVM explained how they were going to regulate IGA (intentional genomic alterations). That is a lot of 3-letter acronyms (the scariest of all acronyms!).

There was lots of discussion of frightening sounding off-target effects, small to large-scale alterations, unintended biological consequences, unknown long term effects not apparent in early generations, deletions, insertions, inversions, lesions, translocations, mutations being deleterious regardless of whether they occur in a coding region, and challenges to addressing unintended on and off target effects. What there was not much discussion of is biology and context. And the fact that there are literally millions of “insertions, inversions, lesions, translocations, and mutations” in every plant and animal on Earth.

As we argue in this open access 2019 paper entitled “Proposed U.S. regulation of gene-edited food animals is not fit for purpose

To put this in perspective, one study of whole genome sequence data from over 2,700 individual cattle in the 1000 Bull Genomes Project revealed more than 86.5 million differences (variants) between different breeds of cattle. These variants included 2.5 million insertions and deletions of one, or more, base pairs of DNA, and 84 million single nucleotide variants, where one of the four nucleotides making up DNA (A, C, G, T) had been changed to a different one. None of these naturally-occurring variants are known to produce ill effects on the consumers of milk or beef products. In fact, every meal we have ever consumed is genetically distinct from every other meal in terms of genomic DNA sequences. Genetic variation per se does not pose a unique hazard as it relates to food safety. All non-processed foods harbor DNA as a natural component and that DNA is different in every individual of every food species (both plants and animals).

Visual representation of the magnitude of DNA sequence variation (i.e. naturally-occurring mutations) that exists between different individuals within a species. Image from Van Eenennaam et al. (2019)

A number of other countries have come out with their regulatory approaches to genome editing in food species, including the USDA opinion regarding genome edited plants, and the FDA is alone in considering a genetic alteration in a food animal to be a drug. And while under proposed U.S. law it is technically not the animal but the IGA (not the grocery store but the “intentional genomic alteration”) that is the drug, short of a centrifuge it is pretty hard to disassociate an animal from its genomic DNA! Animals carrying IGA effectively become unapproved animal drugs that are not allowed to enter commerce in the absence of a multigenerational safety and efficacy evaluation and FDA approval, analogous to the types of studies that are required for the approval of actual new animal drugs.

All of this comes about because 10 years ago the FDA announced its intent to regulate all genetically engineered animals modified by rDNA techniques, including the entire lineage of animals that contain the modification, under the new animal drug provisions of the 1938 Federal Food, Drug, and Cosmetic Act (decades before the discovery of the structure of DNA).  In that act, a new animal drug is defined as “an article (other than food) intended to affect the structure or any function of the body of … animals.”

The 2017 FDA draft guidance on gene edited animals doubles down on this approach by proposing to regulate all genomic alterations introduced into animals by gene editing as new animal drugs. This includes many of the same nucleotide insertions, substitutions, or deletions that could be obtained using conventional breeding. No longer is it the presence of a transgenic rDNA construct that triggers mandatory premarket FDA regulatory oversight prior to commercial release, but rather it is the presence of any “intentionally altered genomic DNA” in an animal that initiates oversight.

What concerns me, after listening to the webinar, is that it was really not stated what unique risks are feared to be associated with IGA, that are not also associated with UGA (unintentional genomic alterations), aka de novo mutations that are very basis of evolution. We do not regulate the millions of spontaneous genetic variations that are in our food because DNA is generally regarded as safe to consume, and it is a routine ingredient of food obtained from any species, irrespective of its sequence. Referring to a DNA sequence variant as a “drug” is likely to confuse or frighten consumers who might infer that there are biologically active substances in their food.

I am of the opinion that this proposed regulatory approach for genome editing in animals will effectively make it cost prohibitive for both U.S. researchers and livestock producers to use and potentially benefit from genome editing in food animal breeding programs. I am not alone in this concern. Over 300 scientists supported a petition calling for  the Harmonization of US gene-edited food regulations which was launched in January at the 2019 Plant and Animal Genome meeting. Signatories include over 260 US scientists from more than 40 academic institutions throughout the nation including members of the National Academy of Science, Engineering and Medicine (NASEM), and a Nobel prize laureate. When scientists are riled up enough to emerge from their laboratories and express an opinion about something as arcane as a regulatory guidance, perhaps it is worth listening.  The petition concluded with the following ask:

“We call for a harmonization of the U.S. regulatory approach to gene editing in food species so that both plant and animal breeders have access to gene editing innovations to introduce useful sustainability traits like disease resistance, climate adaptability, and food quality attributes into U.S. agricultural breeding programs.”

Proposed U.S. regulation of gene-edited food animals is not fit for purpose

It has been more than two years since the FDA released its draft “Guidance for Industry #187” “Regulation of Intentionally Altered Genomic DNA in Animals”, that proposes to regulate ANY “intentionally altered genomic DNA” in food animals as a veterinary drug, irrespective of product novelty or risk. Human intention does not equate to risk. This regulatory trigger seems to be aimed squarely at some taint associated with human intervention . Despite the fact that the public comment period for the FDA’s draft guidance for industry #187 closed on June 19, 2017, there has not yet been a formal response to the many comments by public sector scientists working in this field who see that this regulatory approach will make food animal research in this field cost prohibitive, and effectively preclude the use of gene editing in food animal breeding programs.

Dietary DNA is generally regarded as safe to consume, and is a routine ingredient of food obtained from any species. Millions of naturally-occurring DNA variations are observed when comparing the genomic sequence of any two healthy individuals of a given species. Breeders routinely select desired traits resulting from this DNA variation to develop new cultivars and varieties of food plants and animals. Regulatory agencies do not evaluate these new varieties prior to commercial release.

To put this in perspective, one study of whole genome sequence data from 2,703 individual cattle in the 1000 Bull Genomes Project revealed more than 86.5 million differences (variants) between different breeds of cattle. These variants included 2.5 million insertions and deletions of one, or more, base pairs of DNA, and 84 million single nucleotide variants, where one of the four nucleotides making up DNA  (A, C, G, T) had been changed to a different one.

A small fraction of these mutations have been selected by breeders owing to their beneficial effects on characteristics of agronomic importance. None of these naturally-occurring variants are known to produce ill effects on the consumers of milk or beef products. In fact, every meal we have ever consumed is genetically distinct from every other meal in terms of genomic DNA sequences. Genetic variation per se does not pose a unique hazard as it relates to food safety. All non-processed foods harbor DNA as a natural component and that DNA is different in every individual of every food species (both plants and animals).

Gene editing tools now allow plant and animal breeders to precisely introduce useful genetic variation into agricultural breeding programs. The U.S. Department of Agriculture (USDA) announced that it has no plans to place additional regulations on gene-edited plants that could otherwise have been developed through traditional breeding prior to commercialization. However, the U.S. Food and Drug Administration (FDA) has proposed mandatory premarket new animal drug regulatory evaluation for all food animals whose genomes have been intentionally altered using modern molecular technologies including gene editing technologies.

Mandating premarket regulatory approval for deletions, mutations, and the conversion of one wild-type allele to another wild-type allele in the same species (cisgenic) that could have been obtained using conventional breeding runs counter to the approach that was outlined by OSTP in the 1992 policy announcement (following the 1986 Coordinated Framework document).  There it is stated that, “Exercise of oversight in the scope of discretion afforded by statute should be based on the risk posed by the introduction and should not turn on the fact that an organism has been modified by a particular process or technique”. Additionally, it was clarified that “(O)versight will be exercised only where the risk posed by the introduction is unreasonable, that is, when the value of the reduction in risk obtained by additional oversight is greater than the cost thereby imposed. The extent and type of oversight measure(s) will thus be commensurate with the gravity and type of risk being addressed, the costs of alternative oversight options, and the effect of additional oversight on existing safety incentives.”

At the end of the day, food animals with intentional genomic alterations produce food, and if the food they produce is not biologically active via an oral route of administration it does not make sense to regulate these intentional genomic alterations as drugs. Referring to a DNA sequence variant as a “drug” is likely to confuse or frighten consumers who might infer that there are biologically active substances in their food.

A DNA alteration is not a drug, but rather part of the genetic code uniquely associated with any organism. Through its natural function within a cell, DNA controls how an organism grows and its unique form and function. The phenotype will ultimately be determined by the interaction of an organism’s genomic DNA sequence and the environment in which it lives. We do not regulate the millions of spontaneous genetic alterations that are in our food because DNA is generally regarded as safe to consume, and it is a routine ingredient of food obtained from any species, irrespective of its sequence.

The FDA’s draft “Guidance for Industry #187” entitled “Regulation of Intentionally Altered Genomic DNA in Animals” is not fit for purpose as it relates to food animals that could otherwise have been developed through traditional breeding techniques.   Myself and fellow academic researchers reject the idea that intentional genomic DNA alterations should be regulated as a veterinary drug in food animals, and consider that the proposed approach will thwart the development of genetic approaches by public sector researchers and small companies to use gene editing to solve zoonotic disease and animal welfare problems in the United States.

Please support the petition above calling for harmonization of the U.S. biotechnology regulatory system so that both plants and food animals that could otherwise have been developed through traditional breeding techniques are not subject to additional premarket regulatory requirements based solely on the fact that intentional genomic alterations were introduced using modern biotechnologies or rDNA techniques in the breeding process.

Harmonizing the regulations associated with gene editing in food species is imperative to allow both plant and animal breeders access to gene editing tools to introduce useful sustainability traits like disease resistance, climate adaptability, and food quality attributes into U.S. agricultural breeding programs.

Proposition 12 – Humane vs. Humane

Back in January I wrote a blog entitled Proposition 2 déjà vu about a proposed  California ballot initiative entitled “The Prevention of Cruelty to Farm Animals Act”. Sure enough that initiative qualified for the 2018 ballot, despite the clear data on the impacts as detailed in my three blog posts on this issue (Six hens a laying, Evidence-based animal welfare recommendations, Proposition 2 déjà vu).

I am quaintly of the opinion that objective evidence should drive public policy, and not emotions, despite having lived in California for over 30 years. And as a public scientist I remain convinced that objective facts and data are the best way to inform policy.

However, ballot initiatives in California are basically a pay-to-play scorecard. If you have the money to get the requisite number of signatures (365,880 valid signatures), then your initiative will be on the ballot, facts be damned. And so it was with Proposition 12, a Humane Society of the United States (HSUS)‐backed initiative addressing animal confinement, which has raised $5.37 million to date… And so now let’s cue the opposition funding which will no doubt be “big ag” or “corporate farming” or “evil egg” or “big chicken”, or a tearful segment of a mother on Dr. Oz, or a shockumentary on NetFlix…..but no – crickets (actually cage-free, mute crickets to be precise). As in no organized-opposition from those who grow your food, or research the best way to produce food sustainably (Hint: people who might know some things).

Wait – what? Agriculture and scientists have had enough. We know science and facts are useless (see my previous 3 blogs re this initiative and almost all of the outreach work I have ever done in agricultural science), and there just is no point in fighting initiatives funded by wealthy animal activist industry groups who use persuasive arguments based entirely on emotion while conveniently failing to mention the multiple trade-offs and unintended consequences associated with their proposed course of action. And so the usual adversaries of demonstrably bad agricultural policy i.e. “big ag”, known as farmers by the general public, and “tobacco scientists”,  known as public university faculty and researchers to most, have thrown in the towel.

And I understand that response. It is exhausting trying to fight these large, well-funded activist groups who will stop at nothing to get their way – facts and scientific consensus be damned, and it can be a lucrative pastime. Ask those trying to fight the anti-vaxxers, or the anti-GMO industry. Slowly I see my animal scientist colleagues quietly retreating into the “spiral of silence” – a tranquil place where no one fabricates facts, and where pure science can be carried out peacefully sans messy public confrontations – sometimes referred to as “the ivory tower.”

Last time UC Davis got involved in this discussion by providing objective facts regarding Proposition 2 “Treatment of Farm Animals” over a decade ago in 2008, it cost the taxpayers more than a million dollars in a lawsuit with HSUS – money that did not go to educating our students or carrying out research, and the lawsuit about wore out one of my faculty colleagues. Likely UC administration is happy we are playing dead this time around on Proposition 12 too.

And who can blame the University? It is not fun to be in the middle of a politicized, scientific controversy. However, if professionals in the field are unwilling to stand up for objective data and evidence-based decisions, who will? And that is where this discussion gets interesting.

Who is opposing Proposition 12 – if not industry or subject-matter experts? The Humane Farming Association (HFA), an animal cruelty organization that opposes the proposition on the grounds that it legalizes for several more years some practices HFA opposes. So Proposition 12 does not move fast enough for the Humane Farming Association.

Say again? With a modest $550,000, a committee backed entirely by the Humane Farming Association, is the sole funder of opposition to Proposition 12, the “The Prevention of Cruelty to Farm Animals”. And here is where it gets good. Who doesn’t like a little Humane vs Humane mud wrestling?

Bradley Miller, spokesperson for HFA’s Californian’s Against Cruelty, Cages, and Fraud “Stop the Rotten Egg Initiative” stated of rival HSUS

The Humane Society of the United States [HSUS] is once again deceiving voters, flip-flopping on the issue of cages, and perpetuating the suffering of egg-laying hens”                                            HFA

There is a video made by HFA (below and can be accessed here) summarizing their version of the June 19, 2018 California State Legislature hearing regarding Proposition 12 which contains some interesting conflict-of-interest footage, including some questioning as to how much money HSUS was making from Proposition 12 (Spoiler alert: HSUS does not have those numbers).

According to HFA, HSUS ended up collecting 664,000 signatures for the ballot, but less than a quarter (164,000) of those were collected by volunteers, the remaining signatures were collected by HSUS paid-“bounty-hunter” signature gatherers, like the one I met at the CA Davis market in January, telling me that Proposition 12 would remove non-existent “veal-crates”, and sow “gestation crates” from California production systems. This video is worth a listen, as Miller suggests the major opposition to Proposition 12 will be the humane farming associations.

Miller further stated on the HFA “Stop the Rotten Egg” page:

Prop 12 is now just a publicity stunt in search of a lawsuit. Not only does this come at taxpayer expense, HSUS’s reckless exploitation of California’s ballot measure system is putting in grave danger a wide array of existing consumer, animal, and environmental protection laws. Of the initiatives appearing on the November ballot, Proposition 12 is the dirtiest of the dozenWe’re confident that California voters won’t get fooled again and that this fraudulent initiative will be decisively rejected.”                                                                                                                                 HFA

And then there is a quote from Friends of Animals (FoA) on the HFA “Stop the Rotten Egg” page,

“This initiative should be fiercely opposed by everyone who cares about farm animal suffering. HSUS’s collusion with the egg industry is disturbing. From legalizing battery cages to allowing as little as one square foot of space per hen — this initiative would be a disaster for millions of egg-laying hens who would still be left suffering in battery cages throughout California.”                     FoA

And yet another quote from People for the Ethical Treatment of Animals (PETA) on the HFA “Stop the Rotten Egg” page

Beware! This initiative is being painted in rosy terms, but don’t be fooled… What it would actually do is allow farms to keep egg-laying hens in cages until 2022, at which time factory farms would still be able to confine uncaged hens to massive, crowded sheds with only 1 square foot of space per bird.”                                                                                                                                                        PETA

And finally this from Animals 24/7 on the HFA “Stop the Rotten Egg” page

“Time and again HFA has accurately identified fatal flaws in legislation advanced by HSUS.”    Animals 24/7

So what is a voter to do? Be guided by The Humane Society of the United States (HSUS), the Humane Farming Association (HFA), People for the Ethical Treatment of Animals (PETA), Friends of Animals (FoA), or Animals 24/7? Some of the above, none of the above, one of the above? Who is representing animal welfare, and how can you tell? You could try asking the scientific community who have spent their careers researching these questions, or farmers who happen to know a thing or two about farming – but that does not seem to be a popular route.

In the absence of objective, evidence-based measurements – there is just a “blob” of emotions, competing world-views, and fund-raising agendas. And that is not a great foundation upon which to base decisions around animal agriculture or public policy. Case in point: Proposition 2 from 2008 (see what that did to California farmers: Six hens a laying).

So it seems some cracks are appearing in the humpty dumpty coalition of “animal-themed corporations” also known as the “humane community”.  And perhaps nowhere is this rift more bizarrely illustrated than in this “Stop the Rotten Egg” page  animated video, “Proposition 12: California’s Caged Chickens Say NO!”.

For anyone that has ever met the former President and CEO of HSUS, Wayne Pecelle, who resigned February 2018 in a #MeToo moment  after a number of women accused him of sexual harassment,  the big-toothed male lead featured in this animated video is a thinly disguised provocation from one humane society (HFA) whose operations are based on the West Coast in California to another (HSUS) based on the East Coast in Maryland. Ironically the largest egg producing state in the US by far is Iowa.

On an unrelated note, buried in the fine print of Proposition 12, are the following strikeouts (and additions) that remove the scientific and agricultural research exemptions that were previously written into SECTION 5. SECTION 25992 OF THE CALIFORNIA HEALTH AND SAFETY CODE (line A below).

The proposed Proposition 12 language includes the following exemptions:

“This Chapter will not apply:

(a) During scientific or agricultural medical research.”

In other words, scientific and agricultural research animals at universities and other research facilities are subject to the provisions of the initiative – just like all of the farm animls. The implications of this change to the research exemption on things such as teaching, scientific or agricultural research, especially for genetic and nutrition research (we need individual cages to collect observations or phenotypes on each animal, and to record which egg comes from which hen), may well not be discovered until after the ballot votes are cast when agriculturalists and scientists go to perform specialized research on calves, pigs, or poultry.

It may be that those university researchers retreating to the “spiral of silence” to avoid the discomfort of a heated public discussion of Proposition 12, will eventually find their research projects thwarted by the inevitable passage of the initiative (I may have quaint opinions on how objective evidence should drive public policy, but I am a realist living in California). Yet another casualty of public policy based on emotion and propaganda, rather than informed by objective evidence and science-based recommendations.

As Mr. Miller, spokesperson for HFA’s Californian’s Against Cruelty, Cages, and Fraud, ironically lamented during his testimony before the California State Legislature, including the words “farm animal” and “protection” in a ballot initiative in California is enough to get it passed, irrespective of how the text reads, and what the ultimate impacts of its passage will be on the welfare of animals, and the people of California.

Antibiotic Use and Food Animals

Because I did not think biotechnology and hen housing were controversial enough topics, I thought I would wade into antibiotic use in food animals. Actually, the only reason I am doing this blog is because of a Twitter exchange with Marc Brazeau from Food and Farm Discussion Lab late last year. He posed several questions to me and I postponed responding unitl I had a little time to delve into the science. The answers are necessarily a bit sciency – if you want to cut to the chase, scroll directly down to Question 7.

1. How much are antibiotics used in food animal agriculture?

We have sales records from 2009-2016 from the FDA for food animal sales, but I couldn’t find any on the human side of things since April of 2012 (2011 data). The quality of the data is not great – in that it is sales data – and because some food animal products are labelled for multiple species it is a bit hard to interpret use – was that drug sold to treat a horse or a cow or a dog? The data are broken down into “medically-important” versus “not medically-important” as determined by the FDA (Appendix A).

In 2016, there were 8.36 million kg of “medically-important” and 5.62 million kg of “not medically-important” antimicrobial drugs (e.g. ionophores) sold. The good news is that these numbers represent 14% and 4% decreases, respectively, over 2015 sales data. These can be contrasted to the last data available for humans which is 3.29 million kg sold in the U.S. market in 2011. Hard to detemine the trend in human prescriptions in the absence of data.

The FDA warns that there are a number of differences in the circumstances in which antimicrobial drugs are used in human and veterinary medicine that must be carefully considered before making comparisons between human and animal use, including:

  • The number of humans in the U.S. population (approx. 320 million) compared to the much, much larger number of animals in each of the many animal species (e.g., approx. 9 billion chickens slaughtered annually)
  • The differences in physical characteristics of humans compared to various animal species (e.g., physiology and weight– average adult human, 182 lb vs adult cattle live weight, 1,363 lb).
  • Veterinarians commonly utilize human antimicrobial drugs in their companion animal patients; therefore, amounts presented for certain human antimicrobial drugs may represent some unknown portion sold for use in companion animals. More on this point later!

According to the FDA it is, therefore “difficult to draw conclusions from any direct comparisons between the quantity of antimicrobial drugs sold for use in humans and the animal drug sales and distribution data (and species specific estimates) for use in animals.”

2. What types of antibiotics are used in animal agriculture?

It should be noted that there were some fairly sweeping changes that went into effect in 2017  as part of an effort to promote the judicious use of “medically-important” antimicrobial drugs in food animals.

The FDA has approved antibiotics for only these 3 uses in food animals:

  • Disease treatment for animals that are sick;
  • Disease control for a group of animals when some of the animals are sick;
  • Disease prevention for animals that are at risk of becoming sick.

Animal health companies, farmers and veterinarians cooperated with the FDA to develop a guidance which ended the use of antibiotics important to human medicine to promote growth in animals or to improve feed efficiency (i.e., production purposes). The remaining therapeutic uses in feed and water are required to be under the supervision of licensed veterinarians through the Veterinary Feed Directive (VFD) (feed uses) or prescriptions (water uses) which went into effect on 1/1/2017. These changes were enacted to ensure these drugs are used judiciously and only when appropriate for specific animal health purposes.

As can be seen from the graph above, by far the biggest class of antibiotics used in food-producing animals in 2016 was tetracyclines, a class of antibiotics which represented only ~ 3.5% of human antibiotic sales in 2011. This number will likely fall in 2017 as a result of the cessation of the use of “medically-important” antibiotics  for production purposes.

3. What is the current state of knowledge about the transfer of resistant bacteria from livestock farms and manure use to human populations? Farm workers first and foremost.

Based on the available literature, direct transfer to humans seems to occur at a pretty minor level. One paper estimated that direct infection with resistant bacteria from an animal source, or through ingestion of bacteria from contaminated meat or water, was a relatively small risk in comparison with the overall burden of resistant disease. There was one example in the US in the past year where a Salmonella outbreak of S. heidelberg infected 54 people of whom 34 (63%) reported contact with ill calves (0 deaths). To put this in perspective, there are 1.2 million food-borne Salmonella infections per year (450 deaths). Interestingly, dogs and cats can also carry and transmit Salmonella and Campylobacter organisms, along with other pathogens traditionally associated with “foodborne diseases”.  One older paper raises the question of whether dogs or other companion animals are involved in transmitting such pathogens to food-producing animals or humans, an issue which is often overlooked.

We share our homes and our microbiota with our companion animals

According to one paper examining the prevalence of within-household sharing of fecal Escherichia coli between dogs and their owners, both direct contact and environmental reservoirs were seen to be routes of cross-species sharing of bacteria and genes for resistance. The authors warned that cross-species bacterial sharing is a potential public health concern, and good hygiene is recommended (i.e. wash your hands after cleaning up after your pets!!).

It is known than human exposure to zoonotic nematodes and cestodes and other parasites associated with feces of companion animals in the United States is an ongoing public health problem. And statistically it is more likely most people will come into contact with one of the 140,000,000 dogs and cats in the US, than directly with livestock.  The transmission of antimicrobial-resistant organisms between humans and pets warrants further investigation, especially as pets can be treated with  “medically-important” antimicrobial drugs.

4. Is there evidence showing resistance originates in the animal population and then moves to humans?

A recent 2017 systematic review and meta-analysis to summarise the effect that interventions to reduce antibiotic use in food-producing animals have on the presence of antibiotic-resistant bacteria in animals and humans, and funded by the WHO, concluded:

Interventions that restrict antibiotic use in food-producing animals are associated with a reduction in the presence of antibiotic-resistant bacteria in these animals. A smaller body of evidence suggests a similar association in the studied human populations, particularly those with direct exposure to food-producing animals. The implications for the general human population are less clear, given the low number of studies. 

The Centers for Disease Control (CDC) issued a 2013 study on the most concerning antibiotic resistance threats and none of the most urgent threats have any relation to farm animals. On the broader CDC list, which includes less urgent threats, only two of 18 involve bacteria associated with farm animals.

A comprehensive 2016 review of 50 studies published in Critical Reviews in Food Science and Nutrition concluded that there is an established connection between animal antibiotic use and antibiotic resistance in animals, but no established causal relationship between animal antibiotic use and human resistance related to campylobacter.

There is an interesting example of an antibiotic drug called avoparcin that was used in EU agriculture for livestock growth promotion. The human equivalent is vancomycin which is used to treat E. faecium, and there was concern around vancomycin-resistant E. faecium (VRE). Avoparcin was banned in Denmark in 1997 as part of their elimination of production uses of antibiotics, and as a result VRE declined in farm animals but increased in hospitals where human vancomycin use & VRE are highly correlated. The US never approved avoparcin in livestock yet VRE started here in the 1990s due most likely to human vancomycin usage or quite possibly use in companion animals as VRE precursors have been isolated in dogs.

Likewise, this paper states that in 2005 the emergence of fluoroquinolone-resistant Campylobacter jejuni in the clinical setting in conjunction with fluoroquinolone administration in animals prompted the FDA to ban fluoroquinolone use in poultry, although it remains unclear if the dramatic increase of fluoroquinolone-resistant strains was due to fluoroquinolone use in livestock. In the USA, no decline in the levels of ciprofloxacin resistance was observed following the ban of fluoroquinolones in chickens. While it is possible that insufficient time has elapsed for trends to be detectable, it is also possible that fluoroquinolone-resistant strains may remain in the environment in the absence of antibiotic selective pressure.

On a broader scale, the EU and especially Sweden and Denmark have removed all growth promoting uses of antibiotics, and I am not familiar with any data showing this has moved the needle on resistance in human populations.

5. How reasonable is it to be concerned that bacteria resistant to an Ag-centric ABx becomes just a mutation or two away from resistance to medically important ABx with a similar mode of action.

According to the WHO-funded 2017 systematic review and meta-analysis,

There is currently no consensus regarding the effect that antibiotic use in food-producing animals has on antibiotic resistance in the human population. Furthermore, the effect of interventions that restrict antibiotics in food-producing animals on antibiotic resistance in both animals and humans is somewhat unclear.”

In the discussion section, this 2015 paper states that,

The topic of agricultural antibiotic use is complex. As we noted at the start, many believe that agricultural antibiotics have become a critical threat to human health. While the concern is not unwarranted, the extent of the problem may be exaggerated. There is no evidence that agriculture is ‘largely to blame’ for the increase in resistant strains and we should not be distracted from finding adequate ways to ensure appropriate antibiotic use in all settings, the most important of which being clinical medicine.”

You can be worried about it, but I think the objective data is much stronger on resistance coming for the most part by way of human medicine use. Anytime antibiotics are used they will lead to resistance – whether used to treat livestock, dogs or people.

6 . What are the recommendations of the World Health Organization Guidelines on use of medically important antimicrobials in food-producing animals ?

The first three recommendations of the WHO guidelines are based on “low quality evidence

  1. We recommend an overall reduction in use of all classes of medically important antimicrobials in food-producing animals.
  2. We recommend complete restriction of use of all classes of medically important antimicrobials in food-producing animals for growth promotion.
  3. We recommend complete restriction of use of all classes of medically important antimicrobials in food-producing animals for prevention of infectious diseases that have not yet been clinically diagnosed.

And the last two are conditional recommendations based on “very low quality evidence

Recommendation: Control and treatment use (in the presence of disease)

4a. Recommendation: We suggest that antimicrobials classified as critically important for human medicine should not be used for control of the dissemination of a clinically diagnosed infectious disease identified within a group of food-producing animals.

4b. Recommendation: We suggest that antimicrobials classified as highest priority critically important for human medicine should not be used for treatment of food-producing animals with a clinically diagnosed infectious disease.

The fact that the WHO acknowledges there is low or very low quality evidence to support these apparently logical recommendations, does suggest that there is little data on the transfer of resistant bacteria from livestock farms. Irrespective, the first recommendation for an overall reduction in use of all classes of medically important antimicrobials in food-producing animals to me lacks the required nuance when dealing with disease. A blanket reduction (as in just decreasing the physical mass or amount) of antibiotics used in food animals does not necessarily mean improvement.

For example, replacing an effective antimicrobial with an ineffective antimicrobial that is used at a lower dose would result in an overall reduction in the use of antibiotics, but not with the desired effect as the animal would still be sick. And some “medically-important” antibiotics are more important/critical than others. It is analogous to the comparison that is sometimes made that the weight of glyphosate herbicide use has gone up in recent years, but that has to be looked at in terms of the effectiveness and weight and toxicity of alternative herbicides that were used to control the weed problem. Same thing here – what are alternatives for treatment and how effective are they (i.e. weigh up pros and cons and determine the most judicious choice of treatment)?

Recommendations 4a and 4b are based on very low evidence. The report states that when a veterinarian is faced with treating a clinically diagnosed infectious disease in food animal(s), “The GDG [Guideline Development Group] concluded that although evidence from the systematic reviews and additional studies indicates it will achieve the human health benefit of lowered antimicrobial resistance in bacteria, this recommendation should be conditional due to the very low quality of available evidence. ….Furthermore, the undesirable consequences associated with such a restriction of use of antimicrobials appear to be relatively small or non-existent. Finally, several countries have successfully accomplished such a restriction of antimicrobials in food-producing animals, demonstrating its feasibility.

The second to last sentence seems rather callous in its regard for the sick animal and is particularly worrying from an animal welfare perspective. There is a remark in the guidance that states,

To prevent harm to animal health and welfare, exceptions to recommendations 4a and 4b can be made when, in the judgment of veterinary professionals, bacterial culture and sensitivity results demonstrate that the selected drug is the only treatment option.”

To my knowledge there is no country that does not allow treatment of animals with a clinically diagnosed infectious disease. And so one wonders where that leaves veterinarians when their only option is a drug that is critically important to human medicine – do they use avoid using “antimicrobials classified as highest priority critically important for human medicine” based on very low quality evidence or do they use them to prevent harm to animal health and welfare?

Some of the replacements of antibiotics that have been used in Europe are themselves associated with their own set of problems, for example the application of zinc oxide has been a key alternative to the reduction of antibiotics usage in Sweden and Denmark. The European Commission, however, has pointed to zinc oxide as having a serious impact on the environment as much of the substance gets excreted and ends up in fields when the manure is applied on the lands. In some studies, the use of zinc oxide has been associated with the occurrence of methicillin-resistant Staphylococcus aureus (MRSA) as the resistant bacteria might carry zinc-resistance genes.  That is, as always, tradeoffs associated with different choices and the antibiotic replacements are not without their own set of risks and tradeoffs.

7. I don’t care – I just want food animals never to get treated with antibiotics irrespective

We still don’t have strong evidence linking animal use with antibiotic resistance in the human population. Antibiotics along with other management and health factors go into animal welfare – if we can’t use them animals will get sicker and this can affect One Health (the unity of multiple practices that work together locally, nationally, and globally to help achieve optimal health for people, animals, and the environment) goals.

For example, the “no antibiotics ever” (never ever) marketing campaign may actually put the food supply at risk. If there is more untreated infectious disease, then pathogen prevalence could increase and this would increase the pathogen load of the  raw product coming into plant which could affect food safety from the perspective of food-borne pathogens.

And more generally is the question of what should be done with sick animals then? At the moment there are three choices:

  • treat the animal(s) and dump the animals into someone else’s supply chain
  • leave untreated and sell the ones that survive which seems rather callous and Darwinian
  • euthanize sick animals (including entire flocks) which comes with its own set of sustainability issues

Dairy Heifer with a bad case of pinkeye and blindness in that eye in a production system that prohibits the use of antibiotics for treatment of the bacteria which cause that disease

There is an understanding that this is an important issue and the industry is working to address it but I personally think there is both a One Health and welfare need to keep access to strategic uses. The dairy heifer in the picture above has a raging pink eye in her right eye as you can see and was on a “never ever” antibiotic farm in Northern California – so she never ever got antibiotics and her eye just blew up and developed a perforated ulcer. At the time the picture was taken, she was 14 months away from producing milk. Personally I will take the conventional milk that allowed her to get treatment in the same way I treated my own kid’s pink eye with antibiotics.

If the entire food supply chain mandated never ever treatment regimen,  there would be a real welfare dilemma in terms of what to do with sick animals. At the current time the conventional supply chain takes in the “rejects” (i.e. sick animals that needed to be treated with antibiotics) of the never ever supply chain. To me there is something just not right about a system that depends, in fact relies, upon the fact that someone else’s customers will consume their rejects so that their value-added (i.e. more expensive) product can carry an absence label for what is an essential tool in their own production system. It is a bit like the EU rejecting the cultivation of GMO crops and then importing GMO soybean and corn grown in other countries to feed their livestock populations – exporting the problem to someone else’s backyard does not solve the problem. And pretending that sick animals don’t  exist does not address this problem either. Our food animals deserve a more honest and transparent discussion of this topic.







Proposition 2 déjà vu (Part 3 of 3)

Recently at the Davis Farmer’s Market, I was approached by a volunteer who was collecting signatures for a new initiative for the 2018 CA ballot. These ballot initiatives are a part of the California landscape and in 2016 posed questions to voters ranging from marijuana legalization (it was approved) to use of condoms in pornographic films (it was defeated). California allows measures to be placed on the ballot through citizen-led signature petitions. For an initiative to be placed on the statewide ballot in November 2018, proponents need to collect 365,880 signatures within 180 days.

This particular initiative would impose new standards for confining certain farm animals. The proposed title is “”The Prevention of Cruelty to Farm Animals Act”. Needless to say, most people would be hard pressed to come up with a reason to refuse to sign on for a proposal with such a title. It would be like refusing to sign an act that requires parents to love their children. But unfortunately, this innocent-sounding initiative does little to inform voters of the nuanced tradeoffs associated with the wording contained in the proposed initiative. And further questioning revealed the signature-gathering volunteer (who probably in retrospect wished they had asked some other than me to sign) had very little understanding of hen housing systems, or the likely impacts of the initiative.

This proposed measure sounds eerily reminiscent to Proposition 2, an initiative that was passed by California voters in 2008. In 2008 the initiative was to “allow these animals to lie down, stand up, fully extend their limbs and turn around freely” which was judged to be 116 square inches of floor space per bird. According to HSUS, the new initiative, “will require housing systems by 2019 that are impractical for cage confinement. And by 2021, it’s an absolute cage-free requirement.”

The L.A. Times reports the new 2018 initiative sets the standard for egg-producing hens initially at 144 square inches per bird — one square foot — which is the level at which a hen is considered by activists to be cage free by December 31, 2019. By 2022, the hens and other animals will have to be actually cage free, and allowed to roam inside barns.

The initiative’s language, submitted to the state by the Humane Society of the United States, states also prohibits businesses in California from buying or selling liquid eggs, pork, and veal that were produced from animals confined in more restrictive enclosures that would not comply with the measure’s requirements. This prohibition applies to both in-state and out-of-state production of these livestock commodities. Violation of the measure would be a misdemeanor punishable by a fine, imprisonment, or both. The measure also requires CDFA and the California Department of Public Health to issue regulations to implement its provisions.”

One thing that the large $6 million Coalition for Sustainable Egg Supply (CSES) study on hen housing systems showed clearly, was that cage-free egg production systems, which are effectively mandated by this new initiative, are not without their drawbacks, specifically this hen housing system was “the most expensive in terms of egg production costs and had the greatest hen mortality, the worst indoor air quality (with consequently greater risks for worker respiratory health related issues due to inhalation of dust and endotoxins), the greatest dust emissions, the greatest feed usage and hence carbon footprint, the greatest nutrient losses, and the greatest potential for microbiological contamination (aerobic organisms and coliforms) of eggs.”  It was also “substantially worse” in terms of cannibalism relative to conventional cages (CC) and enriched colony (EC) cages (Mench et al. 2016).

For some people, providing hens with the most freedom of movement and opportunity to perform natural behaviors (flight, foraging, and dust bathing) may outweigh these other considerations, however for others different considerations like environmental footprint of food production, food safety and cost may come into play. Especially given eggs constitute a valuable and inexpensive protein staple for low-income families. Currently those choices are available in the marketplace – if this image is representative of current choices evidentially not all California consumers are interested in choosing to purchase cage free eggs – but the proposed initiative will mandate an absolute cage-free requirement for all hens producing eggs for California.

It is estimated that Californians now pay between $0.48 and $1.08 more for a dozen eggs as a result of existing Proposition 2, and that was for the CA SEFS Compliant (California Shell Egg Food Safety Compliant) 116 square inches of floor space per bird. Presumably 144 square inches per bird and then cage free will result in even higher prices.

According to HSUS, “Since Prop 2, the HSUS has led a national campaign to convince food retailers to phase in cage-free purchasing practices and to stop buying any eggs that come from hens in cages.” A number of food retailers including, Nestle, Subway, McDonald’s, Dunkin’ Donuts, Walmart, Target, Costco and other businesses have said they will make a transition to eggs from cage-free hens by 2025. HSUS keeps an updated list here. According to HSUS senior director of food policy, Josh Balk, “McDonald’s announcement in September [2015] started a landslide from the rest of the food industry”. According to Balk, “There’s nothing more powerful in talking about this issue to a company than stating that its competitors are doing it and they are not.”

And to add a little salt to this evidence-based wound,  McDonald’s USA was member of the CSES study that showed there were clear hen welfare drawbacks to the cage-free egg production systems, and that in many of the metrics the enriched colony (EC) cages scored considerably better than the cage-free aviary (AV) systems. In their announcement, Marion Gross, senior vice president and Chief Supply Chain Officer of McDonald’s North America said “We’re proud of the work we’re doing with farmers and suppliers to advance environmentally and socially conscious practices for the animals in our supply chain.  This is a bold move and we’re confident in our ability to provide a quality, safe, and consistent supply.”

So what are the environmental implications of cage-free egg production systems? Well according to the CSES, of which McDonalds was a member and so presumably aware of its findings, cage free (AV) was worse in terms of carbon footprint, indoor air quality, manure management, particulate emissions, and natural resource use efficiency. And it rates consistently worse, in many cases “exceptionally worse”, for all food affordability metrics than enriched colony (EC) cages.

And then there is the sticky issue of worker health and safety – rarely considered but again substantially worse for  metrics like ergonomics and worker exposure to endotoxins and particulate matter for the cage-free aviary (AV) system. How do companies rank hen welfare versus consumer, farmer, and worker welfare in” socially conscious” decisions?

In the food companies’ rush to promise buying only cage-free eggs in the years to come, I wonder if anyone is paying attention  to animal, consumer, farmer, and worker welfare implications of  cage-free aviary (AV) systems. One would think groups portending to be interested in animal welfare, rather than perhaps dissuading animal protein consumption, might at least be interested in this. As this piece in the Seattle Times, featuring undercover video footage of chickens in a cage free environment warns,

The egg industry has long warned that hens living cage-free in aviary systems will experience higher mortality rates and more disease. Research by the Coalition for Sustainable Egg Supply, which is financed by egg producers and food companies, found “substantially worse” levels of aggression and cannibalism in cage-free systems, also known as aviary systems, compared to caged systems. It has also found more damage to the birds’ sternums.”

It is too easy to paint a simplistic story that portrays one production system as bad using undercover video and selected imagery, and an alternative as idyllic by using terms like “allowed to roam inside barns” while ignoring the substantially worse rates of keel damage and cannibalism, but the inconvenient truth is that all production systems have pros and cons, and those that appeal emotionally to humans as being the most natural, are also associated with real welfare concerns and big sustainability tradeoffs.

So we have a dilemma. Who gets to define animal welfare parameters of agricultural production systems? One could argue the consumer and that might be appropriate if tradeoffs are clearly communicated, and different production systems that provide that choice are allowed to coexist. Another might legitimately be the animals. My UC Davis colleague who studies chicken welfare, says her job is to look at production systems from the viewpoint of the chicken, not as how humans might imagine a chicken might perfer. Dr. Temple Grandin famously did something analogous in terms of slaughterhouse facility design.

I have a feeling that choice as it relates to the production system used to produce the eggs for California consumers will soon be limited to only cage-free options if  the initiative “The Prevention of Cruelty to Farm Animals Act” is on the 2018 ballot, despite the sustainability concerns around the environmental, economic and other implications of this proposition.

I hope that rather than ignoring the very real impacts of this proposition, there will be a transparent public discussion of the evidence-based tradeoffs and interplay among food safety, environmental, animal health & well-being, worker health & safety, and food affordability implications of this proposed initiative. Perhaps we could also include producer welfare in there as well. And that this time around public sector scientists won’t get sued for trying to give California voters an objective assessment of the likely impacts of passing the initiative.

Evidence-based animal welfare recommendations (Part 2 of 3)

Proposition 2, an initiative passed by California voters in 2008, required that egg-laying hens (and calves raised for veal and pregnant pigs) be confined only in ways that “allow these animals to lie down, stand up, fully extend their limbs and turn around freely”. Unfortunately no further clarification was given to guide producers as to how the needed to alter their production systems to be compliant with the law.

Some voters might have interpreted this initiative to mean “cage-free”, however in 2013 California Department of Food and Agriculture issued regulations stipulating the minimum number of square inches of floor space per laying hen, effectively requiring less hens per cage or bigger cages  to be CA SEFS Compliant (California Shell Egg Food Safety Compliant).

So by January 1, 2015 producers in California, and those out of state producers seeking to export their shell eggs for consumption in California had to comply with this law. Strangely, liquid eggs (whole, yolk, or white), frozen/dried eggs, hard-boiled eggs (in shell or peeled), cooked eggs (e.g. breakfast sandwiches), and shell eggs that are pasteurized in the shell are exempt from the law. The chickens producing these eggs are exempt from the Proposition 2 standards.
The question I think many might be interested in knowing, is whether this initiative has helped hen welfare? And the answer to that is complicated, as there is no agreed upon definition of “good” welfare. All production systems come with their own set of pros and cons and tradeoffs.

To help answer this question, the Coalition for Sustainable Egg Supply (CSES) was formed to support research evaluating the sustainability of laying hen housing systems. The CSES members represented a variety of stakeholders, including food retailers and distributors, egg producers, universities, and governmental (USDA ARS) and nongovernmental organizations. According to their FAQs members include the American Humane Association; Bob Evans Farms; British Columbia Egg Marketing Board; Burnbrae Farms Limited; Cargill Kitchen Solutions; CCF Brands; Cracker Barrel Old Country Store; Daybreak Foods, Inc.; Egg Farmers of Canada; Egg Farmers of Ontario; Flowers Foods, Inc.; Forsman Farms; Fremont Farms of Iowa; General Mills; Herbruck Poultry Ranch, Inc.; Iowa State University; McDonald’s USA; Michael Foods, Inc.; Michigan State University; Midwest Poultry Services; Ohio Egg Marketing Program; Poultry Science Association; Purdue University; Sparboe Farms; Sysco Corporation; Tyson Foods; United Egg Producers; University of California, Davis; and University of Guelph.

The goal of the CSES was to provide scientifically based information on the trade-offs related to the sustainability of egg production by conducting holistic research on a commercial farm that had 3 different hen housing systems. This $6M study examined “various laying hen housing systems and potential impacts on food safety, the environment, hen health and well-being, worker health and safety and food affordability, providing food system stakeholders with science-based information on sustainability factors to guide informed production and purchasing decisions” (Mench et al. 2016).

The three hen housing systems that were evaluated in the study were: conventional caged (CC), enriched colony (EC) and cage-free aviary (AV). According to the CSES “the conventional cage system was chosen because the vast majority of eggs used by the U.S. food system at the time the research was planned and today originate from this system. The enriched colony and cage-free aviary systems were chosen as the most modern alternative types of systems that were available at the time and that were also beginning to be adopted by U.S. egg producers. The conventional cage system was comparable to other conventional cage systems widely used in the industry. In this case there were six hens per enclosure, with each hen provided 80 square inches.” This is less than the “minimum of 116 square inches of floor space per bird” for an enclosure containing nine or more egg-laying hens to be CA SEFS (Proposition 2) Compliant .

The CSES did a nice job of presenting the data in a comprehendible format for the general public, and their graphical interface is particularly useful. There you can find drop down menus looking at different attributes of sustainability: Food Safety and Quality, Animal Health and Wellbeing, Environment, Worker Health and Safety, and Food Affordability. This image from the Animal Health and Wellbeing dropdown is a useful example of the fact that no system is all good or all bad.

Results demonstrated the complexity of addressing sustainability problems, in that each housing system had negative and positive aspects. According to Mench et al. (2016), “The cage-free aviary (AV) provided hens with the most freedom of movement and opportunity to perform natural behaviors (flight, foraging, and dust bathing) and was also associated with some hen health benefits (best leg and wing bone strength, good feather cover, and low overall incidence of foot problems), but it was also the most expensive in terms of egg production costs and had the greatest hen mortality, the worst indoor air quality (with consequently greater risks for worker respiratory health related issues due to inhalation of dust and endotoxins), the greatest dust emissions, the greatest feed usage and hence carbon footprint, the greatest nutrient losses, and the greatest potential for microbiological contamination (aerobic organisms and coliforms) of eggs.”  It was also substantially worse in terms of cannibalism. The term “hen-pecked” and “pecking order” are in our vernacular for a reason.

So which is the most sustainable system? Well that depends upon what attributes of sustainability you value. Is it the one that best protects animal health/welfare, the one with the lowest environmental footprint per unit of product, or the most efficient, or the best one for worker health and safety, or that system which increases affordability, or some combination of the above?  Often there are direct conflicts between what “feels” like the best system from a purely emotional standpoint, and the objective data quantifying the impacts of that system. As with all dietary decisions there are tradeoffs among the various pillars of sustainability, and consumers will need to make the choices they consider to be best for their particular family values, budget, and circumstances.

Unfortunately, marketers or special interest groups will sometimes focus on a single sustainability component of a production system that is of particular interest or value to them, without holistically addressing the accompanying food safety, environmental, animal and worker health and safety, and food affordability implications and tradeoffs. This presents the public with a simplistic binary choice, avoid this production practice or buy my product that does not contain antibiotics/hormones/GMOS/gluten/etc. and does not objectively represent the complexities and nuances associated with imposing production system requirements on producers. That is the importance of choice in the marketplace – to allow consumers to purchase products that align with their values. However, groups are increasingly working to remove that choice and impose their unique set of values on the general population. More on that next.

Six hens a laying (Part 1 of 3)

On a trip to my local grocery story on Christmas Eve, I was struck by a phenomena in the egg case. There were plenty of choices available to shoppers, and this picture says a thousand words. Shoppers purchased the least expensive eggs. They had the choice of more expensive cage-free, organic and pasture-raised eggs, but at this grocery store in the fairly wealthy town of Davis, when given the choice, the less expensive eggs.

And just so I don’t get accused of cherry picking my data I went to the more exclusive specialty grocery store in town, (because they have the best goat’s cheese), and there I saw a similar phenomenon. I do realize that this is now only an N of two!

 The $2.99/ dozen large eggs outsold the other choices including the $6.99/dozen enhanced omega-3 eggs and the $8.99/dozen pasture-raised eggs. If you look carefully you will see all of these eggs say they are CA SEFS Compliant (California Shell Egg Food Safety Compliant). What does this actually mean?

Almost a decade ago, in 2008, California voters passed Proposition 2. The proposition, sponsored by Humane Society of the United States (HSUS), required that egg-laying hens (and calves raised for veal and pregnant pigs) be confined only in ways that “allow these animals to lie down, stand up, fully extend their limbs and turn around freely”. Given we don’t raise many calves for veal or pigs in California – the full impact of the initiative was mostly felt by the egg-layer industry. The full implementation of the law took effect January 1, 2015.

The vagueness of the language in this proposition was challenged by some egg producers. One company, JS West built two new barns in the style of those found in Europe called enriched colony (EC) cages where the chickens have almost twice as much space, as well as perching, nesting, and scratching area. According to Modern Farmer,

“The construction cost $7.2 million, and the eggs, sold under the name “Comfort Coop,” are sometimes marked up by grocery stores as high as a dollar over conventional eggs. When that’s the case, [Senior Vice President Jill Benson] says, “The sales are drastically reduced.” So much for giving voters what they want.”

Finally on May 6, 2013, the California Department of Food and Agriculture issued regulations stipulating the minimum number of square inches of floor space per laying hen that shall be deemed to constitute compliance with Prop 2, i.e. CA SEFS Compliant. The regulations say, in part: “An enclosure containing nine or more egg-laying hens shall provide a minimum of 116 square inches of floor space per bird.” And that is the standard CA SEFS Compliant eggs have been adhering to since January 1, 2015.

When Californians were debating Proposition 2, proponents assured consumers that the price of eggs would increase only a little, if at all. However, the University of California Agricultural Issues Center (AIC), attached to UC-Davis, issued a July 2008 study about the fiscal impact. That study said: “The best evidence from a variety of sources suggests that (non-organic) non-cage systems incur costs of production that are at least 20 percent higher than the common cage housing systems. This is due to higher feed costs, higher hen laying mortality, higher direct housing costs, and higher labor costs. The study also estimated that the California egg industry would relocate to other states during the 5-year adjustment period. The study concluded that the cost to consumers of the cheapest California-produced eggs would increase by at least 25%.”

Proponents of Proposition 2 suggested that the additional cost would amount to only about a penny an egg, or 12 cents per dozen.

So what actually happened? According to USDA NASS statistics the number of eggs produced in CA from 2008 to 2016 dropped ~34% from 5.271 billion eggs to 3.474 billion eggs.

This decrease in egg production was accompanied by a decline of egg-laying hens in California. A 2014 Washington Post BLOG estimated the loss of 10 million egg laying chickens in CA, a prediction that was pretty accurate as evidenced by this graphic posted on Jason Lusk’s BLOG

The egg prices have bounced around a little. The USDA Market News Service reported that California wholesale egg prices for the small benchmark egg increased 24 percent, from $1.13 a dozen on Jan. 16, 2014, to $1.40 on Jan. 2, 2015, when Proposition 2 went into effect. According to Jason Lusk’s BLOG “We find that the average price paid per dozen eggs was about 22% higher from December 2014 through September 2016 than it would have been in the absence of the hen housing restrictions. The price impact fell over time, from an initial impact of about 33% per dozen to about 9% over the last six months of the observed time horizon.” That number is pretty close to the 25% predicted by the University of California AIC.

And for their efforts in trying to give objective evidence-based estimates to the California public voting on this initiative in 2008, HSUS sued the UC Davis AIC alleging that their cost study characterized Proposition 2 “as having a negative economic effect on California citizens”. They claimed in the state voter’s pamphlet that anyone who said egg prices would increase as a result of its passage was using “scare tactics.”

According to Lusk “These [egg] price increases correspond to welfare losses of at least $117 million for the three California markets [in LA, San Diego, and San Francisco from December 2014 to September 2016]. Our results suggest annual average welfare losses of at least $2 per California household in future years.” Lusk is obviously referring to human welfare in this case.

He also has a very “economicy” peer-reviewed paper looking at this which concludes Californians now pay between $0.48 and $1.08 more for a dozen eggs as a result of Proposition 2. The estimates suggest an annual reduction in California consumer surplus of between $400 million and $850 million. This cost increase is important as eggs provide a nutritious staple food used disproportionately by low-income families. California has the dubious honor of being home to the nation’s highest (20.6) percent poverty rate when considering the U.S. Census Bureau’s Supplemental Poverty Measure which takes into account the cost of living.

So what have been the actual impacts of Proposition 2? There are many less egg-laying chickens and eggs being produced in California, the state is importing more eggs to make up the shortfall, the cost of eggs has gone up around 25%, the choice to purchase eggs from hens in conventional cages is no longer an option for the 39.25 million California consumers, and California consumers are spending between $400 million and $850 million more on eggs. Pretty much exactly what the AIC study predicted. And has the welfare of chickens actually improved? More on that in my next BLOG.

Two pendulous nipples

An academic colleague of mine recently tweeted that Netflix’s Okja was worth watching. He is not an agricultural scientist or breeder, but he is a geneticist, and I was surprised that the image of Okja did not trigger his scientific angst. I realize Okja is a science-fiction fantasy movie – but the science makes no sense. The most glaring problem for me is that for some reason, the movie makers who had a budget of $50 million, decided to reimagine a female of a litter-bearing mammalian species that normally has two rows of nipples, and give her a random goat udder with two pendulous nipples that appear to be slighly engorged with milk despite the fact she has never given birth to any offspring. Why??

Okja Credit: Netflix

According to an interview entitled “How the ‘Okja’ VFX Team Created the Creature That Turned Us All Vegetarian” with Okja’s visual effects supervisor, Erik De Boer

“Since Okja was designed as a GMO, she had to come across as a believable meat producer. So it was very important for us and for Bong that she had a very healthy and luxurious feel to her skin and her mast. You could harvest a lot of pork from her”.  Erik De Boer

For those of you that have not seen Okja, the premise of the movie begins with an evil biotechnology company that starts with M… not that one…..(get it? wink wink). It is Mirando Corporation, and they have been surreptitiously using genetic engineering to breed a special kind of “super pig”. According to Mirando CEO (Tilda Swinton) the “super pigs will be big and beautiful, leave a minimal footprint on the environment, consume less feed, and produce less excretions, and most importantly they need to taste F#$%#@$ good.”

I guess the “F” bomb had to be in there for dramatic effect. Because the rest of those goals are a pretty close estimate of the overall bereding objective of probably every animal breeding company in the world. Probably disease resistance would be in there too. And before you write off this as being irrelevant to your life, what would be the implications of having pigs and cows and chickens that leave a maximal footprint on the environment, consume more feed, and produce more excretions? In other words what would happen if there were no genetic improvement programs for food animal species?

Let’s consider pigs, the second largest provider of meat after fish (wild & cultured).

Over the years selection goals for pig genetic improvement programs have included

  • Increased litter size
  • Increase the number of litters per year
  • Increase the amount of lean meat (pork/bacon) per pig
  • Decrease the amount of time needed to get to market weight
  • Improve the efficiency of feed digestion (feed conversion ratio)
  • Decrease the feed needed to produce a finished pig (increase growth rate)

And as a result of those goals the US industry has improved the pork production per sow more than 5 fold, from 800 lb in 1930 to 4,200 lb in 2015 .

Without these productivity improvements over the past 85 years, it would take an additional 25.5 million sows (approximately 31.5 million in total) compared with today’s 6 million sows to achieve the current level of US pork production. Now you might not eat pork for personal or religious reasons, or even any animal protein at all – but as long as some people on earth do, there is a strong environmental agrument to be made for genetically improving the plants and animal species we use for food production. And the way to achieve this is not 6-ton females with goat udders.

And really this is where Okja loses the plot to me in more ways than one. This so called super pig that was meant to come  across as a believable meat producer took 10 years to reach her 6-ton maturity weight (actual pigs take 5-6 months and weigh around 1/8 ton), and was still barren after a decade. Most sows have more than two litters per year – on average marketing a total of around 22 piglets/sow/year . See the rows of teats on this litter-bearing pig below?

No udder on her – and she has a snout not a hippopotamus face, and a curly tail. That is what makes a pig.  And her feed conversion (feed/gain) ratio is 2.6; down from 3.2 just 25 years ago – making her “consume less feed” which is a good thing – would you prefer a Prius or a Hummer in terms of fuel efficiency and the resultant environmental footprint of food production systems?

According to Okja’s writer and director, Bong Joon-ho in an interview with Vulture

“I don’t think of Okja as a metaphor. It doesn’t have any symbolism of any kind. I simply want to make the audience think that this animal is something that could happen in the very near future, like five years from now. In reality, there are such animals being developed. They’re developing a genetically modified pig.”                                                                                                                       Bong Joon-ho

Yes “they” are developing a genetically modified pig, well actually public sector scientists at the University of Guelph developed the so-called Enviropig, more than a decade ago, a pig that  had a 75% reduction in undigested phosphorus in its manure. It literally was a  pig that “produced less excretions” to avoid phosphorus pollution.  But public opposition to genetic engineering, fueled by activist fearmongering and dare I say the long lasting impacts of science-fiction movies like Jurassic Park, have effectively kept such pigs from commercialization. We have over a billion pigs being reared globally, and they still are unable digest inorganic phytate , and so the inorganic phosphorus pollution problem in their manure still exists. Precluding access to the Enviropig  did not make the pig poop phosphorus pollution problem go away, it just precluded one potential solution.

Recently public sector researchers at the University of Missouri and the Roslin Institute in Scotland, have produced gene edited pigs that are immune to the Porcine Reproductive and Respiratory Syndrome (PRRS) virus, a devastating disease of pigs. These groups inactivated a protein that was known to be the gateway for this virus to infect pigs.

University of Missouri research team that developed disease-resistant gene edited pigs

Shockingly the public sector researchers that developed these pigs, academic colleagues of mine, look and behave nothing like the deranged zoologist and TV personality Johnny Wilcox in Okja, played by Jake Gyllenhaal, but rather “they” look more like a group of mundane university professors (apologies Kristin, Kevin and Randy)  trying to produce disease-resistant pigs to solve an animal disease problem. Sometimes life does not imitate art at all.

In the darkest part of the movie – spoiler alert – Okja is taken by Mirando Corporation to be raped by a super boar for no apparent purpose other than presumably to shock the audience, and then a sample of her flesh is taken by plunging a circular probe into her side. Apparently the non-invasive ultrasound examination that is typically done to evaluate back fat thickness and meat quality was not gruesome enough for the movie makers. And then she, and the 25 other genetically modified super pigs that were developed as a new genetic line, are inexplicably placed in what appears to be a cattle feedyard with 100s of other super pigs (not sure where they all came from as there were only 26 to start with) to be slaughtered for food. Talk about eating your seed corn – that would have been the end of Okja’s genetics as she did not produce a single offspring to carry on her super pig line.

Of course at the end of the movie – spoiler alert – Okja is spared from becoming ham and bacon, and goes off to live the life of a 6-ton pet pig in Korea. That is how fairy tales, even science fiction fairytales, are supposed to end.  That  is part of the reason that  Erik De Boer made Okja pet-like stating

“In terms of Okja’s demeanor and personality, Bong and I always discussed it as a very happy, friendly Labrador. I think we can all relate to that slightly older dog that is just happy to tag along, lumbers a bit, with floppy ears, looking up over its brows. That was the personality we wanted to give Okja: just a very content Labrador inside a super-pig body”.                                                         Erik De Boer

I can understand that some people want pigs as pets, but the vast majority of them are grown for food production. Pigs are actually a very important source of meat in Asia, especially China. Over one billion pigs are conusumed annually worldwide, an average of 23 million pigs a week. China, European Union and United States, eat about 12 million, 5 million and 2 million pigs per week, respectively.  That is the source of all breakfast bacon and holiday hams.

So while it is fun to imagine a pet 6 ton pig, it is also important to be seriously cognizant of the 2050 projections shown in the figure below.

Milk, egg, broiler, beef and pork production since 1970 and projected to 2050 (FAOSTAT 2030 report & database as of 2017.

Ultimately, the livestock sector collectively will need to produce more with less while enhancing health and welfare for humans, animals and the environment. Okja can demonize this objective, and promote a pigs as pets fairytale, but livestock play an important role in global food security today, providing essential micronutrients and high quality protein to billions, and they provide important contributions to livelihoods and economic opportunities for many as well as providing draught power, manure for crop production and many by-products.

I wish science fiction movies and fairytales could do a better job of “sciencing the shit” out of agriculture and food production, in the way that Mark Watney was able to use innovation to get off Mars in The Martian. With no apparent sense of irony, towards the end of the interview regarding the complexities of shooting Okja, visual effects  supervisor, Erik De Boer emphasized the importance of pushing technology to try to do better in his chosen field.

“From a technology point of view, we’re always trying to push ourselves further and try to do better.”                Erik De Boer

There is probably no more pressing problem facing humanity than climate-smart agriculture to feed projected population growth, and it disappoints me that Okja yet again perpetuated the tired old story of scientists as disturbed, money-hungry corporate sell outs. As long as agricultural research continues to be painted in such a negative light, it will be difficult to obtain public support for agricultural technology and the importance of “sciencing the excretion” out of problems facing agricultural production systems.


A look back at 2017

My first BLOG for 2017, and in fact all 9 of this year’s BLOGs, were triggered by either bad science or blatant misinformation about agriculture. Typically the only way a topic raises to the level of justifying me writing a BLOG is that the balance of my annoyance at the erroneous material that is being put out there outweighs everything other thing that needs to be accomplished that day, and so it tends to be I blog more in the early half of the year than in the later part of the year when reading theses, and chapter deadlines loom heavy at the end of year approaches.

This has been a busy #scicomm year for me and despite my best intentions to be a frequent blogger, I have not been able to keep up with that in addition to my “day” job which also tends to be an evening and sometimes night job as well. This map gives you some idea of my speaking schedule in 2017 – some 46 cities, 23 US states, and 9 countries. Typically I speak at producer or allied industry meetings, or scientific conferences. Sometimes I even get to tour the farms in conjunction with speaking engagements which helps me keep current with farmers and the issues they are facing in different areas. In that regard I think extension educators are a unique segment of academia. Fly geneticists who study the nervous system probably don’t get out into the applied end of neuroscience in clinics in the same way as often.

Most people do not know the realities of the job of a Cooperative Extension specialist, we translate public land-grant university research into application. It is our job to get out and talk to people applying science in farming and in the food production industry and to hear about the problems they need help solving. Extension has literally be doing #scicomm “for the average person” since the Smith-Lever Act was signed into law in 1914. Historically audiences have been farmers, as the US was a nation of farmers.

Today, less than two percent of the population engages in farming. There is now an urgent need to translate the intricacies and science of farming to the “average person”, because there is no use translating technology to a farming audience, if the general public is just going to turn around and reject the use of that technology in their food production systems based on misinformation they obtained on the internet or social media! This to me is the #scicomm challenge of the 21st century – how to counter the whack-a-mole of alternative facts as it relates to food and agriculture production systems. Extension needs to extend further now.

There are too few people with expertise in agricultural science addressing the discussions around “food systems”. It seems like everyone gets asked their opinion by the media, or to serve on panels about agriculture and food production – chefs, actors, book writers, celebrity bloggers, journalists, mommies, activists – everyone except farmers and agricultural scientists.

Just for fun I googled “what percentage of the population are agricultural and food scientists?” According to the Bureau of Labor and Statistics there were only 43,000 of us in 2016! That is 0.013% of the US population working as “Agricultural and food scientists research ways to improve the efficiency and safety of agricultural establishments and products”! We are literally like hen’s teeth. There are actually more Yoga instructors registered in the US. By way of comparison in 2016 there were 1,028,700 “Farmers, Ranchers, and Other Agricultural Managers” That is about 24 researchers for every farmer. That is a relatively small number of agricultural practitioners and researchers compared to the  US population of 323 million people.

I sometimes think that because there is such a small proportion of the population involved in fulfilling the most fundamental lower order needs of Maslow’s hierarchy of human needs, having those basic needs met becomes assumed in the developed world, somehow devaluing the professions that enable that privilege.

Maslov’s hierachy of needs – image from

But I digress, back to #scicomm.  I realize everyone is busy, yoga teachers, farmers and agricultural scientists alike. But those with agricultural experience and expertise have to become involved in discussions around food and agriculture, or the future of agriculture will be decided devoid of objective-information and more importantly without a nuanced understanding of the various pros, cons and tradeoffs associated with any production system. We need to become very proactive in telling the stories of farming and food production.

As Dwight D. Eisenhower famously quipped, “Farming looks mighty easy when your plow is a pencil and you’re a thousand miles from the corn field.” More and more I am making time to be involved in these public discussions, so I apologize in advance to my 2018 manuscripts, graduate students, grant reports and of course committee meeting obligations (I am a faculty member after all), but this agricultural #scicomm challenge is too important to ignore.

Perhaps the most unique #scicomm experience I was involved with in 2017, was Food Evolution, a documentary by director Scott Hamilton-Kennedy, producer Trace Sheehan, and narrated by Neil deGrasse Tyson. In his words

“….the film explores all the ways science has been used and abused in public discourse surrounding the genetic engineering of food. In a world of misinformation and disinformation, nothing could be more timely.”                                      Neil deGrasse Tyson

Agricultural scientists are not often involved in documentary movies. That is probably an understatement. They are almost never involved in documentary movies might be closer to the truth.  Entertainment does not really align well with the patience and dispassion required by science, most days in the laboratory are not exactly riveting watching, nor are most scientists.

What was amazing for me, working with these film makers over a three or so year period, was watching how their product came together. Not in the logical, chronological, methodical, boring way that I would have crafted a movie, but in a narrative, storytelling, emotional, entertaining way that was miraculous to behold. Like making cinematic sausages. But more interesting were the parallels between science and movie making. Both are creative processes, borne out of passion, but with a completely different set of constraints and objectives.

Science Movie making
Science requires a creative mind harnessed by the rigors of the scientific method and data Movie making requires emotion, creative story telling, and an appreciation of visual impacts
You start with an idea and  a hypothesis you want to test, then develop a well-designed experiment to produce data that  either supports or disproves it You start with an idea of the story you want to cover and make use of good journalism to uncover the truth about that topic, driven by facts not ideology
Your favorite hypothesis gets disproven by data that turned out differently to what you predicted The story you thought you were going to tell was very different from the story you ended up telling
A lot of experiments don’t yield useful data, and exceptions sometimes lead to new discovery A lot of raw footage never makes the film and sometimes the story reveals itself during filming
A lot of experiments are tedious and require extraordinary attention to minutia and detail A lot of movie editing is tedious and requires extraordinary attention to minutia and detail
You never know if or where your publication will be accepted, or the exact publication date You never know if or where your movie will be shown, screened, or the exact release date
You hope your colleagues value your work You hope the entire world watches your movie

This film was a proactive and narrative way to tell the side of the story that has not been well described so far– about how scientists saved the cherished papaya industry in Hawaii, and how Ugandan scientists are trying now to save a culturally important food crop they call matoke. Watching audience reaction to Food Evolution has been the #scicomm highlight of my year. I have gone to screenings around the US and in a couple of other countries, including at the Food and Agriculture Organization in Rome.

Trace Sheehan, Neil DeGrasse Tyson, Scott Hamilton Kennedy and I doing Q and A panel following screening of Food Evolution in New York City

In addition, the film has been screened in many cities around the world with local discussion panels to help address the issues. The discussions following the movie have been encouraging. Rather than repeating tired old fallacies, many of which were debunked in the movie, questions were elevated to more nuanced conversations about agriculture or science communication. The best screenings for me were those at film festivals with an urban audience, totally naïve to the fractious GMO debate. These are the target audience, the silent majority that it is hard to reach with agricultural #scicomm, and the response was so positive.

Apparently critics liked the movie too as it has an impressive 100% rating on Rotten Tomatoes. It has really been a privilege and an honor to be associated with the movie, and I got to meet Neil deGrasse Tyson too! I encourage anyone that has not seen it to check it out on Hulu, or rent it on  itunesAmazon, or YouTube. And hats off to the Institute for Food Technologists (IFT) for funding to take food and agricultural science to the movies!  We need more of this – Hollywood does not have a great relationship with agricultural facts. And there are a number of terrible food documentaries that are not helping the public discourse. Reacting to them is tedious, but important given the powerful influence of film.

OK that is it for 2017. I have actually been working on a series of BLOGS over this holiday break ‘cause that what #scicommers do during quarter breaks, and so to start the New Year right  I am going to try to publish one BLOG a day for the next week on topics that have been sticking in my craw, some bad science, some bad policy, and some bad cinema before the quarter gets rolling. To start the series – I am coming for you Okja – tomorrow.

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