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

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Funding Announced for Cooperative Research Centre (CRC) for Zero Net Emissions from Australian Agriculture

AMAZING. Today the Australian Government Department of Industry, Science, Energy and Resources announced it is funding the Cooperative Research Centre (CRC) for Zero Net Emissions from Agriculture  (ZNE-Ag) to the tune of AUD $87 million to further develop and scale up technologies to reduce methane emissions from grazing cattle and sheep, and to improve crop quality and production. The same week that the FAO released a report at COP28 to map pathways towards lower livestock emissions through the support of application of best practices in animal management such as reduced time to market. It is a Christmas miracle.

This ZNE-Ag agricultural sector-led public-private partnership has secured AUD $300 million in funding over 10 years which, in combination with the Federal Government’s contribution of $87 million, makes it the largest CRC in the program’s history. This ZNE-Ag was brokered by The University of Queensland and Queensland Department of Agriculture and Fisheries and involves a consortium of 73 partners across industry, education and government. The collaboration includes 16 major industry groups, all six state governments and the Northern Territory, 10 universities, 3 Indigenous organizations and many small and medium enterprise (SMEs) and grower groups.

There are four research programs including plant and animal production systems, deriving value from net zero, whole-farm and mixed enterprise systems analyses, and a fifth cross-cutting education, training and adoption program to integrate all the science emerging from the CRC to provide farmers with the guidelines, resources, metrics, and benchmarking tools required for a profitable transition to net-zero emissions. Agriculture and land management more broadly have the unique potential to drive down emissions within the agricultural sector. 

Figure 1. The ZNE-Ag CRC will harness and coordinate rapid research, development and adoption of science and technology-led solutions at scale.

The ZNE-Ag CRC’s strategy is designed to ensure Australia’s agricultural sectors increase their economic viability, profitability and long term asset building as they simultaneously implement strategies and actions to meet and exceed emissions reduction targets by 2050. As importantly for economic sustainability, are plans to grow the agricultural sector value to $100 billion per annum by 2030, and maintain food and ag sovereignty, and market access (Figure 1).

This project is particularly good news for pastoral systems. Emissions from animal production account for 78 percent of Australia’s agriculture emissions. Most of that (88 percent) is methane from enteric fermentation derived from ruminants. There is a lot of dryland in Australia that is not suitable for the production of food, or feed for monogastrics. In 2017-18, ten times more land (328 million ha) was used for grazing than was used for crop production (31 million ha).

There is often some talk of eliminating ruminants from these landscapes due to their high emissions intensity, discounting their magic superpower of producing more high-quality protein & micronutrients than they consume thanks to the cellulose conversion enabled by their gut microbes. However, what would become of that land with no other productive food use? Would it become fodder for fires where  ironically the emissions would be considered transient as they return to the pre-fire level relatively quickly? Overrun by invasive plant and animal species? And what of the agricultural community that is built up around those properties?

Fortunately, the low-emissions animal solutions research program of the ZNE-Ag CRC headed by Research Director Professor Ben Hayes, plans to address the methane challenge in pasture systems that account for 90 percent of livestock production by the development of novel animal and plant genetic and management approaches to reduce CH4 production, and propose to research and develop an evidence-based whole of system approaches to tap into the sequestration potential in large pasture-dominated landscapes.

Ultimately the ZNE-Ag CRC aims to “create large scale action through integrated frameworks to accelerate industry-led research, development, adoption and commercialization of science and technology-based solutions at scale. As reflected in the CRC structure and program design, the efforts are co-designed with industry and government partners and focussed on where the most benefit can be achieved”  Notice the emphasis on including stakeholders in problem-identification, and outcome-focused research.  And what excites me is that education, training and adoption (aka extension) is actually baked into the pie (layer 5), rather than an afterthought to the research (Figure 2). Demonstration sites will provide a hub for sector-wide outreach and engagement that is both feasible and accessible to drive adoption of emission reduction activities, methods and initiatives from the CRC.

Figure 2. There are four ZNE-Ag CRC Research Programs, and a fifth cross-cutting Education, Training and Adoption Program

In full disclosure I have just spent six months in Australia on sabbatical at Queensland Alliance for Agriculture and Food Innovation (QAAFI) housed within The University of Queensland and so I am excited to see this CRC funded. I have seen the positive outcome of previous CRCs.  For example, the Sheep CRC started in 2001 and by its completion in 2019, the gross value of the Australian sheep industry  was more than $8.6 billion. In real terms this represented an increase of almost 50% compared to  2001, despite the national flock decreasing in size by more than 40% over this period. On a ‘per sheep’ basis the real gross value of production had increased 2.6-fold.

During my time in Australia, I had the opportunity to meet with a variety of livestock producers, mostly those running ruminants on non-arable land. I recently had the pleasure of speaking at a Holbrook LandCare event in southern New South Wales. This Landcare Network is a not-for-profit community network. It manages a range of agricultural and Natural Resource Management projects to deliver information and support the community, predominately farmers. They  support farmers in achieving environmental care and improved management; the adoption of sustainable and productive agricultural practices and the support of innovation. Sounds a lot like the ZNE-Ag CRC’s goal of taking science and innovations to the farmer.

The vision of the Landcare Network is to foster “an economically and socially resilient rural community demonstrating strong environmental stewardship”, and their membership is comprised of farmers, many livestock producers raising sheep and cattle on rain-fed, undulating land, teeming with biodiversity, and with no other productive food use.

Such land is the backbone of rural Australia – not to mention an economic powerhouse for the nation. These are the types of communities that are keen for answers and eager to adopt emissions reducing technologies that are evidence-based and cost-effective for their operation. They will most benefit from the outcomes of the ZNE-Ag CRC, and networks such as LandCare would be obvious conduits for dissemination for the types of evidence-based emission reduction activities, methods and initiatives developed by ZNE-Ag CRC.

What is refreshing about the ZNE-Ag CRC is that it is leveraging talent from all over Australia (16 major industry groups, all six state governments and the Northern Territory, 10 universities, 3 Indigenous organizations and many SMEs and grower groups) and collaborating with farmers to use science and innovation to meet and exceed emissions reduction targets, while ensuring Australia’s agricultural sector remains economically viable. If history is any guide, the return on this investment in agricultural innovation will be many fold the sticker price, in addition to the emissions reduction. The ZNE-Ag CRC is a wonderful early Christmas present  for Australian agriculture.

Extension Critical to Mitigate Anticipated Increase in Livestock Sector GHG Emissions

A 2023 report from the FAO “Pathways towards lower emissions: A global assessment of the greenhouse gas emissions and mitigation options from livestock agrifood systems” revised their previous lifecycle assessment (LCA) estimate of the percentage of greenhouse gas (GHG) due to livestock to be 6.2 gigatonnes (Gt) of carbon dioxide equivalent (CO2eq), equating to approximately 12% of of the estimated 50 to 52 Gt CO2eq total anthropogenic GHG emissions in 2015.

Direct emissions from the livestock sector globally, encompassing CH4 from enteric fermentation, and CH4 and N2O from manure management, amount to 3.7 Gt CO2eq which is equivalent to approximately 60 percent of livestock emissions, or 7.2% of total emissions. Terrestrial animal source foods (TASF) were associated with emissions contributed by cattle (62%), followed by pigs (14%), chickens (9%), buffaloes (8%), and small ruminants (sheep and goats, 7%) (Figure 1).

Figure 1. Sankey diagram of emission sources in 2015 by species, products, sources of emissions and gasses. CH4 = methane (red), N2O = nitrous oxide (blue), CO2 = carbon dioxide (grey). 

The report further estimated that population and demand growth, primarily in Africa, will drive a further 20% increase in animal product demand by 2050 compared to 2020 levels. In the absence of any intervention or improvements in productivity it is estimated that this increase will drive global livestock emissions to nearly 9.1 Gt CO2eq by 2050.

A comprehensive literature review included in the study suggested that improvements in animal production, adoption of known feed and nutrition practices, and improving animal health and welfare were the most promising interventions to reduce GHG from this sector. Other practices such as breeding, changes in consumption of TASF, reducing food loss and waste, and rumen manipulation were considered to lower but still important mitigation potentials (Figure 2).

Figure 2. Base year and projected emissions from livestock systems shown as a waterfall chart with a range of mitigation measures applied to 2050 with their technical potential Note: 100 percent adoption is assumed. Interventions are assumed to have cumulative impacts and the order of interventions is thematically structured, without the intention to rank them for their importance.

The most significant reductions in both absolute and relative emissions can be achieved by prioritizing improvements in productivity, not only per animal but also by optimizing efficiency at each stage of the production chain.”    FAO (2023) Pathways towards lower emissions

This report succinctly summarizes the impact of what many animal scientists like myself have been working on for years, innovations in the three main disciplines of animal science; genetics, nutrition and health, historically supported by extension programs that facilitate adoption of best practices, have been associated with large decreases in the emissions intensity (emissions produced per unit of product) in developed countries.  However, this improvement has not been universal, and many low and middle income countries (LMIC) have production systems with high emissions intensities.Global average values of emission intensities hide a lot of heterogeneity, and mask the decreases enabled by the adoption of innovations.

Figure 3 shows that high income countries have dramatically decreased the emissions intensity of cattle meat relative to those seen in low income countries. LMIC are home to 76% of the global cattle herd and contribute 75% of the global ruminant greenhouse gas emission emissions. Chang (2021) estimated that improving livestock production efficiencies in the 10 countries with the largest emission reduction potential (Madagascar, Morocco, Niger, South Africa, Tanzania), Asia (China, India, Iran, Turkey) and South America (Brazil) could contribute 60%–65% of the global reduction in livestock emissions by 2050 (compared to a baseline where emissions intensities are held constant in the future). These authors stated that improving production efficiency has a much greater mitigating effect than demand-side efforts, and should be prioritized in a few countries

Figure 3. Beef GHG emissions intensity per regions. Note: Estimates are based on historical time series from the FAOSTAT Emissions Agriculture databases which are extended with the Agricultural Outlook projections. CO2 equivalents are calculated using the global warming potential of each gas as reported in the IPCC Sixth Assessment Report (AR6). Image from

Academic animal scientists making nuanced, well-supported points about the importance of global livestock production systems, the need for innovation, explaining that emission sources and the specific gases involved vary considerably across locations, livestock species and production systems and emphasizing that global averages conceal important local differences, are often dismissed outright by critics as having a vested interest, or being industry apologists, or even worse they are accused of being  paid sock-puppets as I wrote about in BLOG last year. Something similar happened to me when I dared to speak out on the science and considerable evidence base on the safety of the highly politicized topic of genetically modified food, and dared to publish a peer-reviewed paper suggesting that there is no scientific evidence that the literally billions of livestock eating GMO feed every year had suffered any ill-effects.

The multitude of complex trade-offs that should legitimately be part of conversations around differing food production systems and dietary shifts are often dichotomously framed, frequently envisaging a future where people have to pick a kingdom – plant or animal – for dinner. These needlessly simplistic binaries are unproductive, often alienating or disaffecting the very people whose goodwill, cooperation and knowledge will collectively be required to reduce the environmental footprint of food production while addressing projected demand. This binary led over 1,000  scientists  working in a multitude of disciplines from universites and research institutions around the globe to sign The Dublin Declaration on the Societal Role of Livestock which states:

Livestock systems must progress on the basis of the highest scientific standards. They are too precious to society to become the victim of simplification, reductionism or zealotry. These systems must continue to be embedded in and have broad approval of society. For that, scientists are asked to provide reliable evidence of their nutrition and health benefits, environmental sustainability, socio-cultural and economic values, as well as for solutions for the many improvements that are needed. This declaration aims to give voice to the many scientists around the world who research diligently, honestly and successfully in the various disciplines in order to achieve a balanced view of the future of animal agriculture.

The integrity of the scientists who wrote this declaration has been questioned in the media, and in fact even the FAO itself, has recently come under attack for daring to revise its livestock emmisions estimates in GLEAM 3 based on incorporating refinements made to the 2006 guidelines of IPCC in 2019. Science does that over time, revises based on new data. A response from one of the authors of the Declaration Prof. Frédéric Leroy (CoI; Vrije Universiteit Brussel, Belgium to these criticisms is detailed in his BLOG entitled, “Activist tactics and the discrediting of scientists.” He writes, “This opinion piece was written in protest to persistent attempts to undermine the credibility of established experts and organizations in the domain of animal source foods and livestock agriculture. This is now typically done by unfairly labelling prominent research and science communication that do not align with certain (largely ideological) perspectives as untrustworthy and perversely influenced by industry. Yet, the validity of the actual scientific arguments and evidence, that have been diligently provided by numerous established experts in the interdisciplinary domain of animal production (and far beyond), are rarely addressed in an appropriate manner. The recent smear campaign against the Dublin Declaration is an illustration of this ongoing trend to silence ‘inconvenient’ science”.

Scientists who are subject matter experts willing to speak up on politicized topics have frequently become the target of online attacks and harassment campaigns, seemingly intended to silence their viewpoint. False accusations of industry connection with “BIG” [insert relevant industry here] are made to delegitimize their voice,  and unfortunately, this has often proven effective at discouraging those who are unwilling to subject themselves and their reputation to such harms. This is particularly problematic when the topic is agricultural innovations because demonizing agricultural scientists and basing agricultural decisions on ideology rather than evidence has a long history of mass famines and economic collapse including the Great Leap Forward, the “Holodomor”, and most recently the 2022 collapse of the Sri Lankan economy.

I have no doubt this FAO report will come under fire for putting the reduction potential from changes in consumption of TASF at only 4%, calculated by “prorating the emissions reductions of 0.19–0.53 Gt CO2eq per year” estimated by Behrens (2017). This paper “Evaluating the environmental impacts of dietary recommendations the global food systems”, was published in PNAS. The authors reported that  compared with average diets, nationally recommended diets (NRDs) in high-income, upper-middle–income nations are associated with reductions in GHG from 13.0 to 24.8%, and 0.8–12.2%, respectively, and increases in GHG by 12.4–17.0% in and poorer middle-income countries. The majority (54%) of the reduced environmental impact in high-income countries was driven by reductions in calories  (i.e. eating the recommended number of calories rather than in excess of what is needed), and 46% by shifting the increased fruit, vegetables and nuts at the expense of sugars, oils, meat, and dairy! The increased GHGs of NRDs in LMIC were associated with recommendations for increased intake in animal products, partly due to the relatively high prevalence of undernutrition and micronutrient deficiencies in these regions. The authors of this study concluded that “Overall, our results show that in many cases, there are environmental impact benefits to adopting NRDs. At present these benefits are smaller than other interventions in the environmental impact of food systems such as reductions in food waste.”

The fact is that improvements in animal production were seen as the most promising interventions to reduce GHG from this sector in the FAO report, based on an analysis of FAOSTAT production data at regional level, coupled with assumed 100% adoption of known feed and nutrition practices, breeding, rumen manipulation and improving animal health and welfare suggests animal scientists and extensionists are going to be key players in helping to reduce TASF emissions by 2050. I might posit that this might be an easier task than convincing 100% of high income consumers that they need to reduce consumption to the NRD-recommended number of calories, even though perhaps everyone can agree that this would be good for both human health and the envronment. The FAO report concludes,

to realize the modelled pathways and effectively reduce emissions by 2050, the adoption of proposed practices at the local level is essential. Given the complexity and diversity of farming systems, mitigation interventions should be customized to suit specific local contexts. Collaborative efforts from all industry stakeholders are critical to successfully mitigate the anticipated increase in sectoral GHG emissions. Based on the presently available data, this path appears both viable and effective.” FAO (2023) Pathways towards lower emissions

The wide adoption of relatively simple, proven animal science innovations has had, and will continue to have, considerable potential to improve the efficiency of milk and meat production in both high income and developing countries. The challenge in LMIC is that these technologies are often too expensive or difficult to implement in the absence of the required infrastructure and technical expertise. The adoption of agricultural technology in now developed countries has historically been done in collaboration with publicly-funded extension efforts to work with developers to field test and refine products, optimize efficient and practical protocols, perform field demonstrations with farmer collaborators to ground truth and ultimately promote the adoption of cost-effective, evidence-based agricultural innovations.

Such a strategy, including public-private partnerships and investment, will likely be required to facilitate widespread (or even the 100%  ambitiously assumed in the FAO report) adoption of  proven technologies.  This will undoubtedly require collaborations among established experts in the interdisciplinary domain of animal production and most importantly the producers that will implement these practies. As someone who has worked in two controversial fields: animal science (and furthermore cattle!) and biotechnology,  as an extensionist and researcher for my entire career, I worry that students, early career academics and allies interested in pursuing efforts to help to produce TASF with higher quality, efficiency and environmental and economic sustainability will be dissuaded from working in this important field based on misinformation regarding the integrity of animal science, right at the time when the adoption of innovation is most needed to ensure future demand is addressed by more efficient animal production systems, rather than an ever increasing number of animals.

New York Times Reporting on Agriculture

Look I get it. The New York Times (NYT) does not like GMOs, industrial agriculture, factory farming or meat consumption. But I question the decision of such an influential media source to feature TWO front page articles detailing agriculture industry funding of agricultural scientists, Prof. Kevin Folta in 2015 and in 2022 Prof. Frank Mitloehner, who work doing public outreach in these fields. With the implication that they are “on the take” and promoting misinformation as a result of this funding. But what the NYT failed to show in these stories was that either of these public sector scientists, whose reputations the NYT has forever brought into question, ever made statements that were unsupported by peer-reviewed literature. There is a term for when someone attacks the character, motive, or some other attribute of the person making an argument, rather than the argument itself; it is called an “ad hominem” attack.

The most recent article featured one of my departmental colleagues at UC Davis, Professor Frank Mitloehner. The title of the article “He’s an Outspoken Defender of Meat. Industry Funds His Research, Files Show” was a little confusing, as it seemed to be suggesting the source of Professor Mitloehner’ s research funding was what was concerning, but in fact most of the article was about communication and outreach done by the Clarity and Leadership for Environmental Awareness and Research (CLEAR) Center at UC Davis, which receives almost all its funding from industry donations. Something that Professor Mitloehner has been very open about as detailed in his blog post, and on the CLEAR website. Prof. Mitloehner provides his response to the NYT article and accompanying Greenpeace hit piece here. The irony of Greenpeace, which itself has shamelessly ignored the scientific consensus  on the safety of GMOS and has engaged in ‘Tobacco-style’ PR on this topic for 30 years, accusing  Prof. Mitloehner of being  “a sock puppet” is projection at its finest.

The evidence that the NYT article provides to suggest that these communications are slanted is a statement by Matthew Hayek, an assistant professor in environmental studies at New York University. He states “Almost everything that I’ve seen from Prof. Mitloehner’s communications has downplayed every impact of livestock,” he said. “His communications are discordant from the scientific consensus, and the evidence that he has brought to bear against that consensus has not been, in my eyes, sufficient to challenge it.”

I am not sure exactly which specific scientific consensus Prof. Mitloehner’s communications are discordant from, but in presentations I have not heard Dr. Mitloehner make a statement that was not supported by peer-reviewed papers. I have heard him clearly state on multiple occasions that livestock are responsible for 14.5% of global emissions, and that cows and other ruminants account for 4% of US greenhouse gases (GHG) in concordance with the scientific consensus.

I am no GHG expert, but what really seems to be at the heart of people’s “beef” with Prof. Mitloehner’s communications is whether methane (CH4), as a short lived GHG, should be treated differently to CO2 which is a long-lived GHG in predictions of global warming impacts. This particularly impacts ruminants whose rumen-dwelling methanogenic bacteria produce (CH4) when breaking down otherwise indigestible cellulose. This is discussed on the CLEAR site.

This is actually NOT a settled science.  The commonly utilized ‘carbon footprint’ impact assessment makes use of the GWP100 metric, i.e., the global warming potential over a 100-year time horizon, while standardizing the atmospheric effects of all GHG to CO2-equivalents (CO 2-eq). It is typically claimed under GWP100 that methane (CH4) is, as a greenhouse gas, 28 times more potent than CO2. GWP100 became the standard metric more than 30 years ago when it was selected for in the Kyoto protocol. It has had a history of critiques in relation to characterizing the climate impacts of CH4 (Pierrehumbert, 2014). The authors of the Intergovernmental Panel on Climate Change Fifth Assessment Report themselves state that the GWP100 climate metric should not be considered to have any special significance.

A newer metric, GWP*, was developed by researchers at the Environmental Change Institute, School of Geography and the Environment, University of Oxford (Allen et al., 2018, Cain et al., 2019). These scientists argue that this metric more aptly represent how CH4 emissions translate into temperature outcomes at various points in time, by treating CH4 as a flow gas rather than a stock gas like CO2. This metric was not developed by the livestock industry. The New York Times article includes a quote “the use of that method [GWP*] by an industry “as a way of justifying high current emissions is very inappropriate.” However,  this metric is not necessarily “livestock friendly” under all conditions (Costa et al., 2021). In fact if livestock populations are increasing, the global warming impacts when using GWP* are higher than using the GWP100 metric. And Professor Mitloehner is not alone in suggesting that “expressing CH4 emissions as ‘CO2-equivalent’ emissions based on the GWP100 could misdirect attention from the need to reduce global net CO2 emissions to zero as quickly as possible” (Reisinger et al., 2021). Some have further argued that avoiding animal-sourced foods based on the GWP100 metric may result in trading a short-term climate benefit from reducing short-lived CH4 emissions, with a longer-term problem of increased CO2 and N2O emissions, making climate stabilization even more difficult.

Even the most recent IPCC technical report (2021; doi:10.1017/9781009157896.002) includes discussion of the GWP* metric

“New emissions metric approaches, such as GWP* and Combined GTP (CGTP), relate changes in the emissions rate of short-lived greenhouse gases to equivalent cumulative emissions of CO2 (CO2-e). Global surface temperature response from aggregated emissions of short-lived greenhouse gases over time is determined by multiplying these cumulative CO2-e by TCRE (see Section TS.3.2.1). When GHGs are aggregated using standard metrics such as GWP or GTP, cumulative CO2-e emissions are not necessarily proportional to future global surface temperature outcomes (high confidence).”

The best way to do environmental assessments of the livestock sector is not a settled science. All-too frequently assessments are stated in simplistic terms, making use of a myopic selection of metrics, and overlooking underlying heterogeneity and complexities. If the New York Times has problems with the way that Prof. Mitloehner and the CLEAR center communicate these topics then they should provide their science-based arguments as to why the approach he is using is incorrect. Not malign his reputation by implying he is putting out information that is “discordant from the scientific consensus” with no further elaboration as to what exactly he said that was incorrect, or which specific consensus his information is discordant from. Nor discredit his work solely because of the industry funding he clearly discloses. Because that is how science works, not through “ad hominem” attacks.

A Word About Funding Graduate Students

When I started as a professor at Davis 20 years ago, the cost of in-state graduate student fees was $5,037 per year (including health insurance of $966/year). Today they are $19,378 (including $5,472/year in health insurance). Add an additional $15,102 if the student is from out of state or international for a whopping $34.5K/year. To be clear the faculty advisor pays this cost, NOT the graduate student. And that does not cover a stipend for the student to actually live. A 50% teaching assistantship pays around $2,583 per month, or $30,995 per year. So faculty need to budget $19,378 + $30,995 = $50,373 per year for in-state graduate students and $65,475 per year for out of state and foreign students. Whereas a first year postdoc salary, where the scholar already has their PhD and who works 100% time and takes no classes, is $55,632 salary + $11,905 benefits = $67,537/year.

So there is now a perverse incentive to employ postdocs rather than train graduate students, especially foreign graduate students, which leaves the obvious question of who is going to train graduate students? When hiring a graduate student at 50% time is almost the same cost as hiring a 100% time postdoc something is wrong with the system. In times past, graduate student fees for students on research assistantships used to be paid by the State on so-called “19900” funds, a benefit that was quietly eliminated last year. And way back when I did my graduate training in the 1990s as a foreign student the University waived my out-of-state tuition, rather than charging my faculty advisor. I can foresee a time when it will be cost-prohibitive for faculty to train graduate students, especially foreign students.

This is especially true if faculty are using extramural grant funds that have been charged full overhead, which is currently set at 59.5%, and will be 60% in 2023. What this means is that for each $100,000 in grant funds, only $40,500 is available as direct costs to pay salaries and benefits, the remainder goes to indirect costs.  So faculty effectively need to bring in $95,810 of extramural research funds annually to cover the expenses of a single year of an in-state graduate student, of which a total of ~$65K does not go the student ($45,477 goes to indirect costs, and $19,378 goes to fees and health insurance). And that does not begin to pay research expenses associated with the student’s project.

One way out of this is to have the graduate student take a teaching assistantship which covers their fees and stipend for the quarters in which they are teaching. But by definition they are working 50% time teaching during that quarter which leaves little time for research.

When I started as a professor 20 years ago this month, graduate students were a very small part of the research budget, because for the most part their fees were covered by the State, and the faculty were typically only responsible for the stipend. Training graduate students is a core part of the University’s mission. But it really is becoming cost-prohibitive to take on new graduate students and given projected increases in overhead rates and fees, I do not see this situation improving.

DNA is NOT a drug. And regulating genome edited research animals as a drug is unworkable.

Investigational research animals that have been genome edited CANNOT enter the food supply in the United States, irrespective of the edits they carry, unless the researcher that has produced that animal has submitted an FDA Investigational New Animal Drug (INAD), and additionally has obtained a food use authorization which requires a TON of paperwork and also data collection. PERIOD. So when I read the headline, “Gene-edited beef cattle receive regulatory clearance in U.S.”, I felt the need to pen this BLOG. And it is a little wonky (in the political sense) because that is the nature of regulatory discussions.

While it is true that the FDA decided to exercise enforcement discretion for two slick founder animals produced by a company, Recombinetics, this “enforcement discretion” option is only available to developers. And this decision was not a “regulatory approval”, but rather it was a determination by the FDA that this product was low risk enough that it is not an FDA enforcement priority. In other words, a blind eye will be turned to the sale of this “unapproved animal drug” as it is deemed low risk. And that would be quite appropriate given the low risk of this product. But what is not obvious from the press coverage is 1) This decision is made on an individual animal basis (i.e. the data for EACH genome edited animal needs to be submitted to the FDA) and this particular decision was for two cattle and their future offspring, and 2) This path is only available to commercial developers who are bringing a product to market, not academic or university researchers who are researching genome editing.

If I, as an academic researcher, was to perform exactly the same edit and make a slick genome edited cow, the only way that I could have that animal enter commerce and the food supply would be to open an INAD, and then request a food use authorization. And I know exactly the amount of work involved in doing that as I have spent basically the entire pandemic trying to obtain food use authorization for some genome edited knock-out (gene deletion) research sheep and cattle we have produced at UC Davis. Spoiler alert – I did not obtain a food use authorization. However, I was eventually given permission to render them – meaning their carcasses could enter the animal feed chain (i.e. dog food).

To request an INAD, the sponsor (i.e. me in the case of a university professor), must provide the FDA information including an overview of the project objectives, a description of the constructs or genomic alterations in the animal, a description of the method(s) or technologies used to produce and deliver/introduce the genomic alteration, and a description any completed studies including any relevant information from other animals in which the same genes have been knocked out (e.g., references to published articles characterizing knockout mice). Additionally, a request for “a categorical exclusion from the requirements to prepare an environmental assessment” must be submitted to accompany the INAD file. When FDA reviews and approves new animal drugs, it has to comply with the requirements of the National Environmental Policy Act, which includes a review of environmental risks, if any, where required. Requesting this exclusion entailed certifying that no extraordinary circumstances existed whereby the gene-edited cattle could significantly affect the quality of the human environment. This required documenting the location of facilities where the animals were housed, containment measures, management practices and conditions for all facilities, animal waste and animal disposal, and a description of standard operating procedures, and submitting this information to allow for a determination to be made.

Upon obtaining an INAD, then an investigational food use authorization (FUA) must be requested to introduce the knock-out sheep and cattle into the food supply at the completion of the experiment, rather than incinerating them. For this, the information in Table 1 was requested.

The “Predicted Off-targets” in silico analysis included 10 sequences with three mismatches to the guide sequence in the reference cattle genome. There were no sequences with less than three mismatches other than our target, as per our guide design. Given the (graduate student) time and experimental expense involved with performing this off-target sequence verification for 10 loci for each of the animals, and the fact that these analyses were unrelated to the graduate student’s  scientific interest in these animals (meaning we would be doing these analyses solely for the FUA), the FUA was abandoned in favor of requesting a rendering use authorization.  This meant that the animals would be allowed to enter the animal feed chain, rather than the human food chain at the completion of the experiment.  To obtain rendering authorization required a separate application to the FDA Division of Animal Feeds. Similar information to that outlined in Table 1 for the FUA was requested, but this request did not require off-target sequence verification.

Such regulatory interactions are not a routine part of basic academic research in animal breeding and genetics. Neither is disposing of all animals by incineration, burial, or composting at the completion of a research project. This is particularly expensive when working with large livestock species, and is a unique expense associated with the use of gene-editing in food animals not incurred when researching conventional breeding methods. Further, these regulatory data are typically being requested prior to the conclusion of the experimental work, rather than at the completion of the research when manuscripts describing and detailing the methods and results are typically being compiled and written. As such, preparing these documents required that I dedicated a substantial amount of time solely for regulatory compliance, and pursuing a FUA would have required further additional experimental work. This experience has definitely dampened my enthusiasm about performing further research with genome edited livestock in the United States.

I should mention that there are also fees associated with all of this. As an academic institution, UC Davis is eligible for a fee waiver, however the Animal Drug User Product and Sponsor (ADUFA) Fees are substantial. And while these fees might be quite reasonable for an actual new animal chemical drug evaluation, it becomes hard to wrap your head around a half million dollar fee to get a single nucleotide polymorphism approved, when nature has made literally millions of unregulated SNPs in cattle genomes. UC Davis actually recently received an errant  ADUFA bill for over $140,000 as the fee waiver requests to the FDA were apparently misplaced, and that definitely got the attention of the University!At the end of the day, most academic researchers did not sign up to be regulatory scientists. And while I appreciate the need for such scientists to provide data to get approval for commercial products, it is not something that is of academic interest to me. I have little desire to undertake research to show that there are no substantial differences in nutritional or composition content of edible tissues between edited and non-edited animals unless that was the purpose of the edit (my upcoming paper on the meat and milk composition of the offspring of a genome edited polled bull not withstanding! Spoiler alert **** THERE WAS NO DIFFERENCE BECAUSE HORNS ARE UNRELATED TO MILK AND MEAT COMPOSITION OR SAFETY*****), nor in verifying the absence of hypothetical off-target sites in the genome so that our experimental knock-out animals can enter the food chain. I fear that this regulatory approach will effectively preclude public sector research into genome editing with food animals in the United States.

Public Acceptance of Animal Genomics and Biotechnology

Animal biotechnology is the application of modern molecular techniques to animals. Genetic engineering and cloning are two older forms of animal biotechnology , and genome editing is a more recent entrant. Animal genomics is the scientific study of structure, function and interrelationships of both individual genes and the genome in its entirety. Utilization of genomic information in breeding is often referred to as genomic selection (GS). In my view these two fields – biotechnology and genomics – face entirely different public acceptance issues. I wrote a conference proceedings paper for a forthcoming conference  in November 2021, and drew on some of my work in the past in this area. However the “My thoughts” section of the paper is new and published here for the first time. The entire paper  (which is not yet peer-reviewed) is available on my laboratory website . 

My thoughts

                There exists a considerable literature castigating “scientists” (typically meaning research professionals and bench practitioners) for poor communication with the public on the topic of genetic engineering and cloning, and more recently genome editing and GS. The contention seems to be that this failure to communicate uncertainty is what historically “provoked public alienation and fomented controversy” around these technologies, and that this will likely cause problems for genome editing and GS. I beg to differ. Unless these later two topics become politicized, or perhaps more importantly competing business interests develop an approach to monetize fear around these technologies by inflating public perceptions of risks and arousing opposition in an attempt to trigger a spiral of silence (Scheufele, 2014), they will be integrated into livestock breeding programs largely without public scrutiny in the same way as other breeding advancements have been. Artificial insemination has not been recently communicated to the public, and yet its use is routine. However, if they become targeted, both bench and social scientists will have a hard time being heard above the drone of misinformation on social media where science and politics are inextricably linked, similar to what we observed with communications around uncertainties and relative risks associated with COVID vaccines and treatments.

I use the following evidence and observations to support these assertions. There is no money to be made opposing GS. There is no “Non-GS Project” label. There are no large multinational companies controlling its use that can be used as a proxy for evil (e.g. Monsanto). I do not foresee a targeted campaign to preclude the use of GS in genetic improvement programs, in part because it is founded on naturally-occurring genetic variations, and in part because it is hard to problematize into a clean, dichotomous framing i.e. genomic bulls are “bad”, and conventionally-selected bulls are “good”. And while many of the same criticisms leveled against GE and cloning can be equally associated with GS (e.g. increasing the rates of inbreeding), these concerns are likewise associated with conventional selection programs.

Artificial insemination reduces genetic diversity, and conventional selection programs include traits like docility which could be considered a behavioral disenhancement. Layers are selected to not exhibit broody behavior. I am unaware of any campaigns to preclude the incorporation of temperament traits into breeding goals for ethical reasons, despite the fact this clearly alters the telos of the animal. Additionally, there are glaring disparities when it comes to the implementation of GS in the developing world, and even in small breeds; it is expensive to develop large populations of genotyped, phenotyped animals. It is not a scale-neutral technology, advantaging large breeds and genetic providers over small ones. Such inequality concerns would be problematic for a GE application, yet these concerns are rarely even discussed as it relates to GS, and they have not precluded the adoption of this technology. Genomic selection is not a perfect science, there are uncertainties and emerging issues (Misztal et al., 2021), but it is the most accurate tool we have to select the future performance of the offspring of an individual. The absence of an additional regulatory layer to the use of genomic testing has allowed the unfettered, uncontested and rapid adoption of GS in livestock breeding programs globally.   

Cloning is clearly unnatural, well at least somatic cell nuclear transfer (SCNT) cloning is unnatural in that it takes place in a laboratory. Cloning is actually rather common in nature, as evidenced by identical twins. Cloning elite animals has no obvious benefit to the consumer, and really is not that useful in breeding programs as it replicates the current generation rather than the next generation. It has had limited application in serving as a genetic insurance policy, and at times enabling the production of elite sires using less resources (Kasinathan et al., 2015).

By these metrics it would appear cloning is destined for market failure. And it has been effectively banned in the EU. In the Netherlands, the Dutch Animal Health and Welfare Act and Animal Biotechnology Decree prohibited the application of biotechnology to animals without a specific license. Criteria for being given a license included: the goal serves a public interest, has no unacceptable impacts on health and welfare of animals and does not raise any overriding ethical objections.  It is characterized as a ‘No Unless’ policy – no application of biotechnology to animals unless there is a very good reason for doing so. Since 2005, Denmark has required special licensing for animal biotechnology through the Act on Cloning and Genetic Modification of Animals. This legislation came about in large part due to ethical concerns surrounding the impact of biotechnological applications on animal integrity. This Act effectively limits the commercial use of animal cloning and genetic engineering to “creating and breeding animals producing substances essentially benefitting health and the environment”.

However, in countries where cloning is allowed, opposition to cloning has slowly faded, and it is being adopted where it is cost-effective – mostly in high-value recreational animals like bucking bulls and polo ponies. I would argue in countries where clones are not regulated differently to conventional breeding, and products from clones are not labeled as they are in fact impossible to differentiate from products from non-cloned animals –(despite the apparent green milk moustache in Figure 1!), there has been no way to effectively monetize fear around clones.

Figure 1. The Center for Food Safety depiction of cloned milk from their 2007 campaign against animal clones.

The Center for Food Safety, Consumers Union, Food and Water Watch, The Humane Society of the United States, the American Anti-Vivisection Society, the Consumer Federation of America and the Organic Consumers Association tried hard in the early days of cloning, but at the end of the day it is hard to create a convincing argument that a cloned product is somehow more dangerous than its identical progenitor. And in the absence of tracking or labeling requirements, it was just not possible to create a cost-effective “absence-labeling” campaign as was done with rBST and GMOs. 

It is worth noting that a lucrative pet cloning industry has emerged in the absence of regulatory oversight of non-food applications of cloning. In fact, Barbara Streisand recently took on two puppies cloned from her dead dog for the fee of $50,000.  If there is a direct benefit, at least in the mind of the person cloning their pet dog or bucking bull, then people are willing to overcome their hesitations regarding cloning. And as to the entry of these clones into the food supply, it is mostly a moot point. Undoubtedly products from cloned livestock – elite breeding stock at the end of their productive life, and even bucking bulls at the end of their bucking career have entered the food supply on a limited scale.  And considering that the US exported 190 million dollars’ worth of bovine semen in 2018, it is more than likely that there are offspring of clones running around globally.

And so we come to genome editing, the new kid on the block. And its fate is currently uncertain. Public perception is still forming around this technology, but I have a sinking feeling that genome editing will suffer the same fate as GE animals for the following reasons. Firstly, competing market forces have already started to conflate the two technologies. The Non-GMO project has come out with the following announcement “GMOs are now being created with newer genetic engineering techniques, some of which do not involve transgenic technologies. The Non-GMO Project is committed to preventing these new GMOs from entering the non-GMO supply chain.” The National Organic Standards Board voted to exclude all genetic modification and manipulation from organic production in 2016, including genome editing. And Greenpeace in their 2021 position paper entitled “Danger Ahead. Why genome editing is not the answer to the EU’s environmental challenges”, warns that the use of so-called gene (or genome) editing techniques like CRISPR-Cas could not only exacerbate the negative effects of industrial farming on nature, animals and people, but it could effectively turn both nature and ourselves (through the food we eat) into a gigantic genetic engineering experiment with unknown, potentially irrevocable outcomes.“ And so we again have a situation where activist groups and the natural and organic food industry will monetize fear and run a campaign of misinformation to suggest that genome edited animals are “unsafe”, whilst animals with naturally occurring genetic variants are “pure” (and also more expensive!).

Secondly, irrespective of the nature of the genome edit, the proposed regulatory approach to genome edited animals is the same as for GE animals, in both the EU and the United States. Even SNPs and deletions are being treated as drugs in the US. The absence of one intentionally altered base pair among 3 billion in the bovine genome thus results in an unsaleable new animal drug. By capitulating to this regulatory logic and tacitly agreeing that the emperor is wearing clothes, we replicate the situation where only large companies will be able to afford the regulatory and IP costs of bringing a genome edited animal product to market. Hitherto, the IP in livestock breeding has been primarily protected by secrecy and use of cross-breeding (Bruce, 2017). Small companies and academic laboratories will be unable to make use of a technology that originally resulted from public research funds. They will again be relegated to the sidelines, unable to afford even experimental work in large animals as all milk, meat and eggs from all genome edited “investigational animals” are unsaleable, and the animals themselves have to be composted, buried, or incinerated. There is then little incentive for public sector scientists to stick their neck out doing public communication around a technology they cannot use. Especially when doing so will likely result in hostile freedom-of-information act requests, and reputational defamation by front groups financed by the natural and organic food industry such as U.S. Right To Know (Kloor, 2015).

Figure 2. There are four species of transgenic fluorescent GloFish® available in six colors. Photo courtesy GloFish.

At the end of the day, I am not convinced widespread public opposition is what is preventing the adoption of new animal biotechnologies. The prevailing narrative repeated verbatim is that the public outright rejects GMOs. But that is not observed in actual purchasing behavior when GMO products are available. For example, GloFish® (Figure 2) are marketed to aquarists in the US, where they are now sold in every state in the nation, as well as throughout Canada. Sales represent approximately 15% of US aquarium fish sales. Although some authors raised early environmental and ethical concerns about GloFish (Rao, 2005), these concerns have waned over time.

GloFish is subject to enforcement discretion in the US. This is not a determination of “safety” under the Federal Food, Drug, and Cosmetic Act but is instead a determination that, based on risk, FDA does not believe it would be a good use of its limited resources to act against sponsors for the marketing and distribution of these unapproved products. Its sale is prohibited in other jurisdictions, including Europe, Australia, and Singapore. The success of this product suggests that consumers are willing to purchase GE animals, at least as aquarium pets. Alan Blake, CEO of the company marketing GloFish, wrote regarding public acceptance that consumers will purchase a product that they desire, irrespective of the breeding method that was used to produce it. In his words, “It is not about the process [of genetic engineering], it is about the product” (Blake, 2016).

Similarly, the Impossible Burger, a soy-based food product is proudly GMO with it recombinantly produced, bleeding leghemoglobin, has been a market success. Ironically the same anti-GMO groups that targeted GE in agriculture; GMO Watch, Consumer Reports, and the Center for Food Safety, went after Impossible Burger for using GMO heme and soy. They perpetuated the same fearmongering around GMO in Impossible Burgers as they had used around GMO in corn – claiming it hurt rats in a feeding study. And Impossible Food fought back, Rachel Conrad, Chief Communications officer wrote, “Finally, we’d like to request that Consumer Reports disclose its anti-GMO agenda in full transparency, and the biases of its activist employees. For years Consumers Reports, and fellow anti-GMO ideologues have been waging a PR war against GMOs — whether in vaccines, insulin, cheese or more recently the Impossible Burger.” And likewise, the PinkGlow GE pineapple that contains lycopene, a pigment that gives some produce its red color has been success, fetching a premium of as high as $50 per pineapple.

These GE applications might be considered frivolous, after all we can live without fluorescent aquarium fish and pink pineapples. But they are market successes because 1) they were allowed to come to market, and 2) they are products that the customer wanted with at least a perceived benefit. One thing is for sure – if products are not commercially available because it is cost-prohibitive, or even impossible to get regulatory approval, then the public will not be able to indicate their acceptance by purchasing them. That has essentially been the situation for GE food animals for the past 35 years (Van Eenennaam et al., 2021). And for GE food in Europe more generally, although there is of course a glaring incongruity there. In 2018 alone, the EU imported more than 30 million metric tons (MT) of soybean products, 10 to 15 million MT of corn products, and 2.5 to 4.5 million MT of rapeseed products, mainly for livestock feed. The EU’s main suppliers are Argentina, Brazil and the United States. The share of GE products of total imports is estimated at 90-95 percent for soybean products, 20-25 percent for corn, and less than 20 percent for rapeseed (USDA Foreign Agricultural Service, 2018), suggesting GMO feeds are a resounding market success! Again the lack of a requirement to label milk, meat and eggs from animals fed GE feed avoided demonization of these products and has facilitated the widespread use of GE feed in animal production systems globally.  

I’ll leave you with a 60 second video of a delicious meal we prepared recently featuring the first approved GE food animal – the AquAdvantage salmon. Delicious.

Contemplated Regulatory Framework (Part #4)

This is part 4 of a 1, 2, 3, 4 part series on Regulation of Genetically Modified Animals

I am in perhaps a somewhat rare position regarding the contemplated USDA regulatory framework, as I actually have several animals from amenable species (sheep, cattle) on the ground that were developed using “techniques that use recombinant, synthesized, or amplified nucleic acids to modify or create a genome” for “agricultural purposes”.  I have not published these data and they are the dissertation research projects of graduate students, and so I will only say that these animals were produced using CRISPR/Cas9 genome editing and a sgRNA to produce a gene knockout. This was done by introducing a Cas9-sgRNA ribonucleoprotein (RNP) into single cell zygotes following in vitro fertilization of in-vitro matured oocytes.  The resulting double strand break (DSB) was repaired by the non-homologous end joining (NHEJ) pathway, and subsequent embryo transfer to surrogate dams. In other words, each animal is a unique individual, and there was no foreign template or intergeneric combination of genetic material introduced into the editing process at any time. None of the genome editing target genes were intended to impact animal health, nor was the application intended to have an animal health claim. So as I read through the contemplated regulatory framework, I cant help but personalize how it would affect my research, and how it compares to the existing regulations.

By way of background, it is perhaps important to emphasize that the animals that make up the research herds and flocks at land-grant universities are typically entering the food supply at the end of experiments.  Our dairy cattle getting fed different experimental rations keep getting milked, the calves from a beef cattle crossbreeding study are finished in our feedlot and enter commerce at the end of the study, and our poultry produce eggs that are sold to the public, along with meat products from all our animal facilities (except the horses!).  There we sell foals at the UC Davis foal auction. The food animals are actually processed at our USDA-inspected slaughter facility, and butchered by meat science students. The income from the “meat lab” sales goes back into the operational account for the animal facilities.

So back to the genome-edited knockout animals I have on campus. Under the existing FDA regulations, they are considered unapproved animal drugs and cannot enter the food supply without a new animal drug approval or prior authorization. According to the FDA, I would need to apply for an investigational new animal drug (INAD) for these animals, and then request a Food Use Authorization (FUA) for these experimental animals to enter the food supply at the end of the experiment. I have actually already started to apply for that and the FDA have requested an answer to the following questions before they can even open an INAD, let alone tell me what information I need to provide to them to potentially obtain a FUA for my experimental gene knockout sheep and cattle. I have started on this paperwork, but it will take some time to prepare it all and submit it through their electronic portal.

  • Description of the project, including the goal of the intentional genomic alterations (IGAs), any relevant information from other animals in which the same genes have been knocked out (e.g., references to published articles characterizing knockout mice), and a description of the planned studies
  • Description of how the IGAs were produced, including detailed experimental design
    • Include information such as which Cas9 nuclease variant was used (e.g., SpCas9, SpCas9-HF1) and any associated information regarding the variant’s fidelity, criteria used to design and select guide RNAs, and any controls utilized to mitigate the potential for unintended alterations
  • Available molecular characterization data, including a description of the methods used (e.g., PCR, Sanger sequencing, long-range PCR, etc.)

So under the USDA contemplated regulatory framework, published in the Federal Register 12/28/2020, these knockout animals would clearly fit under the “amenable species modified or developed using genetic engineering and intended for agricultural purposes and human food”. If they were knockout plants they would have an up-front exemption from regulation under the SECURE revision as they “result from natural cellular repair of a targeted DNA break without any introduced DNA to direct the repair”.

For the USDA animal health safety review I would need to show that “the animal under review is found to pose no greater risk to animal health than the animal from which it was derived”. This is where is gets a little unclear.  The term “the animal from which it was derived” suggests that the animals are being derived from a known unmodified animal, presumably through genetic engineering of a cell line derived from that animal, followed by somatic cell nuclear transfer cloning of the edited cells. But my animals are derived from editing multiple zygotes, so each edited animal has its own unique genomic sequence i.e. there is no animal from which these animals were derived, and conceptually editing outcomes differ between all of these different individuals, especially because the DSB was repaired using the error-prone NHEJ pathway.  So does each individual animal have to have a different evaluation?

The safety review requires “a molecular characterization of the modification and an understanding of the process by which it was introduced, that the intended change was made and that there were no unintended disruptions of endogenous genes, unintended DNA insertions, or off-target changes if the genome was modified without inserting DNA.” It is not hard to prove that the intended change was made, we typically do that with a PCR amplification of the target locus, and sequencing of the amplified PCR product. But to answer the rest of those questions will require, at a minimum, whole genome sequencing of every animal, and proving a negative i.e. proving no unintended disruptions of endogenous genes, unintended DNA insertions, or off-target changes if the genome was modified without inserting DNA.  Both the sequencing and the bioinformatics to try to answer these questions would be very expensive, well beyond the cost of a sheep, or even a cow. This is especially true when every animal has a unique genotype, and there is no way to differentiate off-target changes from spontaneous de novo mutations.

Further, at a minimum, the animal health risk assessment would include an evaluation of the following issues:

  • Molecular Characterization: What is the genetic modification(s) in the animal, how was the genetic modification(s) introduced, and how does the genetic modification(s) alter protein or ribonucleic acid (RNA expression)?
  • Animal Health: Is there scientific evidence that the modified animal could plausibly, either directly or indirectly, increase susceptibility of livestock, including of the animal itself, to pests, non-infectious diseases, or infectious diseases of livestock, including zoonotic diseases? Is there scientific evidence that the modified animal could plausibly increase the spread of pests or infectious diseases of livestock, including zoonotic diseases?  When a plausible pathway to such an increased risk is identified, further analysis would be conducted to evaluate the pathway.  When an animal health claim is made or a modification is known to adversely affect animal health, the review would assess the animal health claim.
  • Environmental Factors: Is there scientific evidence that introduction of the modified animal into the environment may result in environmental impacts that would warrant review pursuant to the National Environmental Policy Act (NEPA) or other statutes?

And in addition, the FSIS review would include an evaluation of the following issues (theoretically pre-slaughter, although obtaining meat for compositional analysis from animals pre-slaughter is obviously problematic):

  • Evaluation of expressed substances: Is there scientific evidence that the genetic modification could result, directly or indirectly, in toxins, chemical residues, or other potentially deleterious substances in meat or poultry products?
  • Allergenicity: Is there scientific evidence that the genetic modification would directly or indirectly alter the allergenic potential of meat or poultry products derived from the animal?
  • Food storage and processing: Is there scientific evidence that meat or poultry products derived from the modified animal could mislead consumers regarding wholesomeness or the need for appropriate storage (e.g., meat that maintains a red appearance even when spoiled)?
  • Compositional analyses of key components: Is there scientific evidence that meat or poultry products from the modified animal are compositionally (e.g., nutritionally or functionally) no different than meat from conventional animals, such that it meets any regulatory definition, standard of identity or other labeling requirement, and consumer expectations for the applicable product?

Needless to say, providing answers to all of these questions for each individual knockout animal would be an unsurmountable hurdle for an academic laboratory. Throughout the USDA contemplated regulatory framework the term “developer” is used. For example, “Under the contemplated regulatory framework, developers could request that USDA conduct a risk-based and science-based safety review focused on animal health”. Historically, developers of genetically engineered plants have been large multinational companies who have the resources to provide the regulatory data to support commercialization and ultimately deregulation of their products. Research universities are not developers in this sense, but we still produce amenable species modified using genetic engineering and intended for agricultural purposes and human food.

One of the questions the USDA poses in the request for comments is,

“How often does a start-up company or not-for-profit university or research organization modify or develop an animal using genetic engineering?”

My answer would be never.  Researchers at universities often modify animals using genetic engineering but never has one developed and commercialized an “amenable species modified or developed using genetic engineering and intended for agricultural purposes and human food.” The two food approvals for genetically engineered animals were both obtained by companies, albeit small companies. AquaBounty for the “AquAdvantage” salmon, and Revivicor for the “GalSafe” pig.  To date neither of these products has been sold for food in the United States, although AquaBounty is getting mighty close.

In closing, as long as animals produced using genetic engineering, even those that could have been produced using conventional breeding,  are subjected to unique regulatory scrutiny not required of identical products produced using conventional breeding, research in food animals using genetic engineering for agricultural applications will be cost-prohibitive in the United States.

Another question the USDA poses is,

“Should USDA exempt certain types of genetic modifications of amenable species intended for agricultural use from regulation?  If so, what types of modifications and why?”

I would suggest that the SECURE up-front exemptions for certain types of modifications in plants, specifically a modification (1) resulting from natural cellular repair of a targeted DNA break without any introduced DNA to direct the repair;  (2) that is a targeted single base pair substitution; or (3) that introduces a gene known to occur in the plant’s gene pool, or causes a change in a gene that corresponds to a version of that gene present in the organism’s gene pool should be extended to genetically engineered animals.  These exemptions were primarily designed to exclude from regulatory oversight organisms that could have been achieved using conventional breeding. Just like the Coordinated Framework calls for.

If you have comments on the contemplated regulatory framework, there is a 60 day public comment period that closes 2/26/2021. I would encourage all people working in this field to post comments. Comments can be posted Federal eRulemaking Portal: Go to  Supporting documents and any comments that are received on this Advance Notice of Proposed Rulemaking may be viewed at

In the words of one commentator

“It, of course, remains to be seen what will be the Biden Administration’s approach to ag biotech; however, given the consistency of approach to the evolving ag biotech regulatory structure by both the Obama and Trump Administrations, it would not be surprising if the Biden Administration also continued the evolution of a more science-based, evidence-based, and risk-based approach to regulation of ag biotech – including genetically engineered animals. It would behoove stakeholders that would support such consistency of regulatory approach to submit detailed comments that would assist USDA in developing such a notice of proposed rulemaking (NPRM).

As with all opportunities to provide comments on Federal agency proposals, it is important to submit concise, substantive, and well-supported and well-documented comments to the administrative docket. In this case, given the trans-Administrations nature of the action, it is important that interested stakeholders use this opportunity to best advantage to urge the Biden Administration to continue a 21st Century approach to regulating ag biotech.”         Keith Matthews, Wiley Rein LLP

Regulation of Genetically Modified Animals Part #3

This is part 3 of a 1, 2, 3, 4 part series on Regulation of Genetically Modified Animals

So what is the USDA’s proposal for the regulation of genetically engineered animals? In a nutshell, it proposes moving regulation of food animals that are genetically engineered for agricultural purposes such as human or animal food, fiber, and labor from FDA to USDA. This means that intentional genomic alterations in food animals would no longer be automatically and mandatorily regulated by the FDA as “drugs”. That is good news, because genetic variation between individuals cannot reasonably be considered a drug. All life on Earth is made up of genetic alterations. It is the very foundation of all selection programs, and indeed evolution itself. In some ways it is going back to the future, as APHIS oversight of  agriculture and forestry products developed by modern biotechnology was envisioned in early discussions of the regulation of biotechnology.

APHIS would conduct a safety assessment of animals that have been modified or developed using genetic engineering subject to the Federal Meat Inspection Act (FMIA), and the Poultry Products Inspection Act (PPIA) with a specific eye to alterations that may increase the animal’s susceptibility to pests or diseases of livestock, including zoonotic diseases, or ability to transmit the same. The Food Safety and Inspection Service (FSIS) would also conduct a pre-slaughter food safety assessment to ensure that the slaughter and processing of certain animals modified or developed using genetic engineering would not result in a product that is adulterated or misbranded, as they do with animals produced using conventional breeding.

This is a definite improvement over the FDA approach. Period. Clearly the approach being proposed has been used in plants, and has allowed at least some genetically engineered crops to come to market, albeit mostly those developed by large biotechnology companies. However, there are still some logical inconsistencies in the proposal as it stands. And I realize that perfect is the enemy of good enough, but I can’t help but look at this from my perspective as an academic working in livestock improvement, who has seen the promise of genetic engineering wither on the vine. Regulatory evaluations have included “Alice-in-Wonderland” evaluations that include questions that have no right or wrong answer. If there is no hypothesis to test it is not possible to do a power analysis or design a sensible experiment. Studies that product developers have conducted to try to address these questions have been used by groups opposed to the technology to suggest the whatever data is provided indicates unacceptable risks as discussed here. At least the USDA proposal is seeking to identifying “plausible” risks, suggesting the need to test at least some hypothesis, rather than a fishing expedition.

First, lets look at what genomic alterations are covered. Specifically, those that are introduced into animals of the “amenable species” (cattle, sheep, goats, swine, horses, mules, other equines, fish of the order Siluriformes (catfish), chickens, turkeys, ducks, geese, guineas, ratites, and squabs) modified or developed using genetic engineering that are “intended for agricultural purposes” such as human or animal food, fiber, and labor. FDA would continue its review of amenable species modified or developed using genetic engineering intended for non-agricultural purposes, including medical and pharmaceutical purposes (other than veterinary biologics), and gene therapies; and in non-amenable species. So genomic alterations in non-food animals remain with the FDA, and so does non-agricultural genetic engineering. Sorry dog and cat people – you remain with the FDA, irrespective of the nature of your edit.

And what is “genetic engineering” in this case? It is defined to mean “techniques that use recombinant, synthesized, or amplified nucleic acids to modify or create a genome”.  Note how this is a technique-based definition. Already, we have run afoul of the 1986 Coordinated Framework for Regulation of Biotechnology which states, exercise of regulatory oversight should be product-risk based…”and should not turn on the fact that an organism has been modified by a particular process or technique.”

The proposed rule goes on to clarify it would “not include conventional breeding methods such as directed breeding, artificial insemination, embryo transfer, selective breeding, cross breeding, genetic backgrounding for purposes of studding, or other practices commonly available to and employed by producers.” I have worked in animal genetics my entire career, and have not the slightest idea what “genetic backgrounding for purposes of studding” means. Seriously. NO IDEA. I am also not sure the difference between directed breeding and selective breeding, but maybe I do not get out enough.

Onwards to some other concerns, there does not seem to be any clear distinction between genome edited animals without intergeneric DNA combinations that could have been achieved using conventional breeding, albeit likely less efficiently that can be achieved using traditional approaches, and genetically engineered animals harboring an rDNA transgene. This distinction was clearly made in the SECURE revision of APHIS’ biotechnology regulations for plants; but not in this contemplated regulatory framework for animals. This seems strange.

The proposal reads “The regulatory framework that USDA is considering would be conceptually similar to the recently updated USDA regulations for the movement of organisms, notably plants, modified or developed using genetic engineering, (i.e. SECURE).  However, due to the differences in experience, biology, and breeding practices of animals as compared to plants, there would be some differences between these regulatory frameworks.  For example, although SECURE includes up-front exemptions from the regulations for certain types of modifications [i.e. plants without intergeneric DNA combinations that could have been achieved using conventional breeding], we envision that all amenable species modified or developed using genetic engineering and intended for agricultural purposes would be subject to permitting requirements for their import, interstate movement, or environmental release until they have undergone an expedited safety review or an animal health risk assessment and been determined not to pose an increased risk to animal health.  We do seek comment on this issue.“

Well I certainly have some comment on this issue!  What are the “differences in experience, biology, and breeding practices of animals as compared to plants” that make a SNP in a plant eligible for an up-front exemption from the regulations, but a SNP in an animal not? Crops naturally produce allergens, toxins, or other anti-nutritional substances, and some rare safety issues that have been associated with conventional plant breeding, such as allergens in Kiwi fruit, or high levels of solanine in potatoes. I have a hard time coming up with analogous examples from animal breeding despite intensive selection for traits of interest. So what is uniquely hazardous, or even risky, about genomic alterations that could have been achieved using conventional breeding in animals, but not plants, that makes cisgenics, SNPs and deletions ineligible for an up-front exemption from the regulations? At the end of the day – both kingdoms provide food, and different regulations for the different kingdoms makes little scientific sense.

I have many more specific comments on this proposal, but they all will come back to this basic point. Regulation should be proportionate to risk, and agnostic to method. If regulations are being proposed that mandate a more onerous pathway for identical products produced one way as compared to another, or differ between kingdoms, or require additional testing only of products produced using one method, then they will tilt the scale to the less onerous pathway. This may not always be in the best interests of society. For over 30 years now animal geneticists have had little ability to employ genetic engineering in animal breeding programs. This comes with an opportunity cost as detailed here.

In contemplating  an improved regulatory approach for genetically modified animals, perhaps it is time to ditch the process-based trigger which requires additional regulatory scrutiny of plants and animals that could have been achieved using conventional breeding, and rather take the advice of the 1996 Coordinated Framework, and that is that regulatory review should be confined to organisms deliberately formed to contain an intergeneric combination of genetic material from sources in different genera (aka foreign or transgenic DNA that could plausibly produce a toxin or an allergen), and that oversight should 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 regulatory oversight is greater than the cost thereby imposed.

Regulation of Genetically Modified Animals Part #2

This is part 2 of a 1, 2, 3, 4 part series on Regulation of Genetically Modified Animals

The “Guidance for Industry #187” entitled, “Regulation of Intentionally Altered Genomic DNA in Animals” was published in the Federal Register in 2017, and a public comment period followed. I wrote about my concerns regarding this approach in a previous BLOG. The FDA took comments on this draft revised guidance during the 90-day public comment period which closed June 19, 2017. As I wrote in a BLOG in January 2019, and what remains true today, is that there has been ZERO formal response to the many comments by public sector scientists working in this field who submitted detailed comments, and who see that this regulatory approach will make food animal research using genome editing cost prohibitive, and effectively preclude the use of gene editing in food animal breeding programs.

To date, there have been two food use approvals for genetically engineered animals in the US, ever. One, the AquAdvantage salmon, the founder event of which occurred in 1989, and which has still yet to be sold in the US despite approval in 2015 as discussed here. AquaBounty estimated it has spent $8.8 million on regulatory activities to date including $6.0 million in regulatory approval costs through approval in 2015, $1.6 million (and continuing) in legal fees in defense of the regulatory approval, $0.5 million in legal fees in defense of congressional actions, $0.7 million in regulatory compliance costs (~$200,000/year for on-going monitoring and reporting including the testing of every batch of eggs), not to mention the $20 million spent for maintaining the fish while the regulatory process was on-going from 1995 through 2015.

And on December 14, 2020 the FDA announced it second food animal approval for an Alpha-gal (galactose-α-1,3-galactose) knockout “GalSafe” pig. The press release announced the “First-of-its-Kind Intentional Genomic Alteration in Line of Domestic Pigs for Both Human Food, Potential Therapeutic Uses.” This wording “intentional genomic alteration”, at first made me think this was approval for a genome edited knockout. But then I read an article quoting a spokesperson for the developer saying they have been working on the GalSafe pigs since 2007. That is pre-genome editing in food animals. I searched PubMed and realized that this approval was for a traditional gene knockout approach to achieve a homozygous founder event that was followed by cloning, aka old school genetic engineering, and that was first published in the peer-reviewed literature in 2003.

A petition calling 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 was launched at the Plant and Animal Genome Conference in 2018, and signed by over 300 scientists, and was shared with the federal regulatory agencies in June 2018.

Comments from scientists included:

“It is long-standing U.S. policy to regulate an item derived from biotechnology as a product, not by the process through which it was produced. We must base oversight based on assessed risk, not on the basis of political considerations.”

“Regulatory uncertainty and inconsistency are barriers to innovation. Importantly, it prevents small to medium businesses from having a pathway to market for products that could be of immense benefit, including the welfare of animals. Draft Guidance for Industry #187 is out of step with crop plants and is not consistent with a science-based risk based regulatory framework. It is disappointing that this Draft undermines a regulatory system that has, until now, been regarded as robust and well respected. The Draft is not fit for purpose.”

In the meantime, USDA announced the SECURE (Sustainable, Ecological, Consistent, Uniform, Responsible, Efficient) revision of APHIS’ biotechnology regulations that was published in the Federal Register on May 18, 2020 following a detailed response to the public comments. It includes up-front exemptions from the regulations for certain types of modifications, specifically a modification (1) resulting from natural cellular repair of a targeted DNA break without any introduced DNA to direct the repair;  (2) that is a targeted single base pair substitution; or (3) that introduces a gene known to occur in the plant’s gene pool, or causes a change in a gene that corresponds to a version of that gene present in the organism’s gene pool.  These exemptions were primarily designed to exclude from oversight plants without intergeneric DNA combinations that could have been achieved using conventional breeding, albeit likely less efficiently. Food (e.g high oleic oil from company Calyx) from genome edited plants has already entered the US market.

The FDA doubled down on their new animal drug regulatory approach in a 2020 Nature Biotechnology correspondence entitled “Genome editing in animals: why FDA regulations matters” There, FDA Center for Veterinary Medicine (CVM) Director Steven M. Solomon made the case for

“why it is necessary for there to be regulatory oversight of intentional genomic alterations in animals, even when the intended modification seeks to replicate a naturally occurring mutation.” He then specifically distances his argument from intentional genomic alterations performed in organisms from other kingdoms that we eat, i.e. plants and microbes, with the statement “Readers should note that our statement here relates to intentional genomic alterations in animals; we are not commenting on alterations in plants or other organisms.”                      FDA CVM

As I wrote in my BLOG earlier this year, Nature Biotechnology published its own editorial response the FDA’s correspondence countering that, “the origin of a DNA arrangement (conventional breeding, recombinant DNA or gene editing) makes little difference to an animal. The genomes of domestic cattle contain millions of natural variants: the 1000 Bull Genomes Project found >86.5 million differences (insertions, deletions and single nucleotide variants) among cattle breeds. According to prominent researchers in the field, none of these variants has been shown to produce ill effects on consumers of milk or meat. Amidst this background of innocuous variation, how can the presence of one identifiable variant justify the costs and delays of mandatory FDA oversight?

Nature Biotechnology finishes with the argument that,

“A cautious, process-based regulatory route keeps the FDA out of trouble and lowers litigation risks for CVM’s lawyers. But the agency could still alter course without reversing direction completely.

Mandatory oversight could be phased out to a system whereby the agency exercises discretion over which gene-edited animals are regulated according to the hazard represented by the introduced trait. This would be consistent with USDA policy and longstanding US regulatory policy. It would give the animal biotech sector a chance to bloom. And it would counter the narrative of fearmongers who would taint all gene-edited animals as hazardous to public health and injurious to animal welfare.”                                          Nature Biotechnology

And so we come to December 2020, and the UDSA advance notice of proposed rulemaking “Regulation of the Movement of Animals Modified or Developed by Genetic Engineering “ which was published in the Federal Register on 12/28/2020. What is the USDA proposing? And how does it differ from the FDA’s approach? Does the contemplated regulatory framework improve things? More on that in the next BLOG.


Regulation of Genetically Modified Animals Part #1

This is part 1 of a 1, 2, 3, 4 part series on Regulation of Genetically Modified Animals

Ever since the US Food and Drug Administration (FDA) announced its plans to regulate genomic alterations in genome edited animals as veterinary drugs in January 2017, I have been a vocal critic of this regulatory approach. I am a livestock geneticist, and have seen the negative impact that this expensive and unpredictable regulatory approach has had on the development of genetically engineered animals. Even today, there has not yet been the sale of a single food product from a genetically engineered animal in the United States, although AquaBounty is getting close with their approved, fast-growing AquAdvantage Atlantic salmon. And just this month a second product, a gene knock-out pig was approved by the FDA, although the company has also not yet sold any pork product to consumers.

Compare that to the progression of genetically engineered crops which have been commercialized for more than 22 years, and in 2019 alone they were grown on 190.4 million hectares by 17 million farmers in 29 countries. Clearly there is something different about the trajectory of genetically engineered food products developed in the animal kingdom as compared to the plant kingdom. Yet at the end of the day, products from both kingdoms end up on the plate of omnivorous consumers. Is there something inherently risky about genetically engineered food animals that explains this discrepancy?

Recently, the United States Department of Agriculture (USDA) came out with an advance notice of proposed rulemaking which was published in the Federal Register on 12/28/2020. This proposal contemplates a different regulatory approach for genetically engineered animals of certain “amenable” food animal species that are “intended for agricultural purposes”. There is a lot to unpack in this document, and so first some background information might be helpful. This is going get a little wonky.

Thirty five years ago, the first paper documenting the production of genetically engineered food animals was published in 1985. A year earlier, a December 1984 Notice “Biotechnology regulation; coordinated framework” came out in the Federal Register, with the introduction reading, “Only forty years ago, DNA was discovered to be the repository of genetic information…”.

In that document, USDA outlines it plan to use its existing  regulatory framework to regulate agriculture and forestry products developed by modern biotechnology. In 1986, the White House, Office of Science and Technology Policy (OSTP) published the Coordinated Framework for Regulation of Biotechnology. This document states, “This framework has sought to distinguish between those organisms that require a certain level of federal review and those that do not. This follows a traditional approach to regulation. Within agriculture, for example, introductions of new plants, animals and microorganisms have long occurred routinely with only some of those that are not native or are pathogenic requiring regulatory approval.” The document goes on to clarify that for genetically engineered plants, the “regulated article” would be defined as any organism or product altered or produced through genetic engineering, if the donor organism, recipient organism, or vector or vector agent belongs to a group of organisms designated by the proposed regulations as having plant pests or any organism or product which USDA determines is a plant pest. A similar approach was envisioned for the regulation of genetically engineered animals.

The Coordinated Framework was subsequently updated in 1992 to include “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.”

Back in 1992, genetic engineering typically involved random genomic insertion of intergeneric DNA combinations (i.e. transgenic construct) that expressed a protein which resulted in a desired outcome in the target species. For example, fast growth in the case of the AquAdvantage salmon, disease-resistance in the case of a mastitis-resistant cow, or decreased phosphorus in the manure of the “EnviroPig”.

For a number of years, regulatory oversight of the movement of both genetically engineered plants and animals rested with the USDA. Early work with transgenic goats undertaken by my colleagues at UC Davis in the early late 1990s and early 2000s was done in consultation with the USDA’s Animal and Plant Health Inspection Service (APHIS). Under the Animal Health Protection Act (AHPA), APHIS is authorized, among other things, to prohibit or restrict the importation and interstate movement of live animals to prevent the introduction and dissemination of diseases and pests of livestock within the United States.  The AHPA broadly defines the terms “livestock” as “all farm-raised animals”, and “animal” as “any member of the animal kingdom (except a human)”. APHIS currently uses its plant pest authorities under the Plant Protection Act to assess and regulate the movement of genetically engineered plants into the environment.

A chapter in a 2004 PEW report which came out almost 20 years after the first genetically engineered livestock were reported in 1985 entitled “Regulating Genetically Engineered Animals”, read

“because GE animals are so new and are still largely being used only in research, the agencies likely to oversee them have not yet established clear overall or product-specific policies for regulating them under existing laws. Regulators, researchers, developers, and potential consumers are thus currently navigating in uncertain waters, and the discussion of regulatory policies in this chapter is necessarily somewhat speculative.”

In that PEW report the terms “genetically engineered” and “transgenic” were used synonymously, as genetic engineering at the time involved the random insertion of recombinant DNA (rDNA) constructs.

Then in 2009, the FDA Guidance for Industry #187 entitled, “Regulation of Genetically Engineered Animals Containing Heritable rDNA Constructs”, announced FDA’s 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 Federal Food, Drug, and Cosmetic Act (FD&C Act). 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 FDA clarified that they considered the rDNA construct and its expression product in a genetically engineered animal to be the drug, not the genetically engineered animal itself. Although the FDA’s regulatory evaluation was based on attributes of the product, the method used to produce the genetic change, that is rDNA techniques  versus other breeding methods, was the trigger for regulatory oversight. In other words, the trigger for regulatory oversight was based on the process designed to produce the genetically engineered animal, not on the risks associated with the specific characteristics of the animal or its food products (milk, meat or eggs).

And so it continued until January 2017, when the FDA came out with its updated draft “Guidance for Industry #187” entitled, “Regulation of Intentionally Altered Genomic DNA in Animals”. This guidance proposed to regulate all food animals whose genomes have been intentionally altered using modern molecular technologies including gene editing technologies which may include random or targeted DNA sequence changes including nucleotide insertions, substitutions, or deletions, or other technologies that introduce specific changes to the genome of the animal as veterinary drugs.

So there has been a gradual metamorphosis over the past 30 or so years from a proposal for USDA to oversee the regulation of  genetically engineered food animals that pose “unreasonable” risks regarding introduction and dissemination of diseases and pests of livestock under APHIS, to a 2009 draft guidance requiring mandatory FDA premarket new animal drug approval for all animals modified by recombinant DNA techniques; to an updated 2017 draft guidance requiring mandatory FDA premarket new animal drug approval of any “intentionally-introduced genomic DNA alteration in animals produced using modern molecular technologies”, irrespective of risk or even the presence of a heritable rDNA construct. I think that is called regulatory creep. A set of administrative rules giving rise to unintended consequences, because of their broad industry reach.

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