Author: alvane (Page 5 of 5)

A recent article by Danny Hakim on the so-called “agrochemical academic complex” includes a quote, “If you are funded by industry, people are suspicious of your research. If you are not funded by industry, you’re accused of being a tree-hugging greenie activist. There is no scientist who comes out of this unscathed.”

I beg to differ. My research is not funded by industry, and yet to my knowledge I have never been called a “tree-hugging greenie activist.” Quite the opposite – I have been demonized by groups opposed to genetically modified organisms (GMOs) because my publicly-funded research on animal biotechnology and genomics has occasionally published results in line with the weight-of-evidence around the safety of genetically engineered organisms.

After reading the article, I was left with the conclusion that industry (and by this it appears to be any industry associated with the “agrochemical academic complex”, not the activist or NGO industries – the influence of whose funding is noticeably absent from the article) dictates the outcome of the research and public academics are just hapless puppets to be played to produce favorable outcomes for industry.

That is not how my laboratory works. Nor is it how my department operates. Nor my university. Nor in my experience are the public scientists I know willing to trade their hard-won scientific integrity for research funding. Such a move would be career suicide. Publishing incorrect or false data in science sets off a ticking time bomb for retraction when others are unable to repeat these results.

More generally, the article does not seem to understand how academic funding works. And I have found this misunderstanding to be true in interactions with my friends and neighbors too. My university has little control over what I research – it is called “academic freedom”.

As a researcher at UC Davis, I am provided with my salary and a laboratory. The rest is up to me. What I mean by that is if I want to do original research, I need to obtain research funding to conduct that research. Typically this involves writing research grants.

My university has absolutely no say over the topics I chose to research or where I apply for funding. They have absolute direct control over how I spend the funding I do receive in terms of ensuring I abide by all university policies, and that the grant monies are spent appropriately.

By FAR the biggest expense I have in my research program are graduate students. At the current time the annual cost of a UC Davis graduate student is around $26,734 for a 50% time stipend for 12 months, and $17,581 for fees and health insurance for a total of $44,315 annually. So for a 2 year Masters student that is $88,630 and a 5 year Ph.D. student $221,575 – let’s just call that an even quarter of a million.

And that does not include the University’s “indirect rates” which currently adds an additional 57% on top of the stipend, so the amount that needs to be in a research grant for that PhD stipend is an additional $76,192 for a grand total of around $297,767 for a 5-year student, close to an even $300,000 assuming no tuition hikes– and that only gets you 50% time of that student, the other 50% time they are doing their course work!

Each laboratory is effectively a small business within a much larger entity. Their business is to obtain funding to pay student salaries, conduct research, and publish peer-reviewed articles. The University provides the location and facilities to perform that research. And for that the University taxes a 57% “overhead” rate off the top of the grant award.

If I did not write successful grants to fund graduate students, pay for research supplies, travel to field plots and perform my extension activities then I would not have a research program or anything to publish in the peer-reviewed literature. And that is how I am evaluated – by my peer-reviewed publications and research productivity, not by the amount or source of the research funding I am able to secure. It is the researcher, the so-called “principal investigator”, that drives this enterprise and makes the decisions on what to research and where to obtain grant funding, not the university.

If the university as an entity happens to obtain money from a donor to build a building, for example the UC Davis Mondavi Center for the Performing Arts built with a gift from the wine industry, that in no way affects my research funding or what I chose to research, or means that researchers have to perform research that is favorable to the wine industry.

If a researcher chooses to seek industry funding, as many do especially in the information technology, transportation and energy sectors, there are strict guidelines around managing potential conflicts of interest and ability to publish the results of the research. According to UC Davis university policy: “Freedom to publish is a major criterion when determining the appropriateness of a research sponsorship; a contract or grant is normally not acceptable if it limits this freedom. The campus cannot accept grants or contracts that give the sponsoring agency the right to prevent for an unreasonable or unlimited time, the release of the results of work performed.”

It is perhaps not well publicized that an inordinate amount of a University professor’s time is spent writing grants to public agencies, which often have a funding success rate of one grant in 10. As such 9 out of every 10 grants are only ever read by one or two reviewers, and then never see the light of day again. This is not an efficient system, but it is the system we have. If a researcher has public funding, their research has already survived pre-project peer-review by the grant panel. Ironically some have even suggested that public funding is also tainted. If funding from both private and pubic sources is suspect, where does that leave academic laboratories, and who will pay to train the next generation of scientists?

Writing grants is perhaps (actually for sure) the least favorite part of my job, and it is time-consuming. But it is a necessary evil if I am to perform research and fund my graduate students. I have been fortunate to be able to secure public funding for my research mostly from the United States Department of Agriculture (USDA) (thanks NIFA!), but many other researchers quite appropriately work with industry sponsorship in the development and evaluation of new technologies. Industries of all types seek such partnerships with public universities to obtain an impartial evaluation of their technology.

Demonizing industry funding as unilaterally suspect in the absence of wrongdoing fails to take into consideration the checks and balances that are in place at public universities and the importance of public:private partnerships in the development of new technologies, and the unfortunate reality that there is a paucity of public research funding.

I was updating a chapter I am writing about the regulations around genetically engineered  (GE) animals, and both supporters and detractors of GE animals have criticisms of the US regulatory approach.

Criticisms from the biotech industry include:

• the approach is process-triggered rather than being based on the actual, relative risks (if any) associated with the novel phenotype or product as compared to those associated with conventional comparators.
• the process is prohibitively time consuming and expensive to complete all of the mandatory testing. AquaBounty has expended over $60 million in attempting to bring the AquAdvantage® salmon through the regulatory approval process thus far (David Frank, AquaBounty, pers. comm.), and still does not have authorization to market in the US.
• some tests are not based on unique risks (e.g. endogenous allergens), and the absence of a known tolerance level or natural levels of variability means regulatory studies are problematic to design and the results are ambiguous to interpret.
• unpredictable timeline.
• focus is only on risks, no consideration is given to potential benefits of the novel phenotype or product, nor are the risks associated with existing alternative approaches to genetic modification and breeding, or regulatory inaction, considered.

The following table outlines the key events in the timeline of the regulatory process for the AquAdvantage^® salmon since its genesis over a quarter of a century ago in 1989. No other GE food animal has been approved anywhere else in the world.

Criticisms from the activist industry include:

• lack of public participation and transparency – although the entire AquAdvantage data package was made publicly available.
• no consideration of socio-economic issues including ethics and moral concerns.
• concern about impartiality of the data because the regulatory review studies are being conducted by the company seeking approval of the GE animal.
• environmental risk is not given appropriate consideration as the National Environmental Policy Act is procedural in nature and does not give the FDA the authority to deny an application on environmental grounds.
• lack of mandatory process-based labels on food derived from GE animals, although the passage of the 2016 National Bioengineering Food Disclosure Law may pre-empt that concern.

The AquAdvantage^® Atlantic salmon carries an “all fish” growth hormone chimeric gene. The rDNA construct consists of  an antifreeze protein gene promoter from ocean pout linked to a chinook salmon growth hormone cDNA. It was envisioned that this construct would raise less public concern because of the “all-fish” nature of the rDNA construct and the fact that does not include any viral or selection marker sequences. Given the founder of this transgenic line was generated in 1989 and that the commercial product was first approved in December 2015, it is hard to argue that the mandatory process-based regulatory process encountered by the GE AquAdvantage^® salmon  created “an environment of certainty and confidence for researchers, industry and consumers” . It may even have convinced consumers that, since mandatory regulation is required, it must mean that this fast growing fish is somehow more intrinsically risky than conventionally bred fast growing salmon.

One thing is for certain – no small company or university can afford to try to get a GE animal application through regulatory given the unpredictability of the timeline and costs. The protracted regulatory evaluation of this fast-growing Atlantic salmon and uncertainty associated with the process and the timeline has had a chilling effect on investment and development of GE animals for food applications in the US.

If I wanted to create a fake news story – I would lead with a sensational headline. Something that would incense and shock the readers and be extra “clickbaity”. Perhaps a hook about a teenager getting raped to death. That should get some serious traffic.

That seemed to be the approach taken by New York Time’s journalist Michael Moss back in in January 2015 when he wrote “Research Lab Lets Livestock Suffer in Quest for Profit” skewering the US Meat Animal Research Center (US MARC).

Moss began investigating the USDA-research facility after being contacted by Dr. James Keen, a disgruntled ex-employee who is prohibited from setting foot in the center. In the article Keen is quoted as saying that in 1989, “There was a young cow, a teenager, with as many as six bulls,”…”the bulls were being studied for their sexual libido, and normally you would do that by putting a single bull in with a cow for 15 minutes. But these bulls has been in there for hours mounting her”…”Her back legs were broken. Her body was torn up.” According to the article a few hours later the (teenager) cow died.

That is a gut-wrenching image! I have never heard a heifer referred to as a teenager, but that one compelling anecdote was enough for me. If true, this was egregious and unacceptable animal cruelty. However, the scenario did not ring true. I know the protocol for libido testing bulls, and it never involves multiple animals. There would be no reason to EVER put six bulls in with a single heifer for 5 minutes, let alone for hours.

There were numerous other horrific claims in the article. Moss quoted another source, Robert A. Downey, the executive director of the Capital Humane Society, in Lincoln, NE as saying “Experimental surgery is being performed in some (not all) cases by untrained, unskilled and unsupervised staff. This has resulted in the suffering of animals and in some cases the subsequent death of all animals.” During a visit, he said, he saw animals headed to surgery that fell from carts or were pushed to the floor by their handlers, while two other workers in the operating room ate doughnuts.

Again that infuriated me – as an animal scientist I know the very strict animal care protocols we have to comply with to undertake any animal research at UC Davis, even routine herd management is strictly monitored. However, again the scenario did not ring true given what I know of the character of the researchers at US MARC, not to mention the senselessness and research futility of doing a surgery if all the animals subsequently died. That does not pass the common sense smell test. And surgeries do not mix with doughnuts. For obvious reasons.

As I wrote in 2015 “As an animal geneticist, I have worked with the researchers in the Genetics, Breeding and Animal Health research unit at MARC, and personally visited the center on several occasions over the past decade. The story published by The New York Times does not reflect my knowledge of the current research that is being conducted at the center. Nor does it in any way align with my observations as it relates to the handling and treatment of animals at the center.”

Even back then I challenged Micheal Moss’ statement that “the center has one overarching mission: helping producers of beef, pork and lamb turn a higher profit” It is unclear where that demonstrably incorrect statement originated. Moss’ personal opinion perhaps. MARC’s publicly-available mission statement is to develop “scientific information and new technology to solve high priority problems for the U.S. beef, sheep, and swine industries.” Even the article itself then goes on to state that since MARC was founded 50 years ago, it “has fought the spread of disease, fostered food safety, and helped American ranchers compete in a global marketplace.”

However it was the allegations of the death raping of the teenage cow and experimental surgery being undertaken by untrained, unskilled and unsupervised staff that really stuck in my mind. I was therefore glad when the USDA Office of the Inspector General (OIG) announced it was going to investigate and audit the allegations made in the New York Times article. Specifically they stated they were going to investigate “33 statements from the article to evaluate and attempt to determine their veracity”.

I watched with interest as the interim report came out in 2015 to see which 33 statements were going to be investigated, and was satisfied to see that the two most egregious statements about the teenage cow (Statement 14), and that untrained staff performing experimental surgery (Statement 15) were going to be thoroughly investigated. At the time the interim report was released in September 2015, it stated with specific reference to these two statements, “We have no observations on this statement at the current time.”

So imagine my surprise when the OIG final report was released Friday December 16, 2016 and I was none the wiser. The OIG report stated that of the 33 statements made by the New York Times, “we determined that only 7 were materially accurate — 26 were inaccurate, lacked sufficient context or were uncorroborated”. New York Times that is a 21% material accuracy rate – also known as an F in my classes. The OIG report further clarified that “Overall, we did not note evidence indicating a systemic problem with animal welfare at US MARC”

Wait – death raping of a teenage cow and experimental surgery being undertaken by unskilled staff – is that not the definition of an animal welfare problem? So I looked to see what the report specifically said about Statement 14 and 15. It said nothing. Because the entire text was redacted. Both the statements and the findings – blacked out. Even the statement text that was in the interim report was inexplicably redacted.

So of the 26 statements in the New York Times article that were determined to be “inaccurate, lacked sufficient context or were uncorroborated” which was which? How many were inaccurate? There is a HUGE difference between inaccurate (i.e. fake news), and lacking sufficient context. And hopefully any journalist worth their salt would corroborate statements from a disgruntled employee and an executive director of a Humane Society in an article about animal welfare at an animal research facility with at least one independent source. Isn’t that how journalism works? Only two of the statements were listed as inaccurate in the OIG report, but the OIG conclusions on several others was bizarrely redacted. So your guess is as good as mine.

In its 12/20/2016 article about the report “U.S. Animal Research Center Needs More Oversight, Audit Says”, the New York Times explained that “The Times did not answer questions from the auditors, telling the inspector general’s office that the article spoke for itself.” Actually it didn’t, that is why there was an OIG investigation and audit which found only about one in five statements were correct. Nary a mention of that failing grade in material accuracy.

And in perhaps the ultimate piece of irony, the OIG report concluded that US MARC “could make its research more transparent to the public”. I might say the same to the OIG in its report! What are the privacy concerns that required the redaction of a simple conclusion of either materially accurate, inaccurate, lacked sufficient context or uncorroborated? Those sensational allegations and emotive images are out there now – right or wrong – unchallenged.

At the end of the day we will never know if the bull libido test heifer incident ever happened, or if untrained, staff performed experimental surgeries. All we have is OIG report conclusion that they “did not note evidence indicating a systemic problem with animal welfare at US MARC.” The OIG investigators said the Pulitzer Prize-winning reporter Michael Moss did not agree to be interviewed for their audit of the veracity of his article’s statements.

Rather than being shamed by his failing grade, in a recent email Moss doubled down his assertion that US MARC pushes the biology of livestock for profit, a statement that was graded plain “incorrect” in the OIG report. Repeating something does not make it true. Once again the facts are that US MARC develops “scientific information and new technology to solve high priority problems for the U.S. beef, sheep, and swine industries.”

But as has been evidenced repeatedly in recent months perception soon becomes reality and the truth gets left in the dust. And policy based on perception ensues which seems to have been the article’s original objective. Facts be damned.

This blog post was also posted in Science 2.0

The following is an excerpt of a presentation I gave to the California Academy of Nutrition and Dietetics Annual Conference and Exhibition 2016 in Riverside on April 21, 2016. The full paper which goes into MUCH greater detail and includes more scientific references is available on their conference website. Seemed an appropriate topic for my blog given Earth Day is tomorrow.

What is the “best” source of sustainable animal protein? There is no easy answer to that question. It all depends upon what sustainable means to you, and which metric(s) of sustainability you want to guide your decisions. Definitions of sustainability generally have to do with living within the limits of, and understanding the interconnections among, the three pillars of sustainability: economic, environmental and social. People put varying emphasis on these different pillars. Consider this graphic below – which is the sustainable system (1)? There is no one correct answer since it will depend upon the weighting you put on the various competing pillars of sustainability. There are pros and cons to each of the various scenarios.

Which system is sustainable (1)?

These tradeoffs occur more generally in all of our food choices. For example, some people swear by grass fed beef – but based on a carbon footprint per unit of protein perspective, it is much less efficient and therefore has a bigger carbon footprint per kg beef than intensively raised beef (2). Others advocate obtaining protein from nuts, but from a water footprint per unit of protein perspective they are more water intensive than all animal products (3). Others swear by wild-caught fish, but from a carbon footprint perspective, animal products from this source are very energy intensive if they involve bottom trawling and longline fishing (4). And let’s not even get into the issue of air miles which can make even the innocuous asparagus appear to be public enemy number one (5) based on CO₂-equvalents per unit weight of food product as illustrated in the graphic below.

Carbon emissions (CO2-equivalent/kg) for fruits and vegetables on a weight basis (5).

The sustainability question becomes even more complicated when considering the requirements for a nutritionally-balanced diet. Although it may seem like switching to a diet with less red meat and more fruits, fish and milk should be desirable from an environmental perspective, it may actually exacerbate climate change due to the relatively high energy and water use per calorie of these food products. A recent research paper (4) compared 3 different scenarios: 1) a reduced calorie diet (-300 calories/day) with the same mix of food as the average US diet; 2) the USDA-recommended food mix without reducing the total calories of an average diet; 3) reducing calories AND shifting to the USDA-recommended food mix. The first option resulted in a desirable 10% reduction in energy use, water use and emissions. The second scenario increased energy use (43%), water use (16%), and emissions (11%). Even when reducing calories on the USDA-recommended diet, the scenario 3 diet resulted in a significant increase in energy (38%), water use (10%), and emissions (6%) compared with the current status quo.

Why are the “costs” of these scenarios so different? Because fruit, fish, and dairy – as emphasized in the USDA guidelines – are foods that on a per calorie basis require the most energy and water to grow.

Input/emissions per calorie from some common US dietary items on calorie basis (6).

In contrast, added sugars, fats, oils, and grains require fewer resources and create fewer emissions per calorie. So although these might be the most environmentally-friendly sources of calories, they are not likely to be the ones that are recommended for consumption in large quantities as part of a healthy diet. If you totally forget health and consume a diet that would have the least impact on the environment, you would eat a lot more fats and sugars. Additionally, grains are also an excellent source of calories despite the fact they tend to be vilified in US dietary culture.

The bottom line is that food is more than calories and protein, and the dietary mix of foods and their availability will determine the best balance for a healthy diet. Adding in sustainability metrics complicates the discussion, and often conflicting results will be generated depending upon which metric is being optimized. Sometimes the most environmentally friendly diet might be the least healthy option. As with all discussions around sustainability, and agricultural production systems in general (organic, conventional, genetically engineered etc.), it is complicated and there are tradeoffs. Beware of anyone who touts a seemingly magic solution. There will never be black and white answers to the questions of which foods are the most sustainable, other than perhaps just eating less of whatever you are currently eating. Although this is a privileged first-world perspective, as evidenced by the approximately 25,000 people who die of malnutrition or starvation daily. As the saying goes, “A well-fed man (perhaps we could substitute society in here) has many problems (and food choices!), a starving man has but one.”

SUMMARY

There is no one sustainable source of protein, and depending upon the question that is being asked (e.g. carbon emissions/water use/land use/energy use per calorie/unit weight/unit protein), different food products will look like the “most sustainable” choice. There are also ethical and religious concerns around animal welfare and/or consuming meat and/or animal products (e.g. eggs, milk). Often there are direct conflicts between what is perceived as the most sustainable production system. Is it the one that best protects animal health/welfare, the one with the lowest environmental footprint per unit of product, or the most efficient? As with all dietary decisions there are tradeoffs among the various pillars of sustainability, and consumers will need to make the choices they consider to be best for their particular family values, budget, and circumstances.

REFERENCES

1. Stern S, Sonesson U, Gunnarsson S, et al. 2005. Sustainable development of food production: a case study on scenarios for pig production. Ambio 34:402-407.
2. Nijdam D, Rood T, Westhoek H. 2012. The price of protein: Review of land use and carbon footprints from life cycle assessments of animal food products and their substitutes. Food Policy 37:760-770.
3. Mekonnen MM, Hoekstra AY. 2012. A Global Assessment of the Water Footprint of Farm Animal Products. Ecosystems 15:401-415
4. Tom MS, Fischbeck PS, Hendrickson CT. 2015. Energy use, blue water footprint, and greenhouse gas emissions for current food consumption patterns and dietary recommendations in the US. Environment Systems and Decisions 2015:1-12.
5. Heller, M. C. and Keoleian, G. A. 2015. Greenhouse Gas Emission Estimates of U.S. Dietary Choices and Food Loss. Journal of Industrial Ecology, 19: 391–401. doi: 10.1111/jiec.12174

A couple of years ago a science communication paper came out suggesting public trust differs depending upon the perceived warmth and competence of different professional groups.

As can be seen in the graphic below from that paper by Susan T. Fiske and Cydney Dupree (PNAS 2014;111:13593-13597) that was good news for nurses and teachers, and not such great news for lawyers who are seen as competent but not trustworthy. But lawyers are not typically trying to communicate science and so perhaps this lack of trust is not a deal breaker for them.

Warmth–competence ratings of commonly mentioned jobs.

Scientists fared less well than professors, although I am not 100% sure what the difference is between a scientist and a professor. I assume that professors are seen to be those teaching at universities, whereas scientists might include those presumably nefarious industry scientists.

But for scientists interested in scientific communication the take home message of the paper was to attempt to be “warmer”, and show concern for humanity and the environment. As someone who entered agricultural science because of my interest in how genetics can be used to simultaneously increase food production and minimize the environmental footprint of agriculture, those concerns for humanity and the environment are actually the cornerstone of my profession.

However it was another finding of the study that has been rattling around in the back of my brain.

And that finding was that in particular, “Americans seem wary of researchers seeking grant funding”. Think about that. As a public sector scientist who mentors several graduate students in my laboratory, I would perhaps be more wary of scientists who were not seeking grant funding because how else can you pay for research supplies and expenses? That made me think there is a fundamental disconnect between how science is actually funded, and the public perception of how science is funded.

In my own case, I receive a salary from the University of California, an office on the Davis camps, and the holy grail of space, a wet laboratory. The rest of it is up to me. If I want to do research, I have to “seek grant funding”. And as a molecular geneticist working with large animals who need feed and care, this is expensive research.

Perhaps one of the biggest expenses, and undoubtedly the most satisfying part of research, is funding those pesky graduate students who actually do the work. And they do not come cheap. I looked at a recent USDA grant I was awarded and the approximate annual cost of a graduate student is in the ball park of $40K a year in direct costs for fees and living stipend. Apparently students need both an apartment to live in and food to eat.

And with University overhead, which for this grant was 30% of total costs, this brings the annual cost up to around $52,000 a year – so for a 2 years Masters student I have to seek grant funding for $100,000. That is about the approximate cost of new Maserati. And funds for a PhD, which is typically 5 years, is a whopping quarter of a million dollars! And that does not actually pay for any experimental reagents or animal care fees, just brains and boots on the ground.

Therefore if we want graduate students to be trained at public universities their professors need to seek grant funding. I have been fortunate to obtain public funding for my research program, all of which can be freely accessed at my university webpage.

Public research funding programs are highly competitive. In 2014, the last year for which I could find data , at the USDA National Institute of Food and Agriculture’s  flagship competitive grants program, the Agriculture and Food Research Initiative (AFRI), “the success rate in FY 2014, calculated in terms of number of proposals funded (excluding conferences, supplements, continuing increments of the same grant, and NIFA Fellowships) divided by the number of proposals submitted for review, was 11 percent”. That roughly means that for every 100 proposals submitted, 11 got funded.

Imagine spending 90% of your time putting words to paper that no else will read, with the exception of a single grant review panel. Or writing a paper that only has a 1 in 10 chance of being accepted by a peer-reviewed journal. And yet scientists seeking public research funding spend a lot of their time writing grants that never are funded.

Things are a little better for medical research. in 2014 the National Institutes of Health (NIH) received 51,073 research project grant (RPG) applications, out of which they funded 9,241, resulting in a success rate of 18.1 percent.

So make whatever judgment you may about the trustworthiness and perceived warmth of scientists and professors. But please understand that researchers seeking grant funding, especially public grant funding, is not a reason to be suspicious. It is actually a sign of an active scientist who is likely trying to fund graduate students, reagents and experimental supplies to enable them to undertake research in their chosen field of interest.

If the public is wary and untrusting of scientists who seek research funding, we have a real scientific communication problem. Those are most likely public sector scientists trying to secure funding to enable them to support, mentor and train the next generation of scientists.

Cattle grazing in Northern California

Over the past two weeks I have been speaking to livestock producers at locations from Bakersfield in Southern California to Montague on the Oregon border. I was a speaker at a number of “Winter Animal Health” meetings which are organized annually by the University of California Cooperative Extension.

As a geneticist, I was speaking about genetics and how to make better bull selection decisions. Not surprisingly (to all but a geneticist) genetics was only one of several topics covered, and many of the subjects were unrelated to my area of expertise.

Being located on the Davis campus, I relish the opportunity that extension meetings afford me to get out among actual producers and listen to their experiences, concerns and problems. And what really struck me about this series of meetings is that everything is trying to eat our lunch!

What I mean by that is that pests from all kingdoms – microbial, plant and animal – are competing for the resources used by the plants and animals that we eat, or are beating us to the punch by actually eating those same things for themselves!

The traditional definition of a pest is an epidemic disease associated with high mortality; specifically the plague or “pestilence”. It is also defined as something resembling a pest in destructiveness; especially a plant or animal detrimental to humans or human concerns (as in agriculture or livestock production).

The pests that were covered by this series of meetings included the traditional viruses and bacteria that result in animal diseases, weeds that compete with pasture and crops for scarce water and nutrients, a wide-ranging list of insects like ticks and mosquitos that carry disease, ground squirrels that eat vegetation and construct leg-breaking holes and destructive mounds in the middle of fields, wild deer that graze crops, pastures and even watermelons, and wild horses that compete for precious resources on the drought-stricken range.

Listening to the plethora of animal and plant pests discussed at these meetings, it is impressive that the producers are able to preserve any of their product to market for human consumers.

Control measures to address pests were as varied as the pests, and indeed the producers, themselves. Depending upon the production system requirements of their target market, producers are using a variety of chemical, physical, and  temporal pest management approaches.

One thing is constant – all production system face pests. Some pests are common to all – like threat of animal disease and weeds – whereas others are crop and/or species specific.

Google image search for “ideal farm”

Often images of agriculture show a utopian red barn in a green field, and rarely is there even a single pest present in the image. The animals are all healthy, the fields are all weed-free, and there is not a single ground squirrel, tick or other scourge in sight.

Skillful management can help approach that ideal through the judicious use of preventative measures like vaccines to forestall disease, and ploughing or tilling to manage undesired weeds. But in the open outdoor environment of agriculture it is hard to avoid airborne weed seeds, disease-causing microbes and insects, and grazing competition from wild herbivores. And then there are the predators that prey on the livestock themselves.

Failure to correctly or effectively manage pests can result in complete crop failure (i.e. no food), or catastrophic health outcomes for livestock. It has been estimated that without pesticides 70% of the world food crop would be lost and even with pesticide use, 42% is destroyed by insects and fungal damage. Dispensing with pesticides would require at least 90% more cropland to maintain present yields.

The producers present at these meetings spanned the range from backyard hobby farmers, to part-time ranchers with  day jobs in the city, to fulltime commercial family farmers and ranchers. They represented a range of farming systems, including some that prohibited the use of certain pest management methods such as certain herbicides, antibiotics, or selected insecticides.

What was  refreshing to me was that the different control methods and integrated pest management approaches were presented objectively, and the producers listened with respectful interest, rather than judgment, as to how their neighbors were managing their pest problems.

There were no black and white choices or magic silver bullets provided by the various speakers. Different approaches were presented along with their nuanced pros and cons; benefits and tradeoffs were discussed fairly and without prejudice in comparison among the different choices that are available.

In my 20 year experience working with farmers and ranchers, this set of meetings was not atypical. Extension has long presented objective information on solutions to agricultural problems through informal educational meetings.

I just wish more urban people could hear these discussions and see the level of technical competence, professionalism and thought that producers put into their production and pest management decisions, and appreciate the fact that at the end of the day some food remains for their dinner and dessert plates. Including this impressive spread of homemade pies on offer at the conclusion of the Montague cattle health meeting, aka “Pie Night” for obvious reasons. One of the lesser known and most enjoyable perks of an extension meeting in Northern California ! With thanks to Siskiyou County Cattlemen and Cattlewomen!

Home made pies at the 2016 Montague Cattle Health Meeting

The following abstract entitled “Twenty years of TARC: Time to Accelerate Real Change” appears in the February 2016 issue of Transgenic Research  Volume 25, Issue 1, pp 101-122

(Note: Since the 10th Biennial Transgenic Animal Research Conference (TARC X) conference was held in August 2015, the AquAdvantage salmon was technically approved by the FDA in November 2015, although currently it can still not be sold in the United States as explained here.)

The first transgenic animal research conference (TARC I) was held in 1997 and the proceedings were summarized in a book optimistically titled, “Transgenic Animals in Agriculture”. The book contains some interesting quotes, including one attributed to Dr. Robert Wall, USDA-ARS in Beltsville, Maryland, who quipped, “the field of transgenic large animals is one of the few fields where there are more review papers than data papers.”

It is perhaps a useful exercise at this TARC X conference to go back to some of those original papers and see what progress we have made over the past 18 years. At the time it was posited that there were three major limitations to wide-scale application of transgenic technology to improve farm animals: 1) lack of knowledge concerning the genetic basis of factors limiting production traits, 2) identification of tissue and developmentally-specific regulatory sequences for use in developing gene constructs, expression vectors and in gene targeting, and 3) establishment of novel methods to increase the efficiency of transgenic animal production. Considerable progress has been made in all three of these areas in the past 2 decades.

Despite the hopeful projection offered by Dr. George Seidel of the Animal Reproduction and Biotechnology Laboratory at Colorado State University, “At this point in evolution, human society places great emphasis on applications of science and technology. Since use of transgenic technology in farm animals, almost by definition, is an application, this will be viewed favorably by both public and private funding sources”, limited progress has been made in the commercialization of transgenic animals.

Pharmaceutical proteins ATryn® and Ruconest®, produced in transgenic goats and rabbits, respectively, have been approved in both the European Union and the United States. Several varieties of fluorescent transgenic aquarium fish are being marketed throughout the United States as GloFish®, and open field trials of genetically engineered male insects produced by Oxitec have been carried out in several countries to reduce the population numbers for disease-spreading pests. However, no transgenic animal has yet been approved for food purposes anywhere in the world, despite an ongoing long-term attempt by AquaBounty to obtain a U.S. regulatory decision for their fast-growing Atlantic salmon.

Fluorescent Genetically Engineered Aquarium Fish (Glofish)

The lack of progress on agricultural applications can be attributed to a scarcity of both public and private funding sources, and the absence of a clear path to market. Starting in the mid-2000s, the annual USDA request for grant applications included the following ominous text, “Applications whose primary aim is to improve the efficiency in the production of clones or transgenic animals through manipulation of the nucleus will no longer be accepted by the Animal Genome program”. This directive continued for almost a decade. There has likewise been little private sector interest in taking transgenic food animals, such as the phytase-expressing Enviropig™, through an expensive and unpredictable regulatory process. In the absence of any approved food animal applications, there has been little support or market pull for transgenic animals from the livestock breeding sector.

As a scientific community, we have continued to make progress in transgenic animal research methods, funded mostly by granting sources interested in the biomedical application of transgenic animals, and also the USDA Biotechnology Risk Assessment Grant (BRAG) program. This program has funded research to test some nontraditional hypotheses to provide rigorous scientific data for risk assessments.

Dr. Matthew Wheeler, University of Illinois, answered the question of whether transgenes can be transferred directly from transgenic pigs to control swine by physical association or contact, by mating, or from a transgenic dam to her non-transgenic offspring during lactation. Spoiler alert # 1: The data showed no transfer.

In another project, Dr. Elizabeth Maga, University of California, Davis (UCD) answered the question of whether transgenic goats expressing lysozyme in their milk behave differently to control goats. Spoiler alert # 2: The data showed no difference.

In the first chapter of “Transgenic Animals in Agriculture”, Dr. Jim Murray, UCD wrote, “Our role as scientists, consumers, and regulators is, in part, to decide at what level or stages and to what degree the development of agriculturally important transgenic animals must be monitored and regulated to ensure consumer safety and animal well-being, and address societal concerns. A further corollary to this responsibility is to ensure that the consuming public understands the processes to the extent that they can accept government approval of such animals in the food chain.”

I would argue that less progress has been made in this area. In the chapter penned by Dr. Joy Mench, UCD, which focused on the ethics and animal welfare of transgenic farm animals, she warned, “In the past scientists have tended to isolate themselves from these debates. This posture needs to change. Scientists need to become full and fully informed participants in the debate about the ethical effects of the technologies that their work is instrumental in developing. Otherwise, consumer confidence in science and scientists may well be lost.”

Is it finally time for the transgenic animal scientific community to take these suggestions to heart and address both the regulatory impasse and the consumer concerns head on? The current recombinant DNA (rDNA) process-based trigger for regulatory evaluation of transgenic animals is disincentivizing the development of beneficial transgenic animal applications. As a community, we need to push for sensible regulatory reform.

Regulatory effort should be proportional to the risks posed by the product. Required regulatory studies should be hypothesis-driven based upon the novel attributes of new varieties in relation to known risks associated with existing varieties, and not on the breeding method used to develop the new variety.

The closing speaker at the 1997 conference, Dr. George Seidel suggested, “One mistake that animal scientists are rightly accused of making is to emphasize production traits when low production is not a problem. More attention needs to be paid to non-production traits such as animal welfare, animal health, consumer acceptance, and so on.” I contend that we now have applications that address these non-production traits and it is time for scientists to more effectively communicate the compelling narratives associated with the potential benefits of these technologies.

It would be ironic if,  as was portended by Joy Mench at TARC I in 1997, “genetic engineering turned out to be the fastest and best solution for some of the welfare problems that we have created using traditional breeding methods like leg problems in broilers.”

Scientific and technological advances in disparate animal breeding research communities over the past two decades are now undergoing a form of scientific convergent evolution. The thousands of SNP markers discovered through livestock sequencing projects, the information obtained from numerous genome wide association studies, the discovery of causative SNP (QTNs), the development of genomic selection statistical methodology to include molecular data in genetic merit estimates, genome editing techniques, and transgenic technologies are all useful individually. But collectively, they offer a powerful approach to accelerate real genetic change in our food animal species to the advantage of food security and agricultural sustainability globally.

I have had a long standing interest in omega-3 fatty acids. Increasing the intake of omega-3 fatty acids has been linked to beneficial health outcomes. Mammals cannot make omega-3 fatty acids, they must obtain them from their diet.

Milking mice

In fact, one of the first research projects I undertook when I started at UC Davis in 2002 was to produce genetically engineered mice (by adding an omega-3 desaturase gene) that could produce their own omega-3 fatty acids in their milk! Yes I have spent time milking mice – they have a lot of teats (10-12) compared to a cow (so this milking mice image is technically incorrect!).

When in 2004 I  wrote a follow on grant to take my preliminary research in mice onto larger animals (i.e. cows), the grant was not funded with the reviewer’s comment being  “Given the “pure and wholesome” public perception of milk products, it may be particularly difficult to gain widespread public acceptance for transgenic milk products – despite their health benefits.”

So began my decade plus of focusing my research on breeding methods other than genetic engineering. However, I still think that if cows could produce their own omega-3 fatty acids that would be a good thing for public health, and perhaps if the public sector had been able to obtain research funding to bring some of these consumer benefit traits to market then public acceptance of transgenic products might be different today.

But back to omega-3s in milk. Because cows cannot produce their own omega-3 fatty acids they must obtain them from their diet. And because cows are ruminants, almost all of the feed they consume is first “digested” by the microbes in their rumen. And bacteria love to derive energy by converting polyunsaturated fatty acids into saturated fatty acids (biohydrogenation).

Hence, ruminant products are relatively high in saturated fatty acids relative to single stomach animals who tend to more faithfully reflect the fatty acid composition of their diet. And one group that eat a lot of omega-3 fatty acids in their diet is oily fish, such as salmon, herring, mackerel, anchovies, menhaden, and sardines.

Like cows, fish do not synthesize omega-3 fatty acids; they obtain them from the plankton in their diets. Fish are a particularly valuable source of the long-chain omega-3 fatty acids (20:5 EPA and 22:6 DHA). Evidence supports a dietary recommendation of ≈ 0.5 g/d of EPA and DHA for cardiovascular disease risk reduction. As a result, the American Heart Association recommends eating fish (particularly fatty fish) at least two times (two servings) per week.

So is milk an important dietary source of omega-3 fatty acids? Not really. Not to criticize milk – it is valuable source of protein, Vitamin D, Riboflavin,  Vitamin B12, Phosphorus and Calcium, and my kids drink a glass of pasteurized milk with every meal.

I am not a trained dietician, but as a Mom I do feed humans nutrients and therefore compare the nutritional content of foods. According to the USDA standard reference database, an eight fluid ounce cup (244 g) of 3.25% fat milk has 0.183 grams of omega-3s, most of it 18:3 (ALA). A half fillet serving (178 g) of salmon has 4.023 grams of omega-3s,  most of it EPA and DHA. In other words I get more than 20 times the omega-3 fatty acids from a serving of salmon that I get from a glass of milk, and they are the long-chain varieties. And if the milk is non-fat or skim the amount goes down to 0.0049 grams of omega-3s, because – well they removed the fat!

Dairy cows on California drought-stricken pasture in Sonoma County in 2014

The omega-3 composition of milk can be influenced by the cow’s diet – if cows eat a diet high in omega-3 fatty acids, then a small fraction of them “bypass” biohydrogenation by the rumen microbes, and so make it to the true stomach. So feeding cows lush omega-3 rich green grass, rather than the drought-stricken pastures that have been on offer here in California for the past 4 years, is associated with a slight increase in omega-3 fatty acids. The high content of polyunsaturated fatty acids (especially ALA) in grasses at early stage of maturity is the main reason for the positive effects of pasture on the fatty acid composition of milk.

I should mention my husband (of 26 years as of today – Happy Anniversary!)  is also a researcher at UC Davis, and he works in aquaculture. So we have had a surf and turf rivalry going on for more than a quarter century in our house. I think we only survived together so long because we recognize that different foods – four legs, two legs, no legs – all have their pros and cons! And little of each in moderation seems to be a recipe that my whole family can live with.

Should I start a blog? I have been thinking about this question for a while. I certainly have plenty of other things to keep me occupied – students, grants, research, presentations to prepare, reports to write, oh and my own kids and husband (Happy Valentine’s day BTW) and family duties.

What really spurred me to actually bite the bullet and start a site was a couple of recent interactions with work colleagues. One was an email asking me if I had ever interacted with a particular journalist. The question was whether this journalist had a history of misrepresenting the science around animal breeding methods. The default assumption seemed to be that it was most likely that the scientifically-accurate information that was being freely given by this public sector scientist to the journalist would be spun to misrepresent what the scientist said or distort the facts.

And then there was a discussion with some faculty members in my department about correcting some misinformation regarding the consumption of animal products. There was a collective sigh that yes the information was incorrect, but was it worth our while to challenge it? Such things take time and energy, and often such challenges fall of deaf ears. And everyone has plenty of other pressing work to do with their own students, teaching, research etc. to more than occupy the day.

So who then is left to stand up for science, especially around agriculture, and speak out to challenge incorrect information which is often used as the basis of public policy? If not public sector scientists and researchers working in the field, then who? Unfortunately I think we all know the answer to that question.

I know as a researcher working in the field of animal biotechnology (my current research projects are listed on my faculty website – and are publicly funded), I deal with controversial topics. My interest is to use this blog to try to interject scientific nuance into these controversial and often politicized scientific topics.

Science is rarely black and white, and agriculture never is. I know you should never say never, but in this case I think never is warranted. I also remember thinking to myself  I would never write a blog. That is the beauty of science – you are allowed to change your mind based on new information.