Thursday, February 23, 2017

Comments on Rules for Gene-Editing Technology

From the literature:

“We found that the improvement of a plant variety through the acquisition of a new desired trait, using either mutagenesis or transgenesis, may cause stress and thus lead to an altered expression of untargeted genes. In all of the cases studied, the observed alteration was more extensive in mutagenized than in transgenic plants” - (Batista, et al; 2008)

So what are the implications of this? Currently the FDA is accepting public comments related to genome editing in new plant varieties used for foods. https://www.regulations.gov/document?D=FDA-2016-N-4389-0001

Gene editing represents an opportunity to move forward with advanced technologies to sustainably feed the planet without the same regulatory hurdles that make development costs for transgenic plant varieties (aka GMO) up to 20x greater than conventionally bred plants(Conko and Miller, 2003). Similar to organically certified crop varieties that use chemical and radiological methods to create in-genome changes, gene edited technologies operate within genome, vs. across species.  (one popular example of gene editing includes the CRISPR-Cas9 system).  Unlike mutagenic approaches used in organically approved plant breeding systems,  these in-genome tweaks are planned, controlled, and designed to bring about very specific outcomes. Gene edited plants are not ‘gmo’ in the manner that the term has traditionally been used (or misused) by regulatory proponents, and in fact are just as natural as their organically approved counterparts in terms of their development. However they stand out in very important and positive ways.

The article above does not specifically address gene edited plants, while it does indicate that genomic disruptions (which are what we should be concerned about regulating if we are concerned at all) are greater in mutagenic plants vs standard transgenic plants. With greater disruptions, one might favor increased regulatory scrutiny over the existing framework in place for transgenics. However, we do not have a framework in place for mutagenically improved crop varieties that have been safely used for decades and approved by the organic food industry as well as consumers.  Because both mutagenic and gene edited technologies represent similar in-genome approaches to crop improvement, this in fact argues against additional regulation for both mutagenic and gene edited plants, or it begs for the possibility of a revision of the existing regulatory framework for transgenics.

The benefits of gene editing technology are far greater than either conventional and organic mutagenically improved or even traditional ‘GMO’ or transgenic crops while the risks to human health and the environment are equally minimal. To impose new costly regulations on gene-edited plants would be to create huge hurdles for the development of next generation green technologies in food and fiber production in the United States and have significant environmental, public, and personal health implications for the rest of the world.

References:

Batista R, Saibo N, Lourenço T, Oliveira MM. Microarray analyses reveal that
plant mutagenesis may induce more transcriptomic changes than transgene
insertion. Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3640-5. doi:
10.1073/pnas.0707881105. PubMed PMID: 18303117; PubMed Central PMCID: PMC2265136



Henry Miller and Gregory Conko. Bootleggers and Biotechs. Regulation. Summer 2003

Convergence of Big Data and Genomics (from WillAg closing market report)

Last week there was an interesting interview on the closing market report with Robb Fraley, Chief Technology Officer at Monsanto. The discussion related to possible future spending on R&D related to the potential merger with Bayer. Some interesting comparisons were made between R&D spending by Monsanto vs other research intensive industries like Samsung and Apple and pharma.  The takeaway is that the combined company would have more resources to invest, and based on what is spent on R&D in other sectors there is a lot of untapped opportunity here that the combined companies could take advantage of.

I would love to know how much is spent on regulatory compliance given the extreme overkill in this area related to biotech making transgenic varieties cost as much as 20X more to develop vs conventional technologies. I'd like to know direct costs and indirect compliance costs in terms of lost revenue due to delays in approvals etc. One would wonder how much better these companies could serve the industry if those resources could be re-allocated to more productive R&D?

But to me the interesting question related to what kind of people are they looking to hire going forward? The answer included people working in or studying data science, engineers, mathematicians, statisticians. This is not a surprise to anyone following the industry, but its indicative of the kind of company that Monsanto has transformed and is transforming into. The phrase that stuck with me most was "breeding gene by gene and farming plant by plant".

The future direction, merger or not, is the integration of agronomy, bioechemistry, molecular biology, and data science to develop new products, solutions, and services that serve producers, consumers, and the planet as a whole. This is what I have written about before in terms of the convergence of big ag, genomics, and big data.

And this means more choices and opportunities going forward:

"the disruptions of new technology, big data and genomics (applications like FieldScripts, ACRES, MyJohnDeere or the new concept Kinze planters that switch hybrids on the go etc.) will require the market to continue to offer a range of choices in seeds and genetics to tailor to each producer's circumstances of time and place. There are numerous margins that growers look at when optimizing their seed choices and it will require a number of firms and seed choices to meet these needs as the industry's focus moves from the farm and field level to the data gathered by the row foot with each pass over the field." - From Big Data + Genomics ≠ Your Grandparent's Monoculture

References:

http://will.illinois.edu/closingmarketreport/program/feb-16-closing-market-report

Henry Miller and Gregory Conko. 'Bootleggers and Biotechs.' Regulation. Summer 2003 

Tuesday, February 21, 2017

The Biotech Story: As told in the scientific literature

Has biotechnology lived up to its promises? What were the ‘promises’ of biotechnology? Does genetic engineering present food safety risks greater than conventional plant breeding methods? These are controversial questions. There is one version of the story that indicates that biotechnology has not lived up to so called promises expressed by critics and creates risks to the environment and consumers. However the story that we find in the scientific literature tells us that biotechnology in crop production and applications in the livestock industry is just as safe or safer than traditional technologies, promotes biodiversity, reduces the levels and toxicity of herbicides and pesticides used in row crop production, improves food safety, and reduces our carbon footprint. This annotated review of key scientific papers from sources including The Proceedings of the National Academy of Sciences, Science, Nature Biotechnology, Crop Science, Ecological Economics, and others tells this story.
 
Matt Bogard. "The biotech story: as told in the scientific literature" (2017)
Available at: http://works.bepress.com/matt_bogard/35/ 

See also: Modern Sustainable Agriculture (video)

Tuesday, February 07, 2017

The progressive way to deny climate change

Julie Kelly makes an interesting point with this question:

"who are the real deniers: those who are reasonably skeptical about climate change or those who give lots of lip service to it while living a lifestyle totally inimical to every tenet of the climate change creed?"

A different but related argument is given by Steve Horwitz:

“It is perfectly possible to accept the science of global warming but reject the policies most often put forward to combat it.  One can think humans are causing the planet to warm but logically and humanely conclude that we should do nothing about it. In fact, those who think they can go directly from science to policy are, as it turns out, engaged in denial” 

This is not that different from what I have argued before. To me this is the fundamental problem of climate change:

Without being able to accurately predict future damages, or discount them to evaluate them in today's dollars, it's hard to value future climate related gains that today's sacrifices (driving less or smaller or hybrid cars, switching from coal fired electricity to natural gas or solar, changing our diet or other lifestyle changes, lost income or returns from capital investment etc.) will buy. In other words it's hard to know to what extent it makes any sense to do anything about climate change.

Bringing these perspectives together, some of the most ardent proponents of doing something about climate change based on 'science' are in denial about real world workable solutions:

Unfortunately, many of the same people so vocal about adopting policies based on the so called science of climate change (taxes, permits, dietary restrictions, regulations etc.) are also many of the same people that would restrict us (via GMO labeling laws, bans, strict limitations on hormone and antibiotic use, demonization of LFTB via derogatory terms like 'pink slime' etc.) from doing the very things that would have the greatest positive impact on our climate and environment. 

So it seems we have some people that want to as Steve says, jump straight from the science to policy and skip over asking the hard questions or making a critical case for it. At the same time they are they are ignoring real world workable solutions, which are in fact based on solid science, if not actually trying to block them. For progressives of this flavor its not about science, its about invoking the name and prestige of science to override other people's choices while being in denial about rigorous evidence to support their position.

See also:
Doing Nothing: A science based policy prescription for climate change
Facts, Alternative Facts, Evidence, and Marching for Science 
Science + Economics = Sound Policy



Saturday, January 28, 2017

Facts, Alternative Facts, Evidence, and Marching for Science

From:

Scientists planning their own march in Washington (CNN Politics)

http://www.cnn.com/2017/01/25/politics/scientists-march-dc-trnd/index.html

"There are certain things that we accept as facts with no alternatives," according to the site. "The Earth is becoming warmer due to human action. The diversity of life arose by evolution. ... An American government that ignores science to pursue ideological agendas endangers the world."

While I could not agree more with this, one thing that concerns me especially since this last election is the extreme emphasis given to isolated facts vs critical thinking and evidence.  Ideological agendas thrive on isolated facts. The real danger as economist Thomas Sowell points out in some of his writings is when an American government invokes the name and prestige of science to override other people's choices.

Take for example the following "facts" we often hear from activists in the agriculture space.:

1)  Over the last two decades we have seen increased plantings of "GMO" crops resistant to roundup as well as weeds resistant to roundup herbicide. 

2) GMOs have lead to increased use of chemicals in agriculture and that increases risks to health and the environment.

3) Industrial scale farms get subsidies from government to grow mostly monocrops of corn and soybeans which are primary ingredients going into cheap unhealthy foods at the same time we are seeing an obesity epidemic

 And this fact from the article above:

4) The Earth is becoming warmer due to human action.

One could take these "facts" and then lobby for policies to address all of these concerns including increased regulation, carbon taxes, changing farm subsidies, labeling laws, or taxing foods. In every case we are pushing an agenda to override the choices of millions in the name of science, based on "facts".  But there is a big difference between facts and evidence that supports one policy or another. When we consider each of these facts in the proper context, when we begin to think critically instead of ideologically, science based policy becomes something different.  For instance, we know that roundup (or glyphosate) has largely replaced other chemicals much more toxic and persistent in the environment (USDA, 2000). We also know that monoculture and its implications for genetic diversity and sustainability  are quite different than what popular stigmas imply. And finally, the links between farm subsidies, commodity crops and obesity are very very frail when we look at the actual impact these policies have on food prices or even the potential for things like soda taxes. But what about climate change?  If we are going to make progress here we have to accept that it does not make one a climate change denier to understand that our response to climate change also has to be based on facts and evidence held to the same level of rigor and scrutiny as the science supporting its existence.

 Economics teaches us that the world is complicated. There are numerous facts and details to consider when trying to solve a problem. While it is certainly bad for governments to deny the truthfulness of established facts based on sound science, we must also understand how to make sense of them. Economics provides a theory for deciding which facts are central and which are periphreal.* To quote Paul Heyne, Boettke, and David Prychiko in their text the economic way of thinking (10th ed) "we can observe facts but it takes a theory to explain causes. It takes theory to weed out the irrelevant facts from the relevant ones".

As I stated before economics can put science, good or bad, into a context relevant to the things we really care about.

So while I support a march for science and appreciate the driving concerns around politicians efforts to muzzle science, at the end of the day lets emphasize critical thinking and sound theory over isolated facts and talking points. While the "facts" stated in the article may have no alternatives, there are numerous alternatives with regard to the policies so called purveyors of truth may have in mind to address them. These policies imply numerous margins and tradeoffs to be considered. Only critical thinking, evidence, and sound theory can help us find the best path among many for addressing these issues. Economics provides mathematically precise theories and empirically sound methods that together provide a rigorous policy analysis framework for addressing these problems. 

Isolated facts grounded in the truth of science but devoid of critical thinking about causal relationships and policy tradeoffs can be just as dangerous and little better than alternative facts that deny the truth of science.

It's probably also true that the truth of science can risk losing ground to alternative facts if not properly communicated. We know this when it comes to alternative facts about biotechnology that currently drive the snake oil marketing practices of many food companies and lobbying for related policies.

From what I can tell the March for Science is nonpartisan and its more about freedom of speech and science communication than taking a stance on one policy vs another, so I don't think they are attempting to recruit activists for one policy vs another. But the march for science could present an awesome opportunity for science communication about many of the issues in agriculture related to biotechnology, genomics, technology, and modern production practices that so often come under the radar of activists, politicians, and the media. Or, at least the chance to segway into conversation.


See also:

Diversity in Agricultural Production

Modern Sustainable Agriculture -  Video with Annotated Bibliography

Genetically Engineered Crops: Has Adoption Reduced Pesticide Use? Agricultural Outlook ERS/USDA Aug 2000

*taken from Alan Stockman, Introduction to Marcoeconomics. 2nd Edition.

Left vs Right vs Propensity to Regulate http://ageconomist.blogspot.com/2016/06/left-vs-right-science-vs-risk-vs.html

Fat Tails, the Precautionary Principle and GMOS http://ageconomist.blogspot.com/2015/01/fat-tails-precautionary-principle-and.html

Saturday, August 20, 2016

GMOs and QR Codes: Consumers need more than a label they need a learning path

I recently came across an article in national geographic about the new GMO labeling compromise that I thought was well written:

http://www.nationalgeographic.com/people-and-culture/food/the-plate/2016/07/gmo-label/  

The article asks:

"But what good is a label if people don't know what it means?"

That's the point...a blatant politically charged label with direct language or terms like "genetically engineered" is meaningless. I've discussed before how this can increase information asymmetry (i.e.consumer confusion).

One thing the article discusses in the huge gap in the science related to biotechnology and consumer knowledge and perceptions (something I have been studying since graduate school):

"Despite thousands of scientific studies, support from the World Health Organization, the American Medical Association, and the National Academy of Sciences, and, most recently, the concerted advocacy of 107 concerned Nobel laureates, the bulk of the public remains firmly convinced that GMOs are at best undesirable and at worst, downright dangerous. In other words, to the majority of Americans, a GMO label on a can of corn might as well be a skull-and-crossbones. What we’ve got here is a gaping divide between reputable scientific research and public perception. Unfounded GMO fear-mongering is doing us, as a planet, more harm than good."


There is huge burden on the consumer in terms of understanding complex modern agriculture. Earlier in the article there is some criticism of the currently proposed labeling paradigm:

"The federally approved warning label can consist of a QR (Quick Response) code, accessible by smartphone, or an 800 number that customers can call for information. These alternatives are not immediately helpful, and require time and effort on the part of consumers, many burdened with long grocery lists and fractious toddlers."

But given the huge gap in information I'm not sure there is any label that can be immediately helpful. The last thing we need is a shortcut label with confusing language like "genetically modified" that information economizing consumers will just interpret as a skull and cross-bones and move on. That approach is no better. It may in fact be the case that the QR code, if implemented properly may be the best way to attempt to fill that gap. It accomplishes a couple important things:

1) It can provide full disclosure and transparency
2) For consumers that truly want to understand what is in their food, it *can* potentially provide a learning path that helps fill this gap of knowledge from farm to fork

As I understand it, the details around the content and format of information related to QR codes is yet to be decided. I think a few things are necessary to make this work.

First, if this issue is important enough to be addressed FEDERALLY with a national labeling standard, then lets make this work for all food. Maybe require in some format that all foods that fall under this legislation have a "more information" section and a QR code, not just foods that contain so called "genetically engineered" ingredients.  If a label with a QR code becomes a proxy indicator for GMOs, that will defeat the whole purpose of an effort genuinely designed to inform the consumer. After all there are lots of approaches to food production out there- conventional breeding and hybridization, recombinant DNA, mutagenic approaches, and on the horizon CRISPR cas technology (HT: John Phipps).

Second, what should the 'landing page' look like for a QR code? What kind of information should it contain and how should it be presented? This is where the government needs to elicit the help of experts in science and communication. I am not sure, but I propose a learning path. Before saying anything about how a specific food product was produced, the consumer should quickly and effectively be exposed to a summary or survey of the many ways plants and animals are modified in agriculture to produce the foods we have today. (again conentional breeding/selection/hybridization/mutagenic/recombinant/CRISPR cas9/fermentation/cheese cultures etc.). Also they should be informed about the safety, regulations etc. about these technologies and the consensus views of groups like World Health Organization, the American Medical Association, and the National Academy of Sciences etc.

Finally they should be informed about the specifics of the food they are considering to purchase. All of this info can be standardized and used as stock for all food products, with more specific information for each food product detailed at the end of the 'learning path.' Maybe this could all be accomplished with a video or interactive infographic. But I firmly believe that a more comprehensive universal learning path approach like this is the most honest and transparent way to inform consumers about current and new technologies on the horizon and their safety and benefits. Not some politically loaded unscientific term like "genetically engineered" or "genetically modified."

Tuesday, August 16, 2016

An Econometric and Game Theoretic Analysis of Producer and Consumer Preferences Toward Agricultural Biotechnology

It is no secret these days that there are anti-biotech activists that reject the science related to the safety and benefits of biotechnology but yet have no issues accepting the science related to climate change or other fields. In my early days, back in graduate school I hypothesized that beliefs about the safety of biotechnology were more related or driven by political constructs than knowledge or acceptance of science itself. This was crude (I wish I had the floppy with the actual paper...and a drive to read it) but my general findings were that those that believed in climate change or were supportive of stem cell research were less likely (45-50% less using the divide by 4 rule for marginal effects) to believe in the safety of biotech foods. 

Of course this work had some drawbacks, including small sample size and power. But also, after a few years on the job and working on a limited basis with structural equation modeling, there are more powerful methods I could have used looking at these effects. But I think it was an interesting preliminary finding that seems to still hold true almost a decade later.

See also:

Perceptions of GMO Foods: A Hypothetical Application of SEM 

Left vs Right Science vs Risk vs Propensity to Regulate 

Monsantophobia Explained

Reference:

Matt Bogard. "An Econometric and Game Theoretic Analysis of Producer and Consumer Preferences Toward Agricultural Biotechnology" Western Kentucky University (2005)
Available at: http://works.bepress.com/matt_bogard/31/ 

 Abstract:

Agricultural biotechnology offers tremendous benefits to farmers and to society as it provides tools for mitigation of a number of environmental externalities related to water quality, food safety, and climate change. However, perceptions of the safety of recombinant DNA technology on the part of consumers and management decisions by producers can shape the policy environment in ways that may inhibit expanded use of biotech traits in agriculture. This presentation presents a summary of results from an econometric and game theoretic analysis of consumer perceptions and producer decisions as they relate to agricultural biotechnology.

Submitted in partial fulfillment of AGRI 597 Independent Study/Special Problems in Agriculture.





Wednesday, July 06, 2016

CRISPR Technology

A nice article related to CRISPR technology and an application with waxy corn in a recent DTN article:

https://www.dtnpf.com/agriculture/web/ag/news/article/2016/06/17/gene-editing-comes-agriculture 

A very nice description of CRISPR technology:

"The letters CRISPR stand for "clustered regularly interspaced short palindromic repeats," that is, snippets of DNA….They work as part of the bacteria's defense system, in partnership with a group of special, DNA-cutting Cas ("Crispr-associated") proteins and RNA molecules….When viruses invade, the bacterial CRISPR-Cas copies DNA sequences from the virus and saves this information as a short CRISPR repeat -- a sort of molecular mug shot. When that virus invades again, these repeats are remobilized as RNA molecules, which recognize the virus DNA sequence and guide the CRISPR complex to it. There, the Cas protein snips the offending DNA sequence out, disabling the virus."

"Using a specific protein, Cas9, researchers are now using this CRISPR complex to target specific genes in the genome of plants, animals and even humans. The RNA guides the CRISPR complex to the gene sequence in question, and Cas9 cuts it out. Researchers can leave the DNA to heal on its own or they can insert a desired gene in its place."


The article goes on to discuss the regulatory environment and applications related to a new variety of waxy corn in the development pipeline for Pioneer.