Monday, June 19, 2017

Food Facts: Food Insecurity and Food Deserts

According to the USDA, "an estimated 12.7 percent of American households were food insecure at least some time during the year in 2015, meaning they lacked access to enough food for an active, healthy life for all household members."

Here are a few more notes:

1) 5.0 percent of U.S. households (6.3 million households) had very low food security
2) There were sizable differences by state
3)   ~59% used SNAP, WIC, or the national school lunch program in the previous month
4)  The median food-secure household spent 27 percent more for food than the typical food-insecure household

Prices Matter

In a 2013 Applied Economic Perspectives and Policy article, researchers found a significant impact of local food prices on food insecurity developing a novel index of local food prices:

“We find that the average effect of food prices on the probability of food insecurity is positive and significant: a one-standard deviation increase in food prices is associated with increases of 2.7, 2.6, and 3.1 percentage points in household, adult, and child food insecurity, respectively. These marginal effects amount to 5.0%, 5.1%, and 12.4% increases in the prevalence of food insecurity for SNAP households, adults, and children, respectively. These results suggest that indexing SNAP benefits to local food prices could improve the ability of the program to reduce food insecurity and economic hardship more generally in areas with high food prices.”

Food Insecurity, SNAP, and Health Outcomes

In 2012, researchers publishing in the Journal of the American Statistical Association found that SNAP can have positive mitigating effects on the health of children.

"Under stronger but plausible assumptions used to address the selection and classification error problems, we find that commonly cited relationships between SNAP and poor health outcomes provide a misleading picture about the true impacts of the program. Our tightest bounds identify favorable impacts of SNAP on child health."

Gundersen (2015) finds a relationship between food insecurity and health outcomes for children and seniors.

"after confounding risk factors were controlled for, studies found that food-insecure children are at least twice as likely to report being in fair or poor health and at least 1.4 times more likely to have asthma, compared to food-secure children; and food-insecure seniors have limitations in activities of daily living comparable to those of food-secure seniors fourteen years older. The Supplemental Nutrition Assistance Program (SNAP) substantially reduces the prevalence of food insecurity and thus is critical to reducing negative health outcomes"

What we can conclude from this research is that  prices matter - while policies that help reduce or subsidize the purchase price of food can help reduce food insecurity and provide positive outcomes, policies that increase prices could have the opposite effect.

What about food deserts?

Over at the UofI Policy Matters blog, Craig Gundersen and others discuss the relationship between food deserts and prices. They cite a few studies:

Availability And Prices Of Foods Across Stores And Neighborhoods: The Case Of New Haven, Connecticut. Health Aff September 2008 vol. 27 no. 5 1381-1388

The above was a case study looking at stores across lower vs higher income neighborhoods. They find lower quality and fewer options in the lower income stores.

Does Healthy Food Cost More in Poor Neighborhoods? An Analysis of Retail Food Cost and Spatial Competition. Patrick L. Hatzenbuehler, Jeffrey M. Gillespie, and Carol E. O’Neil. Agricultural and Resource Economics Review 41/1 (April 2012) 43–56 

The above was an interesting study that found that the impacts of spatial distribution of store locations impacted consumption, although there were no price effects.

 In their blog post, the authors discuss how they develop a local price index for food bundles and compare prices for areas that are and are not classified as food deserts.

"Our findings suggest that living in a food desert affects the overall food prices faced by households to a small extent when consumers can shop within their home census tracts and in contiguous census tracts. The difference in prices is largely driven by differences in available variety. As such, while higher food prices are associated with higher rates of food insecurity, the results of our work suggest that living in a food desert is unlikely to influence food insecurity to a great extent"

In their related paper, presented at the 2015 Agricultural and Applied Economics Association and Western Agricultural Economics Association annual meeting you can read more.

References:

Alisha Coleman-Jensen, Matthew P. Rabbitt, Christian A. Gregory, and Anita Singh.
Household Food Security in the United States in 2015, ERR-215, U.S. Department of
Agriculture, Economic Research Service, September 2016.

Christian A. Gregory, Alisha Coleman-Jensen; Do High Food Prices Increase Food Insecurity in the United States?. Appl Econ Perspect Policy 2013; 35 (4): 679-707. doi: 10.1093/aepp/ppt024

Kreider, B., Pepper, J. V., Gundersen, C., & Jolliffe, D. (2012). Identifying the effects of SNAP (Food Stamps) on child health outcomes when participation is endogenous and misreported. Journal of the American Statistical Association, 107(499), 958-975. DOI: 10.1080/01621459.2012.682828

Gundersen C, Ziliak J. Food insecurity and health outcomes. Health Affairs 2015;34(11):1830-1839.

Sustainably Feeding the World: Organic Food and Vegetables vs Conventional Commodities

Can we feed the world sustainably using organic crop production methods? Several studies have indicated that there is a yield penalty for organic crops

The crop yield gap between organic and conventional agriculture. Agricultural Systems
Volume 108, April 2012, Pages 1-9

The above indicates ~ 20% yield penalties for organic vs conventional production

Comparing the yields of organic and conventional agriculture. Nature 485,229–232.(10 May 2012) doi:10.1038/nature11069 

The above finds a range of differences in yield between organic and conventional agriculture, from 5-35% depending on different crops, practices, and conditions.

Alexandra N. Kravchenko, Sieglinde S. Snapp, and G. Philip Robertson. Field-scale experiments reveal persistent yield gaps in low-input and organic cropping systems
PNAS 2017 114 (5) 926-931; published ahead of print January 17, 2017, doi:10.1073/pnas.1612311114 


The above indicates much of the previous research was based on research plots, and penalties for organic vs conventional yields could actually be worse when scaled up to field size production practices.

To what extent does organic farming rely on nutrient inflows from conventional farming?
Benjamin Nowak1,2, Thomas Nesme1,2, Christophe David3 and Sylvain Pellerin1,2
Published 5 December 2013  2013 IOP Publishing Ltd
Environmental Research Letters, Volume 8, Number 4 

The above research indicates there are significant inflows of N, P, K from conventional sources. For example, many organic production systems may rely on manure from animals raised or fed conventionally. If these positive exteranalities were excluded, the increased energy and land devoted to organic production would reduce its sustainability further.

 Often in addition to some calling for increased organic food production, you will hear additional criticisms of commodity or 'monocrop' agriculture. Themes include criticisms of agricultural policies favoring 'industrial' agriculture at the expense of healthy fruits and vegetables. However, these criticisms ignore the importance of calorie density and consumption at a global level. According to the FAO rice, corn, and wheat provide 60% of the world's energy intake. Costs of production and economies of scale favor large scale production of these staples over specialty crops like broccoli and tomatoes when it terms of providing affordable calorie dense food to a growing population.

Additional References:

Greenhouse gas mitigation by agricultural intensification Jennifer A. Burneya,Steven J. Davisc, and David B. Lobella.PNAS  June 29, 2010   vol. 107  no. 26  12052-12057

Thursday, June 08, 2017

CRISPR Mediated Off Target Mutations in Mice

In a very recent paper in Nature Methods , researchers used CRISPR technology to repair a gene mutation related to blindness in mice. But what they found was a large number of off target mutations compared to what is typically expected.

An article in The Conversation discusses some of the possible explanations for these findings. Some critics have suggested that the large number of off target mutations could be related to the specific methods used to control the activity of the Cas9 enzyme, which would impact the number of cuts/edits made in the host DNA that occur.

Others have pointed out that there are various flavors of CRISPR, and even temperature can impact enzyme activity and off target impacts, as well as better and worse methods of detection of off target mutations.    

See:
Xiang et al. (2017). Temperature effect on CRISPR-Cas9 mediated genome editing. J. Genetics & Genomics. (Apr 20) 44(4):199-205.

High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529, 490–495 (28 January 2016)

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases Genome Res. 2014. 24: 132-141

When it comes to food crop applications, critics of CRISPR technology, as well as older recombinant DNA technologies have been largely concerned with genetic disruptions. These criticisms imply that genetic disruptions indicate increased risk to consumers. I think a very relevant question in this regard (give or take the Nature Methods paper) is related to the comparative differences in genetic disruptions between CRISPR mediated genetic improvements vs traditional plant breeding methods including mutation breeding (chemical and radiological mutagenesis used in conventional and organic foods).

Given that previous risk management/regulatory reviews and agencies have found little evidence to restrict or highly regulate traditional and mutagenic crop improvement methods, if genetic disruptions for CRISPR mediated crop improvements are comparable the argument for increased scrutiny of CRISPR based crops is weakened. Previous research indicates that genetic disruptions for traditional plant breeding methods are actually greater than what we observe in recombinant DNA methods.

See:
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

Baudo MM, Lyons R, Powers S, Pastori GM, Edwards KJ, Holdsworth MJ, Shewry PR. (2006). Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. Plant Biotechnol J. 2006 Jul;4(4):369-80

 To reiterate two important questions in relation to the Nature Methods paper as it may apply to food seem to be:

1) are the drastically higher than expected off target mutations based on sound methods/application of CRISPR

2) What is the weight of evidence comparing genetic disruptions in CRISPR vs conventional crop improvement methods.

Wednesday, June 07, 2017

TalkingBiotech- Technology and Society

TalkingBiotech 079: Technology and Society (link)

Very nice. One thing that moved me toward studying both genetics and economics was the realization that science does not occur in a vacuum. No matter how great the scientific discovery or technological breakthrough, its ability to make a positive impact is governed and shaped by political, social, economic, and financial forces. Everything from venture capital funding, regulatory constraints, government grants, to the influences of food marketers and celebrity tweets.

 "There are scientists that help define the social reaction to science and the way that scientists need to communicate issues in technology.  Dr. Matthew Harsh is an Assistant Professor at the Centre for Engineering Technology at Concordia University in Montreal Canada.  The discussion talks about the interface of natural sciences and social sciences, and how discussions can affect policy"

Monday, June 05, 2017

Game Theory and Antibiotic Resistance

I found an interesting article in Quanta Magazing discussing a 2012 paper in PNAS discussing game theory in the context of evolutionary processes. The article in Quanta is very detailed and nicely written as well as accessible.

This was interesting because in graduate school and other work I am familiar with, the context of games is defined around human-environment interactions leading to a Nash Equilibrium/prisoner's dilemma situation where the dominating strategies involve overuse of a given technology (antibiotics, herbicide resistant crops, insect resistant crops). In this context the equilibrium strategies create selection pressure which ultimately lead to insects, weeds, or bacteria that are resistant to the given technology. However, the Quanta article provides some examples where researchers are using game theory to describe actual behavior in nature (i.e. fish, monkeys, or the bacteria themselves). Here is a slice:

"For example, scientists studying antibiotic resistance are using a game theory scenario called the snowdrift game, in which a player always benefits from cooperating. (If you’re stuck in your apartment building after a blizzard, you benefit by shoveling the driveway, but so does everyone else who lives there and doesn’t shovel.) Some bacteria can produce and secrete an enzyme capable of deactivating antibiotic drugs. The enzyme is costly to produce, and lazy bacteria that don’t make it can benefit by using enzymes produced by their more industrious neighbors. In a strict prisoner’s dilemma scenario, the slackers would eventually kill off the producers, harming the entire population. But in the snowdrift game, the producers have greater access to the enzyme, thus improving their fitness, and the two types of bacteria can coexist."

Below is the citation related to the Dyson and Press paper discussed in the Quanta article:

Press, W. H., & Dyson, F. J. (2012). Iterated Prisoner’s Dilemma contains strategies that dominate any evolutionary opponent. Proceedings of the National Academy of Sciences of the United States of America, 109(26), 10409–10413. http://doi.org/10.1073/pnas.1206569109




Game Theory- Applications in Trait Resistance Managment

See also: Game Theory- Selected Works

In graduate school  (2005) I worked on an independent studies project exploring the idea of combining population genetics and game theory to model pest resistance to Bt traits in corn. Recently I decided to look at the literature in that space to see what others have been doing in this space. Below are some articles I have found from a quick search:

Press, William H., and Freeman J. Dyson. “Iterated Prisoner’s Dilemma Contains Strategies That Dominate Any Evolutionary Opponent.” Proceedings of the National Academy of Sciences of the United States of America 109.26 (2012): 10409–10413. PMC. Web. 5 June 2017.

Miranowski, J.A., & Lacy, K.M. (2016). When do resistance management practices pay for the farmer and society? The case of Western Corn Rootworm. AgBioForum, 19(2), 173-183. Available on the World Wide Web: http://www.agbioforum.org.

Joel S Brown, Kateřina Staňková, Game theory as a conceptual framework for managing insect pests, Current Opinion in Insect Science, Volume 21, June 2017, Pages 26-32, ISSN 2214-5745, https://doi.org/10.1016/j.cois.2017.05.007.

Jussaume, R., & Ervin, D. (2016). Understanding Weed Resistance as a Wicked Problem to Improve Weed Management Decisions. Weed Science, 64(SP1), 559-569. doi:10.1614/WS-D-15-00131.1

Ervin, D., & Frisvold, G. (2016). Community-Based Approaches to Herbicide-Resistant Weed Management: Lessons from Science and Practice. Weed Science, 64(SP1), 609-626. doi:10.1614/WS-D-15-00122.1

Nicole Haynes McCoy, Pradyumna Amatya, Games People Play: Human Behavior and Invasive Weed Management, Rangelands, Volume 27, Issue 6, December 2005, Pages 8-14, ISSN 0190-0528, https://doi.org/10.2111/1551-501X(2005)27.6[8:GPP]2.0.CO;2.

Game Theory - Selected Works

In graduate school I looked at trait resistance management through  the lens of game theory. Below are some links to some related posts, references, and short articles that I have written.

Game Theory- TalkPython podcast

Game Theory- An Introduction

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/

Matt Bogard. "An Introduction to Game Theory: Applications in Environmental Economics and Public Choice with Mathematical Appendix" (2012) Available at: http://works.bepress.com/matt_bogard/22/   

Matt Bogard. "Game Theory, A Foundation for Agricultural Economics" (2004) Available at: http://works.bepress.com/matt_bogard/32/ 

Molecular Genetics and Economics

A really interesting article in JEP:

A slice:

"In fact, the costs of comprehensively genotyping human subjects have fallen to the point where major funding bodies, even in the social sciences, are beginning to incorporate genetic and biological markers into major social surveys. The National Longitudinal Study of Adolescent Health, the Wisconsin Longitudinal Study, and the Health and Retirement Survey have launched, or are in the process of launching, datasets with comprehensively genotyped subjects…These samples contain, or will soon contain, data on hundreds of thousands of genetic markers for each individual in the sample as well as, in most cases, basic economic variables. How, if at all, should economists use and combine molecular genetic and economic data? What challenges arise when analyzing genetically informative data?"


Link:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306008/


Reference:
Beauchamp JP, Cesarini D, Johannesson M, et al. Molecular Genetics and Economics. The journal of economic perspectives : a journal of the American Economic Association. 2011;25(4):57-82.