Can A 10,000-Year-Old GMO Change How We Think About GMOs?

Researchers at Ghent University in Belgium have discovered ancient transgenic DNA from Agrobacterium in the sweet potato genome. The finding that DNA from the same microbe used to produce human-made transgenic crops—or genetically modified organisms, GMOs—resides in one of the world’s most important crops calls into question the classification of GMOs as unnatural. This new research could challenge the basis for regulating GMOs separately from non-transgenic crops and perhaps help rescue GMOs from their increasingly negative public image.

That is, if biotech advocates can harness this story to retell the GMO narrative from a new perspective.

The sweet potato was domesticated 8,000-10,000 years ago in South America, and today more than 100 million tons are grown every year around the world. It is grown for its fleshy storage root and leafy greens and, despite the name, is unrelated to the potato.  

While searching for regulatory bits of DNA in the sweet potato genome, the Belgian scientists discovered portions strikingly similar to well-known segments of DNA inserted by the bacteria Agrobacterium. Agrobacterium is a plant parasite. It inserts short sections of its DNA into plant cells that reprogram them to grow tumor-like structures called galls, which are often seen on tree trunks or crop plants. These galls are where the bacteria thrives when it gets the chance.

That Agrobacterium DNA might be in a crop plant is neither new nor altogether surprising. It has been found in tobacco before, although not in food crops. And a lot of DNA detritus floats around all of our genomes—viral DNA that does not function anymore, or truncated genes that are DOA.

But these microbial genes in sweet potato are actually active, albeit at a low level. What’s more, in studying hundreds of domesticated and wild sweet potato relatives, the researchers found that all of the crop plants, and none of their wild relatives, had one portion of this transgenic DNA. Although not proof, this strong association between the Agrobacterium DNA and the plants humans have domesticated is good evidence that the foreign DNA was selected for. That is, it might have helped produce a trait that humans kept around when taming sweet potatoes.

However, the scientists did not find a clear link between the DNA and the root we eat. It might be that the bacterial DNA produced stronger sweet potato plants, or conferred other useful traits, even if it does not account for the engorged root.

As a new lesson in the malleability of genomes during evolution, this study is fascinating enough. But the reason it was the cover of the latest issue of the Proceedings of the National Academy of Sciences has much more to do with the article’s final sentence:

“This finding could influence the public’s current perception that transgenic crops are ‘unnatural.’”

But will it?

In a recent survey by the Pew Research Center comparing the opinions of scientists and the general public, no topic—not vaccines, not evolution, not climate change—had as big of a gap between the two groups as whether GMOs are safe to eat. Google “GMOs” and the first hit is the non-GMO Project. Switch over to images and you’ll find that one syringe in a tomato just doesn't cut it these days, we've upped it to three!

Clearly companies like Monsanto, Syngenta and Bayer failed, and failed hard, in their consumer-oriented communication. They’re trying to make up for lost time. But the general public are not their customers, farmers are. And by the numbers, corn, cotton and soybean farmers sure like GMOs, so much so that 9 in 10 of each of these crops in the United States is genetically engineered. If biotech advocates want to pivot the conversation in the public sphere, this article could be that fulcrum. But there are no guarantees it will work.

Already the popular press has written it up and jump-started the conversation in a positive light. Biotech advocates should call into question the unnecessary exclusion of GMOs from the USDA organic label. Are organic sweet potatoes still a thing? If the organic label was changed to be exclusively about growing practices and not germplasm, we could have organic GMOs, as envisioned by rice geneticist Pamela Ronald and her organic farmer husband Raoul Adamchak.

Biotech advocates should call into question the label of GMO. Period.

This sweet potato study blurs the already unclear boundaries between crops created by artificial selection, induced mutation, hybridization, and genetic engineering. New genetic engineering methods that introduce no foreign DNA muddy the waters even more. By some definitions, organic sweet potatoes will be GMOs while genetically engineered potatoes won’t be. Before we start playing definitional Twister, let’s simplify the conversation so we can speak meaningfully about what matters—allergenicity, gene escape, industrial agriculture, and feeding billions of people healthfully in the era of climate change.

Audio File #4: Civil, Civic Discussions

Our conversations about civic matters—economic policies, schooling systems, religion, science, and social institutions—are severely lacking in nuance and reasoned debate. Instead, what flourishes are simplistic arguments and ad hominem attacks. This trend is strengthened by a media environment where we can easily consume pieces tailored to our point of view, avoiding challenge and change.

On Being is a weekly public radio show hosted by Krista Tippett ostensibly about religion and spirituality, but now the host of a broader series of discussions called the Civil Conversations Project. I used to turn off On Being when it came on my radio Sunday afternoons, put off by the wispy quality, assuming it was a liberal echo chamber of feel-good, empty spirituality.

But as I would listen in snippets, or accidentally turn it on in the car, I found it to be a series of careful, respectful dialogues about difficult subjects, with religion, of course, among the trickiest.

So it did not altogether surprise me to find myself enchanted by a recent episode on gay marriage, which really became a window into how to have civil debates. An interview of David Blankenhorn and Jonathon Rauch—originally on opposite sides of the gay marriage debate, and now friends in agreement on many issues—the discussion covered David’s changed mind on gay marriage, but much more interestingly their process of what they called “achieving disagreement.”

For this post I really want to excerpt some longer segments that, I think, speak for themselves. I encourage listening to the full episode. To have two people agree about how to disagree, that are intellectually honest in their point of view and empathetic enough to consider the other side is tragically rare these days and models a better way to converse. I think we can learn from them how to continue to passionately disagree while remaining not just polite, but truly civil.

Following are minimally-edited excerpts.

Listening in on Plant Defenses

It’s enchanting to consider that classical music might help plants grow better, like something out of a fairy tale. A simple Google search shows that a lot of people are interested in it, from the throngs at Yahoo Answers to marijuana growers looking for an edge. Mythbusters tested it, with mixed results. Academic researchers have explored the effects of tones on plant growth, finding frequency-specific gene regulation and growth responses. But it remains unclear what evolutionary benefit sensitivity to sound could provide, and a solid understanding of what is sometimes called ‘plant bioacoustics’ eludes researchers.

In a widely-reported study released last year, two researchers over at the University of Missouri, Columbia tested the effects on plant defenses of the vibrations caused by a caterpillar chewing on a leaf. Although much of the reporting fell prey to the temptation to claim the plants “heard” the chewing and responded, the real answer is both more complicated and more interesting. I had the opportunity to attend a talk Drs. Appel and Cocroft gave at Washington University a few months ago where I learned more than I could have extracted from their paper, published in Oecologia, alone.

Sound waves are longitudinal. Insect vibrations are transverse

Dr. Cocroft studies insect communication, especially the ability of insects to find mates and prey by sensing the vibrations of other insects on a plant. Like sound, the information is encoded in vibrational waves passing through a substance. Instead of a pressure wave like sound that varies in the same direction of travel—a longitudinal wave—insect vibrations on plants are transverse waves, moving up and down like a wave on the ocean (see figure).

We could never hear these kinds of waves ourselves, but their frequency can be directly translated to sounds we can hear. Cocroft played a number of humming soundscapes recorded with a laser on a wild prairie—the result of hundreds or thousands of insects communicating silently on stalks of grass. A plant, Cocroft noted, is a great conductor for these vibrations, flexible yet strong. His field studies how insects benefit from communicating this way, but he joined forces with Appel to ask: Do plants respond to the vibrations of insect herbivores in an adaptive way?

One major defense that plants have against pests is producing noxious compounds to deter feeding. Appel and Cocroft hypothesized that Arabidopsis plants would produce more defense compounds if they were exposed to the vibrations of herbivorous insects before actually being attacked. This effect is called priming, and could help defend against a second wave of insect damage.

To test this, the researchers first used lasers to record the vibrations of caterpillars allowed to eat the leaves of Arabidopsis plants. To play the vibrations back to undamaged plants, Cocroft attached leaves to tiny pistons driven, essentially, by speakers, ones that could replicate the vibrations of an insect chewing. Then caterpillars were allowed to feed on either the leaf that was vibrated or another, untouched leaf.

Both vibrated and distant leaves responded more vigorously to caterpillar attack than leaves on untouched plants. The plants that were primed by recorded caterpillar vibrations produced more glucosinolates, or mustard oils, than those of unvibrated plants. This is evidence of an adaptive response to insect vibrations, but leaves open the possibility that any vibration encouraged plant defenses.

To see if the effect really was specific to the herbivorous caterpillars, Appel and Cocroft played back vibrations of harmless insects, wind, or caterpillars on different plants and again measured defense compounds—this time anthocyanins, responsible for the deep reds and purples of many plants. Only caterpillar vibrations could prime plants to increase their defense response to herbivory; wind and the neutral insects had no effect.

One important caveat: although the researchers looked for an effect of vibrations alone, they found none. Only vibrations plus actual insect feeding induced higher defenses; the plants were primed for future attack, but vibrations alone made no difference. Of course, a real insect is more than just its vibrations. Herbivore attack is a physical, chemical, and auditory assault, and plants likely respond to each stimulus in different ways.

But how are plants able to sense the vibrations of caterpillars, and even differentiate them from similar sounds in nature? It’s entirely unknown. A very good candidate is a diverse group of proteins bound together by their responsiveness to physical forces—mechanoreceptors. These proteins can signal within a cell in response to vibration or touch and are potentially behind the priming effect that Appel and Cocroft observed.

In fact, to test this, the Haswell lab is working with Appel and Cocroft to see if our favorite mechanosensitive ion channels are part of the vibrational-response pathway. I got to see Liz’s face pop up in the corner at the end of their presentation over on the medical campus as they told us that work was underway. We’ll just have to wait to find out.

[A version of this post first appeared on my lab's blog]

Visualizing Our Changing Cities

Photos by Brian Villa for St. Louis Public Radio and Richard
Moore via the Missouri History Museum

In 1950, St. Louis was the eight-largest city in America at a bulging 850,000 residents. It was a twentieth-century city, buoyed by diverse manufacturing and a busy port. It was also a highly-segregated city, split strikingly into a largely-black north city and whiter, richer south city—but the entire urban core suffered from flight to the suburbs and industrial Midwest decline.

Six decades later, the city is drastically different. The County bests the City's 300,000 population by three-to-one after sixty years of uninterrupted population loss.

Understanding the causes and consequences of urban decline and evolving city life is difficult. It requires ten-, fifty-, and hundred-year perspectives and a close knowledge of economic and political contexts. One way we can better appreciate how our cities have changed is to visualize the effects of time, in maps and data.

I was drawn to the hypnotizing displays of changing Midwest cities put together by the University of Oklahoma's Institute for Quality Communities. Simple sliders reveal cities universally carved up by the Interstate Highway System and uniquely altered by the effects of and responses to urban decline, such as the Arch grounds and Pruitt-Igoe projects in St. Louis. In each case we can directly observe how dense, residential neighborhoods were transformed into offices, or simply wiped clean by population loss and decay.

One of my first exposures to the stark changes that St. Louis has undergone since its mid-century heyday was the simple and excellent Mapping Decline website to accompany Colin Gordon's book of the same name. Four maps show the great exodus from the city center and the racial covenants that forced black residents to remain in decaying neighborhoods, patterns that resulted in an intentionally divided region. The consequences of these policies and demographic shifts are felt now, decades later. Ferguson became a household name this past August in part because of unaddressed divides, seen clearly in Gordon's work.

Visualizing how my city has changed is simply fascinating as well, not always so serious. I stumbled upon Elizabeth McNulty's St. Louis Then and Now at Dunaway Books on South Grand, just the kind of architectural coffee table book I was keeping an eye out for. In almost 70 paired photographs, McNulty shows us a St. Louis rising at the end of 19th century, barreling into the 20th, and the state of its urban neighborhoods today. The dramatic shift from bustling port to sleepy, abandoned riverfront is especially striking to see. Similar sets of photos were assembled as part of St. Louis' 250th anniversary celebration, where streetcars make way for regular ones, and grand boulevards were once populated by throngs of downtown residents that have since left.

Cities are as dynamic as the people who inhabit them and bring them to life. Many Midwestern cities have struggled for several decades, while coastal cities have largely prospered. The pendulum may be swinging back now as people—especially the young—increasingly seek out cities for their liveliness and density. These once-grand cities have serious problems to contend with, from racial divides to ailing school systems, but perhaps the twenty-first century will again see a rise of the cities that seemed to peak in the middle of the twentieth.

Local Politics at Work: Celebrating Cycling in St. Louis

24th Ward Alderman Scott Ogilvie

Around 30 people gathered this past Friday in the new bike shop Spoked in the rapidly changing Cherokee neighborhood. There were two half kegs of Civil Life beer on ice and free pizza from the wine shop next door. One wall is painted a bright, invigorating orange and the silvered tin ceiling looms overhead above bike rims hung up high. I met up with several friends and ran into others I knew from Gateway Greening and CityArchRiver who, like me, had come to bond over cycling, hear about new bike infrastructure and, yes, drink the free beer.

My mom was visiting too, and was by far the oldest person in the room. But she shared stories of biking in Boston almost 40 years ago and how she knew it was too cold to bike to work that day if her nose hairs froze on the way to the bike shed behind her apartment. Everyone was welcome.

Spoked was hosting a happy hour principally to celebrate the huge success of painting buffered bike lanes on Tower Grove Avenue ahead of the closure of the largest north-south thoroughfare in the city, which will divert traffic to Tower Grove and other detours—this effectively preserves my only route for cycling to work.

Scott Ogilvie , the alderman for the 24th ward and an avid cyclist, leapt up on the counter to welcome everyone and entreat us to be active advocates for biking in St. Louis. He introduced Matt Wyczalkowski, the man who led the fight to stripe Tower Grove before the Kingshighway closure. Matt told us how he had used Tower Grove to commute to Washington University for years and felt passionate about this short mile that is so crucial to bike commuters in the city.

Matt Wyczalkowski

When he learned that the planned bike lanes would be postponed until after the construction to allow more car traffic to use the route—essentially closing the street to all but the most diehard cyclists—he gathered a coalition of biking advocates and neighborhood associations. Together they held votes that convinced my alderman, Stephen Conway of the 8th ward, to expedite the bike lanes. It was done days later. Without Matt's intervention, Conway was prepared to let the planned striping lapse for two more years. At the behest of his constituents, persuaded by Matt, this important route is maintained.

I owe Matt two years worth of my biking commute: hundreds of hours worth of both pleasant and difficult exercise that starts and ends my working day.

Matt took questions and I asked him, "What's next for you?" His response was to ask me the same, and to point out how focused determination on a finite problem can lead to real results. His pet project was expediting bike lanes on a short stretch of his local street. If each of us in the room that day found our own tractable issue and pursued it by building coalitions of neighbors and friends, we could accomplish the same.

Rhonda Smythe

Rhonda Smythe, until recently the policy and advocacy manager at Trailnet, closed out the speeches by outlining her goal of including more people in the cycling community by reducing the barriers to biking. Outside of the spandex-wearing road cyclists, Rhonda wanted to get people who bike once a month to start biking four times a month. By creating low-speed, low-traffic routes through neighborhoods, she wanted to encourage families to bike for more of their short trips.

In my former neighborhood of Skinker-DeBaliviere, this takes the form of the Des Peres bicycle boulevard that improves through-access for cyclists over cars and has highly-visible markings to encourage more relaxed biking.

The owners of Spoked, Matt and Shane, also encouraged us to be advocates mainly by getting on our bikes and riding. Improving the visibility of the cycling community, they said, attracts the attention of neighbors and local leaders so they can internalize how vital it is for our city.

Somewhat unexpectedly, this event became the highlight of my week and a resounding lesson in the power of local politics that, I believe, lifted up everyone in attendance and left us all feeling energized and ready to act, alone and together, to make our home better.

Having an Impact: The Appeal of Mid-sized Cities to Millennials

“There is a vibrant bar and restaurant scene, social sports leagues through which hundreds of young people get together to play kickball and other games, even a monthly bike ride – sponsored by a group working to make [the city] less car dependent – in which participants dress up in costume and ride through the city.”

I thought I was reading about St. Louis and wanted to look up this monthly cycling event that sounded like the Naked Bike Ride but more frequent. The city in question is not Portland, either, but rather Baltimore. In a profile of “The New ‘Cool’ Cities for Millennials,” The Christian Science Monitor uses Baltimore as the example of a series of infamously rundown, increasingly vibrant and even hip urban centers that increasingly draw the urban Millennial generation. Cleveland. Detroit. Nashville. St. Louis. Mid-sized cities with cheap rent, storied histories, and surprising economic opportunities for a generation pummeled by the Great Recession but still searching for places to make their mark.

And although New York, San Francisco, and other metropolises draw the lion’s share of young, educated adults, these other, often overlooked cities are beginning to see rapid increases in these populations. Even as St. Louis has continued a six-decade population death spiral, the number of 25-to-34-year-olds with a college degree near the urban core has more than doubled, rising 138% from 2000 to 2010, the largest such surge in the country. Although this relative increase obscures absolute changes, St. Louis attracted more than half the demographic increase Seattle did over this same period (4,227 versus 8,209). St. Louis and other struggling cities have far to go, but they are going, and changing faster than many would have anticipated just a few years ago.

In St. Louis, Downtown, Midtown and other central corridor neighborhoods were the only ones to gain residents from 2000 to 2010, when the city overall saw an 8% drop in population, perhaps a bellwether of a turning tide in the exodus from the city center. These neighborhoods include startup incubators like T-REX and Cortex, revitalized loft apartments, and convenient public transit.

And St. Louis is the fastest-growing city for new technology jobs. ArchGrants, founded in 2011, provides non-equity funding to tech startups—as long as they remain in or move to St. Louis. LaunchCode, which rapidly trains new programmers and places them at area businesses, was recently lauded by President Obama for its successes and is expanding nationally. Tech may not be sufficient to power the city’s economy, but St. Louis’ low cost of living and access to capital make it a top place for starting other businesses as well. 

Although demographers cannot untangle the economic causes from the cultural behind the Millennial move toward cities, The Christian Science Monitor and other sources have identified a self-reported interest in dense, walkable, community-oriented neighborhoods over suburban sprawl among the young. The people profiled in the CSM piece—employees at tech startups and nonprofits—claimed Baltimore as a city where they could have an impact, where a vibrant urban lifestyle coincided with a small enough community to feel absorbed, not “carried along”.

St. Louis offers the same opportunities to contribute to a quirky, very much in progress revitalization of the city. Upstart politicians can win by a mere 90 votes against an entrenched incumbent; individuals can ensure that local representatives listen to their constituents about critical bike infrastructure projects; shuttered corner businesses can be reopened to create a new community space; a brand new brewery can be self-funded.

As a full-time graduate student, I can still find a way to contribute to outreach to the community gardening scene in St. Louis where other cities, San Francisco for example, might have those kinds of niches saturated by individuals who can commit more fully to single projects. In many areas of this city, there is both a need and room for interested individuals and small groups to get their hands dirty in making their communities better—the results are obvious, the actions of individuals visible.

Demographers quibble over whether the Millennial move toward cities is stable, or whether family life, schools, and age will push us back out to the suburbs in the next decade or two. Time will tell. But it may be that the economic forces that favor urban centers only reinforce an intentional return to lively, dense cities. And that St. Louis, Baltimore, Cleveland or Detroit offer the more civic-minded—and more financially constrained—of our generation an opportunity to help forge the cities we will inhabit for decades to come. 

The Limits of the DOJ Ferguson Report in a Fractured Region

The Department of Justice released the findings of its investigation into civil rights abuses in Ferguson this week. The report is unsparing in its indictment of intentional racial bias within the police department and city government, and the unequal application of the law on black residents without cause. Analysis by people familiar with the DOJ’s involvement with other police forces suggests that the DOJ will forcefully compel their suggested changes, or dissolve the police department entirely.

As striking as this report is—and as clear as it is to dispel the myth that race is not a factor—its effects are inherently limited. Ferguson is home to only 21,000 people, one of 90 municipalities in St. Louis County, which has a total population greater than one million. The independent City of St. Louis houses another 320,000 residents, more than half of whom are non-white. The DOJ may reform the Ferguson police department into an exemplary force, or dissolve it altogether and allow the St. Louis County police to patrol the town. Neither will sufficiently address the widespread problems facing the St. Louis region or the country as a whole.

St. Louis is fragmented, divided intentionally over decades into white and black, rich and poor. Many other cities are similarly fractured. Forceful reform of a single police department, representing barely one percent of the region’s population, is nearly meaningless. The divisions that have contributed to St. Louis’ problems must be addressed alongside raking the Ferguson police department over the coals. Unnecessary police forces should be dissolved, and many of their cities absorbed into larger municipalities. The City of St. Louis and the County should be reunited in order to work together, not compete. 

Only a region so strengthened will be poised to lead the nation in meaningful reforms. Only if we heal these longstanding divisions can we turn a conversation into action. Bust open Ferguson, break it down and build it up into a city and a police force that serves its residents proudly and well. But to stop at Ferguson would fail St. Louis to an extent we cannot afford.