I’m blogging after my first day at an awesome scientific conference: The Keystone Symposia joint meeting covering DNA Replication & Recombination and Genomic Instability & DNA Repair. The talks today were all top-notch. I wanted to give a run-down of some of the radical research I’ve seen thus far, but I don’t want to hit you, my readers, with a firehose of data, so instead I think I’ll summarize the plenary session, and leave the rest of the genomic gymnastics for another post.
Our first speaker, Stephen Jackson, kicked off the conference with an exhortation for collaboration. He encouraged scientists working on similar topics to reach out and promote synergy rather than trying to scoop each other. I really appreciated his message of cooperation: the point of conferences is the productive exchange of ideas, not a giant scientific pissing match. Jackson made a point to acknowledge all of the other researchers who contributed to the work he presented during his talk. He mentioned that a night in the bar with Alan Ashworth led to the screen of small molecule DNA-repair inhibitors against many mutant cell lines that gave rise to a recently approved cancer drug.
Jackson gave a retrospective of 25 years of research leading to one of the hottest new cancer drugs on the market right now: Lynparza (olaparib).This compound is exciting because it is a first-in-class PARP-inhibitor drug especially for personalized cancer medicine. Traditional cancer treatments, like chemotherapy and radiation, kill cancer by destroying any rapidly dividing cells within the body. This blunt approach works reasonably well for fast growing tumors, but it causes NASTY side effects. Hair, skin, and cells in the gut all also happen to also be fast-growing, which is why Chemo hits people like a sledgehammer. Additionally, chemotherapy and radiation don’t take into account the innate differences between different types of tumors. These approaches won’t work on all tumors (like Chondrosarcomas…Hi Mom!) On the surface it’s obvious that breasts and bones and brains are RADICALLY different body parts, and therefore treating cancers of each organ identically is insane. We wouldn’t wear brassieres as hats, why would we treat a breast and a brain tumor with the same drug? However, even within a single type of tissue, different genetic mutations can give rise to different kinds of cancers. The premise behind personalized medicine is that each type of tumor carries its own particular set of changes that contribute to causing disease.
As we get better and better at sequencing genomes we’ve started to better understand the underlying causes of different kinds of cancers; concomitantly, clinicians are becoming more and more adept at targeting these specific differences to destroy tumor cells. One particularly aggressive type of cancer is distinguished by defects in the BRCA genes. The BRCA genes are vital for DNA break-repair. Lynparza inhibits a different DNA repair protein called PARP; PARP inhibitors are highly effective for treating cancers with BRCA mutations. The concept of treating cancer with a drug that prevents DNA repair is, at first glance, a shocking strategy. After all, isn’t cancer CAUSED by DNA damage? Don’t defects in DNA repair genes (like BRCA) LEAD TO cancer? Wont there be lots MORE DNA damage in cancer cells if you treat them with this inhibitor?
The fact that cancers carrying BRCA mutations are defective for DNA repair is precisely the phenomenon behind Lynparza’s success. The idea behind this strategy is that normal human cells have many different pathways to deal with DNA damage; there are back-up mechanisms in place if Lynparza takes down PARP. Cancer cells, by contrast, have lost most of their repair capability (due to mutations in BRCA, or other genes) and thus don’t have many options to fix their DNA. Therefore, DNA repair inhibitors become potent poisons specifically for cancer cells. This concept, where a particular deficiency only becomes a problem in the context of another defect is called synthetic lethality.
Jackson talked about the extensive findings that helped uncover Lynparza’s synthetic lethal effect for cancers with BRCA mutations, and showed the data from phase II clinical trials demonstrating its dramatic efficacy. Not only did the researchers observe prevention of disease progression in 34% of patients, the side effects associated with Lynparza are a walk in the park compared to conventional chemotherapy. The FDA just granted accelerated approval status to Lynparza for treatment of advanced ovarian cancers, based on promising results from these Phase II clinical trials.
The talk, of course, contained lots more mechanistic details about which components of the DNA Damage Response do what, and how scientists in Stephen’s group (and others) figured all of this out. I really enjoyed seeing a multi-decade long story where basic science (mechanisms of DNA repair) eventually led to an awesome new cancer drug.
I could go on, and on, and ON about what else I saw today (There were TWO Plenary speakers…a whole session on single-molecule studies of the replisome…a workshop on genome editing…CRISPRS! I’m in DNA-nerd heaven). However, after explaining synthetic lethality, I think that I want to go to bed so that I’m bright eyed and bushy tailed for my poster presentation tomorrow.
I’ll keep writing up some of the cool stuff I see all this week (I might even sneak in some skiing as well).
In the meantime, I hope everybody’s having a killer Monday!
Has everybody heard the latest buzz that gerbils, not rats, likely were responsible for spreading the black plague around Europe? The paper (published in PNAS) looked at historical death records and tree-ring data and determined that climate shifts played a huge role in driving plague outbreaks. The authors saw big fluctuations in plague cases across Europe, which correlated with shifts in temperatures (according to the sizes of tree rings). Plague is caused by a nasty bacteria named Yersinia pestis; Yersinia spreads from little rodent-y mammals to big human-y mammals through fleas. Because the rat populations in cities are usually pretty stable, not affected by changes in climate, the authors speculate that some other environmental host in Asia was responsible for the persistent re-intorduction and spread of plague in Europe.
The idea is that colder conditions killed off the Asian varmints (like gerbils) that plague was infecting; the fleas jumped ship and headed towards warmer environs (potentially by hitching a ride on camels along trade routes).
In other words: climate chang can have huge impacts beyond just changing temperatures, epidemiology is ALWAYS more complicated than it first appears, rats might not be so dastardly after all, Gerbils are filthy vermin, and Plague is a nasty pathogen.
But I digress.
The point of today’s post wasn’t supposed to be a discussion of the Black Plague. I was hoping to provide my gentle readers with an apology and an announcement.
I’m sorry I haven’t posted anything since my return from the graduate student retreat on San Juan Island. Life has been pretty hectic over here, and some…changes have been happening.
It’s too soon to announce anything just yet, but some opportunities are cropping up on my radar. My life might get RADICALLY different in the next few months. I’m trying not to get too optimistic, but I’m excited. I’m also a little bit terrified.
The real world might be looming large in my horizons. After four super-speedy years in academia, I’m not sure if I’m ready to take the leap.
I had a ton of fun at the last meeting I attended (FASEB’s DNA Dynamics, a.k.a. DNA-Disneyland). This conference will be even bigger, with a ton of super-star speakers doing top-notch science. The fact that the schedule leaves afternoons open to go skiing is another, not so minor, perk.
I’ll be blogging along throughout the week’s activities: expect to see reports on both epic chromosome contortions and sick skiing conditions.
HAPPY FRIDAY! What are YOU looking forward to this weekend?
I’m lazing around Seattle on this Sunday afternoon after a fun-filled weekend spent on San Juan Island.
Each year the graduate students in my microbiology department spend a weekend together away from the lab at our annual retreat on San Juan Island. We always have a great time getting to know one another, talking science, and exploring the pastoral paradise on Puget Sound.
I love our retreat–it’s a great opportunity to make connections with the other graduate students and have some fun together in a non-science setting. It certainly helps that the particular setting we choose for our get-away is a mind-blowingly great place. I’ve been attending this event for four years, and each time I discover some new and interesting thing to do on San Juan Island.
We kicked off our adventures Friday morning by loading up a fleet of UCars and making our way to the ferry terminal.
A brief moment of panic ensued when it appeared that there would not be sufficient space for our merry crew on the ferry. Luckily, even though we were sailing standby, we were able to embark upon the good ship Sealth, and cast off into the well-charted waters of Puget Sound.
The ferry ride from Anacortes to Friday Harbor takes about an hour and a half. Luckily we had on board activities to keep us occupied.
The University of Washington maintains a functional marine-biology research laboratory on San Juan Isand, called Friday Harbor Labs. We stay in the dorms at Friday Harbor Labs every year. In addition to being just a generally gorgeous place, F.H.L. is home to an important bit of scientific history. A sizable chunk of the early work on isolating Green Fluorescent Protein (one of the most widely-used fluorescent tags in molecular biology) was performed under F.H.L.’s roof. The protein comes from a tiny jellyfish named Aequoria, which is native to the northern waters of puget sound. We don’t need tons and tons of Jellyfish to get the protein anymore, now that we know the sequence of the G.F.P. gene, and have mutated it into all the colors of the rainbow. However, it’s cool to see the origins of an important tool (that I, in fact, have used in my own research).
After arriving at F.H.L., we unloaded our belongings into the dorms, and set off to explore the beaches on the east side of the island. You will never find a happier (nor nerdier) group of individuals than seventeen microbiologists let loose among intertidal pools.
On Saturday morning, I got up early and went for an 8-mile run, which is the longest I’ve been out since recovering from my (second) stress fracture this past fall. I had a moment of frustration, because last year at this time I was running 14 miles, at a significantly quicker pace. However, I quickly reminded myself that: incremental progress is still progress, it’s important not to overdo EVERYTHING all of the time, and any time on the road is better than no time at all. I also snapped a quick photo of the island’s resident camel when I reached my turn-around point.
After I showered off and shoved some oatmeal in my face, it was time to continue my explorations. Three other grad students and I decided to go check out a State Park for some hiking. On our way to the trails we spotted this delightfully romantic yard display.
The State Park offered some spectacular ocean views. Apparently Orcas traverse the surrounding waters during the summer months, but we didn’t see any marine mammals during this particular visit.
San Juan Island used to be an important shipping hub for both British and American industries. The Park Service still maintains an active lighthouse to guide vessels through Puget Sound.
The Island also used to have a limestone quarry. We walked to the retired Lime Kilns, which were used to burn away impurities from the raw stone to yield calcium carbonate.
Quarry workers would shovel limestone into the top of the kiln, then heat it to over 1000 degrees Celcius. The cooked rock would then get loaded onto ships and distributed to manufacturers all over the west coast.
We explored the retired kilns for a little bit, and also wandered around the trails. I’m always blown away by the lush, unearthly greenery in the Pacific Northwest.
After our adventures we returned to Friday Harbor Labs and proceeded to engage in some SERIOUS, INTENSE, HIGH-PERFORMANCE….relaxation.
Overall it was a phenomenal weekend. It’s always fun to escape Seattle for a little bit, learn about my colleagues, and take in some pastoral pleasures on the islands. I hope everyone out there in internet-land is having a GREAT Sunday!
OK- I gotta ask: I spent my February 14th having fun with friends and co-workers. Bacteriology is my Valentine. did anyone do anything romantic for V-day?
Hi ho, hi ho gentle readers! How are you doing on this delightful Thursday? I hope that you aren’t feeling dwarfed by deadlines as we come to the conclusion of another workweek.
Astute observers may have noticed certain…changes around this little corner of the internet.
If you came to this blog looking for Marathonsam, running rascal and raconteur, don’t worry, you’ve come to the right place. However, as I continue in my quest for global dominationeffective scientific communication, I’ve decided that my online presence should more accurately reflect my daily identity.
I’m going to keep on blogging about running, the things I like, racing, the environment, running, food, and, occasionally, running. However, I realized that calling myself “marathonsam” in perpetuity limits the scope and scale of what I hope to accomplish with this blog. After all, I can’t run races ALL of the time.
Welcome to the new-and-improved melange of miscellany, now entitled “Million-Weaver’s Musings.” It’s totally different, but pretty much the same as marathonsam.com. Using my real name, however, lends this plucky Ph.D. candidate just a little bit more gravitas as I build up my portfolio of science writing posts. After registering a shiny new domain name, I decided to tinker with the formatting and layout of my little blog as well. Please excuse any (additional) weirdness as I get my pages organized, eyes crossed, and tees dotted.
If you notice anything that impedes your enjoyment of Million-Weaver’s musings, drop me a comment so that I can get everything ship-shape. If you read something you like and you have any questions, send me an email. Finally, before I sign off for today, let’s appreciate some high culture: Lou Henry Hoover and Kitten LaRue’s elegant rendition of truly classical piece. (warning, this video is a seriously strange and wonderful burlesque performance, therefore it may not be appropriate for conservative workplaces, like the supreme court)
Friends, countrymen, constituents, taxpayers, campaign contributors, lend me your ears!
Four score and seven years ago our forefathers…were drinking bathtub gin and dancing the Charleston.
Now we are engaged in a great congressional clusterfuck, testing whether our nation or any nation so conceived can long endure such gratuitous gridlock and puerile partisan poppycock.
As a patriotic plucky Ph.D. candidate at a public institution, I have a passing interest in the fiscal well-being of my funding bodies. Today I’m taking a break from long-form ranting writing about GMOs to play at politics. Watch out, Washington, this blogger-backslash-scientist is going to hit you harder than a sequester!
This past Friday, the University of Washington’s Graduate and Professional Student Senate took a field trip to the State Capitol in Olympia to lobby legislators in support of funding higher education. I decided that this would be the perfect opportunity to rub elbows with the political elite and practice talking science to a non-technical audience, so naturally I jumped at the opportunity to tag along.
During Huskies on the Hill Legislative Lobby Day we were given the opportunity to explaining our publicly funded research to politicians. Catherine and I put up our posters and prepared to present our work to any interested congresspeople.
Unfortunately, our boundless enthusiasm for scientific inquiry was matched only by the total lack of interest on the part of any legislators. It turns out that if you want to liaison with the legislative branch, Friday afternoon is NOT the ideal time to try and locate your lawmaker.
The Capitol building was empty, with the exception of one horde of highly-motivated huskies trying to talk to somebody, ANYBODY, about our agenda.
Even though I didn’t get to meet the governor, the day was not a total loss. Catherine and I had a total blast seeing the sights at the state capitol.
I also got a chance to practice my skills as a scientific communicator by explaining DNA dynamics to a few law students. I chatted up an aide about my buddy Bacillus subtilis. I saw the world’s largest Tiffany chandelier.
The hackneyed old saying “those who love the law and sausages would do well to avoid watching either being made” contains a small kernel of truth. I don’t particularly love the law, but it was HIGHLY informative to learn that NOTHING gets done after one p.m. on Friday in the State Capitol.
As a plucky Ph.D. candidate, used to working on B. subtilis’schedule (a.k.a. “cells grow just as well on Thanksgiving as any other day”), I must say that the hours associated with a government position seem pretty plush. I don’t think I could ever find satisfaction in being a politician.
However, somebody’s got to serve as an interpreter between scientists and the taxpayers that fund our research. The ongoing public misconceptions over vaccine safety, climate change denial, and (my latest pet project) GMOs are just a few examples where poor communication by scientists has undercut our efforts to improve the world. Anti-science sentiment doesn’t arise in a vacuum, it’s our responsibility as researchers to explain our results in a clear non-threatening manner. Unfortunately, the very qualities that make for excellent science such as careful word choice, an utter aversion to dogmatic pronouncements, refusal to generalize, and consideration of every possible caveat, make for lousy headlines on the six o’clock news.
Scientist speak in a different language of certainty than pundits. We still call gravity and natural selection theories, for crying out loud.
Occasionally our careful language gets interpreted as uncertainty. But we don’t have to be our own worst enemies. I’m not advocating for scientists to start making dogmatic pronouncements.
Instead I’m trying to carve out a little niche for myself as an interpreter between academia and the general public audience at large. I will always be devoted to science, and right now I think that the best way I can move the field forward is by communicating interesting findings in an accurate and informative manner.
So I’ll put it to YOU gentle readers! Got any questions? What controversies are on your mind? I want to explain science to anyone who asks! Drop me an email or a comment, and I’ll find out whatever answers you want.
Today’s post is a continuation in my long-form series on genetically modified organisms (GMOs): Marathonsam’s Pragmatic Perspectives (click the link to read my initial foray into longer-form journalism). I’m going to share an opinion editorial that I researched and wrote a few months ago covering the impacts of propagating GMO plants on American Agriculture. While I was writing this piece, voters in both Orgeon and Colorado rejected ballot initiatives that would have mandated labeling food made with GMOs. The campaigns on both sides of the issues fought ferociously; in Oregon the final outcome hinged upon a difference of merely 802 votes. In both cases the opposition SERIOUSLY out-spent the pro-labeling campaigns (over 15 million dollars flowed into Colorado alone). The anti-GMO-labeling coalition, led by the grocery manufacturers of America, PepsiCo, and our old friends at monsanto, tripled their lobbying dollars during 2014, spending over $27 million to oppose efforts to label GMO products.
Supporters of GMO labeling spent roughly $1.9 million in 2014. Clearly, the spending balance is seriously skewed, which further complicates getting quality information. Opponents of GMO labeling effectively launch a media blitzkrieg whenever the merest hint of a ballot measure begins to take shape.
In the face of the onslaught of opposition, the pro-GMO labeling groups tend to rely on shrill, provocative pronouncements warning consumers about toxic tomatoes waiting to pounce off of their supermarket shelves and poison their children.
Unfortunately, this strategy undercuts their arguments for many reasons. For one thing, most fresh produce available for purchase is categorically NOT produced using GMOs.
The most common GMO crops in the united states are corn and soybeans. Most Americans only eat corn on the cob on the fourth of July, and would only willingly eat a soybean if they were held at samurai-sword point.
However, given the ubiquity of King Corn and his Syrup in processed food, Americans truly do consume a SHOCKING amount of GMO products without their knowledge. Every kernel of candy corn came from GMO corn syrup. GMOs aren’t glowing rutabagas, GMOs look like anything and everything that comes in a package and contains high-fructose cornsyrup.
Whatever a GMO may or may not look like, the claim that these products are innately harmful to human health is PATENTLY UNTRUE. Nothing inside of the tissues of a GMO plant is harmful to humans in and of itself. Nothing. Nada. Zilch. These products are subject to EXTREMELY careful, extensive, long term scrutiny and the basic process of genetically modifying an organism does not do anything to make these products harmful.
Obviously, one COULD genetically modify a potato to produce ricin, if one felt so inclined. That would be one hell of a toxic GMO. However, the modifications that are approved for human consumption do not cause any detrimental impacts on human health. Frankly, it’s more dangerous to eat a serving of unmodified french fries that to sample a GMO soybean.
When proponents of GMO labeling rely on shrill claims that aren’t substantiated by science they undercut their own valid arguments. I believe that GMO products should be labeled because GMO agriculture relies on horrifically bad farming practices and Americans need to know how their food is produced. I wrote up a screed opinion piece making my own case. I’m delighted to share it with you, my gentle readers. I’ve included footnotes with the references that I used to make my claims, in case anyone is interested in pursuing the topic further. Chime in in the comments with your own opinions about GMO labeling, I’d love to hear what you think. Let’s hit the trails to talk GMO labeling!
The process is the product: label GMO foods
The term genetically modified organism (GMO) conjures up images of a chimeric cornucopia overflowing with eternally firm FLAVR-SAVR tomatoes and freeze-resistant flounder-spliced fruit. In reality, the prototypical GMO product sold in America today more closely resembles a common candy bar. While a humble GMO cornstalk may fail to capture the public’s imagination, high-fructose corn syrup derived from amber waves of genetically engineered grain saturates supermarkets from sea to shining sea .
American consumers are largely uniformed about which items on the shelves of their local grocery stores originate from GMOs. Only 43% of respondents to a recent online survey were aware that food made with GMOs is currently available for sale in this country, and three quarters of those surveyed were under the impression that they had never consumed such a product . Labeling goods generated using GMOs would reveal the ubiquity of these products in our food supply. Current FDA regulations mandate labeling GMO products only if “a bioengineered food is significantly different from its traditional counterpart” . Most GMO products themselves likely are indistinguishable from unmodified food in terms of human health risks. However, GMO plant production is radically different than conventional cultivation techniques. Foods produced using GMOs should be labeled so that consumers may make informed decisions about the agricultural practices that they wish to support.
A deluge of emotionally charged declarations surrounds the debate over labeling GMOs. Proponents of GMOs claim that they are equivalent to un-modified foodstuffs; opponents assert that these products present a risk to human health. Both statements are misleading. Extensive long-term feeding studies in animals demonstrate that GMO foods are broken down into their nucleic acid and protein building blocks and digested just like any other plant . No investigation has ever found any direct negative health effects associated with eating GMO foods  and the only paper ever to purport that GMOs are potentially hazardous to humans was widely discredited and subsequently retracted . However, the agricultural methods used to produce these products render them distinct from un-modified organisms, changing the way that farmers cultivate their fields. The farming practices associated with GMOs deserve careful scrutiny, and consumers deserve to know how their food is produced.
GMO agriculture has fundamentally altered farming in the United States. Since the advent of the first commercially available GMO crops in 1996, adoption of these technologies has expanded to such a degree that the majority of American agriculture is produced using GMOs. Genetically modified organisms made up 93% of American corn crops and 94% of soybeans in 2014 . Corn and soybeans cover roughly half of the United States’ 335 million acres of commercial cropland (85 million and 73.8 million acres, respectively) and these commodities are extensively used as livestock-feed . Proponents argue that these products are a boon to the economy, noting that agricultural yield has increased by 22% and that farmers have seen a 68% increase in profits over the past two decades . This increased productivity stems from farmers sidestepping costly traditional pest control measures, through the cultivation of genetically engineered insect-resistant or herbicide tolerant organisms [1,7].
Insect-resistant GMOs encode proteins that are harmless to humans but lethal to any lunching pests. Herbicide-tolerant GMOs are immune to the effects of a particular plant-killing chemical, which allows farmers to easily eliminate invasive weeds while sparing their crops . Both have changed the ways farmers treat their fields: the widespread adoption of insect-resistant crops has seen a 40% reduction in insecticide usage . However, while the use of chemical pesticides targeting insects has declined, the ubiquity of herbicide-tolerant crops has led to an additional 527 million pounds of weed killing chemicals applied to crops over the past 15 years . Despite the reduction in insecticides, pest-management chemical usage overall has increased by 8.9% every year since the advent of GMO agriculture .
The dramatic increase in herbicide use associated with wide-scale GMO adoption deserves further scrutiny. The most common commercially available herbicide-tolerant GMO crops carry genes rendering them immune to the toxic effects of glyphosphate, the active ingredient in RoundUp weed-killer [1,7,8]. Glyphosphate is regarded as safe to humans . However, the chemical is not used in isolation: any herbicide must be mixed with adjuvants and surfactants before it is applied to plants. While the active ingredient alone is innocuous, the adjuvants are toxic and mutagenic to human cells [10,11]. Indeed, long-term exposure to glyphosphate-containing herbicides is associated with an increased risk of non-hodgkin’s lymphoma . While the herbicide-resistant GMO and glyphosphate alone are both likely completely harmless to humans, dramatic increases in the usage of glyphosphate-containing herbicides have potentially dangerous impacts on health. This is a case where the total risk of the whole system is much greater than the sum of its individually innocuous parts.
In addition to potential human health risks, herbicide-intensive GMO agriculture alters entire ecosystems. One concern associated with any pest-management practice is the emergence of resistant organisms. Just as antibiotic-resistant “super-bacteria” strike terror into clinicians by rendering traditional treatments ineffective, super-weeds and immune-insects have the potential to devastate a farming system founded in GMOs. Since 2005, over 135 novel glyphosphate resistant weed species have emerged , raising concerns about the long-term viability of continuously applying large volumes of this agent to our fields. Insects, by contrast, are slower to develop resistance to the bacterial toxins produced within GMO plants . The presence of alternate non-GMO food sources in the environment and recessive genetic inheritance decreases the selective pressures that facilitate fast spread of a resistance trait . Despite this, resistant species have emerged on several occasions , devastating crop yields in the Midwest .
The environmental impacts and human-health risks of herbicide-intensive large-scale GMO agriculture have largely been overshadowed by the irrelevant debate over the nature of the products themselves. Even though recent initiatives in Colorado, Oregon, and California failed to garner sufficient votes to mandate labeling GMO products, a 2013 online survey determined that, when asked directly, 73% of respondents believed that GMO food should be labeled . Labeling items produced with GMOs will reveal the sheer omnipresence of these products to consumers, opening the door for a long overdue conversation about American agricultural practices.
7) Klümper W, Qaim M. A meta-analysis of the impacts of genetically modified crops. PLoS ONE. 2014;9(11):e111629.
8) Impacts of genetically engineered crops on pesticide use in the U.S. — the first sixteen years. Environmental Sciences Europe. 2012;24(1):24.
9) Henderson, A. M.; Gervais, J. A.; Luukinen, B.; Buhl, K.; Stone, D. 2010. Glyphosate Technical Fact Sheet; National Pesticide Information Center, Oregon State University Extension Services. http://npic.orst.edu/factsheets/glyphotech.html.
10) Mesnage R, Bernay B, Séralini GE. Ethoxylated adjuvants of glyphosate-based herbicides are active principles of human cell toxicity. Toxicology. 2013;313(2-3):122-8.
11) Chaufan G, Coalova I, Ríos de molina Mdel C. Glyphosate commercial formulation causes cytotoxicity, oxidative effects, and apoptosis on human cells: differences with its active ingredient. Int J Toxicol. 2014;33(1):29-38.
12) Schinasi L, Leon ME. Non-Hodgkin lymphoma and occupational exposure to agricultural pesticide chemical groups and active ingredients: a systematic review and meta-analysis. Int J Environ Res Public Health. 2014;11(4):4449-527.
13) Heap, I. The International Survey of Herbicide Resistant Weeds. Accessed: Friday, November 7th 2014. www.weedscience.org
14) Tabashnik BE, Brévault T, Carrière Y. Insect resistance to Bt crops: lessons from the first billion acres. Nat Biotechnol. 2013;31(6):510-21.
15) Gassmann AJ, Petzold-maxwell JL, Clifton EH, et al. Field-evolved resistance by western corn rootworm to multiple Bacillus thuringiensis toxins in transgenic maize. Proc Natl Acad Sci USA. 2014;111(14):5141-6.
Today’s post will be a slight departure from the regularly scheduled programming normally available here on marathonsam.com. I believe that you, my gentle readers, will find this content informative and entertaining, but today’s post will be slightly longer on written words and shorter on selfies in spandex.
One of my main goals for this itty-bitty blog is to hone my abilities as an effective science communicator. I’ve explored the data behind the benefits of meditation and tempo runs. I like to learn about the nutrition claims behind some of my favorite “superfoods” whenever I try my hand at recipe writing. I have also, of course, written ranted ad nauseum about climate change.
While I am proud of my previous efforts, each topic deserves more in-depth analysis than 1,000 words and a smattering of selfies. I would love the opportunity to exhaustively investigate a topic over the course of multiple articles. Maybe I’m just catching the “Serial” fever, but I like the idea of rigorously researching and explaining a single issue for you, my gentle readers.
Without further wasted words, let me introduce a new feature for 2015: Marathonsam’s Pragmatic Perspective. As a blogger, scientist, and part-time superhero I get EXCEEDINGLY frustrated when I hear or read pieces by pundits that COMPLETELY over-interpret, misinterpret, or miss the point of a new scientific study. The problem is particularly pernicious when it comes to a ubiquitous, scary-sounding, and poorly understood topic: Genetically Modified Organisms (GMOs) in the food supply. Break out your forks and knives! We are going to learn-along together about franken-fruits and vegetables.
I’ll be writing about just what exactly a GMO is (this becomes trickier to define by the decade), how GMO plants are constructed (we stole a trick from, surprise! Bacteria), whether GMO foods pose a risk to human health (they might, but definitely not in the way that people claim they do), the impacts of GMOs on the environment (negative), the economy (positive…for a select few), agriculture in general (definitely atrocious), and any other juicy topics that I turn up in my research.
Today I’m using some recent news as a jumping off point to begin to address the question: “How the heck do GMOs turn up in our food, anyway?” The USDA just approved a new GMO product for the United States market: a potato, patented by the privately held food and agribusiness company Simplot. Simplot’s potatoes have two claims to fame: they don’t develop brown spots when their flesh is exposed to air, and they don’t produce acrylamide when heated to high temperatures. Simplot is aggressively marketing their special potato to fast food venues—purporting that this technology will yield pristine French Fries with a bonus health boost! For the moment, let’s leave aside the fact that the minute amount of acrylamide generated in potato-flesh at high heat is, frankly, small potatoes health-wise (pun intended) as compared to the truckload of oil, starch, and salt served up with a carton of French Fries. Instead, let’s focus on why this potato represents a few important “firsts” for GMO agriculture.
In order to tackle this question, it’s important to define a few terms. Most GMOs take genes from one organism and splice them into another, producing a hybrid with desirable traits from both. Think of it as technologically advanced extreme selective breeding.
One example of multi-genome-mash-ups is freeze resistant citrus fruit. Oranges are delicious, but their cells burst when temperatures fall; flounders swim happily through sub-freezing waters because their cells make a protein that protects them from the cold. It would be pretty difficult to make a flounder have sex with an orange tree, but swapping chunks of DNA around is as easy as pie. Insert the flounder cold-tolerance gene into an orange’s genome…voila! Cold-tolerant tasty tangerines all winter long!
The cold resistant citrus that I described (which is no longer available for sale in the US, apparently the idea eked out consumers) is an example of a transgenic GMO: an organism that carries genes from a different life form within in its own genome. Bt corn and Round Up Ready soybeans (the most common GMOs in the United States) are also both examples of transgenic technology.
Simplot’s potato is NOT a transgenic. Scientists didn’t add any genes from another organism into its genome. Unmodified potatoes go brown and make acrylamide because of natural processes happening in their own cells. The clever scientists at Simplot just figured out how to turn the dimmer-switch down on these processes. GMOs that don’t have any DNA from different species in their genomes are called cisgenic organisms. Simplot isn’t the first company to make a cisgenic GMO: the widely hyped and widely reviled FLAVR-SAVR tomato was generated using a related strategy.
So why is the scientific community excited about Simplot’s potato? A mildly healthier, more aesthetically pleasing tuber isn’t exactly a cure for cancer. However, this potato is a technological achievement. Simplot’s scientists used a newer technique called RNAi to turn the dimmer switch down on those undesirable genes that cause browning and acrylamide in French fries. RNAi has been kicking around research labs for a few years, but the potato is the first commercial product created with this method.
The second, and more interesting, reason why this potato might represent the start of a sea change for GMOs (in the United States, at least—Europe has highly strict regulations on these types of products) is because of who produced it. Simplot is a giant food and agriculture company, at first glance interchangeable with any other large, soulless corporation. However, the fact that Simplot gained approval for a new GMO product is notable precisely because of whom they are NOT.
Monsanto has been the major player in GMO products in the United States for the past two decades. Monsanto owns the patents on (among other products) Round-Up Ready Soybeans and Bt corn. Given that these two GMOs cover approximately 94% of the agricultural land in America (more on THAT later), Monsanto effectively has a stranglehold on farming in general in the United States, through its dominance of the GMO market. A new GMO gaining approval produced by someone OTHER than Monsanto could portend an important shift in the prevailing winds of commerce.
Or maybe not. Shortly after the USDA approved the Simplot potato, McDonalds publicly announced that it would NOT appear on menus at the golden arches. Anti-GMO advocates tout this as a victory: apparently a GMO potato is simply unpalatable to McDonald’s customers. However, before we start congratulating uncle Ronald McDonald for a principled stance against GMOs, let’s stop to consider what ELSE appears on McDonalds’ menus: burgers (made from corn-fed American beef), soda (made with high-fructose corn syrup), chicken McNuggets (corn-breaded, fried in soybean oil and made from…well let’s just not go there).
I can 100% guarantee that every single drop of corn syrup, and every kernel of livestock feed that goes into producing all of the other McFoods on McDonalds’ McMenus come from GMO sources. GMO corn is ubiquitous in America. McDonalds’ hypocritical high-profile rejection of Simplot’s potatoes does not source from some deeply held concern for their customers’ health. McDonalds made a token anti-GMO gesture, which stifled a potential innovator in the marketplace, while solidly maintaining the status quo. The GMO potato is dead, long live corn, the GMO king.
Personally, I am conflicted about the Simplot potato. I think that it, as a product, is a solution in search of a problem. French fried potatoes are pretty much delivery vehicles for grease, salt, and ketchup.
The world was not clamoring for a spot-free fry. The lower acrylamide levels are interesting, but fries are NEVER going to be a “healthy” choice. McDonalds’ gesture against GMOs is encouraging, yet empty. Monsanto will likely continue to lord over GMOs in general and thus the majority of agriculture for years to come. However, I think that the (non)-story of the Simplot potato nicely illustrates the complexity of the issue. The label GMO encompasses many different types of products. It is not appropriate to casually throw this term around without some understanding of what exactly the particular GMO is, how it was made, and how it is used. I’ll be tackling those topics (and many more) in later posts.
Thanks for reading, I’m interested to know: What is the first thing that pops into your head when you hear the term GMO?
I’m pecking out this post with a spring in my step and a song in my heart, gentle readers. Would anybody care to hazard a guess why this plucky Ph.D. candidate blogger is in such a merry mood?
I’m feeling elated and elevated because yesterday evening was my induction into an organization that guarantees a lyrical and lovely outlook on life. Don’t worry, gentle readers, I haven’t joined a cult or gone gluten-free.
The reason I’m feeling so merry is because yesterday night was my first choir practice with the O.K. Chorale.
I am not a singer by any stretch of the imagination. I did musical theater in high school, and I took a gospel choir class in college, but it’s been YEARS since I have sang in a group. I don’t know how to read music, and I wouldn’t know a harmonic major chord if it bit me in the ass. E sharp major might as well be a hashtag on twitter for all of my music theory knowledge.
Fortunately, the OK Chorale doesn’t care about any of that. Our fearless leader started the rehearsal by emphasizing that the goal of this choir is not to achieve technically perfect four part harmony, but rather to get people singing in a way that works for them. Last night we went over a few of the songs we’ll be learning over the course of the next 8 weeks. I’d like to share these terrific tunes with you, my gentle readers. These melodies are going to be stuck in my mind for the rest of the day, maybe y’all can hum this classic music along with me.
You’re Just in Love (Irving Berlin)
God Only Knows (Brian Wilson)
As you can see, we’re mostly doing classics, with some Irish and Scottish folk tunes. I was pretty thrilled to see some Beach Boys included into the mix. Enjoy the listening.
I apologize for my conspicuous absence during the past few days week. I made such a big deal about announcing my un-retirement, then proceeded to promptly vanish off of the face of the Earth.
I could bore you with an excruciating description of what it’s like to do mutation rate estimation experiments for 12 days in row.
However, this blog is supposed to be a space for things that are amusing and interesting, so I will spare you the gory details of my latest laboratory labors. I grew a bunch of bacteria, I found a bunch of mutants, I made a nice graph about it and then I moved on with my life.
That particular chapter of my research is officially in the history books, so let’s turn the page because today I want to talk about my new winter weather hobby: nordic skate-skiing!
Cross country skiing is an awesome way to get outside during the winter and enjoy some scenery at sub-zero temperatures.
I’ve always enjoyed classic cross-country skiing, gliding over the snow for a three-hour tour is a meditative, low impact way to connect with nature.
Classic cross country is awesome, but I was recently introduced to a faster, fiercer member of the nordic skiing family tree: skating.
My Dad got me in to skate skiing on my most recent visit to Colorado (in case anybody is keeping score, this is that latest in a long string of examples where my Dad inspires me to do something interesting; I refer my gentle readers to : triathlons, cooking, meditation, etc… for other evidence that the apple steals all of his cool ideas from the tree).
I instantly fell in love with the experience of flying over freshly groomed corduroy. Skate skiing is awesome because it combines all of my favorite activities: sweating, wearing spandex, playing in the snow, endurance sports, the outdoors, and stache-sickles.
If cross country skiing is comparable to hiking, skate skiing is analogous to trail running. It’s great to get outside and explore nature. It’s even better to experience the outdoors while exploring your anaerobic threshold. Skate skiing is fun because it happens to be SERIOUSLY difficult.
I was poking around on the internet and found a ton of articles espousing the benefits of skate skiing as cross training for runners. An older, but nicely controlled, European study compared the endurance benefits gained by a group of athletes embarking on either a cross-country skiing or running training program over the course of two successive winters; each activity led to identical performance gains. According to competitor.com, nordic skiers have the highest VO2 maxes of ANY endurance athletes. Nordic skiing isn’t just a great cardio workout in general, the skating motions work some muscle groups in areas that runners are notorious for neglecting such as: shins, ankles, hip adductors and the pelvic girdle, not to mention the solid upper-body workout provided by the poling motion. Also, because skiing is low impact (gliding, rather than pounding), it’s a great option for injured runners to get outside while they recover.
The one disadvantage of skating compared to running is that the sport has a few more requirements than simply: “put on some shoes, then put your feet on the pavement.” You can’t skate without a pair of skis, poles, and the associated accoutrement.
You also need a place to GO once you’ve acquired your gear. Skate skiing is a little different from typical backcountry; you can’t just go tromping through the woods through three feet of fresh powder, those skinny little skis won’t get very far. The ideal substrate for a skating session is nice, cold, hard-packed, freshly-groomed corduroy.
I was nervous about whether it would be easy to go skate skiing in my adopted habitat of Washinton State. Seattle is awesome, but the emerald city loses it’s collective shit and shuts down entirely if it snows an inch within the major metropolitan area.
I needn’t have worried. The Kornsberger Ski Club maintains (and grooms!) roughly 20 km of premium trail-goodness at the Snoqualmie Summit less than an hour’s drive along I-90 from my house!
On Saturday morning I got up bright and early, loaded my skis into my Subaru, and headed east to check out what the Cabin Creek Nordic Ski Area is all about.
I intended to do a quicky 10K loop, but promptly got distracted by a fork in the trail leading to Mt. Amabilis.
The Mt. Amabilis trail is a winding, five mile tour through delightful scenery…straight up a mountain.
My skate to the summit was punishing, but totally worth it for the pristine vistas. The second half of my skating session was certainly a LOT easier (and faster) than the first.
Overall I’m stoked on the fact that I can indulge in my new favorite winter sport while I’m based in Seattle. It was great to get outside and really push myself for a long challenging endurance session. I’m easing my way back into running after a stress fracture right now, which means that my time on my feet on the streets is limited. Covering 10 miles on the snow takes my mind to the same meditative place that I find on my long runs. Even though Cliff Mass’ forecasts are a little grim for the PNW’s downhill ski season, I will DEFINITELY be making more journeys to cabin creek over the next coming weeks.
Happy Monday maniacs! I hope you are starting your week off on the right foot.
I’m still measuring mutation rates, which means growing lots and lots of individual bacterial cultures. These experiments aren’t my favorite thing to do in the entire world, which sometimes makes it a little bit difficult to stoke up my motivation to leave my house for lab in the morning.
I ride my bike to work every day. I love using pedal-power to explore uncharted frontiers, but sometimes wintry weather makes bike-commuting seem downright daunting. Limited daylight, frigid temperatures, and unfriendly weather conspire against even the bravest bicyclist.
Seattle in particular presents a challenge for cyclists. Our winters are rainy and WET.
However, I have a few tricks up my sleeve to avoid the dreaded stripe-up-the-butt syndrome and keep commuting by bicycle through the moist months.
Without further ado I offer you, my gentle readers, in no particular order, my top tricks of the trade to ride through the rain all winter long!
1) GoreTex is a gift from the almighty!
Invest in a high-quality waterproof jacket to keep yourself dry.
2) What you wear to BIKE TO WORK doesn’t necessarily have to be what you wear AT WORK
Even with the very best moisture-wicking, waterproof, ultra-light, technologically advanced fabrics, you still may find yourself somewhat damp when you arrive at your final destination. If you plan ahead, you can avoid the indignity of a damp posterior all day at work. Stash a pair of pants in your backpack before you head out the door, then change when you arrive at the office.
3) Don’t forget about your feet!
Walking around all day with soggy socks is just the WORST. A good pair of cycling booties can help protect your toes. A simpler (and more cost-effective solution) is to carry a spare pair of socks.
4) LIGHT up the night!
Dark and stormy winter mornings come with decreased visibility conditions. As cyclists, we have a responsibility to obey all traffic laws and share the roads. Tragically, far too many bikers are struck by cars each year. In 2012 (the most recent year from which statistics are available) the United States saw 49,000 bicycle injuries and 726 fatalities. “Collision with car” was, and remains, the most common cause of cycling accidents. Even in my fair city of Seattle, with its extensive bike lanes and cyclist advocacy by the Cascade Bicycle Club, accidents still occur. The devastating death of Sher Kung in autumn 2014 was one chilling example of a life cut short because of a driver’s lack of attention. To protect ourselves as we pedal, we cyclists need to be VISIBLE, especially during the dark winter months! Invest in BRIGHT bicycle lights.
Make friends with Neon.
Biking through dark and rainy streets is no time to be a shrinking violet, let your inner raver shine through!
Techno music is optional. Being visible is non-negotiable. Maximize your chances of being seen to minimize your chances of getting hit.
Riding through the rain doesn’t have to be miserable. With a little forward planning, you can arrive at your workplace safely, then dry off and CRUSH IT all day long. Don’t let a little bit of water scare you off of your bicycle for months at a time.
Bike commuting is ecologically friendly, fantastic exercise, and a whole lot of fun. By making a few minor tweaks to your routine you can keep up this healthy habit rain or shine. However, my most important final tip, a principle I apply to every facet of my existence, from riding through the rain or sailing through space, comes courtesy of the Hitchhiker’s Guide to the Galaxy: ALWAYS KNOW WHERE YOUR TOWEL IS!