Genetic Maize » academia

Poster competition woes

Anastasia — Tue, 14 Oct 2008 13:15:33 +0000

One topic of this blog is the graduate student experience, with the aim of passing on a little advice to prospective graduate students. The lesson for today is: stand up for yourself.
Today was the Seventh Annual Norman Borlaug Lectureship Poster Competition For Graduate and Undergraduate Students. I was very excited about the competition this year, because my research is very important to world food issues. The poster is: Characterizing seed storage proteins in teosinte and tripsicum, with the objective statement “To find unique seed storage proteins in relatives of maize that might be used to improve maize nutritional qualities.” I like to imagine that Norm Borlaug would approve. I purposefully chose a table at the opening of the room, just as I did last year, so I would be easily noticeable. I even brought samples of the seed so people could see for themselves how different teosinte and tripsicum are from maize, because everyone likes hand-on science. I thought I did all the right things to make a good showing, even if my poster wasn’t the best. Unfortunately, the judging was less than smooth.

Each poster was assigned two judges from a pool of about six judges. My first judge, who I’ve interacted with before, read my poster and joked with me for a bit. I was concerned that he didn’t ask many specific questions about my research. His last question was “how would this affect food policy?” I talked about intellectual property, and how we should somehow compensate people who “own” wild plants or at least not profit from the commons, but I’m not a lawyer, policy maker, or ethnobiologist. I did my best and felt fairly confident.
At some point, one of the judges came by to talk to me about my poster, but he specifically said that he wasn’t my judge. We talked a bit about protein identification (he’s a protein chemist) and he gave me some great tips on how I might be able to better separate my proteins with SDS-Page.
Then, I waited. For over an hour, I waited for a second judge to come by. Multiple times, I commented to the poster competition coordinator that I had only been judged once, and asked if she could tell me who my judges were. She sort of politely walked away, but never told me who my judges were. Finally, I noticed the judges sitting down together, presumably to compare results. I again reminded the coordinator that I was only judged once. She walked away.
At the end of the event, I asked the coordinator what I could do next year to ensure that I was judged by two people. She said that two people did judge me, she saw their score sheets. I asked if I could have their comments, so as to learn from them, and she said she didn’t think so because the judges left and took their score sheets.
My husband says that I wasn’t forceful enough, that I should have walked up to the judges’ huddle to ask why I wasn’t judged twice. He says that I should talk to my major professor about this and ask him to intervene on my behalf, to ensure that this doesn’t happen to another student (or to me next year, if I decide to enter). I’m not sure what to do, or if I should do anything. Should I have been more forceful at the competition? Am I being a push-over? Advice on this would be appreciated.
Maybe my poster is terrible, maybe I’m just horrible at presenting myself and my research. Maybe I’m just not a winner. Ok, I can work on those things, if necessary. I’m not really concerned about that, though. What concerns me is that I was ignored, and what concerns me even more is that this isn’t the first time.
Last year’s poster was Bioavailable iron in maize endosperm can be increased with overexpression of maize hemoglobin. Here’s what I wrote in my LiveJournal on Oct 16th 2007 after the poster competition:

I presented my first poster tonight at the World Food Prize Lecture. Overall, it was nice. I got to explain this really awesome research to people, and they understood. They walked away having learned about something totally new, something that could really impact world health. My major professor thought it was good, and so did the project leader professor. The judges, however, not so much. We were supposed to be judged by two people. The first asked me to explain my poster. Unfortunately it was the first time I’d been through it, so I was a little awkward. I don’t think I was terrible, though. Then he asked how I thought the research would affect policies on GMOs. I really felt like he was baiting me, even though he has similar ideas about it all. I mean, how are my personal feelings on these issues relevant to the research? Anyway, I was trying to explain that RoundUp Ready is fundamentally different from our high iron maize because ours improves nutrition while RoundUp Ready encourages the use of additional pesticides. He told me that RoundUp is not a pesticide. I said a pesticide is any chemical that is used to kill pests, such as fungicide, algicide, etc. He said that I needed to go look up the definition of pesticide. Dude, I gotta tell you, I’ve been a DoD Certified Pest Controller for 8 years. I think I know what a pesticide is. I told him that I agree that technology such as BT actually has a huge environmental benefit but that I believe our research would be more palatable to laymen. He didn’t get it. The second judge listened to a few minutes of the pesticide conversation, then left without returning. I feel discriminated against. Most of the poster winners had posters about growing gardens in African villages. Horray for the villagers having eggplant (I still don’t understand why the eggplant, as it has no nutrients, according to Alton Brown, but whatever) but this is not research. Yes, you proved that people with food are better off than people without food. Good job. The project I’m working on will take time, yes. However, the results are really promising. Alleviating iron deficiency in the world would be massive. As far as I’m concerned, they were being short-sighted. Oh, and just to clarify, I’m not bothered by not winning, I’m bothered by having my intelligence insulted by one judge and by being ignored by the other. Whatever.

Life cycle analysis in animal agriculture

Anastasia — Tue, 23 Sep 2008 10:47:32 +0000

In Reducing the environmental impact of farming, I talked about Nathan Pelliter’s work on Agricultural Life Cycle Analysis as a way to evaluate which farming methods have the least environmental impact. While the ideas apply to any type of farming (or really to the production of anything), his main work is actually on animal agriculture.
The return on investment of most types of animal agriculture is small compared to that of plant agriculture. For example, cattle require about 6 pounds of feed to produce 1 pound of muscle. All of the water, fertilizer, and pesticides required to grow 1 pound of plant material is thus multiplied by 6 to produce 1 pound of beef. Granted, it isn’t quite that simple, as parts of plants that aren’t used for human food can be fed to animals, but the point holds, even in organic systems.
Demand for animal protein is increasing rapidly both in developed and developing countries. This means that the amount of land used to produce food for animals will also increase. Some lands that aren’t suitable for plant agriculture may be better put to use as pasture land, but those areas can not possibly supply per capita demand for meat – more than 200 lbs per year per person in the US, according to the USDA (and that’s an average, theoretically factoring in the 3.2% of vegetarian and vegan Americans). This image from the University of Arizona concerning the uses of the US corn crop is a little old, but is essentially still true (and the story is similar for soybeans).

Ironically, many people condemn corn ethanol as wasteful and environmentally damaging but continue to consume animal products that account for a far higher percentage of the US grain crop – but that’s another story.
So, what are we to do? The planet would breathe a metaphorical (metaphysical?) sigh of relief if each person just ate lower on the food chain a few meals per week (see Nathan’s pictorial presentation Calories in Context). We’ve been told to reduce meat consumption for our health and for the planet, but it seems like no one is listening. Nathan’s response to the environmental degradation associated with animal protein production is to use LCAs to find which types of animal agriculture provide the most return on investment. At his seminar at Iowa State, I asked how his results can be used to influence consumer habits. We talked about possible taxes based on environmental impact so that food prices reflect the actual price to the environment, but we’ll leave that to the economists.
Nathan, along with Peter Tyedmers, wrote about LCAs in Biophysical accounting in aquaculture: insights from current practice and the need for methodological development, which was part of the FAO Fisheries document Comparative assessment of the environmental costs of aquaculture and other food production sectors. One of the most striking tables in the paper was a ranking of foods “by ratio of edible protein energy output to industrial energy inputs” on page 234. Intensive carp farming is by far the most efficient (when done properly, carp is even better than plants), while cultured shrimp grown in Thailand are by far the worst. Pastured beef is better than feedlot beef (barely), and industrial eggs are a terrible waste of inputs. See the full table at the end of this post.
Industrial energy inputs only tell part of the story, though, because they do not consider any negative outputs like waste or negative effects like spread of disease to wild populations. Ecological impact assessments also do not consider many effects. That’s why we need LCAs. According to the paper, LCAs frequently consider the following Impact Categories:

Impact Category	Description of Impacts
Global Warming	Contributes to atmospheric absorption of infrared radiation
Acidification	Contributes to acid deposition
Eutrophication	Provision of nutrients contributes to Biological Oxygen Demand
Photochemical	Oxidant Formation Contributes to photochemical smog
Aquatic/Terrestrial	Ecotoxicity Creates conditions toxic to aquatic or terrestrial flora and fauna
Human Toxicity	Creates conditions toxic to humans
Energy Use	Depletes non-renewable energy resources
Abiotic Resource Use	Depletes non-renewable resources
Biotic Resource Use	Depletes potential primary production
Ozone Depletion	Contributes to depletion of stratospheric ozone

Nathan and Peter have focused on salmon farming, which can greatly benefit from LCAs. Production of feed is the most energy intensive and environmentally damaging aspect of aquaculture (and all animal agriculture). Replacing conventionally grown plant based feed with organic had a little effect, but replacing animal based feed with plant based has a huge effect. Some might say that we should just eat wild salmon instead, but again, the problem is demand. Wild salmon would be extinct if we tried to supply the current demand with them exclusively.
All of the options are complex, but two lessons of LCAs stand firm – reduce or eliminate synthetic nitrogen fertilizer (which can be done at least partially with genetic engineering), and decrease per capita meat consumption.

Food Type	technology, environment, locale	Protein Energy Output/Industrial Energy Input (percent)
Carp	extensive freshwater pond culture, various	100 – 11
Herring	purse seining, North Atlantic	50-33
Vegetable Crops	various	50-33
Seaweed	marine culture, West Indies	50-25
Chicken	intensive, U.S.A.	25
Salmon	purse seine, gillnet, troll, NE Pacific	15 – 7
Tilapia	extensive freshwater pond culture, Indonesia	13
Cod	trawl and longline, North Atlantic	10 – 8
Mussel	marine longline culture, Scandinavia	10 – 5
Turkey	intensive, U.S.A.	10
Carp	unspecified culture system, Israel	8.4
Wild caught seafood	all gears, marine waters, global average	8
Milk	U.S.A.	7.1
Swine	U.S.A.	7.1
Tilapia	freshwater unspecific culture system, Israel	6.6
Tilapia	freshwater pond culture, Zimbabwe	6
Shrimp	trawl, North Atlantic and Pacific	6.0 – 1.9
Beef	pasture-based, U.S.A.	5
Catfish	intensive freshwater pond culture, U.S.A.	3
Eggs	U.S.A.	2.5
Beef	feedlot, U.S.A.	2.5
Tilapia	intensive freshwater cage culture, Zimbabwe	2.5
Atlantic salmon	intensive marine net-pen culture, Canada	2.5
Shrimp	semi-intensive culture, Colombia	2
Chinook salmon	intensive marine net-pen culture, Canada	2
Lamb	U.S.A.	1.8
Seabass	intensive marine cage culture, Thailand	1.5
Shrimp	intensive culture, Thailand	1.4

Reducing the environmental impact of farming

Anastasia — Sat, 13 Sep 2008 02:34:19 +0000

Atmospheric concentrations of greenhouse gasses are rising, but reducing them isn’t as simple as taking cars off the road. A significant part of the problem rests is agriculture. What is it about agriculture that is such a problem and how can we develop changes that will have the most benefit?
Agricultural Life Cycle Analysis is a useful tool in collecting information and making decisions. LCAs take every input and every output into consideration including difficult to consider ouputs like greenhouse gas emissions.
Nathan Pelletier from Dalhouse Uni in Nova Scotia presented his work on ag LCAs at Iowa State recently. He explains that actually conducting LCAs can be difficult. First, we need to define the scope of the analysis. For example, if we consider milk production, we should likely include the cow herself, food, water, and waste. We probably should include all of the inputs and outputs associated with feed production and transportation. We might include the inputs and outputs of pasteurizing and transporting the milk. Also difficult is actually quantifying all of the inputs and outputs to air, soil, and water. Finally, it is difficult to complete a meaningful impact assessment including the identification of “hotspots” or most negative impacts. Despite the difficulties, LCAs are worth the effort. Nathan reminds us that agriculture produces 1/3 of global warming emissions. The demand for food will will double by 2050, so we need to half the impact to continue a constant level of damage.
Nathan used LCAs to evaluate different cropping systems. He found that fuel and field emissions for a variety of crops was similar for organic and conventional (although he did not account for the vast variability in each category). It’s surprising that the field emissions were not different, but we have to consider that many conventional farms are no till, instead treating for weeds with pesticides like Roundup. I imagine that the overall number of times a farmer drives over his field is similar, accounting for the similar fuel costs, even though the reasons might differ.
Even though overall farming methods don’t make that large of a difference with regard to greenhouse gasses and other negative outputs, nitrogen fertilizer source has a huge effect. Synthetic N, commonly used in conventional farming, is produced with natural gas, and CO2 is a coproduct of the process. Additionally, because of the type of N that is applied, not all of the applied N is taken up by plants, leaving the rest to evaporate as greenhouse gases or to be washed off the land into streams, rivers, and oceans.
The issue of replacing synthetic fertilizer is very complex, though, because we need to consider so many factors. For one, transporting and spreading organic N sources like manure is costly because a lot of weight is needed to provide enough N to see yield increases. Transporting and spreading all of this weight has its own greenhouse gas issues. If we use manure, the animals need food, water, and land, but some of this is offset because the animals themselves are a valuable output. Crop rotation is another option, but depending on the plants used, more land will be needed to produce the same amount of food. Nathan’s models considered out of season cover crops as non-synthetic N sources, but this method might not produce all of the N that is needed for various crop types and soil types.
It is possible that the complications of alternatives make synthetic nitrogen seem more attractive. However, a lot of these drawbacks might become non-issues when fuel costs cause synthetic N, P, and K prices to skyrocket. As you can see, deciding how to best fertilize your crops is far from easy.
One way to at least decrease the N problem is with genetic engineering. Newly developed “nitrogen use efficient” or NUE crops are able to take up more of the nitrogen that is applied, leaving less to run off. This, in combination with optomized nitrogen application techniques, could significantly decrease the amount of N needed. I asked Nathan what he thought about NUE but he said he didn’t know much about it. I hope he looks into it, because NUE crops would be useful no matter what type of fertilizer is used.
Nathan’s work with LCAs included an analysis of various types of animal agriculture, which I’ll save for another post.

Even scientists make mistakes

Anastasia — Fri, 12 Sep 2008 13:25:58 +0000

I went to a seminar titled “Harvesting ecosystem services from cellulosic biofuel landscapes” at Iowa State yesterday. The speaker was Michigan State Professor of Entomology Douglas Landis. His research is very practical, focusing on which types of plants should be used in biomass production for biofuels to encourage the highest biodiversity of insects. This is important because insects provide many ecosystem services, including pollination and predation of pests.
His work shows that switchgrass and mixed prairie encouraged higher numbers of some native insect species, but also encouraged some invasive insects. Corn likewise had mixed results (especially encouraging native insects that like to eat corn!). His methods of data collection are simply fun – low tech but effective – nets, sticky traps, leaf blowers turned into vacuums, and such.
It’s good work, because we really need people working on the sustainability issues associated with farming. Growing biomass for fuel, as any farming, could be beneficial or detrimental to the environment – it’s up to people like Dr. Landis to make sure it’s the former.
Unfortunately, Dr. Landis seems to be misinformed on one issue – Bt crops. I won’t go into too much detail here, but Bt crops have been shown to increase insect biodiversity because overall levels of pesticide are decreased. I would have thought that an entomologist concerned with biodiversity would at least contemplate a cost-benefit analysis of Bt.
In the introduction of his talk, Dr. Landis mentioned the 2007 PNAS paper “Toxins in transgenic crop byproducts may affect headwater stream ecosystems”. This paper is more than a little controversial, because the authors make broad claims that do not follow from their results. The authors make the typical mistake of lumping that is never appropriate in science. All Bt is not the same, all aquatic insects are not the same, all corn fields are not managed in the same way… Dr. Landis should have at a minimum mentioned that the paper has been contested before trotting it out as evidence.
I wrote about the press release of the paper when it first came out, and I continue to be frustrated by the mediocre science and the terrible way that people twist results to make the point they want. Feel free to read the paper for yourself, but don’t pass up the rebuttals. Beachy, et. al. make the point that papers like this are taken by the popular media and used to fuel debates – regardless of the strength of the science. It truly is the responsibility of every scientist and especially of every reviewer to put aside personal bias for or against the paper and make sure the conclusions are supported as much as possible by hard evidence. The reviewers of this paper should have sent it back, requesting some of the experiments explained in the rebuttals (such as dose-response measurements, as suggested by Parrott).

Dr. Landis showed this pair of images from the Rosi-Marshall paper, implying that corn residues in streams are all the fault of genetic engineering, as if organic corn crops or other crops in general don’t clutter up streamheads. He seems to think that harvesting switchgrass or mixed prarie would somehow not leave the same sorts of residues in streams.
Of course, all crops are going to leave residues in nearby streams, plant matter that is not a natural part of the ecosystem. What I find most ironic is that, if crop residues actually do damage streams, we should start harvesting them for biofuels right now!
To make things even worse, Dr. Landis told the audience (full of impressionable sustainable ag majors) that “the Bt toxin leaches from crop residues into streams where it kills aquatic insects.” This statement is wrong for a lot of reasons, the main one being that there is zero evidence that Bt leaches from the plants that produce it. If you know of any evidence showing that it does, please let me know, but I’m not going to hold my breath.
E. J. Rosi-Marshall, J. L. Tank, T. V. Royer, M. R. Whiles, M. Evans-White, C. Chambers, N. A. Griffiths, J. Pokelsek, M. L. Stephen (2007). Toxins in transgenic crop byproducts may affect headwater stream ecosystems Proceedings of the National Academy of Sciences, 104 (41), 16204-16208 DOI: 10.1073/pnas.0707177104

God is ok with evolution, really.

Anastasia — Wed, 30 Apr 2008 03:36:59 +0000

There’s been a bit of controversy lately at Iowa State on the subject of “intellectual suppression” of intelligent design. Some pent-up drama from Dr. Guillermo Gonzalez’s tenure denial is still around, and Expelled brought the beast back to life. Of course, having Dr. Hector Avalos here helps to keep things interesting. The first ISU Daily article in this round, “Avalos: ‘Expelled’ wrong on Holocaust” has accrued almost as many comments and letters to the editor as the articles about Gay Pride week. The whole subject is frustrating, because I don’t think there is a controversy. No one should dictate what religious beliefs a person can or can not have.

In this country, separation of church and state is a necessity (due to the many faiths or absence of faith present). Therefore, religion can not be taught in state funded schools. Period. If people want to study things other than approved evidence based curricula, they are welcome to do so at home. Dr. Gonzalez is also welcome to study these things, but not while he is on the payroll of a public university to study science. If he was a religious studies professor, things would have been entirely different. The NY Times reports today about Dr. Francisco Ayala, a former Dominican priest and current evolutionary biologist and geneticist at UC, Irvine. Dr. Ayala’s thoughts on the ID / Evolution controversy are amazing, unlike any I have every seen. The article is: “Roving Defender of Evolution, and of Room for God”, which I learned about from the Knight Science Journalism Tracker.

Dr. Ayala [said] that evolution is a well-corroborated scientific theory, but also that belief in evolution does not rule out belief in God. In fact, he said, evolution “is more consistent with belief in a personal god than intelligent design. If God has designed organisms, he has a lot to account for.”

Consider, he said, that at least 20 percent of pregnancies are known to end in spontaneous abortion. If that results from divinely inspired anatomy, Dr. Ayala said, “God is the greatest abortionist of them all.”

Or consider, he said, the “sadism” in parasites that live by devouring their hosts, or the mating habits of insects like female midges, tiny flies that fertilize their eggs by consuming their mates’ genitals, along with all their other parts.

These things makes sense when we consider evolution, but seem absolutely horrible if directed by intelligent design! These and other examples are presented in his book: “Darwin’s Gift to Science and Religion.” According to the comments on Amazon, the book is a straightforward introduction to the ID / evolution controversy. COI Statement: I was elected President of ISU Atheist and Agnostic Society on the day of Dr. Avalos’s lecture (that’s me in the front row of the top photo).

Media Credit: Manfred Strait. Caption:Hector Avalos, professor of religious studies, is applauded at the end of his lecture in response to the anti-evolutionary film Expelled by members of the Atheist and Agnostic Society along with the rest of the room on Tuesday, April 22nd. Avalos was highly critical of the emotional, rather than fact-based approach of the documentary. Photo: Manfred Strait/Iowa State Daily

Brain doping to further science

Anastasia — Thu, 10 Apr 2008 12:17:17 +0000

The 10 April Nature presents the results of a survey that aimed to determine how many scientists are using cognition enhancing drugs. Caffeine is of course the most widely used stimulant, but it seems that quite a few people are using other substances to improve concentration.

For those who choose to use, methylphenidate was the most popular: 62% of users reported taking it. 44% reported taking modafinil, and 15% said they had taken beta blockers such as propanolol, revealing an overlap between drugs. 80 respondents specified other drugs that they were taking. The most common of these was adderall, an amphetamine similar to methylphenidate. But there were also reports of centrophenoxine, piractem, dexedrine and various alternative medicines such as ginkgo and omega-3 fatty acids.

The article, Poll results: Look Who’s Doping, reports that 1 in 5 respondents said they had used the drugs, and that all ages reported use. The whole thing started with an April Fool’s Joke by the Academic Editor in Chief of PLoS Biology! Evolutionary biologist Jonathan Eisen of UC Davis discloses all on his blog. Even thought it started with a joke, this brings up some very interesting ideas about human enhancement. Would it be so bad if people who need pinpoint concentration had the option of using a drug like Ritalin? Would they (we) be more productive, better scientists? I’m not sure. My recreational drug use currently consists of coffee and the occasional glass of wine. I don’t know if I’d try anything else. Even if I didn’t choose to use, I wouldn’t prevent others from using – the same way I feel about low-side-effect drugs like marijuana.
The editorial Defining ‘natural’, in the same issue of Nature, explores the idea that the definition of ‘natural’ should change over time, as technology makes more things possible.

Devices such as glasses, hearing aids, pacemakers and artificial hips are unnatural. Yet they are widely accepted as legitimate ways to enhance the human experience. By the same token, if drugs enhance performance on a standardized test, what is so ‘natural’ about prep courses designed to improve scores?

I heartily agree. We should always examine the ethical issues – but not let ethics overwhelm us. An aside of the Look Who’s Doping article, Worrying Words, lists the four major ethical problems associated with neuroenhancing drugs, confirmed by quotes from poll respondents:

Safety – “The mild side effects will add up to be profound in due course and may even require stronger therapy to control the addiction.” 26–35 years old from Nigeria

Erosion of character – “I wouldn’t use cognitive enhancing drugs because I think it would be dishonest to myself and all the people who look to me as a role model.” 25 or younger from Guyana

Distributive justice - “Morally puts a disadvantage to people without access.” 55–65 years old from the United States

Peer pressure – “As a professional, it is my duty to use my resources to the greatest benefit of humanity. If ‘enhancers’ can contribute to this humane service, it is my duty to do so.” 66 or older from the United States

These are all valid issues, but we can not ignore the possible positive ramifications of these drugs. All sorts of professionals might benefit from enhanced concentration. Breakthroughs in science may take less time. This idea of ethical problems vs benefits is so similar to the arguments for and against genetic engineering. I hope we can all come to a satisfactory compromise on these and other issues facing science.
Note: A lot of scientist bloggers include some posts about academia, graduate student life, etc. I plan to start posting more on these topics.