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Bloggers on the Maize Genome

Update: PolITiGenomics just posted a piece on the corn genome as well.

You know I could keep talking about the maize genome all day (and I may very well do just that), but what are other bloggers saying about the most complicated plant genome ever published, of second most important single species for feeding people around the world? (Clearly I’m not at all excited) (more…)

It never rains but it pours (more analysis of The Organic Center report)

Just this morning I was talking about how I’d hope to see more analysis of The Organic Center’s report on genetic engineering’s effect on pesticides. Just a little while ago I was able to point to a discussion of problems with some of the numbers behind the report. Here’s more perspective (this time from Steve Savage on sustainablog), which brings up another key point I didn’t consider. Much of the increase in pesticide use attributed to herbicide tolerant crops actually came in 2007-2008, the same year that food prices spiked around the world:

There is an old saying – “the best cure for high food commodity prices is high food commodity prices.”  When grain prices are high, growers respond by planting more acres (=more chemical use) and by applying more crop protection chemicals to the crop they grow so that less of this more valuable yield is lost to pests.  Its really simple, rational economics.  Also, remember that the irritating, but not large, food price increases American consumers saw in 2007/8 corresponded to a huge swing in the percent of the family budget spent on food in poor countries.  There were even food riots and export restrictions.  The fact that American farmers ramped up production was a good thing for poor people and the chemicals were part of that.

Bruce Sterling and Kim Stanley Robinson on Climate Change

This post was followed up by More on Why Science Isn’t a Perfect Fit with the Left or the Right

Bruce Sterling writes science fiction cyber-punk. Kim Stanley Robinson writes enormous science fiction trilogies. One on terraforming mars (Red Mars, Green Mars, and Blue Mars) that I read when I was younger and space mad. He’s also put out a more recent trilogy (40 Signs of Rain, 50 Degrees Below, and 60 Days and Counting) which I haven’t had a chance to read yet, but I’m told is quite good, and that at least the first book presents an accurate and depressing picture of the process for funding NSF grant proposals. Not something I want to think about I’m ~24 hours from submitting my own.

Kim Stanley Robinson recently did an interview for his new book Galileo’s Dream (you can find the whole text here). It’s a great read, although there’s plenty of stuff I disagree with.

One thing happening is that the Republican Party in the USA has decided to fight the idea of climate change (polls and studies show the shift over the first decade of this century, in terms of the leadership turning against it and the rank and file following), which is like the Catholic Church denying the Earth went around the sun in Galileo’s time; a big mistake they are going to crawl away from later and pretend never happened. And here the damage could be worse, because we need to act now.

What’s been set up and is playing out now is a huge world historical battle between science and capitalism. Science is insisting more emphatically every day that this is a real and present danger. Capitalism is saying it isn’t, because if it were true it would mean more government control of economies, more social justice (as a climate stabilization technique) and so on. These are the two big players in our civilization, so I say, be aware, watch the heavyweights go at it, and back science every chance you get. I speak to all fellow leftists around the world: science is now a leftism, and thank God; but capitalism is very, very strong. So it’s a dangerous moment. People who like their history dramatic and non-utopian should be pleased.

Reading the answer to this question made me feel a little weird about Mr. Robinson’s claiming of science for one side of the political debate (and also not a big fan science vs. capitalism, the climate change debate is more about the split between short and long term planning). Science isn’t a side in the political process, it’s a set of knowledge and tools that are openly available to all and political movements are free to either accept them, or, as sadly seems more common, toss them aside. Which is why Bruce Sterling’s response cracked me up: (more…)

How to Maintain Anonymity when Rejecting a Paper

Was just forwarded a hilarious post over at scienceblogs. Apparently researchers who are asked to review scientific papers* have to worry about a fair bit about being identified even though comments are supposed to be anonymous…especially if the researcher in question is giving the paper negative reviews.

Many specific fields of research aren’t that big, so an author receiving a paper back with negative reviews can often make educated guesses about who rejected the research he’d spent grant money like it grew on trees, and poured out grad students’ sanity like water to accomplish.

This post proposes a set of tactics for disguising your identity, though not with a straight face. Tactics include: Pretend to be British, pretend to German, pretend to be an American pretending to be German (if you are german), and my personal favorite, pick someone you don’t like and pretend to be them:

Pick one of the people from you own list of 5-6 enemies and pretend to be that person. Heavily cite their work. Reference their obscure conference presentations. Arrogantly suggest that person’s methods in favor of the methods used in the paper, especially where they are clearly inapplicable.

*Since the people who work as editors at the various journals can’t be the top experts in every fascet of the scientific work they cover (and even if they could be, leaving the decision on what science was worthy of publication in the hands of so few might make bias a little too tempting.) The solution is to have the scientific merit of scientific publications submitted for publication evaluated by a group of anonymous researchers, working in the same field. This, usually, makes sure the people reviewing the paper are up-to-date on the science and techniques involved, and since different papers are reviewed by different scientists, there’s less danger of personal opinions biasing the direction of published research. This method of evaluating the validity and relevance of scientific publications isn’t perfect, but it’s the best system we’ve come up with so far for advancing the understanding of the scientific community.

Giant Vegetables and Fruit

Hey folks. I announce I’m going to be working on my NSF fellowship application all week and you all go break the daily traffic record. At this rate you’ll convince me to spend every week writing grant proposals!

What’s a guy gonna do? Apparently dig up more content to show you guys. Here are some cool pictures of giant fruits and vegetables. The giant pumpkin at the end is a particularly awesome 1725 pound monster.

There are also some pictures of things like giant burgers or giant pizzas but I just have trouble getting as exciting about huge versions of prepared food. Given sufficient money and time, humanity could produce a burger much heavier than 150 pounds or a pizza much wider than 42 inches. The size of these food items is limited solely by human motivation.

Cool mutants and horticultural tricks are way more exciting. 😉

Updating the Blog-roll Again

I’ve found two new blogs to link to.

Sustainablog

When Biofortified linked to Steve Savage’s post The Bizarre, Modern Coalition of Anti-Science Forces my first thought was “how can it be I’ve never seen this site before?”

Science has a tendency to tell us some things we don’t want to hear at times – something that challenges our core pre-suppositions. Sometimes what science tells us really matters, so just rejecting it or ignoring it can have serious consequences.

I’ve been following the updates ever since and it’s definitely a good place to check out, especially Steve Savage’s work.

Good to Grow

I try to avoid getting attached to new blogs. Keeping up with posts is hard work, it’s not always rewarding, and the internet is littered with abandoned blogs. Good to Grow is a less than a month old plantie blog*, but so far the author has been keeping up a good pace of updates and once I’d learned how easy it would be to steal a piece of my roommate’s Jade plant I was hooked. The fact that a person can make many more Jade plants starting with a single plant gets back to this morning’s post about how plants breeds are a non-rivalrous good.

*Plantie: Like foodie only focused on the growing of plants rather than the preparation of food. I’m started to discover a whole world of plantie blogs through PlantsAreTheStrangestPeople . I don’t know if they already have a better word to describe their area of interest. I suppose horticulture fits pretty well but maybe it sounds too intimidating?

Disease Resistance and Diversity

Matt has a great new post up on The Scientist Gardener called The Myth of Monocultures. He gives talks about the PBS special on Michael Pollen’s Botany of Desire (which I still need to watch myself), addresses some misconceptions about diversity and monoculture and talks about the best way to ensure crops aren’t wiped out by pathogens that can evolved to overcome a single resistance gene:

Theoretically, it would be useful to maintain crop populations with diverse resistance genes. The industrial application of this (multilines) invovles breeding many different versions of a favorite crop variety that are identical except for their resistance genes. As appealing as this idea is, it hasn’t really worked out in the real world. The alternate approach (pyramiding) seems to be more effective. Here, many different resistance genes are combined into a single crop variety. Pests and pathogens may be able to overcome a single gene at a time, but it’s usually almost impossible to simultaneously overcome several.

Think of it like the story of the three little pigs. [spoilers ahead ;)] (more…)

Microbial Art

Check out some of the gorgeous art people can make in petri dishes.

Clearly the people who create these have far steadier hands than I do when it comes to smearing out colonies.

by Niall Hamilton

by Niall Hamilton

Relaunched Tomorrow’s Table

Yesterday I linked to Pamela Ronald’s relaunched blog at Scienceblogs. There are over one hundred million blogs on the web (and that’s already an outdated number). Many are abandoned, as for all intents and purposed jamesandthegiantcorn was this summer, but even so, simply getting heard over the background noise is a struggle.

Becoming part of a popular and well known community greatly increases those odds of having the voice to each a substantial audience. It’s been a real treat to follow the discussions the posts of the new Tomorrow’s Table have already launched. I highly recommend checking them out.

I can also speak from personal experience in saying that increased traffic and comments definitely make updating a blog more exciting, which in turn leads to more interesting, and just plain more, updates. And so-on in one of those wonderful positive feedback cycles. Given that I expect we’ll be hearing a lot more from Tomorrow’s Table in the future.

I also hope it is ok that I am a litte envious. Will just have to use it as a motivation to work even harder both here and on my actual research.

Putting Prejudice over Science

I read this when it came out, but it was before I’d restarted the site full time, and Pamela Ronald restarted the discussion over on scienceblogs today. Back in May the USDA posted a report on their website about how allowing genetically engineered crops to be certified as organic would have positive environmental effects.

Needless to say the organic movement was not pleased, and the report has since been pulled from the website. Now I previously celebrated the idea that the Obama administration was going to let organic and biotech go head to head and take the best parts of both. I’m confident in the benefits of genetic engineering when people judge the technology based on the data instead of preconceived opinions.

Making reports disappear because they step on the toes of well connected interest groups is not letting the data speak for itself.

h/t’s to Tomorrows Table and Biofortified.

And hey, if you’re willing to spend 10 minutes you can register and vote for Biofortified in the Ashoka Changemakers Contest. There’s a good chance you’ll help win $1500 to support a website fighting the good fight to correct the misinformation about genetic engineering, but even more importantly from my perspective, winning this contest means the guy on the left (yes he’s wearing a corn cob patterned t-shirt) will get a chance to meet with Michael Pollen. There’s also a stuffed corn cob with glasses in the picture.