James and the Giant Corn Genetics: Studying the Source Code of Nature

November 7, 2009

Figure from my Research Proposal

Filed under: biology,research stories — Tags: , , , , , — James @ 7:17 pm

“My budget…triples the number of National Science Foundation graduate research fellowships.  This program was created as part of the space race five decades ago. In the decades since, it’s remained largely the same size –- even as the numbers of students who seek these fellowships has skyrocketed.  We ought to be supporting these young people who are pursuing scientific careers, not putting obstacles in their path.” – President Obama

I’m still feeling brain dead after the final push for submitting.

Speaking of NSF, here’s the one figure I managed to shoehorn into my research proposal.

Blast hits between an orthologous quartet of gene spaces, one in rice, one in sorghum and the two copies created by the maize tetraploidy.

Blast hits between an orthologous quartet of gene spaces, one in rice, one in sorghum and the two copies created by the maize tetraploidy. As usual click the picture to see it fullsized

If you’d like you can even click here to be able to play around with the figure yourself using the CoGe interface. Now I’ve got to try to explain what this figure is about. (more…)

November 6, 2009

It is Done

Filed under: biology,research stories — Tags: , , — James @ 4:21 pm

NSF fellowship application complete and submitted with just under an hour and a half to spare before the deadline. More inside. (more…)

More on why Science Isn’t a Perfect Fit with the Right or Left

Filed under: Politics — Tags: , , — James @ 2:40 am

In a follow up to my post yesterday afternoon.

The opponents of science are those who put ideology over empirical facts, putting how they want the world work over how data shows the world actual does. On one side the extreme left is fine with the observational side of science telling us everything that’s wrong with the world, but when scientists try to come up with ways we could try to solve those problems, we get shouted down. Since I’ve written plenty about genetic engineering, consider how Steve Levitt, the author of Freakonomics*, was received when he simply suggested we should evaluate geo-engineering techniques as one of the ways to mitigate climate change.

The Daily Show With Jon Stewart Mon – Thurs 11p / 10c
Steven Levitt
www.thedailyshow.com
Daily Show
Full Episodes
Political Humor Health Care Crisis

Or watch the interview of Bill Frist (a former Republican Senator) with Bill Maher, and cringe at the discussion of vaccines.

On the other hand the extreme right is mostly ok of with all the goodies scientific reseach produces: modern “Western” medicine (including vaccines and antibiotics), genetically engineered crops, computers, and microwaves. But when it comes to believing anything science tells us from “hey, the planet is getting warmer” to evolution (without which, let me tell you, comparative genomics would be a very boring field of study, an I’m not bored, I’m fascinated!), to not so much.

I am exasperated with the world. Try back tomorrow.

*Freakonomics is a fascinating read. I haven’t had the chance to read Superfreakonomics, which is what apparently generated this controversy.

November 5, 2009

Bruce Sterling and Kim Stanley Robinson on Climate Change

Filed under: biology,Link Posts,Politics — Tags: , , — James @ 4:44 pm

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…)

Why Don’t People Like Corn?

Filed under: agriculture,Feeding the world — Tags: , , — James @ 4:13 am
My favorite crop, but many people don't seem to care for it these days.

My favorite crop, but many people don't seem to care for it these days.

I read an interesting question on the still growing thread on the problems with CSI: Miami’s “Bad Seed” episode.

Between this episode and some other stuff I’ve heard about corn, I started wondering what all the concern is about corn lately. … Can you now help shine some light on why the corn industry has been getting such a bad reputation lately? (more…)

November 4, 2009

How to Maintain Anonymity when Rejecting a Paper

Filed under: Link Posts,research stories — James @ 12:42 pm

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.

November 3, 2009

Giant Vegetables and Fruit

Filed under: Link Posts,Plants — James @ 3:46 pm

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

Filed under: Link Posts — James @ 12:42 pm

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?

Sugar Belle Citrus and Patents

Filed under: agriculture,biology,Plants — Tags: , , — James @ 2:02 am
Mandarin Orange (Not a Sugar Belle)

Mandarin Orange (Not a Sugar Belle) from dungodung on flickr

We’ve been talking about grains and genetic engineering strait for a few days, so I thought it’d be the perfect time to put up a story about conventionally bred citrus. The University of Florida put out a press release about a new mandarin orange breed developed by Fred Gmitter, called Sugar Belle. The fruit is of course described as delicious and it may well be, I can’t say one way or the other. Importantly to a different group of people (producers rather than consumers of citrus fruit), the fruit matures 4-6 weeks earlier than other varieties of mandarin, making the harvest better timed to cater to the demand for citrus around Christmas.

Fred has been developing the breed since 1985, when he found the tree Sugar Belle was bred from in the experimental plot of another plant breeder who’d just retired. That’s twenty-four years of research and development. 1985 is the year “new coke” was released. Soviet and Western forces still faced off against each other across the Berlin Wall. If Sugar Belle was a person, it’d already be old enough to be in grad school right now.

The lesson here (one of them) is that it takes a long time to breed fruit trees.

But that’s not the only interesting thing about this story. (more…)

November 2, 2009

Spam Problems

Filed under: Computers and Coding — James @ 11:59 pm

My spam filter has become drunk with power and is attacking innocent comments while allowing obvious spam to pass unchallenged. I’ve disabled it at least temporarily, I’m sorry if your comments have been disappearing without a trace. If you run into any other problems with the site drop an e-mail to jcs98@(this website’s URL here).

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