Chittenden Locks and the Rambunctious Garden

Today we went to Chittenden Locks (aka the Ballard Locks). I’ve been in Seattle for nearly three years and somehow I’d never been. But I really liked it. After reading The Rambunctious Garden, the integrated space of human uses — tourism, recreation and a working lock system — with gardens, parks and most importantly the fish ladder made me think of what our future should hold. Our cities should be a place where all that goes together. And more of us should be in cities and our agriculture have less impact so that we can let the rest of the world be rambunctious. That’s a short summary of the book and probably one that doesn’t do it justice, so go read it. So instead of going on with my ill-formed thoughts, I’ll just leave you with some photos.

Railway bridge west of Chittenden Locks

Ampitheater into the water at Commodore Park

Water leaving as the locks doors swing shut

Rippling water in equalization basin at Chittenden Locks

Red narrow flowers

Fall Colors at Chittenden Locks

I unfortunately didn’t take any pictures of the fish ladder itself. It’s really cool — there’s a viewing chamber where you can see salmon swimming by! But it was too dark in there for good cell phone photos. In any case, I was too entranced by how simple but complicated a thing a fish ladder is that I forgot! The rest of the photos are in my flickr stream. Enjoy!

Randomness and Samples: Why that GM corn study isn’t as scary as you think

This past week a new study came out finding a connection between glyphosate-tolerant corn and cancer (and also Roundup and cancer). You can read more about the study at the BBC or this Discover post. But here I want to expand on the main reason I was immediately skeptical: the small number of control animals compared to experimental animals. I struggled with how to express what seemed obvious to me (my statistics training is scattered) and a person I follow on twitter put up a post which mostly got there. I later made a comment on a Mother Jones story about the study in a similar fashion. I want to elaborate on that here to hopefully make it clear that (perhaps surprisingly) interesting (or scary in this case) data can actually just be random.

Study Background

First, a quick background on the study (PDF). In this study, 200 rats were raised in various experimental groups. Half the rats were male and half were female and they divided both sexes up into similar treatment groups. Ten rats of each sex were controls: they ate normal diets (rat chow which is usually a combination of corn, soy, and supplements) and drank normal water. In the control cases, they actually ate 33% conventional (non-GM) corn grown by the research team in their rat chow. Three groups of ten rats for each sex ate different amounts of a particular variety of glyphosate-tolerant corn. Three groups of ten rats for each sex ate different amounts of glyphosate-tolerant corn that had been grown in a field actually treated with Roundup1 . Finally, another three groups of ten rats ate the regular (control) rat chow but were only given water spiked with different amounts of Roundup. To make this clearer, here’s a table.

Group Description
C: Control Regular rat chow with 33% non-GM corn, normal water
E1: GM Corn 11% Rat chow with 11% GM-corn
E2: GM Corn 22% Rat chow with 22% GM-corn
E3: GM Corn 33% Rat chow with 33j% GM-corn
E4: GM+R Corn 11% Rat chow with 11% GM-corn grown in a field treated with Roundup
E5: GM+R Corn 22% Rat chow with 22% GM-corn grown in a field treated with Roundup
E6: GM+R Corn 33% Rat chow with 33% GM-corn grown in a field treated with Roundup
E7: Roundup 1 Regular rat chow, water with 0.1 ppb Roundup
E8: Roundup 2 Regular rat chow, water with 0.09% Roundup
E9: Roundup 3 Regular rat chow, water with 0.5% Roundup

Remember, for each sex there are ten rats per group. They then raised the various groups for around two years, keeping track of which rats seemed to get tumors. As this particular breed of rats very commonly gets tumors as it gets older the control groups showed tumors. The researchers recorded when animals died (and in some case euthanizing them2). Their graphs sometimes suggest greater effects for treated groups than control but one reason many scientists look at this study with skepticism is that many treatment groups did better than the controls3. Basically, it’s not clear that the results are consistently showing worse effects from treatments — this might just be a case where tumor-prone rats get tumors and a non-rigorous analysis of the data would suggest a problem.

Simulating Rats Prone to Tumors

Andrew Kniss in his post noted that this rat variety is extremely prone to tumors. He used a study that showed 72% of female rats having tumors by two years old. Others have seen figures around 50% or 60%. He then used that probability of developing tumors to generate simulated groups of ten rats — control groups and experimental ones as in the study. In my comment, I used a figure of 20% because the current study saw anywhere from 20% (males) to 60% (females) of the control rats developing tumors. Using some R code (a statistics-oriented software development language), I then generated several sets of ten groups of ten rats to simulate a control group and the nine experimental groups. The R code is this:

colSums(matrix(sample(c(0, 1), 90, replace = TRUE, prob = c(0.80, 0.20)), nrow = 10, ncol = 10)) 

That code may look complicated, but it’s not. What is does is first generate ten groups of ten random numbers either a 0 or 1. A 0 means no tumor and a 1 means a tumor. The probability for no tumor is 80% and for a tumor 20%. Each group of ten is then added up to give the number of rats with tumors in each experimental group. Remember this is all simulated. I’m just having a computer randomly generate how many rats in a group of ten will get tumors based on an expected probability. I ran this a few times and here are five runs I got. In some sense I am simulating the study experiment five times using random numbers.

Run # C E1 E2 E3 E4 E5 E6 E7 E8 E9
Run #1 0 1 1 0 1 2 1 4 1 0
Run #2 1 3 3 2 1 1 3 5 4 1
Run #3 0 1 2 2 0 2 2 2 3 0
Run #4 0 1 3 3 1 1 2 1 6 0
Run #5 2 2 2 4 2 1 2 2 4 2

I’ve labeled the columns in the above table as with the experimental groups in the original study. So pretend the first column in each row is a control group. Then if you treat the rest of the entries in that row which represent our experiments, it certainly looks like our experimental groups may have done “worse” than the control. For example, for run #2, only one control rat got cancer but the experimental groups 1, 2, 3, 6, 7, and 8 all had more rats with cancer. But this is just randomly generated data. Now for a moment, let’s rethink this and treat more of our groups as controls and not experiments. Pretend that E2, E4, E6, and E8 columns are also control groups and leave E1, E3, E5, E7 and E9 as experimental groups. All of a sudden the data look a lot more random, as it should. Statistical tests let us decide how many control and experimental subjects we need to have enough “power” to determine whether our results are due to actual effects and not chance (and even then, usually we can only say with 95% or 99% confidence the results aren’t due to chance).

Low Tech Rat Study Simulation

But not everyone is a programmer and wants to run programs that will generate random numbers. But you probably have dice or coins. Being nerds, we have a lot of dice. You can roll some six-sided dice (D6s) or some ten-sided dice (D10s):

Some D6s and D10s
The First Run: 3 Tumorous Mice

Actually, you can roll any kind of dice. I rolled D10s (my ranger in my first dungeons and dragon game used D10s for damage rolls). Ten-sided dice have sides labeled with 0, 1, 2, up to 9. For our simulation, we only need 0 or 1 values so I’m going to treat 0, 2, 4, 6, and 8 as a zero and 1, 3, 5, 7 and 9 as a 1. Odd is a tumor, even is no tumor. This changes the probability to 50% for a tumor but is a lot easier to count quickly (and is actually closer to known tumor rates for this breed of rat). Here’s my first roll which is going to be the number of tumors in a group of ten rats for a control group:


And here’s a few full runs. You can see why I wanted to roll ten dice and just wanted to add up the number of odd numbers.

Run # C E1 E2 E3 E4 E5 E6 E7 E8 E9
Run #1 3 3 2 7 3 6 5 6 4 5
Run #2 4 4 5 5 4 5 8 6 7 6
Run #3 5 2 5 4 4 7 3 4 3 5

At this point I got pretty tired of rolling and counting.

But I hope you got the idea: with only one group of ten control rats (per sex), it’s really easy to possibly see harmful effects in the treatment groups that we just don’t know are there. That’s why we have statistics. They let us know with some likelihood how much data we need to collect to know whether we’re seeing true effects. In this study, the authors did not show any standard statistics that would demonstrate one control group of male (or female) rats is enough for nine other groups of experimental rats — and most independent experts are saying this setup just isn’t likely to allow us to rule out random effects. So while this study’s results are admittedly scary, it’s just as likely that the results are random.

  1. The implicit hypothesis for these experimental groups is that a combination of Roundup residues and the glyphosate-tolerant traits in the corn have some kind of effect. I find this doubtful because Roundup is used to control competing plants very early in the season well before ears develop. Moreover, corn ears come with a wrapper. How would much glyphosate even be left on the corn?
  2. The protocol is poorly described in the paper. The explanation of when a decision to euthanize an animal is not clearly given which makes it trivial for the study to be biased merely by an experimenter deciding (even sub-consciously) to let an ill control rat live longer.
  3. For example, in the “GM Corn” groups (no Roundup), the male rats fed a diet of 33% GM corn overall survived longer than the control rats.

Let’s Send Congress The Geek Manifesto

I had a engrossing evening at a Science Online Seattle where we discussed issues of identity and digital “stuff” left after your death (more on that soon). But during drinks after, I remembered the idea of sending a copy of The Geek Manifesto to every member of Congress. Folks in Britain have sent copies to all of their Parliament. Our legislative body varies widely in their understanding of science and evidence. Why don’t we do that here?

A few days ago, I asked Mark Henderson if he knew if anyone was organizing this already and he said he doesn’t know. So who’s with me? This isn’t about convincing politicians of any particular policy position. It’s about convincing them of the importance and power of treating science as a way to make good decisions. Since it’s election season, I think it’s a good time to tell Congress we’re watching how they use and abuse science — and provide them with good reasons to make better use it.

Pasta e Fagioli Mad Libs

As a kid, my mom used to make a very simple version of pasta e fagioli that could mostly come together with canned or dried goods: pasta, canned chick peas, tinned tomatoes, oil, garlic and onion. We also pronounced it “pasta fazool”. As an adult I dress it up and fill in the blanks with whatever I feel like. And I fancily try to pronounce the Italian. Mine is also not a “soupy” pasta e fagioli and tends more towards oily gravy. Since we made it last night with some fresh cranberry beans, I thought I’d share this very simple but awesome vegetarian dinner.

The basic recipe is simple. Cook lots of onion until a bit caramelized and tasty. Add lots of garlic. Add some vegetable(s). Add some (already cooked) beans. Salt, pepper, maybe some chile flake. Toss with pasta. Serve. If you want to get fancy, grate some parmesan over it. Simple.

But really the recipe looks like this:

  • Cook some ________ beans from dried or fresh. Use ________ stock if you have it. A pressure cooker is perfectly okay.
  • After the beans are about done, cook lots of onions in lots of ________ oil until golden and lovely. Use more oil than you think you need. No really.
  • Add ________ quantity of garlic. Don’t let it burn.
  • Start some ________ style pasta. Heavily salt the water.
  • Add some ________ (diced small or in ribbons depending on what kind of veggie you choose).
  • Season with salt, ________ or ________.
  • Add the cooked beans to the onion, garlic and ________ mixture. You might include a bit of bean water for flavor and extra awesome.
  • Toss beans, onions, etc. with the pasta.
  • Serve.

I am a bit obsessed with beans. All kinds. For this recipe, I’ve used:

  • Chickpeas. Of course. Strangely, ones cooked from dried taste a lot better than canned. I don’t know why but I’m pretty sure of it. Anyway, they are a lot cheaper that way.
  • Borlotti or “cranberry beans”. I’ve used dried ones and — the inspiration for this post — fresh ones still in gorgeous red and white mottled pods.
  • Pinto beans. Hey, what can I say? I almost always have pintos on hand1.
  • Christmas limas. These beans are huge. And gorgeous.
  • Small white navy beans. Not spectacular but really it’s all about the garlic-oil-gravy that forms.
  • Probably some I’m forgetting because I buy a lot of bean varieties.

While I made a Mad Lib space for the oil, I have to admit I always just use copious quantities of olive oil. I also must admit that we buy high quality olive oil which I believe matters in a recipe like this. About five years ago, I bought the house brand “virgin olive oil” and a very fancy extra virgin from a Marin County orchard. I tasted them in shot glasses — literally sipped the oil — and discovered that in fact different olive oils taste different. These days we buy not super cheap (but also not super expensive) bulk olive oily from our co-op grocery store. You can in fact taste the oil in this dish. So if you experiment keep that in mind.

The onions and garlic are non-negotiable in this recipe: you absolutely need to get those flavors cooked into the oil because ultimately they, the added veggies and a bit of bean juice will form something almost like a gravy. The traditional vegetable my mother used was a couple tins of diced tomatoes (preferably with not too much “Italian” seasoning in it). I still do that often because the tang of the tomatoes works really well (and the tomatoes melt down into the gravy pleasingly). But I don’t always have tinned tomatoes (or fresh) in the house. For a different (but good!) version, I’ve used kale, chard, spinach, carrots, and more. Obviously you may have to adjust when you add them depending on how cooked down you want them. This is Mad Libs. Go mad.

Seasoning is really simple: a fair bit of salt, some black pepper and maybe chile flake. Googling recipes I find suggestions for thyme, basil, parsley and more. Eh, whatever you like. I’m about the garlic and onions. For pasta, the traditional recipes suggest a small pasta. That’s usually what I use — right now we keep small, whole wheat2, pasta shells in the house as our usual pasta. But basically anything will work, even spaghetti. The important part is to coat that pasta with tasty, tasty oil.

That’s basically it. Sadly I have no picture to share. We ate it all already.

  1. In our house at any one time, we will likely have ten or more dried beans and lentils. Right now we have at least: black beans, pintos, piquintos, jacob’s cattle, good mother stallard, tepary, garbanzo, white navy, limas, red lentils, brown lentils, and probably more. I’m too lazy to do a real inventory now.
  2. Yes, we keep whole wheat pasta at home. Due to the pressure of everyone saying “whole” grains are better, I’ve tried lots of different pasta types. Most whole wheat pastas are gross: almost sandy. These whole wheat shells are, if you believe me, actually better than “white” ones. Nutty, creamy, not sandy. Unfortunately I can’t help you find similarly good ones as they are just the ones in the bulk bin at the grocery store.

A Moral Case for Golden Rice

Golden Rice is in the news again. Sadly, it’s not in the news for saving lives or preventing blindness by decreasing vitamin A deficiency. No, Greenpeace is alleging a recent study on effectiveness was improperly done. Further, they’re trying to halt a field trial in the Philippines1. But I don’t want to talk about the intransigent position of a dogmatically anti-GMO organization which leads them to malign the ethics of scientists with little evidence. I want everyone to know what Golden Rice is and why I think it is good way to improve the lives of millions of people.

What is Golden Rice?

Golden Rice is the name given to rice varieties modified to produce more beta-carotene which when eaten is used by your body to produce vitamin A. The rice plant itself already produces beta-carotene in the green parts of the plant. The difficult part was to make the seed develop beta-carotene. Regular rice is white (with a brown outer husk). Golden Rice is light golden orange. It took scientists Ingo Potrykus and Peter Beyer over ten years to get to the first version of a viable beta-carotene rice. By 2005, the Golden Rice foundation’s research improved the line to produce even more beta-carotene. The recent study in the news demonstrated that the beta-carotene in Golden Rice is just as available to the body as that in spinach or vitamin A supplement capsules2.

Why Golden Rice?

When I was growing up, I was told to eat my carrots or I might go blind. A lack of vitamin A can cause blindness, greater susceptibility to infectious disease and even death. Millions of children worldwide are deficient in vitamin A: hundreds of thousand go blind or die every year because they don’t get enough vitamin A. I was obviously never at risk for this.

Golden Rice is intended to allow families who already depend on rice as a staple to have get significantly more vitamin A and thus lower their risk of health problems caused by its deficiency. People would grow and eat essentially the same rice varieties, including saving and replanting their seed. The Golden Rice project has ensured that any country wanting to breed a locally appropriate Golden Rice variety will be given a free license from all organizations with intellectual property interests. Golden Rice really is intended to be free of all the usual concerns about GMO crops: multinational companies can’t sue farmers; farmers don’t have to use new or expensive farming techniques, fertilizers or pesticides; and replanting from seed is encouraged.

We don’t really need Golden Rice, right?

People are understandably a bit concerned about the idea of transgenic crops. Do we really need to distribute a transgenic crop to solve this deficiency problem? I think that it’s necessary to add Golden Rice to our tool basket because other solutions have fallen short. While Golden Rice will not prevent all vitamin A deficiencies, it could significantly reduce them in rice-eating cultures because its use fits into the existing cultural and economic situation.

Supplementation programs require either local governments or international aid organizations to spend money continuously to maintain a program to give vitamin A shots or pills to the population. People are inevitably missed. Some people are naturally suspicious of being asked to accept a shot or swallow a pill. Worse, it’s easy to let programs go underfunded over time. People in distant rural areas may be overlooked entirely. But a farmer offered a fortified food crop can just keep growing it. The distribution of Golden Rice only has to be done once and is naturally maintainable3. Reducing the need for costly vitamin A supplementation using Golden Rice leaves resources available for other humanitarian efforts.

Another solution given to vitamin A deficiency is understandably seen as the right one: a varied diet. When I was told as a child that I should eat my carrots or “go blind”, it was an idle concern: I, like most everyone I know, grew up with a varied diet. A lack of carrots didn’t matter. In the United States, we are overflowing with a variety of fruits and vegetables such that generally the only barrier to an excellent diet is a person’s dislike of vegetables.

But for millions of people worldwide a varied diet isn’t common. Millions of people worldwide may only have a suitably varied diet part of the year, if at all. There are — and I realize this is hard to believe — millions of people who eat rice every day and little else. This situation has been the case for thousands of years in various parts of the world at different times. I don’t see this situation improving permanently soon. Golden Rice gives us the opportunity to decrease the numbers of children going blind and dying now rather than waiting to solve a problem that has plagued humanity forever4.

Golden Rice has been very slow coming. The experiment that Greenpeace is making noise about was actually completed in 2009. The current Golden Rice traits being field tested in the Philippines were put together in 2005. No one is going to force farmers to grow Golden Rice, but given an informed choice, I believe many will5. Sitting in the West where nutrient deficiency disorders are rare, it’s easy to let our fears of genetic engineering dominate. But transgenic crops are generally safe and the scientists are doing all the right tests to make sure it is in this case. There’s no evidence of harm from Golden Rice and many reasons to think it could do great good. Trying to prevent the testing and distribution of Golden Rice is willfully ignorant. It is also immoral.

  1. Golden Rice is not a single plant variety. The Golden Rice traits are actually bred into regionally appropriate varieties and each variety obviously has to be tested. The idea is to breed the important traits into a variety of rice that is already grown in a particular area so that the only difference will be the additional vitamin A content.
  2. When I read this study I found out how they measure the bio-availability of the beta-carotene in foods and the process is really cool.
  3. Obviously an extreme circumstance such as complete crop failure would disturb Golden Rice as a partial solution to vitamin A deficiency, but obviously any effort to help a deficiency disorder is going to have a problem during periods of crop failures. The IP rights obtained for Golden Rice explicitly allow local trade and sale of rice as well so if one region in a country has a failed crop, rice grown elsewhere can be sold or distributed there.
  4. To answer a question that inevitably gets thrust about by certain organizations: I don’t believe Golden Rice will stop families from eating vegetables. Given the opportunity to eat a varied diet, most choose to. Many don’t have that choice. But we can make it so people don’t go blind.
  5. One of the common arguments against transgenic, bio-fortified crops is that farmers in the developing world will be forced to use them without understanding what they are. I think this idea is repugnant: it assumes that farmers in the developing world who use other modern technologies such as cell phones are stupid and not capable of understanding the kind of information that farmers throughout the world use all the time. But people in the developing world can definitely benefit from scientific advances. A book that helped shake my thinking here was Starved for Science.