Musings about Chipotle

Just went to Chipotle, one of my children's favorite places to eat. Decent burritos, etc. Here are a few things I've noticed about Chipotle:

1. You can always ask for vegetables on anything. Very delicious grilled onions and peppers. A must add.
2. I've been getting double beans (pinto, natch), hold the rice on my burritos, and I LOVE it. I don't like the rice so much, so this is great. But there's a problem: the beans are juicy and there's no rice to soak it up, so be prepared for, umm, breaches in hull integrity. Double beans has a number of other side effects as well.
3. Kids meals are seriously the best deal ever. Tacos/quesadillas with a side of rice, beans, salsa, chips and milk.  All for something like $4-5. I can't tell you the exact price because I don't know it. Literally every time I go through the line, I pay a different amount, depending on whether the count some stuff as sides or extras. Whatever–it's a good deal no matter what.
4. Paul in lab has told me that there's something called the quesarrito, which is a burrito that is wrapped in cheese sandwiched between two tortillas. Sounds divine! But I've never ordered one. I think I keep forgetting, and Paul also said they only like to do it when there's not a lot of people around because it's a bit slow. I gotta try it, sometime, though.

MATLAB figure defaults

Working on a grant, and I have to do SO MUCH fussing in Illustrator just to get stupid MATLAB figures to look even remotely presentable. Why are MATLAB figures so terrible looking?  R makes everything look so much better. And it does it by default–MATLAB can make at least somewhat better looking stuff than what it spits out automatically, but it requires endless tweaking of parameters.

In the remote event that any Mathworks people out there are looking at this, here's a list of problems:

1. Default axes are way overticked. I don't need to have 0, 50, 100, etc. all the way up to 1000.
2. Font sizes are ridiculously small. For publication, figures need to be small. Text gets shrunk to the point of being completely illegible.
3. Line widths are all way too thin by default. Except for axes, which are too thick.
4. Default markers sizes are all way too small.

Please, MATLAB graphics people, help! Make me want to love you, rather than need to have you.

GATTACA and modern biology

I was just watching the movie GATTACA, an old (and fairly mediocre) sci-fi movie from 1997 with Ethan Hawke and Uma Thurman. The movie is about a future in which the vast majority of humans are genetically engineered and constant genetic testing determines your entire future. Ethan Hawke is naturally conceived (a "God child" from a "faith birth") who ends up having all sorts of genetic flaws but somehow conquers the odds to succeed despite his genes.

Throughout the movie, they're always plugging samples into little devices that read out your sequence to determine what you're all about. I guess we're not all that far away from that now. I just got back from a Cold Spring Harbor Lab meeting about systems biology, and certainly in biology, that era's already here–people just sequence everything in sight. What's funny is that maybe the message of the movie applies just as much to modern biology as to society: maybe just sequencing everything won't reveal everything about how a cell works. It just happens to be what we're able to do.

There's an interesting line in the movie when Ethan Hawke takes over the identity of a "valid" (a person with good genes played by Jude Law) and in the process, he notes that "We don't look anything alike", to which the identity swapper agent guy says "When was the last time anyone looked at a photograph?" I was thinking, again, so true in biology, nobody even looks at cells anymore. Ah, but we do, I thought! But before I got too pleased with myself, I remembered that even our images are based on nucleic acid sequences!

Another scene from the lab

Scene: Olivia getting DNA from a PCR purification kit, but the output smells a bit of ethanol.

Olivia: Ah, okay, let’s get this DNA!

[sniffs tube]

Olivia [talking to tube]: Have you been drinking again?

Tube: …

Olivia: You have, haven’t you?

Tube: …

Scene from the lab

Arjun: Hey Sydney, I was just thinking about something and wanted to bother you a bit and interrupt your work by talking about it.

Sydney [loudly, with headphones on]: Sorry, I can't hear you. I've got this song on from the Backstreet Boys. It's so good. It has a really good story.

Arjun: ...

Statistics is not science

[Disclaimer: I am NOT suggesting that statistics is not a science, rather that statistics is not science. Important distinction. Read on. I love stats! Not that I'm particularly good at them...]

I was writing back and forth with Gautham a bit, and he observed that statistics truly is a grim science: the whole point of it is to curb your enthusiasm, be the wet blanket, rain on the parade. I think it’s also true that statistics as applied to science today is perhaps not used the way statisticians really intended it to be used. From what I’ve read (correct me if I’m wrong, dear readers), things like the p-value were designed as quick tests just to make sure that whatever you were observing might not just be a fluke. It is not a substitute for scientific thought. But in our desire to systematize our analyses, we’ve created a system in which the p-value is an end in and of itself. We’ve all heard of people digging through statistical tests to check whether such and such effect is statistically significant, and that is of course bad, and we'd of course never do anything like that ourselves :). But at least there is an effect that someone has reasoned may have scientific significance, so the problem can in principle be rectified with more data. The other situation, where you just look for statistical significance as the scientific finding itself, seems more troubling to me from the perspective of gaining scientific insight (I have been guilty of this myself). We have a tricky situation in biology now, where our measurement tools are getting so good that we can pick up tons of effects with statistical significance. The real question is scientific significance. As an aside, at Nature, I think you can’t even utter the word significant unless it comes with a p-value. To me, this is placing the wrong emphasis on the use of the word significant.

One of my favorite Gautham quotes is “Would Newton have come up with the theory of gravitation by machine learning?” A corollary quote could be “What is the p-value on the theory of gravitation?” Lately, my thinking is that a theory cannot have a p-value: it is the product of scientific thinking and trying to understand our world, and that is what is significant. A theory can lead to a model of a system, which you can use to make predictions which can have p-values (like the five-sigma standard for the discovery of the Higgs) to evaluate whether the theory is right or wrong.  But the theory itself stands or does not stand on the collective judgement of us as scientists and humans as to whether it is telling us the truth about reality. I feel like that is the truest test of significance.

Screen blight

Was watching a talk the other morning from the back of the room, and this was the scene. How many people do you think were actually watching the talk? At least everyone clapped! [Note: I am totally guilty of this myself.]