The hard copy of the Nature Biotechnology with my article in finally came out, so here’s a pic of me posing with it. I designed the cover too, it’s an abstract representation of padlock probes capturing sites in bisulfite-treated DNA, with a color-warped photo of induced pluripotent stem cells in the background.

If you happened to stumble across this site because you’re interested in the profiling methods, please feel free to contact me. Of course, the news about 5-hydroxymethyl-cytosine kind of throws a wrench into the gears of any DNA methylation profiling studies.

Today I produce things of questionable value to society. Five cheezburgers pleez, kthxbai.

moar funny pictures

Ragdoll cats are remarkably calm. Here is my cat pendulum demonstration of this, starring Zoe. I think she only started to object when I started trying to do the rotation motion.

Today I finally framed a painting of California poppies I bought on etsy a while back. You can click on it to see a more detailed photo of the painting itself. The artist retains copyright on the image, please ask her for a print if you’d like one for yourself! 🙂

Yesterday there was a bad smell that kept cropping up in the lab. We thought it might have been the floor drain that is connected to the sewage system; it has a U pipe that should block gas exchange when filled with water but sometimes that evaporates off. So A poured a liter of water into it, but the smell appeared again.

Eventually we discovered it was coming from the 37C incubator where B and C were culturing bacteria as part of a series of experiments I have unflatteringly dubbed “poop-omics”. “Well what do you expect if you culture up a bunch of random ass bacteria!” I said.

In this case the Monroe Interpretation regarding the position of “ass” hyphenation would be the correct one.

The other day I was recalling a required course at Caltech, a science communication writing class that is meant to help students learn how to communicate technical ideas. I remember writing for this class (although I can’t remember what I wrote about!) and in retrospect I’m saddened to think about how many hours I spent in college writing papers that nobody ever read again. There is a large pool of wasted efforts going into writing papers for college coursework.

It occurred to me that it would be wonderful if this sort of course actually had students choose Wikipedia pages that need attention and completely rewrite them. Writing a scientific/technical wikipedia topic addresses many of the same writing skills that science/engineering students need to learn: the article needs to be accessible as possible while remaining technically
accurate, it needs to cover a lot of different pieces of information
while maintaining coherence as a whole, and it needs to be well referenced (and, by implication (one hopes), well researched).

It has been pointed out to me that I’m not the first with this idea and that it has been done — and while they did run into some difficulties it also showed that writing with purpose motivated students to put more effort into their work. I think many of potential pitfalls could be addressed with appropriate foresight. Some concerns are:

• students feeling pressure writing under the spotlight of the public eye
• teachers feeling stressed at having to evaluate whether work is good for Wikipedia rather than focus on helping the student learn to write
• social friction with Wikipedia as students make mistakes in wiki formatting and are unfamiliar with standard protocol

Here is my proposal that I think would address many concerns:

Set up a private mediawiki for the class (or whole school?) into which
all papers are written. Students can see each other’s papers should
they choose, but I don’t see that as a problem. Classes require
students to show their work to other students all the time, and in
this case it’s only if they choose to look and they don’t have to
evaluate each other (unless maybe you want that to be part of the
class). Papers are written into this wiki and instructors read them
there. You could even have a week or two “free for all” editing period near the end where students can improve each other’s articles.

At the end of the course, students can give consent for their work to go onto Wikipedia. It’s optional, but they don’t have to make the decision until after they’re done.

Assign someone a TA position as Wikipedia liason for the group – not a
writing expert, instead someone familiar with Wikipedia, like me. (After an iteration or two of this, prior students are likely to be interested in taking this TA position. If that doesn’t happen perhaps the course isn’t worth continuing.) This person has the following tasks:

1. evaluate the students’ initial choices for topics to write on – check that the target article is poor quality and deserves some
   rewriting work
2. once these are chosen, give notice on the Wikipedia talk pages the possibility of a page rewrite in the next few months.
3. At the end of the course, for those students who give consent to pushing the work to Wikipedia, evaluate whether their versions are an improvement on the article. If there are sections of the article that were lost and should have be preserved, communicate with the students
   to integrate those into their work. If there are wiki style problems they can tell the students what to correct. Give notice on these pages about imminent rewrite. If there are wiki style problems they can tell the students what to correct.
4. The liason can also communicate with relevant Wikiprojects if they doubt their own qualifications for determining the factual accuracy of the rewrite.
5. Update the pages with the rewrites.

This can be a custom Wikipedia account eg. “MIT Wikipedia Liason”.

This way instructors can focus on improving the writing and not worry
about evaluating whether it’s good enough to integrate. Students won’t
be pressured to make their work public, it only happens if they decide
to do so. The liason makes sure the transition of material into
Wikipedia goes smoothly.

Writing a wikipedia article could be an option within a course rather
than a requirement (ie. an alternative to standard dead tree paper
writing) and this set-up could accommodate multiple instructors and
courses should multiple people be interested in offering this style of
writing as an option.

One of the more profound discoveries I’ve made regarding color blindness is that there are only two hues in a color blind person’s world: blue and yellow. For some reason I thought that the hues between blue and green were still vivid colors, like this:

But actually it looks like this (deuteranope simulation):

You can see here that turquoise looks the same as gray/white — in other words, it looks colorless. There are really only two hues: anything between them looks less intense, more gray.

White light is a mixture of all colors – it activates all receptors equally. Because turquoise is right between the two receptors it also activates them equally. The two types of light are providing the same information, it takes a third receptor with a different response to tell the difference. Having a third receptor has a profound effect: all wavelengths become distinct colors, a rainbow of hues is visible. Would adding a fourth receptor have a similarly profound effect? I don’t think so — the spectrum is a linear one-dimensional type of information — but maybe I’m lacking imagination here.

Green traffic lights actually have a bluish tinge to them to distinguish them from the red and yellow lights. Because of this, they actually look white! Here is a digitally merged photo I took, along with a deuteranope simulation:

This colorless white/gray effect for hues that hit both receptors evenly is also visible on the other side of the color wheel, in the “unnatural” hues formed by mixing red and blue.

Thus the colors potentially confused by red-green color blind fellows goes beyond distinguishing between hues in the red-to-green range. Turquoise and magenta can be confused for gray, and purple can look blue. I’ll close here with a series of potential color confusions:

For some time now, I’ve been wanting to write about red-green color blindness, a dramatic perceptual difference with an interesting genetic and evolutionary story. This first post will mostly be an introduction to the topic. If you are color blind: I always feel guilty when I speak of this as a deficiency, or when I emphasize how profound the differences seem to the rest of us. I hope it doesn’t bother you. I always wish I could pee standing up so… there.

Daylight vision in humans is mediated by the opsin proteins, which transmit signals that activate nerves when they are hit with light. Humans have three different opsins with different sensitivities to the colors of the spectrum — it is the different color sensitivities that allow us to see color. You can call these the “blue”, “green” and “red” opsins.

	A normalized diagram of the sensitivities of opsins to different wavelengths of light. “S” = “short wavelength”, is the “blue” opsin. “M” = “medium wavelength”, is the “green” opsin. “L” = “long wavelength”, is the “red” opsin.

In its severe form, red-green color blindness occurs when a man is missing the “green” or “red” opsin – these conditions are respectively known as deuteranopia (1% of all males) and protanopia (another 1% of males). They are fairly similar in effect: a total loss of ability to distinguish hues in the green to red range. There are many less severe forms of color blindness — 6% of males — but that’s a later post.

I say “males” because color blindness is almost always seen in men. This is because the “red” and “green” opsin genes are located on the X chromosome, which men have only one copy of. Women have two X chromosomes; even if one has inherited a deletion mutation, the other can serve as a back-up. For a woman to be color blind, both X’s would have to carry the same mutation, which is much less likely to occur. (e.g. 1% * 1% = 0.01%)

I’ll end this post by showing you what color blindness looks like. Vischeck is a service available online that simulates how images look to a color blind person. To a color blind individual the simulation and original images should look identical (or nearly so – computer monitors vary, so this cannot be perfect). If you’re curious about the algorithm, the program is based on this paper.

Deuteranopia	Original	Protanopia

All colors in the red to green range — green, yellow, orange, red — are simulated here as yellow. As you can see, deuteranopia and protanopia are almost identical – the main difference is that red looks darker to the protanope (look closely at the picture of cars). Also interesting to note: the butterfly picture demonstrates how purple looks like blue to the color blind individual.

Credits: Opsin sensitivity diagram adapted from Wikipedia diagram, credit goes to User:Vanessaezekowitz and from the screenshot for Wavelength 1.3. Photos taken from flickr users Marshall Flickman, Teo, and Oneras under CC and CC-by-SA licenses.

Genetics was on the front page of Wikipedia yesterday as Featured Article of the Day! This was pretty cool, but this of course attracted a crop of editors and comments that wanted to improve on the article — some wonderful and knowledgeable, some newbies, some with an ax to grind.

The one that really got to me was the guy who got really upset with usage of the passive voice:

“With all due respect, I find the drenching of this article in passive voice to be sophomoric and cumbersome. I intend to re-edit the entire article and make it readable to a literate audience, as I believe that Wikipedia articles should be written in a dynamic manner. Should you chose to remove all of my edits, I will seek redress.”

My reply:

“Please don’t get too passive aggressive with me: [1].” …. “I was concerned that your attempt to remove the passive voice made the article harder to read by introducing unnecessary vocabulary. If you can do it in a cleaner manner then you are welcome to it.” …. “While it is hardly arduous for me to comprehend your verbiage, I would importune you to contemplate first the lucidity of your emendations before foisting them upon a somewhat less literate audience.”

That link I made there is worth reading, it’s to a Language Log post “Passive Aggression” that illustrates the fallacy of an absolute injunction against the passive voice.

And so I tend to ignore the injunction, although I do appreciate that it can generally improve readability. But if removing the passive voice from a sentence requires introducing more complicated vocabulary, I think it is actually reducing the clarity of the sentence. Some examples of changes this editor made…

• “For genes that are closer together” was replaced with “For genes located in closer proximity“
• “DNA (rather than protein) was the genetic material of the viruses” was replaced with “DNA (rather than protein) comprised the genetic material of the viruses”
• “A popular theory during Mendel’s time was the concept of blending inheritance” was replaced with “A popular theory during Mendel’s time pertained to the concept of blending inheritance” (the theory was only related to the concept? This one isn’t even correct. I’m not even sure it’s passive??)

I’m really not a writing expert, but I think the article needs to be as accessible as possible — in these cases, the passive voice is preferable to doing some grammatical backflips over fancy vocabulary. Make sure to read that Language Log post, it’s very funny!

Ethan Zuckerman has a couple of recent posts about Darfur and Tibet, I found both very good to read. “China, bias, and misunderstanding” is about the disconnect between Chinese and Western perceptions of Tibet — for example, how and why many Chinese were upset and offended by the Olympic torch protests. “Media, reality, representation: what are we paying attention to when we pay attention to Darfur?” explores the oversimplification made of the Darfur conflict — it’s much more complex than I’ve been led to believe! — and he hypothesizes why this particular conflict has become such a popular cause for activism.