Mad Prime

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.

Bunnie's latest blog post is interesting -- I was fooled as he was. It teaches me that small improvements on the worst mileage cars is more effective than improving the mileage on cars that are already moderately efficient. I recommend it to anyone interested in the general issue of reducing gas consumption.

Here is a short list of some cool words. If you have a cool word, add it with a comment (make say what it means and why it is cool)!

crapulent / crapulence

• definition: sick due to excessive eating or alcohol, excessively drunk
• why it's cool: this should be obvious

pulchritude

• definition: beauty
• why it's cool: ugliest word for beauty I've ever heard

chaotropic

• definition: disrupts the structure of proteins and/or DNA, denaturing them
• why it's cool: sounds bad ass

UPDATE 7/8:

callipygian

• definition: having well-shaped buttocks
• why it's cool: fancy-ass ass-fancy

I don't care if it's not cool anymore, I still love lolcats. Chris found this one - I don't know who made it but I feel I must post it.

I made this picture today in the new version of Inkscape, making extensive use of the new thin/thicken tool.

From Science magazine news Hobbit Redux? article:

Paleoanthropologist Lee Berger of the University of Witwatersrand in Johannesburg discovered the bones while on vacation in Palau in 2006. (His wife had deliberately chosen a remote, young island because it was unlikely to have fossils on it).

Looks like my Genetics article was overdue for a "good article" rating. I think I'll work towards getting a featured article rating, the GA reviewer encouraged me to do this...

The double-blossom article was in the Did you know section of the front page for seven hours yesterday morning. It got the top spot, with the pretty double impatiens photo.