Rhinocrisy

This blog serves to some extent as a barometer of my mental health - when it is effulgent and rife with words, it means I’m doing well, my confidence is overabundant, and I’m willing to project my useless blatherings onto the Interspores. When it becomes ghostlike and silent, except for the occasional tumbleweed post, it’s probably the reflection of some dark stormclouds over my head.

Based on this assumption I can construct for myself a chart of my mental health history over the past few years, using the number of posts per quarter. Here it is:

Evidently 2005 was a very happy year for me. I was in the full bloom of my youth, I was in excellent physical shape, I was living with the best set of housemates I’ve ever had, and I had just taken a step back into graduate school, which at the time seemed fresh and exciting.^* The proceeding three years are clearly the result of grim reality setting in, of a succession of defeats wearing down my patience and self-confidence - the usual business of a PhD program. The last few quarters are understandably muddled; I still haven’t learned how to walk in the surreal mooonscape of San Francisco.

^* I was also the much-beloved neighbor of a bevy of beautiful and charming twenty-year old girls, whose company I sorely miss.

Reiterating the hypocrisy of right-wing Christians in this country is a fruitless exercise, and I’m not exactly sure why I am about to embark on it. I suspect my rational mind must compulsively disentangle their dissonance.

Observe one Paul Broun, a Republican Congressman from Georgia, who wants us to proclaim a “Year of the Bible”, so we can get back to the Biblical principles our laws and fundamental values are based on. He’s most worried about a totalitarian government:

We are headed toward a total government control of everybody’s lives — a loss of freedom, a loss of our money, a loss of our private property — and it’s extremely critical now for us to go back to those foundational principles that this country was founded upon.

I find this infuriating, because it suggests to me that Mr. Broun has never actually read the Bible. The first Christian community, made by the Apostles, whose example we’re all supposed to follow, outlines principles diametrically opposed to what Broun describes above. In Acts Chapters 4 & 5, it clearly describes how the first Christians were meant to live - that is, they were expected to sell all their property and surrender their wealth to the Apostles, who would then dispose of it in the interest of the community. In fact, there’s even an incident where someone cheats a little bit, with drastic consequences:

But a certain man named Ananias, with Sapphira his wife, sold a possession, and kept back part of the price, his wife also being privy to it, and brought a certain part, and laid it at the apostles’ feet. But Peter said, Ananias, why hath Satan filled thine heart to lie to the Holy Ghost, and to keep back part of the price of the land? Whiles it remained, was it not thine own? and after it was sold, was it not in thine own power? why hast thou conceived this thing in thine heart? thou hast not lied unto men, but unto God. And Ananias hearing these words fell down, and gave up the ghost: and great fear came on all them that heard these things. And the young men arose, wound him up, and carried him out, and buried him.

And it was about the space of three hours after, when his wife, not knowing what was done, came in. And Peter answered unto her, Tell me whether ye sold the land for so much? And she said, Yea, for so much. Then Peter said unto her, How is it that ye have agreed together to tempt the Spirit of the Lord? behold, the feet of them which have buried thy husband are at the door, and shall carry thee out. Then fell she down straightway at his feet, and yielded up the ghost: and the young men came in, and found her dead, and, carrying her forth, buried her by her husband.

This seems pretty clear to me: as I’ve suggested before, the early Christians lived according to something resembling Marxist democratic centralism, with a Politburo controlling the community’s wealth and decision-making. This conflicts with Broun’s claim that the Bible upholds the sanctity of private property; whence, then, does he make that argument? The Bible is not text to him, to be read and understood - it’s just a totem to be waved around. I thought that this was the problem that was supposed to have been corrected by the Protestant Reformation, when people first started reading the thing, and saying to themselves, “Wait a minute - none of this shit you’re saying is actually in here.”

When I fold my t-shirts, I hold them by the corners of the shoulders and make a snap-and-fold motion, folding them lengthwise in a single movement. I do this with the ease of long practice, even though I have never consciously noted this action before.

This is the sort of nonsense that would end up on my Twitter feed, if I had one. You guys should feel lucky I don’t.

J. Schwarz over at A Tiny Revolution points us to a 1999 New York Times article on the repeal of a portion of the Glass-Steagall Act of 1933, by the Gramm-Leach-Bliley Act, specifically the portion that prevents banks from offering both savings and investment services. For those more cognizant than I this is probably old hat; you others playing catch-up, like me, might want to read this article by former World Bank economist and Nobel Prize winner Joseph Stiglitz, where he attributes the current mess to five pieces, including the passage of the Gramm-Leach-Bliley act, legalizing maneuvers and consolidation between banks and investment houses that had already occurred (illegally), such as the merger of Travelers Group and Citibank to make Citigroup:

The most important consequence of the repeal of Glass-Steagall was indirect—it lay in the way repeal changed an entire culture. Commercial banks are not supposed to be high-risk ventures; they are supposed to manage other people’s money very conservatively. It is with this understanding that the government agrees to pick up the tab should they fail. Investment banks, on the other hand, have traditionally managed rich people’s money—people who can take bigger risks in order to get bigger returns. When repeal of Glass-Steagall brought investment and commercial banks together, the investment-bank culture came out on top. There was a demand for the kind of high returns that could be obtained only through high leverage and big risktaking.

Of course, once you’ve let the bull out of the paddock, it’s not going to come back in willingly…

UPDATE: See also this excellent Matt Taibbi article documenting this mess with AIG as a case-study.

Famed internet gadfly and comment-thread contrarian abb1^* has been running a weblog for quite some time, now. What else am I missing out on? Post links here, nonexistent readership!

^* Whose name I have always surmised is an abbreviation for ‘anarchist black block’.

“The man who never alters his opinion is like standing water, & breeds reptiles of the mind.” — William Blake

One of my favorite conspiracy theories is that NASA is deliberately false-coloring images so that Mars appears to have a red sky, to cover up the fact that it’s actually blue there. I’m not exactly sure why NASA would be doing this, but I’ll admit I’ve been disappointed by the color of the sky (and the ground) in Mars photos, so I’m on board! Let’s deconvolve:

First, for the uninitiated, our a priori expectation should be a blue sky. The sky everywhere should be blue, because the color of the sky is the product of Rayleigh scattering - which is basically to say, the atmosphere tends to scatter higher-frequency light more than it scatters lower-frequency light. If you look up at any random part of the sky that isn’t the sun, the light you’re seeing is light that has scattered off some part of the atmosphere in that direction; in space, that light would have gone straight to its target, and you would see no light coming from that direction. Since the atmosphere scatters violet light more than red light, this, combined with our human visual system’s spectral bias (weak in the blue end of the spectrum), results in our seeing the sky as blue. This simple phenomenon should apply equally well to all atmospheres.

So it’s a bit glum when we’re told that Mars has a red sky - red because it’s full of thick, choking dust. Well, poop. But maybe it’s not so! Maybe NASA is attempting to pull the dust over our eyes, and Mars is really true-blue. Fortunately, we can verify for ourselves. NASA puts up “raw” JPEGs of all the data the rovers send back. The relevant images are the “PANCAM” ones, which apply a series of fairly narrow bandpass filters before the CCD capture (that is, each filter captures an image of the scene at a specific wavelength of light).

The NASA “true color” images are generated by the PANCAM group at Cornell; their methodology is quite rigorous. The naive method (employed by most conspiracy theorists, notably Keith Laney) is simply to use the three filters that closest approximate the human visual peaks - 600, 530 and 480 nm, for Red, Green and Blue - and slap them together with Ye Olde Photoshop (or in my case, Perl) to make a full-color image. This produces very satisfying images. Check it out!

However, this method has a flaw: the human visual system is additive, meaning that single-wavelengths don’t give the whole picture - each color opsin in your eye is stimulated by the whole spectrum, meaning that what you see as “red” might actually be an amalagam of two individually non-red peaks.^*

Unfortunately, we don’t have data from the whole spectrum available to us - we only have eight wavelengths, six of them in the visual range. PANCAM takes this data and fits a third-order polynomial to it to generate an approximation of the true spectrum. This spectral data is then converted into the XYZ color space (a standard color space) by convolving it with the XYZ standard observer functions that (more or less) define the primary colors of that space.^† Those XYZ values are then mapped to the familiar sRGB space and slapped together to produce a “true color” image. The result, side by side with the “naive” method:

Egad! There’s a world of difference there. So who’s got it right? Hard to tell… unfortunately PANCAM doesn’t have any pictures of the color calibration target that sits on top of the rovers posted in their collection of true color images, so it’s difficult to be sure. However, the average spectra values in the data for the above image for the sky (blue line) vs. the ground (red line) look like so:

This seems to suggest there’s something off about the PANCAM results - the sky should be white-tending-to-blue, and the ground should be red. Of course, it’s possible our visual system is so heavily red-skewed that we’d still see the spectrum on the left as reddish, but I’m inclined to disbelieve it could see the deep, dusty red shown in the PANCAM image. It seems more likely the reconstruction method is flawed somewhere. Furthermore, the naive method should be pretty good at telling us the color of the sky, since the sky color is composed of all wavelengths in varying intensities (which may not be true of rocks on the ground, meaning those colors are more likely to be wrong in the naive method). I’m staying aboard this conspiracy ship!

^* Leading me to wonder if we will, one day, encounter a fully spectrographic visual system - one that sees spectra instead of colors. You’d recognize the chemical composition of everything!

^† Sloth prevents me from recapitulating their method - all the necessary data is linked from here, if you feel inclined to do it for yourself.

The new Obama administration White House website is very snazzy, and apparently done by the same folks who designed his campaign website. I can’t help but feel a little disappointed, though. One of the things I loved most about the Bush website was the easy availability of press briefings. Transcripts were available almost as soon as the briefing was finished. By contrast, the Obama website has nothing, yet. Maybe that will change.

Anyway, to business: Gibbs’ response regarding drone attacks on Waziristan/Pakistan:

Q Exactly. There is skepticism among Republicans whether or not this could happen. What kind of reassurances is he giving? Then, on Pakistan, was he consulted before the strike, or did he consult with Pakistan on that?

MR. GIBBS: Well, let me take your Pakistan question first. As you know, I’m not going to comment on those matters.

What the fuck? If this is “transparent”, I’m going to go replace my windshield glass with corrugated cardboard.^*

^* I just realized I don’t have a windshield glass!^†
† No, it wasn’t stolen. I don’t have a car.^‡
‡ No, my car wasn’t stolen. I never bought one.

Ugh. New Scientist is drumming up subscriptions by pasting the title “DARWIN WAS WRONG” on their cover. Everyone loves a good controversy, right? Let’s swan-dive right into the muck of the inane culture war going on and get good and dirty.

The basic thrust of the article is: the idea of a “tree of life” is wrong. The standard picture of evolution is of a divergent process - an ancestral species separates, differentiates, forms two daughter species. Over time this produces a binary tree of life, which we can trace backwards to its root via comparative genomics. The problem with this neat picture is lateral gene transfer - exchange of DNA across species (or even higher taxonomic classes) boundaries. If DNA can be exchanged back and forth willy-nilly, it confuses the parenting process. If my genome contains both human and frog DNA sequence, am I human, or am I frog? Or both? The graph becomes complex and hard to unravel, and certainly no longer resembles a tree.

This is most problematic in prokaryotic species, which have small genomes with only a few thousand genes, and many mechanisms for exchanging DNA with random strangers (or even taking it up from the environment). That sort of incestuous interchange makes it very hard to draw a simple tree. The stuff gets most confused near the root of the tree, where a debate has long raged about who came first, eukaryotes, prokaryotes, or archaebacteria. The best reading on the subject is W. Ford Doolittle, who rubbishes the notion of a singly-rooted tree in this blessedly free PNAS review:

Some evolutionists believe (i) that a single rooted and dichotomously branching representation of the relationships between all life forms is appropriate (at all levels above species), because it best represents their history; (ii) that we can with available data and methods reconstruct this tree quite accurately; and (iii) that we have in fact done so, at least for the major groups of organisms. … [O]ther evolutionists, ourselves included, question even this most fundamental belief, that there is a single true tree.

So, what am I saying? Is New Scientist right? Well, yes and no. The confusions indicated above are confined: while lateral gene transfer may be rampant in prokaryotes, it’s only sporadic in metazoans (animals), and a tree-of-life metaphor works pretty well there, especially for the species we’re most concerned with (viz., ourselves and our mammalian relatives). There are some notable exceptions, the most famous probably being the discovery that the entire genome of the fruit fly endosymbiont Wolbachia was at some point incorporated into the genome of some Drosophila ancestor. But we shouldn’t expect to find these events playing a significant role in the evolution of large, complex organisms. So while I find this interesting, and don’t mean to contradict Doolittle, et al., in any way, I think the “revolution” is relatively muted, and certainly doesn’t have any of the broad scope that the introduction of Mendelian genetics, for example, had on biology, as New Scientist seems to be suggesting.

Finally, a scrap for the wolves, lest they begin salivating too much, from Doolittle:

Holding onto this ladder of pattern [the tree of life] is an unnecessary hindrance in the understanding of process (which is prior to pattern) both ontologically and in our more down-to-earth conceptualization of how evolution has occurred. And it should not be an essential element in our struggle against those who doubt the validity of evolutionary theory, who can take comfort from this challenge to the TOL only by a willful misunderstanding of its import. The patterns of similarity and difference seen among living things are historical in origin, the product of evolutionary mechanisms that, although various and complex, are not beyond comprehension and can sometimes be reconstructed.

I was late in discovering Nina Simone; I’m lazy in exploring intellectually challenging art, especially with regard to music, more’s the pity since I’m so piercingly affected by it. As music goes I think hearing Nina was kind of a revelation, a demonstration of what a musician can do, and should strive to do. When she sings, it is to make us feel; she is a compelling argument that art is about communicating sentiment much more than it is about aesthetics (never mind egotism). Here’s one of her most powerfully affecting pieces, where she almost berates the audience into accepting the terrible current of emotion she is giving them. She’s an ideal; few musicians come close.