Mad Prime

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.

From Nature News:

When scientists released a draft of the human genome sequence six years ago, they said the data belonged to all of us -- but until now, they have been the only ones able to play with the data therein.

I call bullshit. That data has been publicly available, you can download it from NCBI's FTP site. Go ahead and play.

It makes me sad that most research is published under restrictive copyright licenses and is generally inaccessible to the public. But the fruit of the Human Genome Project *is* available. Find a different hyperbole, please don't needlessly promote the image of science as a monolithically inaccessible tax dollar sink.

An online essay on the Nature website by Phillip Ball (no relation) caught my eye, titled "Arthur Eddington was innocent!" The subject is Arthur Eddington's famous test of Einstein's theory of relativity, in which he compared the observed locations of stars during a solar eclipse to Newtonian and relativistic predictions.

Later historians have noted that Eddington's analysis discarded data from a telescope that did not fit the relativistic predictions. Because Eddington was a supporter of Einstein at the time, the implied accusation is that the experiment was biased and unjustifiably promoted as confirmation of Einstein's theory. However, recent re-examination of the data by Daniel Kennefick concludes that it was not Eddington who chose to discard this data but Dyson, leader of the expedition and much less likely to deliberately discard data in order to favor Einstein's new theory.

I'd like to add to this record of unfair cynicism - I looked into another famous accusation of a lack of scientific integrity while working on Wikipedia genetics pages. In 1936 the statistician R.A. Fisher observed that Mendel's results were "too good to be true". Many have popularized this to imply that Mendel fudged his data (although the ratios he observed were not incorrect). A 2001 review by Fairbanks and Rytting conclude that there are botanical and statistical reasons that could explain Mendel's results. In addition, they note that Mendel published only a subset of his experiments -- it is not surprising that he may have published the better numbers.

Phillip Ball concludes,

The motto of the Royal Society — Nullius in verba, loosely translated as 'take no one's word' — is often praised as an expression of science's guiding principle of empiricism. But it should also be applied to tellings and retellings of history — we shouldn't embrace cynicism about how scientists do their work just because it's become cool to knock historical figures off their pedestals.

I like learning about the uncertain paths that the history of science has taken, but I tend to bristle in response to this other type of relativism -- one that cynically reduces it to the status of social construct. Scientists are fallible and human, but the overall process generally contains an earnest desire for truth and discovery. I prefer this middle path between cynicism and idealization.

I've been getting my little science news snippets these days from Science Now news (Science Magazine, unfortunately restricted access) and Nature News (unrestricted access). I look around for other news sources, I know there's a ton out there. Today I looked at Seed magazine's news.

The top article at the time was this one: "Junk (DNA) In The Trunk".

The article's opening paragraph...

Oooooh, how mysterious! We don't understand 98 percent of our DNA!

Actually, it's not.

It's not a mystery.

It's a bunch of repetitive elements, parasitic self-propagating sequences that occassionally, in frenzied bursts of self-centered replication, manage to insert copies of themselves all around the DNA. They're called transposons. 72% of our DNA is composed of retrotransposons, LINEs, and SINEs, three varieties of selfish, self-propagating junk.

This is just bad reporting. People should not propagate the mystical idea that there's vast tracts of presumably functional DNA that remain a mystery to scientists. It doesn't need a function! We're pretty sure it doesn't have much function. This sort of thing is vexing enough when it takes the form of science fiction but it's totally unacceptable in science reporting.

Of course, the reporter did not actually get any facts wrong. He simply missed the point.

This really is something interesting here. Transposable elements have been a great tool for analysis of transcriptional promotion for Drosophila, and zebrafish is an animal much more relevant. What we really care about here isn't the junk. We care about transcriptional regulatory elements, those small regions preceding genes, and maybe a few small distal elements, that determine when a gene is going to be expressed.

So, yes, there are interesting noncoding portions, but to conflate that with the 98.5% number and the term "junk DNA" is going to propagate the ignorant characterization of this stuff as being of mysterious function, when we're pretty damn sure it ain't.

... And, as if the world conspires to drive me apoplectic, Chris sent me a link to this article about the in silico simulation of a virus. But... what's the point? I mean, sure, it's an impressive computational feat, but what did they learn? The article failed to report on the results!

Here it is, in a quote from Nature News:

See, that's an interesting result. The LiveScience reporter missed it.

Science reporting shouldn't just be about mysteries and pretty toys. I wish science reporters didn't keep misunderstanding science and missing the point of research -- not just for the layman's sake, but mine too, because I like reading about this stuff.

"Those who understand binary, and those who don't." People like dichotomies and people like to simplify. Who wants to listen to the complex opinions of a fox when he could hear the simplified and polarized view of a hedgehog? (A reference to Tatkin's analysis of political predictions .)

I was listening to more Long Now lectures. In particular, I'm thinking about Jim Carse's talk. He's the guy who wrote "Finite and Infinite Games". He talked about belief. He set aside "belief" in its weaker sense to mean "opinions" and focused on what you could call the belief that is religious.

These are some aspects he observed:

• Belief is based on a fundamental and unquestionable source, and the world is interpreted in light of this truth.
• Belief cannot exist in a vacuum; a believer needs an unbeliever to exists in opposition to.

Not all belief is religious, nor do all religious adherents have this style of belief. Some communists have belief in this style, for example. The writings of Karl Marx are their source, capitalism is their opponent. And many religious people are spiritual rather than feeling a polarizing identification to the group.

In my personal reflections on the topic, I was thinking about science. It seems to me that one of the aspects of science is to reject this style of thinking. We might not be perfect at it (it's human nature to dichotomize and simplify), but scientists try to question everything and take no single source as absolute truth. I think this difference causes misunderstanding. To the religious believer, he thinks a scientist simply has a different belief -- that Darwin is his source, and religion his opponent. In this context, science becomes "scientism", just one more belief to exist in opposition to.

PZ Myers linked to a study showing athiests to be "Americas Most Distrusted Minority". I guess it's disappointing. But really, it feels inevitable.

Since 9/11, we have been emphasizing religious tolerance. The propaganda we have heard is this: "Do not blame the Muslims, we respect and accept other religions into the fold of American society." So, yeah, we still distrust Muslims some. But the dialogue has shifted. The Christian belief can't exist in opposition to other religions, not if we're encouraging tolerance.

Well, of course, belief needs an opponent. So the new opponent is natural. If you can't exist in opposition to other religions, then you can exist in opposition to the anti-religion. For atheists to be the most distrusted isn't surprising at all in light of recent propaganda encouraging religious tolerance.

When Nietzsche lamented the death of God, what he meant was the death of a belief in absolutes. But belief can be in Communism, in Scientology, in any number of things that can take the place of religious doctrine. Alas, I lament, I think Nietzsche was wrong. It is human nature to fix our world upon unquestionable truths.