More on flagellum evolution

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So an anonymous comment to my last post on Liu and Ochman’s paper “Stepwise formation of the bacterial flagellar system” directed me to comments by Nick Matzke over on the Panda’s Thumb, which suggest that the L&O results could be an artifact of their methods. I don’t have much experience with the methods at the heart of the issue, but it looks like Matzke could have a point. That’s what I get for being all triumphalist.

That said, for publication at PNAS, L&O did pass peer review by people who know this sort of work. If Matzke feels he has a solid case, he ought to publish a response (he’s previously published on flagellum evolution [subscription], so he should get a hearing), and let the peer review process sort things out. It’s also worth noting that L&O are building on a lot of previous work on the evolution of the flagellum (their introduction section sums it up), which has given scientists good reason to think that the flagellum (1) did evolve in a stepwise fashion and (2) was assembled in part from pre-existing components with other functions.

Well, that about wraps it up for Michael Behe

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Open access article in last week’s PNAS: Stepwise formation of the bacterial flagellar system. Of course, the Intelligent Design crowd will continue saying the same things they’ve always said without blinking, but it’s always nice to have a citation ready at hand for refutation.

The authors look at the relationships of the genes involved in building a flagellum, and are able to deduce that they arose through duplication – mutation and natural selection copied pre-existing components and exapted them to put together more and more advanced structures. It’s possible that all the intricately interdependent components of the flagellum originated from one ancestral protein.

“We’re not a fragile country. Trust us to have that conversation.”

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So, I was pretty excited when I learned Bill Moyers was coming back to PBS with a new interview program, Bill Moyers Journal. And I was even more excited when I learned that it would be podcast, so I can listen to it even though my TV gets nothing but snow and the input from my DVD player. But the icing on the cake? The first interviewee is Jon Stewart.

I love Public Broadcasting.

Beady little eye contact

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The first half of the walk between my apartment and campus goes downhill through a slightly shabby, crowded college-town residential neighborhood that is much improved by the presence of large, shady trees lining the sidewalk. Almost at the bottom of the hill, my walk takes me past a tree whose owner has decided to feed squirrels. The tree is close to the sidewalk on the left as I walk toward campus, and it has two trunks that diverge almost at the ground; nailed to each of these at about the height of my chin is a wooden box about ten inches by ten inches, with an open face looking across the sidewalk to the house of the probable squirrel-feeder and the bottom surface forming a tray, which usually contains seeds or nuts or such. Many times I’ve forgotten that I’m nearing this tree as I walk to campus in the morning, and many times I’ve been jolted by the explosive scutter of squirrels evacuating the feeder as I approached.

Yesterday this didn’t happen. Yesterday, I didn’t think about the approaching feeder until I was right on beside it. Remembering it, I turned left for a glancing look as I passed. And I came eye to eye with a squirrel.

It was sitting atop the farther of the two boxes, right about at my eye level, frozen in that twitchy way that largish rodents sometimes freeze when they’re threatened, as though you might go away if they don’t do anything cute. It was a fox squirrel, I think, rusty gray above and just rusty below, fixing me with a pair of black, shining eyes.

I stood still and looked at it. It twitched its tail.

Then, incredibly, it jumped to the other box, just a foot or so from my face. I could see its handlike little paws gripping the edge of the box, paws that called to mind words like “cunning” and “clever”. The black little eyes stared at me, blank and shiny as freshly-washed chalkboards. The squirrel made a twitchy advance, then backed off, then advanced again. I tried not to move; but this was unnerving.

It advanced again, and I must have stepped back a fraction – the squirrel made an instant U-turn and scuttered up the tree trunk. I was left blinking at the feeder box, listening to the sounds of traffic on the street at the end of the block.

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We are to find God in what we know, not in what we don’t know.

–Dietrich Bonhoeffer, Letters from Prison

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Till we can become divine we must be content to be human, lest in our hurry for change we sink to something lower.

–Anthony Trollope, Barchester Towers

Glory, hallelujah!

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The Supreme Court says (5-4) that the EPA should regulate greenhouse gasses.

Collins versus Dawkins

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NPR’s Fresh Air ran two major interviews on faith and science last week: Richard Dawkins (last Wednesday) followed by Francis Collins (Thursday). Dawkins, of course, made his name as an evolutionary biologist and has recently published The God Delusion, an atheist’s manifesto for the 21st century. Collins is an evangelical Christian who headed the Human Genome Project, now working with the NIH, who has himself just released a defense of scientific Christianity titled The Language of God. The contrasts between the two are informative.

Dawkins comes across as more moderate than I’ve heard him in other interviews; his argument is basically that science explains the physical world better than religion, religion comes with a built-in danger of extremism, and we can find all the meaning we need in science’s explanations of the world. Quoting Douglas Adams, he says that his teenage discovery of evolutionary theory “about wrapped it up for God.”

Collins makes a (to me) highly familiar defense of a theistic scientist’s worldview, making much of his awe before the wonder of the human genome. He points out that science is not necessarily equipped to prove (or disprove) the existence of God, but also persists in talking about “evidence” for the Divine. Citing C. S. Lewis, he argues that faith and evidence are not only compatible, but actually pretty close to the same thing.

My conclusion, after listening to them back to back: they’re both wrong. In this exchange, Dawkins is the more lucid of the two, but his argument founders on his absurd insistence that science’s explanations of the physical world are also adequate to provide that world with meaning. Just because I know why the world is the way it is doesn’t tell me how it should be, especially as regards the best ways for human beings to live together.

Although I’m more in agreement with Collins, his argument feels mushy to me. I can’t agree with his (and Lewis’s) assertion that faith is somehow ultimately based on reasoning from scientific evidence. My judgments of what is (and is not) in accordance with the example of Jesus Christ are far more aesthetic than logical. I can’t quantify why a given behavior is Christly – but I trust that, with prayer, I can make that decision. Likewise, my “evidence” for belief in the Divine is so different from scientific evidence that it probably doesn’t deserve the name. What I have are feelings that are evoked by my experience of Creation and the people in it – this, not scientific fact, is the substance of things hoped for, and the conviction of things unseen.

“It’s the television equivalent of NPR.”

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That’s a publishing spokeperson talking about The Daily Show in a recent New York Times article. Apparently, if you’re hawking a serious book (on politics, economics, or history), Jon Stewart is the guy to go to for a sales-pushing interview.

Ding-dong, the Religious Right is dead?

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In a triumphal column over at Time.com, left-leaning political preacher Jim Wallis declares that “the Religious Right’s era is over.” This week’s New York Times Magazine is running an opinion piece that asks whether Democrats may be “narrowing the religion gap.” Is it time to start celebrating?

Not yet. Here in Moscow, Idaho, the Religious Right is still alive and kicking. Wallis’s will truly have arrived when the most visible representatives of Christianity in this sleepy little college town are no longer the members of near-cultlike Christ Church – and when I don’t have to spend my time in church mostly avoiding talking about my career in science and my time in the lab mostly avoiding talking about my faith. As for the Times article, its thesis is not that the Religious Right is losing steam, but that churchgoing Democrats will bring “welcome moderation” to the Culture Wars. Meanwhile, the worldwide Anglican Communion has given the American Episcopalian Church eight months to stop blessing same-sex unions. Moderation, it seems, may be understood to mean that liberals will tack right – but not that conservatives will give an inch to the left.

Of course, the tide can be turned, and it’s the responsibility of every liberal Christian to present to the world a face of Christ that isn’t defined by prejudice or powerlust. But we’ve still got a long way to go.