July 30, 2006 - August 5, 2006 Archives

Treponema flagellum baseA paper that just came out in Advance Online Publication section of Nature, Murphy et al. 2006, reports the first in situ structure of a flagellar motor in a spirochete, Treponema primitia. Such things have been done before, for the bacterial lab rat Salmonella, but spirochetes are a whole different bacterial phylum, and they have weird flagella. First, instead of the flagella sticking outside of the cell and doing what any self-respecting flagellum would do, the flagella of spirochetes rotate entirely within the periplasm (the space between the inner and outer membrane, which includes the cell wall). You might think that there would be no room for the flagellum to rotate in such a restricted space, or that it would tear apart the membranes – but intuitions are very unreliable at the sub-microscopic scale. The intracellular rotation of the flagella evidently cause the whole cell to gyrate, moving it through liquid in a corkscrew-like fashion.

Thanks, Kansas! Now Back to Ohio

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The success of the recent election in Kansas, in which pro-science moderates took back control of the State Board of Education, depended in part on the willingness of citizens to get out and work on behalf of pro-science candidates, and in part on having strong pro-science candidates on the ballot. Kansas isn’t the only state that will be electing members of its State Board of Education this fall. Ohio will, too, and people and organizations in Ohio are seeking strong pro-science candidates to oppose the ID creationist members of the Ohio Board.

One such organization is HOPE – Help Ohio Public Education. HOPE is actively talking with potential candidates. For example, HOPE is in discussions with a potential pro-science candidate to run in District 7, in northeastern Ohio. That seat is currrently held by one of the two ID creationist thought leaders on the Oho State BOE, the member who made the original “two modesl” motion to the Ohio Board in 2000, first foreshadowed adding global warming to the list of topics to be “critically analyzed” by Ohio school children, and continues to push trash science.

HOPE has been impressed with how much the potential candidate could contribute to solving problems of school funding, state BOE and DOE governance, and curriculum, specifically including science education. He comes with a strong background on education issues and would be an outstanding member of the state board.

Regardless of whether you’re in or out of Ohio you can help. Contact Ohio newspapers, and in particular write a letter to the editor of the Akron Beacon Journal explaining why we need good candidates for the State BOE. Help HOPE improve Ohio education and do it today. If HOPE can persuade good candidates to run we have a good chance of taking out Ohio’s answer to Connie Morris. Help HOPE get a strong candidate on the ballot this fall. Thanks!

Neal McCulskey of the Cato Institute and Matthew Yglesias of The American Prospect have a debate going over whether school choice programs would help resolve the evolution/creationism controversy. Here's McCulskey's first post, Yglesias' reply, and McCulskey's rebuttal.

From here. Almost as good as this one from December 23, 2005:

I imagine that reading scientific journals is mostly a drag for ID advocates: all those papers highlighting evolutionary mechanisms, identifying transitional fossils, veryfing phylogenetic-based predictions must be really irritating. There are, however, few and far between papers that set the ID advocates’ hearts all aflutter, so when one appears, they make sure to milk it for all its P.R. worth. One of the recent examples was a 2003 paper by Hirotsune and colleagues in Nature, which reported that alteration of the pattern of expression of a purported mouse pseudogene (i.e. an apparently inactivated, non-functional gene, part of the so-called “junk DNA”) results unexpectedly in the modification of the activity of its functional counterpart, leading to a series of dramatic developmental defects.

Now, one of the recurrent claims of Intelligent Design is that most if not all of the features of any organism, including its entire genome, should somehow be useful. Thus, ID advocates enthusiastically latched on Hirotsune’s publication as supporting their claim that “junk DNA” is, in fact, not junk at all (indeed, if you Google for “Hirotsune” and “Intelligent design”, you will find over 100 hits). Alas for them, a brand new paper by Todd Gray and colleagues in the Proceedings of the National Academy of Sciences appears to completely refute the original findings.

I found this bit of Discovery Institute fact-mangling to be even more blatant and preposterous than usual.

It seems the good folk at DI are complaining that Paul Nelson May Now be Forever Misquoted, saying

Today there is another urban myth building up a head of steam, and being helped along by Darwinists, about Discovery Fellow Paul Nelson. Gaurdian [sic]reporter Karen Armstrong reports: ‘Great shakings and darkness are descending on Planet Earth,’ says the ID philosopher Paul Nelson, ‘but they will be overshadowed by even more amazing displays of God’s power and light.’ And yet this is pure rubbish because Nelson never said anything like this, and it turns out that Armstrong never even interviewed him. Nelson points this out in his letter to the Guardian demanding a correction. (Note to Paul: don’t hold your breath)

The trouble is, when you visit Nelson’s aforementioned letter, you quickly learn that Paul Nelson is actually thanking

…the indefatigable Nick Matzke for catching a wild misattribution in Karen Armstrong’s Guardian opinion piece of 31 July 2006. I just sent the following letter to the newspaper:

To the editors, In her opinion piece of 31 July, Karen Armstrong attributed remarks to me (as a direct quote) which I did not make: http://www.guardian.co.uk/commentisfree/story/0,,1… The erroneous attribution can be found near my name, Paul Nelson. This was first brought to my attention by the widely-read science blog, The Panda’s Thumb: www.pandasthumb.org

And there we have it. As discussed days ago on the Thumb, a Guardian reporter egregiously misquoted IDer Paul Nelson; the error was posted, corrected and discussed by Nick Matzke here on the Thumb; Paul Nelson complained to the Guardian, citing Nick’s PT blog as his source; … and so, Robert Crowther concludes

Today there is another urban myth building up a head of steam, and being helped along by Darwinists, about Discovery Fellow Paul Nelson.

We’re not making this stuff up! The Moral of the story is that it’s best to put the old brain in gear before engaging the mouth. But when you see evil “Darwinists” around every corner, I guess old habits are hard to break!

Evolution of median fins

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Often, as I've looked at my embryonic zebrafish, I've noticed their prominent median fins. You can see them in this image, although it really doesn't do them justice—they're thin, membranous folds that make the tail paddle-shaped.


These midline fins are everywhere in fish—lampreys have them, sharks have them, teleosts have them, and we've got traces of them in the fossil record. Midline fins are more common and more primitive, yet usually its the paired fins, the pelvic and pectoral fins, that get all the attention, because they are cousins to our paired limbs…and of course, we completely lack any midline fins. A story is beginning to emerge, though, that shows that midline fin development and evolution is a wonderful example of a general principle: modularity and the reuse of hierarchies of genes.

Continue reading "Evolution of median fins" (on Pharyngula)

Now that the voters of Kansas have replaced the pro-ignorance majority on the state school board with a pro-science one, I highlight a comment made today that demonstrates why good standards are important for teachers who come under political pressure.

About a month ago I wrote “Georgia Education on My Mind“, in which I mentioned the struggle of one veteran science teacher, Pat New, to give her students the education they deserved. Eventually, her administrators backed off when they discovered that what she wanted to teach, evolution, was actually part of the state standards. Today she left the following comment:

I was that teacher in Mike Winerip’s New York Times article. I can’t thank the Georgia Citizens for Integrity in Science Education enough for, first of all, their fight to make sure evolution was in the Georgia science standards and, second of all, for their support when I was in the middle of fighting my administrators and parents over my teaching those standards. Having those standards in place was the reason I decided to take the stand in the first place. I knew that, finally, I could teach evolution the way it was supposed to be taught, as the backbone of life science. Thank you, all of you who fought that fight.

Pat New

Let’s keep it up. The teachers need us.

Since U.S. District Judge Casey Rodgers refused to lift a travel ban on Kent Hovind, I’ve been wondering when the itinerary on his web site would change to list “The Hoosegow” for up-coming events. However, ol’ Doc Dino must still be floating in the ether, because he still lists an appearance in my neck of the woods, Coeur d’ Alene, Idaho, for October 21.

It feels good to see the IDist crackpots beaten back a little bit in their bid to control the Kansas school board, and I think it is necessary to keep up the pressure and prevent them from getting a better grip on public school education. However, Paul Nelson actually has a point with his little parable. It's not the point he thinks he's making, but it's important to keep in mind anyway, and I'm going to dash some cold water on any sense of triumphalism on the pro-science side.

Continue reading "In which I (partially) agree with Paul Nelson" (on Pharyngula)

Dembski and Darwinian fascists


Dembski posted an anonymous email he received accusing a "prominent anti-ID proponent" of supressing an "ID-friendly" experiment (actually a computer model) that was developed by an undergraduate student.

Read more (and comment) at Stranger Fruit.

In addition to watching the news on Kansas, we have been meaning to post these to PT but haven’t quite gotten to it, so here is a collection of recent commentary on ID/creationism, Kitzmiller, etc. Much of this has already been noted on the NCSE News page.

Coultergeist – Jerry Coyne reviews Ann Coulter’s book Godless in The New Republic, with about as much respect as she deserves (pass-through link, free registration required). I can’t claim responsibility for the science in Coyne’s essay like Dembski did for Coulter, but I did get to comment on a draft, and Coyne (who is personally targetted repeated by Coulter) did tell me that TNR wanted the review of Coulter’s book to be in the same style that Coulter herself wrote. So that explains the invective (although it appears to me that Coyne wasn’t able to turn his scientific side off completely, there are some low-invective zones). If you want to give the ol’ irony meter a spin, check out this post from an ID blogger who is defending Coulter from Coyne:

I think Coyne might have over-reacted just a tad to the part about Ann Coutler “attacking” him. But again, fact-distorting and insult-hurling have always been favorites for Coyne and the evolution community.

Tangled Bank #59

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If current results hold, it looks like the creationists on the 10-member Kansas Board of Education have lost two seats in the Republican primary. The likelihood is therefore that the new Board of Education will switch from being a 6-4 pro-creationism majority to at least a 6-4 pro-science majority (depending on the November general election). This probably means the pro-ID/creationism science standards are history.

So let’s sum up the last 9 months:

The results of the primary in Kansas election are beginning to come in. The unofficial results are being posted every 10 minutes here on the website of the Kansas Secretary of State.


Many readers of this blog will be familiar with Cold Spring Harbor Laboratory. CSHL is the Long Island educational and research institution that hosts some of the most important professional meetings in several biological disciplines. It has for decades been the “home campus” of phage, bacterial and yeast genetics, as well as of computational neuroscience, developmental biology and various branches of genomics, bioinformatics and systems biology.

As a frequent attendee of meetings and symposia at CSHL, I am on their regular mailing list. I recently got an announcement of a meeting to be inaugurated this December that should be of great interest to followers of Intelligent Design. The meeting, “Engineering Principles in Biological Systems” ought to be exactly the kind of forum at which “Intelligent Design” researchers present their conclusions.

One of the standard talking points from ID advocates these days is that us evolution advocates are just plum crazy to even suggest that policies requiring schools to teach “critical analysis of evolution” are a way to get intelligent design into the classrooms. DI shill Casey Luskin even coined a phrase in February when he claimed that those who think this way are suffering from “false fear syndrome” and exhibiting paranoia. I’m going to suggest that this is argument is transparently false and that the ID side knows it and is pushing it anyway. And I have proof in their own words.

Continue Reading at Dispatches from the Culture Wars. And don’t forget the follow up post, where Dembski’s research assistant admits the fraud.

Here I am, minding my own business, reading this editorial opinion piece in The Guardian about fundamentalists and creationism/ID, stem-cell research, The Rapture, etc. It is by Karen Armstrong, author of the 2000 book The Battle for God. I have not read the book, but I had the impression it was a best-selling history of fundamentalism and a comparative study of the fundamentalist phenomenon in various religions. So I figured that Armstrong probably had some idea of what she was talking about.

So I’m reading the editorial. It overviews some history of Christian fundamentalism and the like, and goes into the Scopes Trial. One minor misstep occurs when “creation science” is dated to 1925, which is not quite accurate (“scientific creationism” was a particular expression of creationism that was codified around 1969 according to Ronald Numbers), but this is the kind of detail that may be lost on people who are not creationism nerds.

But then I read this:

The fundamentalists’ rejection of science is deeply linked to their apocalyptic vision. Even the relatively sober ID theorists segue easily into Rapture-speak. “Great shakings and darkness are descending on Planet Earth,” says the ID philosopher Paul Nelson, “but they will be overshadowed by even more amazing displays of God’s power and light. Ever the long-term strategist, YHVH is raising up a mighty army of cutting-edge Jewish End-time warriors.”

As Jon Stewart would say, Whaaa?


Assuming that none of my readers are perfectly spherical, you all possess notable asymmetries—your top half is different from your bottom half, and your front or ventral half is different from you back or dorsal half. You left and right halves are probably superficially somewhat similar, but internally your organs are arranged in lopsided ways. Even so, the asymmetries are relatively specific: you aren't quite like that Volvox to the right, a ball of cells with specializations scattered randomly within. People predictably have heads on top, eyes in front, arms and legs in useful locations. This is a key feature of development, one so familiar that we take it for granted.

I'd go so far as to suggest that one of the most important events in our evolutionary history was the basic one of taking a symmetrical ball of cells and imposing on it a coordinate system, creating positional information that allowed cells to have specific identities in particular places in the embryo. When the first multicellular colony of identical cells set aside a particular patch of cells to carry out a particular function, say putting one small subset in charge of reproduction, that asymmetry became an anchor point for establishing polarity. If cells could then determine how far away they were from that primitive gonad, evolution could start shaping function by position—maybe cells far away from the gonad could be dedicated to feeding, cells in between to transport, etc., and a specialized multicellular organism could emerge. Those patterns are determined by interactions between genes, and we can try to unravel the evolutionary history of asymmetry with comparative studies of regulatory molecules in early development.

Continue reading "Ancient rules for Bilaterian development" (on Pharyngula)

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