August 2010 Archives

Guardian Science Blogs

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Another group (or as self-styled, “network”) of science blogs is being set up at the Guardian newspaper in order to “entertain, enrage, and inform.” According to the announcement, to start with there will be four blogs covering “evolution and ecology, politics and campaigns, skepticism (with a dollop of righteous anger) and particle physics…”. A fifth will be more generic, and “…will hopefully become a window onto just some of the discussions going on elsewhere. It will also host the Guardian’s first ever science blog festival - a celebration of the best writing on the web.”

We start tomorrow with the supremely thoughtful Mo Costandi of Neurophilosophy. You can also look forward to posts from Ed Yong, Brian Switek, Jenny Rohn, Deborah Blum, Dorothy Bishop and Vaughan Bell among many others.

The Guardian’s science blogs join a growing array of aggregations of science bloggers, most of which are well known to PT readers.

Freshwater: Same song, second verse

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The legal morass into which John Freshwater and his attorney R. Kelly Hamilton have been sinking became deeper today. United States Magistrate Judge Norah McCann King has granted a Motion to Compel compliance with discovery demands and imposed sanctions on Hamilton, John Freshwater’s attorney in Freshwater v. Mount Vernon Board of Education, et al.. This is the second granted Motion to Compel and the second set of sanctions imposed on Hamilton. The first occurred in Doe v. Mount Vernon BOE, et al., when Judge Gregory Frost ordered Hamilton and Freshwater to pay attorney fees and costs to the Dennis family’s attorney. This new order requires Hamilton alone to pay attorney fees and costs to the Board of Education’s lawyer(s) for his dilatory tactics in guiding the evasive responses of the Freshwaters (John and his wife Nancy) to discovery demands. The amount of the fees to be paid isn’t specified in the order; it says only that Hamilton is to pay

… the reasonable attorney’s fees and costs incurred by the moving defendants as a result of the grant of the Motion to Compel. The moving defendants are ORDERED to provide to plaintiffs’ attorney, within fourteen (14) days of the date of this Opinion and Order, a statement of their fees and expenses associated with the filing and grant of the Motion to Compel.

The bill in the similar ruling in Doe v. Mount Vernon Board of Education, et al., was over $28K.

The order also extends the time for the defendants (Board of Education) to identify appropriate expert witnesses, since that depends on the information the Freshwaters were to provide in discovery.

Addendum: The full ruling just went up on NCSE’s site on the case.

The casual assumption of privilege

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See update at the end of the post

One would think after two years of public hoorah in this county over church/state issues in the Freshwater case that there would be a heightened sensitivity to those issues among employees of Knox County (Ohio) schools. But that’s apparently not the case. A Job Training Coordinator at the Knox County Career Center, a vocational high school, is organizing a prayer group for county educators to meet at the local Nazarene University. That in itself is not problematic; such a group has a perfect right to organize and meet in that venue.

However, the organizer publicized his work telephone number and email address as contact information for people interested in the prayer group. More astounding, he specified that contact should be made during school hours!

For more information contact Cagle during school hours at 397-5820, ext. 3051, or e-mail [Enable javascript to see this email address.].

I know it’s a risk publishing the phone number and email address even though he himself has publicized them. Please don’t call or email Cagle to harass him.

Fortunately, I got a swift response from the Superintendent of the Career Center when I complained about the matter in an email sent last night, saying she intended to deal with it today. I also got a swift response from the President of the Mount Vernon Board of Education, who sits on the Career Center Board, giving me the same assurance. She at least has good reason to know the consequences of messing around with the Establishment Clause.

What was surprising was Cagle’s apparent assumption that it is perfectly OK to use his public school email and phone to organize a sectarian religious event on public school time, “during school hours.” That’s the “casual assumption of privilege” the title of this post refers to. I don’t know Cagle, but I don’t doubt that he’s an OK guy and competent at his job. But what part of “Not on the government’s dime, not on the government’s time” is so hard to understand?

I’m reminded of middle school teacher Dino D’Ettore testifying about giving a “salvation message” to students at the middle school, and of Lori Miller testifying about praying over students in the school, neither of them apparently having any idea of the inappropriateness of that behavior. There’s a real deep pool of ignorance of (or disregard for) the Constitution here.

Update

While I don’t see it on the Mount Vernon News web site, corrected contact information for Cagle at his personal phone and email was published in todays print edition.

And the winners are…

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with contributions by Matt Young

Due to some hanging chads, we have two winners this week for the “invasive” category—kinda makes sense—Al Denelsbeck and Malcolm S. Schongalla.

Balanus improvisus, bay barnacle by Al Denelsbeck — They are now showing up far removed from their originating Atlantic home. Here, I caught detail of the “toes” (cirri) during feeding, with a depth of field estimated at less than 2mm. And of course, Darwin spent no small amount of time working with barnacles and their taxonomy.

Apis mellifera, European honeybee, Christchurch Botanic Gardens, New Zealand by Malcolm S. Schongalla — This species was introduced to New Zealand in 1839. It has suffered from worldwide population declines and “colony collapse disorder.” This species holds the unlikely honor of being simultaneously invasive, valued, and in peril.

The Talk Origins Archive Foundation has generously offered to provide the winner with an autographed copy of Why Evolution Works (and Creationism Fails), by Matt Young and Paul Strode. (Update: we may have more options for the winner to choose from.)

(Winners, please send your mailing address to [Enable javascript to see this email address.].)

Birdwatching for creationists

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I question that there is a mexican [sic] gray wolf. Subspecies don’t exist. Its [sic] just a wolf. It breeds and would with any wolf anywhere. Any slight difference in colour of fur etc is ireelevant [sic]. I’m sure the shades of this mexican [sic] are as varied as every mountain. In facxt [sic] its [sic] of a kind. This creationist says the dog kink [sic] is the smae [sic] as the bear kind and the seal kind and probably more. Its [sic] a cute doggy. Its [sic] immigrated but hopefully it assimilates and doesn’t ask for interference on its behalf to the loss of American wolves. Hopefully howls in the same way and doesn’t hyphenate its identity. Be a team member and not another team on the bench. – Robert Byers

Sic, sic, sic. I am always amazed when a so-called expert birdwatcher sees a flash go by and announces, “Oh look! That was a boreal chickadee [or a rosy-breasted pushover or whatever]!” That man claims to have 418 life ticks. According to Robert Byers, he is wasting his time: There is no such thing as a species; in fact there are only kinds. Without claiming anywhere near 418 ticks, I have amassed an almost complete portfolio of ticks – I have seen at least one bird of nearly every kind. Herewith a list of kinds of birds:

Freshwater: More sanctions coming against Hamilton?

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The defendants in Freshwater v. Mount Vernon Board of Education, et al. have requested that R. Kelly Hamilton, John Freshwater’s attorney, be subject to sanctions for failure to comply with discovery demands. What’s interesting about the request (pdf) is that it specifically singles out attorney Hamilton for the sanctions, and not Freshwater.

Recall that in Doe v. Mount Vernon BOE, et al., sanctions were also imposed on Freshwater and Hamilton. In that case the operative paragraph of the Court’s order (pdf) was

6. GRANTS Plaintiffs’ request for attorneys’ fees and costs. The Court ORDERS Freshwater and Attorney R. Kelly Hamilton to pay the reasonable attorneys’ fees and costs that Plaintiffs incurred as a result of Freshwater’s and Attorney Hamilton’s failure to comply with this Court’s Written Order Compelling Production and this Court’s Verbal Order Compelling Production and ORDERS Freshwater and Attorney R. Kelly Hamilton to pay the reasonable attorneys’ fees and costs that Plaintiffs incurred as a result of filing their Motion to Compel. (italics added)

The italicized phrase plainly says that both Freshwater and Hamilton are responsible for the costs. However, what was offered as supposedly satisfying that order was an unrecorded lien on a parcel of land nominally belonging to Freshwater. Hamilton put nothing into the payment pot.

In the new request (pdf) filed in Freshwater v. MVBOE the defendants specifically single out Hamilton for sanctions. They say

Further, this Court should order Attorney Hamilton to pay the expenses incurred by Defendants. “Rule 37 permits a court to order the attorney who advised the conduct necessitating a motion to compel to pay the expenses thereby incurred… when it is clear that discovery was unjustifiably opposed principally at his instigation.” Id. at *19-20 citing Humphreys Extermination Co. v. Poulter, 62 F.R.D. 392, 395 (D. Md. 1974). For the foregoing reasons, it is clear that Attorney Hamilton controlled the disposition of his clients’ discovery responses. Attorney Hamilton chose not to call Defendants’ counsel to notify them that responses were in the mail and chose not to file for an extension of time. It was Attorney Hamilton who did not work with Defendants’ counsel to provide adequate discovery in a timely fashion.

I’ve heard some talk among attorneys not associated with the matter to the effect that Hamilton should be subject to some sort of discipline for his behavior in the several cases involving Freshwater, and this request for sanctions specifically directed at him may foreshadow even more serious measures to come.

And the winner is…

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with contributions by Matt Young

Don’t forget to vote in our new Invasive contest.

The winner of the threatened or endangered category is Dan Stodola for his splendid photograph of a Mexican Gray Wolf.

Canis lupus baileyi, Mexican gray wolf, by Dan Stodola — A subspecies of the gray wolf. Was intentionally eradicated from the wild to protect domestic livestock. Has now been reintroduced to a limited range in Arizona. Photo taken at Brookfield Zoo.

The Talk Origins Archive Foundation has generously offered to provide the winner with an autographed copy of Why Evolution Works (and Creationism Fails), by Matt Young and Paul Strode. (Update: we may have more options for the winner to choose from.)

(Mr. Stodola, Please send your mailing address to [Enable javascript to see this email address.].)

Don’t forget to vote in our new Invasive contest.

Note: Matt Young directed the selection of the finalists and wrote most of this text.

We received approximately 60 photographs from 20 photographers. Most of the pictures were excellent. Approximately half represented endangered or invasive species, very loosely defined. We therefore established 3 categories: general, threatened or endangered, and invasive.

Choosing finalists was difficult. We considered what we thought was the scientific and pictorial qualities of the photographs, and also attempted to represent as many photographers and present as much variety as possible. The text was written by the photographers and lightly edited for style.

Here are the finalists in the invasive category. Please look through them before voting for your favorite. We know it is possible to game these polls. Please act like adults and don’t vote more than once. If we believe that the results are invalid, the contest will be canceled. The photos and poll are below the fold.

The Talk Origins Archive Foundation will provide the winner with an autographed copy of Why Evolution Works (and Creationism Fails), by Matt Young and Paul Strode.

I’m Proud of Wyoming

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granite2500.jpg I recently finished some fieldwork in Wyoming’s Bighorn Mountains, and was favorably impressed with many road signs describing geological formations in the area.

No appeasement of young-earth creationists here! Wyoming is telling visitors just how old the area actually is. Hurrah for Wyoming!

A couple weeks ago, the Skeptic’s Guide to the Universe (the best podcast there is, by the way) covered a horrific story about an Australian couple who tortured a woman after a psychic led them to believe that she was responsible for a theft they had suffered. Their attack on her was really godawful. But then the Rogues got to talking about whether the psychic was herself criminally or civilly liable for her part in the affair, and much of what they said was incorrect. I thought it might serve as an interesting “teaching moment,” but as it has less to do with creationism than with woo in general, you can read more over at Freespace.

And the winner is…

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with contributions by Matt Young

We forgot to declare a winner of the “general” category yesterday The winner is Nicholas Plummer for his splendid photograph of a Robber Fly Eating a Wasp.

Robber fly (possibly Promachus rufipes, red-footed cannibalfly) eating a wasp that it has caught in flight, by Nicholas Plummer.

The Talk Origins Archive Foundation has generously offered to provide the winner with an autographed copy of Why Evolution Works (and Creationism Fails), by Matt Young and Paul Strode. (Update: we may have more options for the winner to choose from.)

(Mr. Plummer, Please send your mailing address to [Enable javascript to see this email address.].)

I generally do not think authors should comment publicly on book reviews, but this spring I came across two reviews of a book that I coauthored, which had somewhat divergent viewpoints and were written by reviewers who were put out by our treatment of religion. Both reviewers, to some extent, project their own views onto us, but for very different reasons, and I thought that this interesting divergence called out for a brief response.

The book in question is Why Evolution Works (and Creationism Fails), by me and Paul Strode. A review in Science Education by Adam Shapiro, now a postdoc at the University of Wisconsin School of Medicine, begins with this enigmatic niggling:

Photo Contest

Voting on the general category has ended. Now is time to vote on the Threatened or Endangered category.

Note: Matt Young directed the selection of the finalists and wrote most of this text.

We received approximately 60 photographs from 20 photographers. Most of the pictures were excellent. Approximately half represented endangered or invasive species, very loosely defined. We therefore established 3 categories: general, threatened or endangered, and invasive.

Choosing finalists was difficult. We considered what we thought was the scientific and pictorial qualities of the photographs, and also attempted to represent as many photographers and present as much variety as possible. The text was written by the photographers and lightly edited for style.

Here are the finalists in the threatened or endangered category. Please look through them before voting for your favorite. We know it is possible to game these polls. Please act like adults and don’t vote more than once. If we believe that the results are invalid, the contest will be canceled. The photos and poll are below the fold.

The Talk Origins Archive Foundation will provide the winner with an autographed copy of Why Evolution Works (and Creationism Fails), by Matt Young and Paul Strode?

Since Comedy Central took Futurama from Adult Swim, I have boycotted watching Futurama on Comedy Central. (Adult Swim is the reason why Futurama lives.) That may have to change.

FuturamaThursdays 10pm / 9c
Preview - Evolution Under Attack
www.comedycentral.com
Futurama New EpisodesRoast of David HasselhoffIt's Always Sunny in Philadelphia

I recently read Casey Luskin’s article (“Zeal for Darwin’s House Consumes Them: How Supporters of Evolution Encourage Violations of the Establishment Clause”) in the Liberty University Law Review. Most of it is tendentious as usual, and Tim Sandefur makes an excellent reply (PT: Luskin, laws, and lies).

However, I think it may be important for us to read Luskin’s article, as it looks like it is laying out a new lawsuit strategy for the ID movement, which would be to provoke parents into suing school districts that use a textbook that has some smidgen of (alleged) materialism, (alleged) endorsement of theistic evolution or accommodationism, or critique of ID/creationism somewhere within its hundreds or thousands of pages.

Luskin, laws, and lies

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Casey Luskin has an article in the Liberty University Law Review which he claims isn’t about Intelligent Design creationism, but is instead meant to show how “zeal for Darwin encourages certain violations of the Establishment Clause.” It will come as no surprise to anyone that Luskin’s argument is flimsy, his evidence illusory, his readings of the case law distorted, and the overall effect essentially a fun-house mirror version of First Amendment law.

Luskin’s thesis is that criticizing Intelligent Design creationism = attacking a religious viewpoint. He combines this with an insistent denial that ID is a religious viewpoint, which is an amusing effort to stick to the Discovery Institute party line, but is not, strictly speaking, illogical. His position is that, if we assume the fact (which is a fact, but he assumes, rather than believing it) that ID creationism is a religious viewpoint, why, then, it violates the First Amendment to disparage it: “Sylvia Mader’s 2007 introductory biology textbook, Essentials of Biology…plainly communicates that ID runs counter to the factual scientific data,” he writes. “If she is correct that ID is a religious viewpoint, is it appropriate for state schools to use her textbooks that unambiguously claim ID is empirically wrong?”

The correct answer is, yes, it’s perfectly constitutional and perfectly appropriate–but of course, to Luskin, the answer is no: “Students who support scientific creationism would thus hear that their ‘set of religious beliefs’ is not only an ‘arbitrary faith,’ but that they are not using their ‘God-given gifts to reason and to understand’ in the way God intended. While many might agree with such arguments, religious neutrality forbids the government from attacking, opposing, and disapproving of such a ‘set of religious beliefs’ in this fashion.”

This is false. The neutrality requirement in the First Amendment forbids the government from taking a position on the truth or falsehood of a religious doctrine in religious terms, but it may take a position on any matter on areligious or non-religious terms. That is, the Constitution forbids the government from endorsing or propagating or censoring the doctrinal truth of a religious proposition, but it does not forbid the government from endorsing or propagating the factual truth of a proposition, even if those propositions turn out to be the same in content. It does not forbid the government from reaching a conclusion, and stating or endorsing that conclusion, from secular premises, even if that conclusion happens to clash with someone’s religious view. Government may not take religious positions, but it take secular positions that happen to clash with positions endorsed by a religious viewpoint.

This ought to be plainly obvious. Some people, for example, believe that AIDS is a punishment sent from God to scourge sodomites, or that blacks are inherently inferior to whites, or that ancient Indian tribes descended from Israelites and fought wars in chariots, or that earthquakes express Vulcan’s displeasure at man’s hubris.* The First Amendment forbids the government from taking any official doctrinal positions on these matters–but it does not forbid, and could not possibly forbid the government from teaching that, in fact, AIDS is caused by a virus, that blacks are not inferior to whites, that American Indian tribes have no relationship to the Israelites and lacked chariots, and that earthquakes are caused by geological activity. The First Amendment does not forbid the government from saying that there is no documentary evidence (or no fossil evidence or no eyewitness evidence) for P, even though P falls within a religious doctrine–and the Amendment cannot sensibly read to require this, because it would make all communication and all activities impossible. The most arbitrary claims would be insulated from challenge, and each person would have a heckler’s veto over government’s actions–the more irrational and mystical, the better.

To put it a bit more technically, if proposition P can be supported by religious argument R and also by secular argument S, government is entirely within its constitutional authority to take an official position on P on the basis of S. In fact, it’s even entitled to throw people in jail for P. But it may do nothing whatsoever on the basis of R. It may not support or oppose or endorse it. That’s why the government can make it illegal for people to use intoxicating drugs–even if they do so for religious purposes–but why it may not prosecute faith healing, even though faith healing is obviously fraudulent bunk.

Now, let’s play “name that logical fallacy” (to steal from our friends at the Skeptic’s Guide): “[E]ither ID is a religious viewpoint that is unconstitutionally opposed, inhibited, and disapproved when this textbook is used in public schools,” writes Luskin, “or ID is not a religious viewpoint and is thereby fair game for all forms of government-sponsored attacks, disparagement, hostility, as well as endorsement.” This is all very clever, no doubt–it is, as Lincoln once said, the kind of logic whereby a horse chestnut turns out to be the same thing as a chestnut horse. It’s the fallacy of the false dichotomy. In fact, ID is a religious viewpoint masquerading as a scientific theory–it is a religious position which is layered in factually untrue or arbitrary assertions. Government is entirely free to denounce the factually untrue statements and explode those arbitrary assertions. No, it cannot say that God does not exist, and it cannot say that man was not created by God through some guided process. On that, Luskin is correct. But government violates no law when it says (and rightly) that there is no factual basis for ID’s scientific claims.

It’s amazing that Luskin can get 88 pages out of this silliness–even if it is through Liberty University. But the bottom line is this: government may inhibit (short of censorship or compelled speech), oppose, and disapprove of any factual proposition whatsoever–including factual propositions that religious groups have taken a position on–so long as it does so from a secular background.

*–Update: I feel so bad. Vulcan was not the god of earthquakes; that was Poseidon/Neptune. I did not mean to denegrate, oppose, or disapprove of this non-materialistic explanation of earthquake generation, and I sincerely apologize to all members of the Supreme Council of Ethniokoi Hellenes.

Columbus (Ohio) Science Pub inaugural event

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Dan Siegal-Gaskins (pdf; scroll to page 8), a Postdoctoral Fellow in the Mathematical Biosciences Institute at The Ohio State University, is starting up a Science Pub in Columbus. Science pubs are a kind of Science Cafe. They’re “live events that involve a face-to-face conversation with a scientist about current science topics. They are open to everyone, and take place in casual settings like pubs and coffeehouses.”

The Columbus Science Pub will hold its inaugural event Tuesday September 7 at 7:00 pm in the basement of (what else?) a bar, Hampton’s on King right by the OSU campus in Columbus. (It is a Science Pub, right?)

The speaker will be Tara C. Smith, Assistant Professor of Epidemiology in the College of Public Health at the University of Iowa, Deputy Director of the University of Iowa Center for Emerging Infectious Diseases, founder of Iowa Citizens for Science, author of the Scienceblog Aetiology, and a participant in the Panda’s Thumb field trip to the Creomuseum. Be warned: The announcement on Facebook says “7:00 pm to 2:30 am”!

I’m going to try hard to make it down to Columbus for (some of) the festivities and other Central Ahia folks are cordially invited to join us, so mark your calendars now. I’ll post a reminder a few days before the meeting.

Note: Matt Young directed the selection of the finalists and wrote most of this text.

We received approximately 60 photographs from 20 photographers. Most of the pictures were excellent. Approximately half represented endangered or invasive species, very loosely defined. We therefore established 3 categories: general, threatened or endangered, and invasive.

Choosing finalists was difficult. We considered what we thought was the scientific and pictorial qualities of the photographs, and also attempted to represent as many photographers and present as much variety as possible.

Here are the finalists in the general category. The text was written by the photographers and lightly edited for style. Please look through them before voting for your favorite. We know it is possible to game these polls. Please act like adults and don’t vote more than once. If we believe that the results are invalid, the contest will be canceled. The photos and poll are below the fold.

The Talk Origins Archive Foundation will provide the winner with an autographed copy of Why Evolution Works (and Creationism Fails), by Matt Young and Paul Strode?

ResearchBlogging.orgRandomness. Shakespeare referred to it. The Bible talks about it. People love to bicker about what it really is, or whether it truly exists. And creationists, especially those of the ID subspecies, consider it a fighting word. A random process, many would say, is a process that doesn't involve God, or direction, or intention, or whatever it is that the culture warriors of the Discovery Institute are so foolishly fighting for. Ah, but it's not just the propagandists of design-think who can mistakenly assume that an ordered process is "directed." Consider this tale of a random process being put to surprising use during vertebrate embryonic development.

Our story comes from Nature about a month ago, and I will present it in four acts.

Act I: The elongation of an embryo

We all know that animal embryos acquire their form through various morphings and twistings. One interesting example is axis elongation, which is just what it sounds like: the embryo stretches out until it clearly has a long axis, then continues to elongate to form something with a head and a tail and everything in between. But "stretch" is a poor term for what's really happening: the tail end of the embryo is growing while the structures closer to the head are beginning to develop into recognizable structures. Developmental biologists know that new cells are added near the tail end, and we know that various directed processes control many similar movements during early development. It was reasonable to assume that these mechanisms would account for embryo elongation, but the actual processes were unknown before the experiments of Bénazéraf and colleagues ("A random cell motility gradient downstream of FGF controls elongation of an amniote embryo," Nature 8 July 2010).

ChickStage11.jpg

The authors employed an old warhorse of developmental biology, the chick embryo. At stage 11, the embryo looks nothing like the animal it will become; it has a head-like thing at one end (the top in the picture on the right), a weird hole at the bottom (Hensen's node), and some blocky structures called somites in between. Down at the bottom, on either side of the hole, is a tissue called the presomitic mesoderm (PSM). The anatomical details needn't concern us; what matters is that we understand that the embryo is elongating toward the bottom, that cells are being made near the top of that hole and that they are moving toward the tail, making it grow. Curious about how this works, Bénazéraf and colleagues started deleting pieces of the tail-end of the embryo, and they found that the PSM was critical for elongation. Good to know.

Act II: Cell movements in the elongating embryo

So, what's going on in the PSM that causes elongation? The authors used a nifty technique called electroporation to label the cells in that region so they could watch them as the embryo grew. Basically, they used an electric field to introduce DNA into the cells of interest the day before; the DNA caused the cells to express the wonderful and famous green fluorescent protein (GFP) so that individual cells could be monitored as the embryo continued to develop in culture outside of the egg. They found something interesting: near the tail of the embryo, the PSM cells were more motile than they were near the front of the PSM. But the cells near the front were more packed together. So try to picture it: in this region on either side of the center of the tail end of the embryo is an area (the PSM) of cells that are moving more frantically near the tail and that are more packed together toward the head. It would seem as though the cells are busily moving toward the tail, and that they get less crowded and more mobile as they get there. And when the authors looked at movement of individual cells, sure enough, there was a directional bias in the movement, meaning simply that cells in the PSM tended to move toward the tail. It looks like a simple case of directed migration of cells toward a target. Interesting, maybe, but not such big news. But then, a noise from the next room. Exeunt.

Act III: Random cell movements in the elongating embryo

So cells seem to move toward the tail. This could mean they're being directed toward the tail by some kind of homing mechanism, and this would be a reasonable expectation. But because the embryo is elongating, it could be that the directed movement of individual cells is an illusion: the cells are moving toward the tail because the space they inhabit is moving toward the tail. The authors addressed this by cancelling out the effect of elongation of the cells' environment, and focusing solely on the movement of cells within that environment. The environment in this case is the extracellular matrix, or ECM, as indicated by one of its components, fibronectin. I'm sorry about the jargon, but I included it so I could quote the authors in full as they describe the results of the experiment:

Surprisingly, the movements of cells relative to the ECM did not show any local directional bias. The mean square displacement of these cells compared to the fibronectin movement scales with time, indicating that cells exhibit a 'random walk'-like diffusive behaviour, with the diffusion of cells relative to the fibronectin following a posterior-to-anterior [back-to-front] gradient.

In other words, the cells are moving randomly, behaving like molecules diffusing in a liquid. The authors verified this by looking at cell protrusions, the telltale signs of a cell's migrational direction. The protrusions all pointed in random directions. Amazingly, this seemingly ordered march of cells toward the back, resulting in the growth of the tail end of the embryo, is the product of random cell movement. And yet it yields an ordered result. How?

Act IV: A gradient of random cell movement controlled by a conserved developmental signaling system

Recall that cell movement in the PSM is not uniform: cells near the tail move (randomly) more. The authors knew that an ancient and well-known signaling system functions in a similarly graded fashion in that tissue. Known as the FGF/MAPK pathway, it's fairly simple to manipulate experimentally. Bénazéraf and colleagues found that whether they turned the signaling up or down, the result was the same: elongation was stunted. This might seem strange, but it makes perfect sense: it's the graded nature of the signaling that matters, so turning it all the way up or all the way down erases the gradient and leads to the same result. What matters, for elongation, is that random cell movement is greater in the back than in the front. This leads to elongation, because the tail end contains cells that move more and have more freedom of motion due to their being less tightly packed.

The upshot is that an ancient conserved signaling system causes a simple gradient of random movement which, in the presence of physical constraints, leads necessarily to elongation of the embryo in one direction. It looks for all the world like homing or some other directed migration, but it's not. And, intriguingly, the authors conclude by suggesting that the mechanism might be quite common in the biosphere:

Axis formation by outgrowth is a common morphogenetic strategy that is widely evident in animals and plants. Thus, the mechanism described here might apply to other well-characterized, polarized axes, such as the limb buds, in which a similar FGF/MAPK gradient is established along the proximo-distal axis.

Randomness. Learn to love it. The End.

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Image credit: "Normal stages of chick embryonic development," poster on Developmental Dynamics site

Bénazéraf, B., Francois, P., Baker, R., Denans, N., Little, C., & Pourquié, O. (2010). A random cell motility gradient downstream of FGF controls elongation of an amniote embryo Nature, 466 (7303), 248-252 DOI: 10.1038/nature09151

Junker_Scherer_2009_edition6.jpgI just came across what is apparently a major online revision to the German creationist textbook Evolution - ein kritisches Lehrbuch, by Reinhard Junker and Siegfried Scherer. The section is section 9.4. There is an HTML summary (original German, google translation) and a 32-page PDF is here (apparently too long for google to translate).

Sadly, while I took German in high school, most of what I remember involves beer-drinking songs, which doesn’t help me out much here. Clearly Matzke (2003/6) and Pallen & Matzke (2006) and perhaps other commentary on flagellum evolution got deep under their skin – most of the chapter seems to be taken up with attempting to refute the evolutionary model for the origin of the flagellum! Regardless, I can tell there are a few issues – they cite the 2003 critiques of the flagellum evolution model by the pseudonymous “Mike Gene”, without noting that several later scientific developments caused Mike Gene to substantially improve his opinion about even the most radical part of Matzke 2003, which was the idea that a good chunk of the flagellum was homologous to the F1Fo-ATPase and relatives. (The original seems to be lost to the internet ghosts, but Ed Brayton blogged it, see: “Mike Gene Admits Matzke was Right”)

Anyway, if anyone knows of a source that can translate PDFs, or if there are any German speakers up for summarizing their main points, it would be interesting to hear if they’ve come up with anything new. I mean, there’s 32 whole pages, so maybe they will actually acknowledge that Luskin & numerous DI sources were wildly wrong about the number of required, flagellum-unique proteins in the flagellum. And actually, it does look kind of like Junker & Scherer are advancing some argument that relies on the idea that the flagellum parts are not unique, but instead were designed to serve multiple independent functions (see Figure 4). How conveniently like evolutionary cooption!

So long, Carrie!

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The National Center for Science Education has a slew of resources to support efforts to keep honest science in classrooms. It has articles, databases, and a great archive. But most important, it has people, smart caring people who are ready to help those of us out in the field with information, advice, and encouragement.

One of those people has been Carrie Sager. I don’t know all her duties, but one of them was maintaining the database devoted to the various legal cases around the country. For me, of course, that means Freshwater. Two federal cases are under way in that matter, and Carrie has been assiduous in sweeping PACER daily for the latest legal documents and court filings and updating the database, notifying me as soon as new docs went up and occasionally commenting on them, giving me ideas for treatment of them. Equally important, she has been unfailingly cheerful in the face of my documentation OCD.

But now she’s leaving NCSE to go to law school. I hate to see her leave, but I wish her all good fortune. ‘Bye, Carrie. And many many thanks.

And to those who haven’t joined NCSE: what are you waiting for?

by Ken Miller, http://www.millerandlevine.com/km/

Two years ago, Louisiana Governor Bobby Jindal signed the Louisiana Science Education Act (LSEA) into law, as noted on The Panda’s Thumb.

When the law was being considered in the Legislature, its proponents were adamant that it wasn’t about “creationism” or “intelligent design.” Folks from the Louisiana Family Forum and the Discovery Institute backed the LSEA, of course, but all they were interested in was good critical thinking, right?

Well, not so much. Now the Livingston Parish School Board is openly using the LSEA as legal justification to implement the teaching of creationism in their public schools. Barbara Forrest, one of the expert witnesses in Kitzmiller v. Dover exposes the maneuverings and alliances of anti-evolution forces in here state in a post at the Louisiana Coalition for Science.

Predictably, the Discovery Institute is now doing the same thing it did back in 2005 to the Dover School Board. They’re turning on their own supporters, and asking how anyone could possibly confuse their ideas with creationism. In this American Spectator article, Bruce Chapman, President of the Discovery Institute, now states that the very people who supported his efforts to get the LSEA passed are “ignorant” of the content of intelligent design theory. Darn. I wonder how those poor folks managed to think that ID equals creationism?

Somehow, the more things change, the more they remain the same. Could it be that the next Kitzmiller Reunion will be in Louisiana?

ResearchBlogging.org

Mutate. Select. Repeat. Mutate. Select. Repeat. You can’t understand evolutionary biology if you don’t get the significance of that process. And yet, if you think that’s all there is to it, you’re way off track. PZ explained this very nicely here last week. Let’s focus on one simple point that he made, and look at some recent and significant work on that subject that shows just how misleading some of the common simplifications of evolutionary biology can become.

Here’s PZ on simple views of mutation and selection:

Stop thinking of mutations as unitary events that either get swiftly culled, because they’re deleterious, or get swiftly hauled into prominence by the uplifting crane of natural selection. Mutations are usually negligible changes that get tossed into the stewpot of the gene pool, where they simmer mostly unnoticed and invisible to selection.

I think this is an extremely important point, both for those seeking to answer creationist propaganda and for anyone else trying to understand the process of evolutionary change. The common picture, painted all too often by commentators of various stripes, depicts a world in which mutations run a harrowing gauntlet of selection that is likely to foolishly discard both the gems and the proto-gems of biological function. Oh sure, the cream eventually rises to the top, but only through the magic of seemingly endless eons and limitless opportunities. I hope that most readers of the Panda’s Thumb are annoyed by this crude caricature, but it’s the standard tale, and when the narrator only has a paragraph, it’s the one we’re most likely to hear.

To improve the situation, we might first add the concept of random drift. And that helps a lot. Then we would emphasize the selective neutrality of the vast majority of all mutations, as PZ did. And that helps a lot, too. Let’s look at another helpful concept, one from the evo-devo playbook, almost crazy at first glance but remarkably interesting and important.

Suppose that one reason many mutations are selectively near-neutral is because genetic systems are able to tolerate mutations that have the capacity to be strongly deleterious. Suppose, in other words, that organisms are robust enough to live with seriously nasty genetic problems. This would mean that such mutations could escape selection, and that populations could harbor even more genetic diversity than our simplistic account would seem to suggest.

Some very nice work in the fruit fly (“Phenotypic robustness conferred by apparently redundant transcriptional enhancers”), performed by Frankel and colleagues and published in Nature in July, shows us one way this sort of thing can work. The authors were studying genetic control elements (called enhancers) that turn genes on and off. Specifically, they were looking at how the expression of a gene called shavenbaby was affected by a set of enhancers. (The shavenbaby gene controls the development of hair-like structures on the surface of the fly larva - i.e., maggot - and so alterations in the embryo’s patterning that result from changes in shavenbaby function are easily detectable by simple microscopy.) Now, like many genes that control development, shavenbaby is regulated by a few different enhancers, some that are close to the gene and others that are apparently redundant and are further away. These latter elements are called “shadow” enhancers, as they are remote and distinct from the primary enhancers but highly similar in activity.

Why all this redundancy? Others had proposed that shadow enhancers might confer “phenotypic robustness” - i.e., developmental or functional robustness - by maintaining function in the face of significant challenges (environmental changes, for example), and Frankel et al. set out to test that hypothesis. First they deleted the shadow enhancer region, and this had a very mild effect, consistent with the idea that the shadow enhancers are redundant with respect to the function of the primary enhancers. But then they examined development in the absence of the shadow enhancers, now introducing environmental stress (extremes of temperature), and found dramatic developmental defects. They concluded that the shavenbaby shadow enhancers normally contribute to phenotypic robustness through what they term “developmental buffering.” In other words, the animal’s critical developmental pathways are buffered against many disastrous alterations, in part through the action of redundant control systems.

That’s interesting all by itself, but the authors went one crucial step further. What if the redundant enhancers can also buffer against genetic disasters? The experiment was straightforward: they deleted one copy of a major developmental control gene (called wingless). Those animals are just fine, until they lose the buffering of the shavenbaby shadow enhancers. Without the redundant system, the loss of one wingless gene leads to a significant change in developmental patterning. The conclusion, I think, is quite interesting: the impact of the shadow enhancers only becomes apparent when the system is stressed, by environmental challenges and even by genetic problems elsewhere in the genome.

Such developmental buffering systems are thought to be common in animal genomes, and this means that animal development is capable of tolerating significant genetic dysfunction. It means, I think, that simplistic stories about deleterious mutants being readily discarded from populations are even less useful than we already should have realized, and that’s without the deliberate misuse of such outlines by anti-evolution spinmeisters.

And one last thing. Why my little comment about the evo-devo playbook? Well, one concept championed by evo-devo thinkers is the notion of “evolvability.” The idea (roughly) is that the ability to generate diversity is something that we should expect to see in evolution. Like most other evo-devo proposals, it’s been savaged by some smart critics. But phenotypic buffering by redundant developmental control elements is just the kind of thing that “evolvability” was meant to encompass when it was discussed by Kirschner and Gerhart more than a decade ago. So I say we give credit where it’s due. Anyone else?

2010-08-02-Uncharted-Planet.png

Find out what happens next. Don’t forget to check the image title.

Judge Gregory Frost has denied a motion by John Freshwater and his attorney R. Kelly Hamilton that sought reconsideration of the sanctions imposed on them for noncompliance with discovery orders (report of the hearing). I’ll link to the ruling as soon as it goes up on NCSE’s site on the suit, but there are a few choice quotations from it below the fold. Judge Frost pretty firmly spanked Hamilton and Freshwater in his ruling.

Update: The ruling should go is now up on NCSE’s site on the case. later today Meanwhile, here’s a teaser, a candidate for the funniest footnote in a federal court ruling this year. It reads in its entirety

In response to a question by the Court, Attorney Hamilton explained that his wife mistakenly believed the Tesla coil was groceries and put it in the freezer at their home.

The Mount Vernon News now has the ruling up on its site here. It’s a good story, too.

Erethizon dorsatum

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Photograph by Susan Bello.

Photography contest, Honorable Mention.

Bello.porcupine.jpg

Erethizon dorsatumNorth American porcupine, Schoodic Peninsula, Acadia National Park, Maine, June, 2006.

Happy Lamarck Day

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by Joe Felsenstein,
http://evolution.gs.washington.edu/felsenstein.html

August 1 is the 266th anniversary of the birth of Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck, born in 1744. Let us all celebrate the birthday of the first evolutionary biologist (and a great pioneer of invertebrate systematics as well). For more information on him see my post a year ago.

Below is a photo I took of the plaque on the back side of the statue of Lamarck in the Jardin des Plantes in Paris. His daughter is shown assuring the aged and blind Lamarck, who died in relative obscurity, that “Posterity will admire you, and she will avenge you, my father.”

lamarckplaque.jpg

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