August 2007 Archives

The Edge of Humanity

Lucy went on display today at the Houston Museum of Natural Science, and there was no way I could resist paying her a visit. I went in to the exhibit with very mixed feelings about it. A lot of people, including quite a few scientists I respect, have been extremely vocal in their opposition to the exhibit. Richard Leakey called the trip “a form of prostitution” and “a gross exploitation of the ancestors of humanity.” Several museums have refused to display the fossil, and the Ethiopian community is calling for a boycott of the exhibit.

Their concerns are hardly unreasonable. Lucy’s bones are very, very old and very, very fragile. Displaying her does involve some risk, particularly in a traveling exhibition that requires packing and unpacking the bones several times. There is no other Lucy. She’s unique. She’s a valuable - priceless - scientific specimen. The opponents of the exhibit think that the risk to the remains is simply too great to justify the exhibit.

For all I know, they might be right. I can tell you this, though. When I walked over next to the display case and looked down at Lucy, all of those concerns evaporated from my mind, replaced by a sense of pure awe.

Read more (at The Questionable Authority, where comments can be left):

Uncommonly Dense blows common descent.

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The Other 95%, a blog devoted to invertebrates, dissects yet another Uncommonly Dense misconception. A recent Science paper (subscription) described the discovery that sea anemones have some genes that are very similar to some human genes. The Science News story says

One of the big surprises of the anemone genome, says Swalla, is the discovery of blocks of DNA that have the same complement of genes as in the human genome. Individual genes may have swapped places, but often they have remained linked together despite hundreds of millions of years of evolution along separate paths, Putnam, Rokhsar, and their colleagues report. Researchers see little conservation of gene linkages in nematodes and fruit flies.

Moreover, the anemone genes look vertebratelike. They often are full of noncoding regions called introns, which are much less common in nematodes and fruit flies than in vertebrates. And more than 80% of the anemone introns are in the same places in humans, suggesting that they probably existed in the common ancestor. “The work presents a missing piece of the puzzle, which people studying intron evolution have been searching for in the past few years,” says Majewski. “They present a strong validation for an intron-rich ancestor,” he says..

With its usual penetrating incomprehension, UD wonders how human genes got into anemones. The Other 95% straightens them out. Read and enjoy.

RBH

Michael Majerus has spent countless hours conducting research on the Peppered Moth (Biston betularia). He’s observed them in the field, bred them in the lab, watched them get eaten by things, kept careful count of the things that he’s seen, and, recently, given a talk about his findings. Jonathan Wells has spent, to the best of my knowledge, absolutely no time doing any actual research on natural selection or moths, but that certainly didn’t stop him from launching a full-throated attack on Majerus.

In this attack, Wells manages to misrepresent a lot of things. This should come as no surprise to those of you who have followed his work in the past, of course. Wells vendetta against all things evolutionary might be a mission from God, but his tactics are hardly heavenly. A Jonathan Wells essay that lies about something is hardly news, and it wouldn’t ordinarily be something that I’d write about. In this case, though, I’m going to make an exception. I simply can’t abide seeing good science and good scientists maligned by a two-bit hack with a defective moral compass.

Read more (at The Questionable Authority, where comments may be left):

After posting Yet Another Creationist Meltdown last July, I began to mull over testing a little hypothesis, namely that right-wing idealogues caught up in embarrassing political or sexual scandals have a better likelihood of being Creationists.

Well, we have a new Data Point. It turns out that Senator Larry Craig, R-Idaho, has been up to more than just allegedly soliciting men in adjacent bathroom stalls.

Courtesy of Jim Fisher’s January 9, 2006 article in the Lewiston Morning Tribune (original here, registration required):

Then there’s U.S. Sen. Larry Craig, who as a House member 16 years ago co-sponsored a constitutional amendment, the “Community Life Amendment,” to authorize teaching “the creation of the earth as accepted in Judeo-Christian tradition.”

And indeed, right there in the 101st Congress, 1989, there is (then Representative) Larry Craig co-sponsoring House Joint Resolution 297:

JOINT RESOLUTION

Proposing an amendment to the Constitution of the United States relating to the right of the people to allow voluntary prayer and the teaching of the Judeo-Christian ethic in public schools. … SECTION 2. For the purpose of section 1, the term ‘teaching of the Judeo-Christian ethic’ shall include the Ten Commandments and the creation of the earth as accepted in Judeo-Christian tradition.

Discuss.

Tangled Bank #87

The Tangled Bank

We have a new Tangled Bank flourishing at Balancing Life.

See Behe Flail

Last week The New York Times ran this article by Kenneth Chang. He was reporting on recent work on protein evolution:

Offering insight into how evolution progresses inside a gene, scientists have pinpointed mutations in an ancient protein that transformed its shape and function more than 400 million years ago.

Scientists at the University of Oregon and the University of North Carolina used modern technologies to conduct an archaeology of genes and help answer a longstanding question about how proteins change over time and develop new roles.

“We have now seen the mechanisms by which a new function evolves at the atomic level, how evolution sculpted the protein structure to produce a new function,” said Joseph W. Thornton, a biology professor at Oregon who led the research.

Fascinating stuff! There's nothing novel in the idea that proteins can acquire new functions through evolution, but the level of detail here is simply astounding.

Of course, this work has obvious relevance to evolution/ID dust-ups. It was not long before Michael Behe devoted a lengthy blog entry to showing -- are you sitting down? -- that this work actually provides stronger evidence for design than it does for evolution. Over at EvolutionBlog, I have a lengthy discussion of why Behe is wrong. Comments can be left there. Enjoy!

Peppered Moths: We Told You So

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The ID movement hasn’t had many successes, but one area where they did pretty much succeed in causing considerable havoc was the classic textbook example of natural selection in action: the change in color of peppered moths (Biston betularia) from peppered white, to black, and back to peppered white again. Through a series of accidents that is still difficult to understand, the idea got started in the late 1990s that leading peppered moth researcher Michael Majerus had debunked Bernard Kettlewell’s famous study confirming the old hypothesis that the change in peppered moth color was due to selective predation of conspicious moths by birds.

Houston Chronicle article

10 of the 15 Texas state board of education members told the Houston Chronicle that they did not favor requiring “intelligent design” in science classes.

That sounds good, but there are a couple of problems.

First off, there’s the “requiring” language. The Discovery Institute Center for the Renewal of Science and Culture has made it a talking point not to ask for IDC to be required in public school science classes, but that teachers should be “permitted” to teach IDC if the Lord so moves them if they want to. So the Chronicle article, useful as it is, doesn’t take us past rhetoric the DI has already deployed.

Second, there’s too much fixation on labels, and not enough on content. We know that the antievolutionists are adept at picking out new labels for the same old tired, bogus, narrowly sectarian arguments they’ve been trying to keep or put back in schools for many decades. We’ve seen “creationism”, “scientific creationism”, “creation science”, “intelligent design”, “critical analysis”, and now it seems to be time for “strengths and weaknesses”, or even just “weaknesses”.

[Original post on the Austringer]

The Expelled movie isn’t yet out so we can’t make fun of it in its entirety, but as everyone knows by now, the filmmakers started things off rather badly by lying to the pro-science people they interviewed, making them think that it was an entirely different film with a different name and a different premise. That’s a good taste of the kind of sleaze we’re dealing with.

Another taste can be found on the movie’s official website, complete with press release and a blog post by Ben Stein. Although they say you can’t judge a book by its cover, one has to assume that the claims being made in the press release and by Stein, who stars in the film, were actually made in all seriousness and truly reflect the content of the movie. I’m going to critique what I’ve seen so far based on these materials. The film could always surprise us of course by avoiding the insane rhetoric and untruthful claims found in its own promotional materials, but that seems unlikely to me. Also, I’m not going into detail about the specific cases mentioned in the press release, which have already been discussed at length and will be discussed in much more detail once the film is out. Instead I’m going to talk more generally about the persecution claims being made.

Continue reading at Sunbeams from Cucumbers

If Answers in Genesis’s creation anti-museum didn’t have enough of lie already, it is beginning to corrupt Kentucky’s government. The tax-funded Northern Kentucky Convention & Visitors Bureau is promoting the anti-museum as a “‘walk through history”” that “counters evolutionary natural history museums that turn countless minds against Christ and Scripture”. This inflammatory lie has rightly upset several organizations, who are fighting to improve the quality of science education in Kentucky. We expect Answers in Genesis to lie, but we hope that government wouldn’t join them in it. So far the visitors bureau has refused to change their website despite having is inflammatory lies pointed out to them. Perhaps some more public pressure can change that.

The Cincinnati Enquirer has the full story.

I recently had the opportunity to return down-under to visit with some esteemed colleagues at Evolution 2007.—I last visited the Evolution meeting in 2005 when it was held in Fairbanks, Alaska.—Prior to the start of this meeting, I blazed across the South Island, in a stylish “rental car”—more like a cardboard box with bicycle tires—with two old drinking companions from the University of Arizona. No sooner had I begun my adventure than I had a close encounter with a truck full of sheep driving down the wrong side of the road. It was a close shave. Now, it turns out those crazy Kiwis drive on the left. Don’t they know “left” and “sinister” are synonymous in certain languages?

I didn’t let their harebrained traffic laws hinder my opportunity to explore as much of the South Island as possible. During my travels, I had the opportunity to become the first panda (and the first J.D.-M.D.-Quintuple Ph.D.) to climb a glacier.

Despite an attempt on my life when one of my companions “fell” in an ice river, I reached the top unscathed. With the help of my guide, Rebecca, I left a University of Ediacara flag upon the Glacier to memorialize my illustrious achievement.

Creationists for genocide

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This is a guest appearance by Hector Avalos. I (Mark Perakh) have not contributed a single word to this essay which I am posting as a courtesy to Professor Avalos.

One of the most common accusations against “Darwinism” and evolutionary theory, as a whole, is that they lead to the devaluation of human life such as was dramatically manifested in the Nazi Holocaust. Such a notion is embodied in Richard Weikart’s From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Racism in Germany (2004). Avalos demonstrates, however, that all of the major ideological precursors of the Holocaust have a long religious history that pre-dates Darwin. We can find such precursors in the work of Martin Luther and among biblical authors. Furthermore, Avalos demonstrates that creationists constitute the most vocal defenders of genocide and infanticide from ancient times to the present day. Therefore, the claim that theistic creationist ethics minimize or eliminate the devaluation of human life is false. Read Creationists for Genocide at Talk Reason.

Last April, I received this nice letter from Mark Mathis.

Hello Mr. Myers,

My name is Mark Mathis. I am a Producer for Rampant Films. We are currently in production of the documentary film, "Crossroads: The Intersection of Science and Religion."

At your convenience I would like to discuss our project with you and to see if we might be able to schedule an interview with you for the film. The interview would take no more than 90 minutes total, including set up and break down of our equipment.

We are interested in asking you a number of questions about the disconnect/controversy that exists in America between Evolution, Creationism and the Intelligent Design movement.

Please let me know what time would be convenient for me to reach you at your office. Also, could you please let me know if you charge a fee for interviews and if so, what that fee would be for 90 minutes of your time.

I look forward to speaking with you soon.

Sincerely,

Mark Mathis
Rampant Films
4414 Woodman Ave. #203
Sherman Oaks, CA 91423
www.rampantfilms.com

Although some have called systems biology a ‘friend of Intelligent Design’, reality is that systems biology is all but a friend of what is best known as ‘ignorance’.

In a recent article in BioSystems 88 (2007) 163–172, titled “Alternative routes and mutational robustness in complex regulatory networks”, Andreas Wagner and Jeremiah White describe how

Alternative pathways through a gene regulation network connect a regulatory molecule to its (indirect) regulatory target via different intermediate regulators. We here show for two large transcriptional regulation networks, and for 15 different signal transduction networks, that multiple alternative pathways between regulator and target pairs are the rule rather than the exception. We find that in the yeast transcriptional regulation network intermediate regulators that are part of many alternative pathways between a regulator and target pair evolve at faster rates. This variation is not solely explicable by higher expression levels of such regulators, nor is it solely explicable by their variable usage in different physiological or environmental conditions, as indicated by their variable expression. This suggests that such pathways can continue to function despite amino acid changes that may impair one intermediate regulator. Our results underscore the importance of systems biology approaches to understand functional and evolutionary constraints on genes and proteins.

So while ID proponents are arguing for an ‘edge’ to evolution, real science is uncovering a remarkable richness for evolution.

So let me ask the following question: Who has contributed to scientific knowledge here?

So Sue Me

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Dr.%20Evil%20copy.JPG Some of you may have heard about the latest in frivolous lawsuit madness: PZ Myers and his blog’s mothership, Seed Magazine, have been sued for FIFTEEN MILLION DOLLARS.

The plaintiff of the case is none else than Dr. Stuart Pivar, NYC businessman and art collector, who burst on the evolution/creationism scene a couple years back claiming that, based on conversations he had with the late Stephen J Gould, he could assert for a fact that Gould really opposed the basic tenets of modern evolutionary theory, and the role of natural selection in particular. According to Pivar, Gould only endorsed evolutionary theory (in dozens of books and hundreds of articles, not to mention sworn court testimony!) under some sort of duress from the iron fist of the enforcers of “Darwinian orthodoxy”.

The obvious nonsense was discussed in various articles here at PT and elsewhere, but of course the absurdity of that canard was not enough to deter the usual peanut gallery of gullible Creationists, Denyse O’Leary foremost among them, from getting all excited about the matter.

At Darwin or Design Jason Rennie talks to Dr Ryan Nichols. Dr Nichols wrote an interesting paper called Scientific content, testability, and the vacuity of Intelligent Design.

There are Hours of additional content

I appreciate Rennie’s link to Scientific content, testability, and the vacuity of Intelligent Design where I discuss Nichols’ paper and the vacuity of ID.

The actual paper by Nichols does not seem to be available online: Ryan Nichols, Scientific content, testability, and the vacuity of Intelligent Design theory The American Catholic Philosophical Quarterly, 2003 ,vol. 77 ,no 4 ,pp. 591 - 611.

Direct link to podcast

Constraints surround us. One of the constraints we have running a popular and well-received weblog is the fact that our CPU cycles and especially our bandwidth are finite commodities on the server. Earlier this year we upgraded the server hardware (with the aid of readers here and at the After the Bar Closes Forum who donated to the TalkOrigins Archive Foundation), which gave us a lot more CPU cycles to play with than we had before. However, just like other popular web sites, there are people who want to profit off of our popularity on the cheap: spammers. They seek to subvert comments and trackbacks for the purpose of advertising their tawdry and/or fraudulent products and services.

A couple of weeks ago, we made the decision to pull the plug on the trackback facility. We were getting upwards of 200 simultaneous connections on the server, the vast majority of those hitting the trackback script, and the overwhelming majority of those were spammers trying to register thousands upon thousands of fake trackbacks. In the interest of keeping up with real users, trackbacks had to go.

We hope to be able to restore trackback functionality soon. Movable Type has released version 4.0 of their weblog software, and there are improvements in the way spam comments and trackbacks are handled. PT will be upgrading soon. We may be using a default template for a while, but we hope to minimize the disruption to posting and commenting.

Tangled Bank #86

The Tangled Bank

The Tangled Bank came early this week — the latest edition is online at Fish Feet.

Well, my time at NCSE is almost up. Next week I will be moving up to Berkeley to start a PhD in for-real, honest to goodness evolutionary biology. It’s quite exciting. Unfortunately, before I go I have to clean all my files out of my cubicle at NCSE to make way for Josh Rosenau (yes, the Thoughts from Kansas guy), who will be occupying my desk. Amongst the stacks of books that I have checked out from libraries, borrowed from various people at NCSE without giving them back, etc., I came across one I hadn’t seen since The Great Hunt for the Origins of Intelligent Design back in early 2005, during the research period of the Kitzmiller case. As everyone now knows, even though the ID guys will never admit it, “intelligent design” as such originated in the 1989 ID textbook Of Pandas and People, with “intelligent design” being the new label chosen after the 1987 Edwards decision made creationist terminology difficult to use in textbooks. Pandas was the first place the term “intelligent design” was used systematically, defined in a glossary, claimed to be something other than creationism, etc. In a desperate attempt to obfuscate this basic historical point, ID guys have dug up various random instances of the words “intelligent” and “design” placed together (although they missed the 1861 Darwin letter, and the 1847 Scientific American article), most of them with absolutely no evidence of having influenced the actual actors in the 1980s who created the ID movement (there are some legitimate precursors, but they are in explicitly creationist works, e.g. Lester and Bohlin’s (1984) The Natural Limits to Biological Change, so the ID guys won’t cite them post-Kitzmiller).

A.E. Wilder-Smith (1915-1995) was a European “creation scientist,” now deceased, sometimes described (pre-Kitzmiller) as inspiring pieces of ID. He was active from the 1960s to the mid-1980s. It is true that Wilder-Smith discusses “information”, “design”, “Design”, Paley, etc., a lot (as well as human tracks next to dinosaur tracks, Noah’s Flood, and other extremely embarassing creationist nonsense). But I have never found the actual phrase “intelligent design” in his work. However, in early 2005, I did come across this, in a 1968 work by Wilder-Smith, discussing a certain oh-so-amazingly-complex organ. For some reason the IDers don’t cite this example as a precursor:

To deny planning when studying such a system is to strain credulity more than to ask one to believe in an intelligent nipple designer, who incidentally must have understood hydraulics rather well.

(pp. 144-145 of: Wilder-Smith, A. E. (1968). Man’s origin, man’s destiny: a critical survey of the principles of evolution and Christianity. Wheaton, Ill., H. Shaw. Italics original, bold added.)

There you have it. The origin of “intelligent…design.”

(In fairness, the full quote is posted below the fold.)

Farewell San Francisco

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I recently finished up my trip with Bora to the Bay Area by attending Science Foo Camp at Google’s Headquarters, where I met several famous people.

Bora has many pictures of our last days in the Bay Area.

1. Last day in San Francisco

2. Science Foo Camp—Friday

3. Science Foo Camp— Saturday Morning

4. Science Foo Camp—Saturday Afternoon

I want to remind you that you can join my Facebook group, or friend me on MySpace. The Facebook group also serves as the fan group for PT. I also have a gallery of pictures from my adventures that you can look through. I working on collecting all my pictures there.

Also don’t forget to submit your best science blogging posts to the 2007 Science Blogging Anthology and join us at the 2008 Science Blogging Conference.

And yes that is me allowing Martha Stewart to examine my kimono.

“Shocking” revelations

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The NCSE reports on some “shocking” developments in Texas

McLeroy accused of hostility to science education and religious tolerance

In a press release dated August 7, 2007, the Texas Freedom Network accused Don McLeroy, who recently was appointed as the new chair of the Texas state Board of Education, of harboring “a shocking hostility to both sound science education and religious tolerance.” TFN’s charge was based on the transcript of a 2005 talk McLeroy gave at Grace Bible Church in Bryan, Texas, on the debate over teaching evolution and “intelligent design.” “This recording makes clear the very real danger that Texas schoolchildren may soon be learning more about the religious beliefs of politicians than about sound science in their biology classes,” TFN President Kathy Miller said. “Even worse, it appears that Don McLeroy believes anyone who disagrees with him can’t be a true Christian.”

I wonder how the many Christians who disagree with McLeroy feel about this?

And for those who were wondering about the nature of Intelligent Design, they need not worry any further:

There are a lot of news articles out today that feature some just-published research on early human research. The research itself - a paper in the journal Nature by a team of scientists including the mother-daughter combinationon of Meave and Louise Leakey- features two partial skulls found east of Lake Turkana in Kenya. One of the fossils, a cranial dome that’s been identified as belonging to a young Homo erectus, has been dated at about 1.55 million years old. The other, a partial upper jaw from Homo habilis, is about 100,000 years younger (1.44 million years old). This shows that the two species overlapped in time, and that both may have occupied at least some of the same places during the period of overlap.

In the media, this is being reported as a find that “casts doubt on the origins of man” (Australian Broadcasting Corporation), “eliminat[es] one reputed ancestor from the human lineage” (LA Times), “challenges standard evolution theory” (Kansas City Star), and “shows us just how utterly ignorant we were about where we came from” (OK, I made that one up). That’s a pretty cool feat for two chunks of bone - if you believe the press reports, anyway. Of course, the press has been known to occasionally blow new research out of proportion every now and then, so it’s probably worth taking a closer look at what’s actually being claimed for these fossils.

Read more (at The Questionable Authority, where comments may be left):

Bless you!

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A blogger has an interesting report on the event that the Discovery Institute just held for teachers at Biola (Bible Institute of Los Angeles) University in order to promote their newest disguise for creationism, the textbook sneakily entitled “Explore Evolution.”

I’m sure it’s a just coincidence that the very first person to blog this event – this no-way-it’s-creationism-no-sirree event – did it from the Old Earth Creation Homeschool blog and works for the old-earth creationist ministry Reasons to Believe.

Anyway, here’s the interesting bit:

Denyse O’Leary notes some of the differences between creationists and Intelligent Design proponents:

Then the creationists in turn help the ID theorists by making clear what creationism is and what it is not. Creationism is about the BIBLE, see? It’s not about intelligent design theories like Behe’s* Edge of Evolution or Dembski’s design inference.

It’s extremely uncommon for me to find myself in agreement with Denyse on anything (and it’s not a comfortable feeling), but in this case I do think she’s got a good point. Creationism is certainly explicitly based on the Bible, and Intelligent Design certainly is not. In fact, that’s probably the Achilles’ Heel of the entire Intelligent Design movement.

Say what you will about the Young-Earth creationists, about Ken Ham and Kent “Prisoner #06452-017” Hovind, they are steadfast in their belief in the literal truth of the Bible, and steadfast in their refusal to lie about that belief. They believe that they are right, and they are not willing to publicly deny their faith. In that, they stand in stark contrast to Intelligent Design.

Read more (at The Questionable Authority, where comments can be left):

by Abbie Smith

Editor’s Note: This is a guest post by Abbie Smith, the blogger behind the Endogenous Retrovirus (ERV) blog (original post), who we marked early as having a special talent for this creationism-rebutting stuff. Abbie works in an HIV lab and has a few things to say about Behe’s argument in The Edge of Evolution that evolution hasn’t/can’t produced any novel adaptations, genes, or protein-protein binding sites during the evolution of HIV, the virus that causes AIDS, unless you are one of the several Discovery Institute fellows who denies this along with denying evolution.

Oh, and speaking of the Discovery Institute and Behe, Behe is apparently going to be on the Colbert Report tonight. Colbert has been setting an excellent example by making a point of it to bring scientists on his show – Kenneth Miller, Neil DeGrasse Tyson, Shubin I think. Hopefully Colbert knows that Behe isn’t quite like these other guys. I recall that Dembski claimed he was sick after he appeared on The Daily Show next to some weird new-ager in 2005.

Anyway, if Colbert doesn’t hit the appropriate snark mark tonight, you’ll get it from Abbie for sure. I thought I got Behe pretty good in Of Cilia and Silliness, but this really takes the cake.

—Nick Matzke


Michael Behe, please allow me to introduce myself…

I’m ERV. This is my dog, Arnold Schwarzenegger. And this is my friend, Vpu. I presume you and Vpu haven’t met, as you recently repeated in an interview with World magazine the same sentiment you gurgled ad nauseam in ‘Edge of Evolution’:

Allons enfants de la ID…

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Perhaps there are still true guardians of human rights and opponents of tyranny within the Council of Europe.

That’s great!, you are probably thinking, Finally the EU has decided to send troops to Darfur; to call for free elections in North Korea; to forcefully condemn human rights abuses in Guantanamo; or demand the right to vote for Saudi women; or to read Mugabe the riot act…

Ah, think again.

Zimmer Profiles Nowak

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Today’s New York Times carries a profile of evolutionary theoretician, Martin Nowak, written by Carl Zimmer: In Games, an Insight Into the Rules of Evolution. Zimmer elaborates on the profile on his blog.

Nowak is the director of the Program for Evolutionary Dynamics at Harvard University. I first encountered his research in graduate school, when I was working on the evolution of language ability. In 2002, at the Evolution of Language: Fourth International Conference, I had the opportunity to have lunch with him.

He is an incredibly gifted scientist, and Zimmer’s article about him is well worth the read.

Tangled Invertebrates

The Tangled Bank

It's a collision! Two great carnivals on the same day. Check out Carnival of the Spineless #23 from sodden Great Britain, where the molluscs are thriving, and also read Tangled Bank #85, the Reductionist's Tale at Migrations.

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