Is Richard Dawkins an Accomodationist?

 
Richard Dawkins was recently interviewed by Newsweek: Darwin’s Rottweiler. Here's an excerpt.

Are those incompatible positions: to believe in God and to believe in evolution?
No, I don't think they're incompatible if only because there are many intelligent evolutionary scientists who also believe in God—to name only Francis Collins [the geneticist and Christian believer recently chosen to head the National Institutes of Health] as an outstanding example. So it clearly is possible to be both. This book more or less begins by accepting that there is that compatibility. The God Delusion did make a case against that compatibility in my own mind.

I interpret this to mean that in Dawkins' own mind the two are incompatible as he explained in The God Delusion, but that there are many scientists, like Francis Collins, who think that science and religion are compatible.

But on reading this, the real accommodationists had a conniption. Josh Rosenau thinks that Dawkins may have converted to his side and the side promoted by NCSE (who back Collins over Dawkins) [Richard Dawkins, accommodationist?].

This, for what it's worth, looks like the position NCSE has taken, and is, to the best of my knowledge, the sort of rhetoric Matt Nisbet and Chris Mooney and Sheril Kirshenbaum have been calling for from folks like Dawkins. It matches my own views, too, though I've been less vocal in these debates than many others.

It will be interesting to see whether the usual suspects go after Dawkins with quite the same vehemence that has met others advancing similar lines of argument.

Matt Nisbet is delighted because he's been saying all along that Dawkins needs to re-frame his argument to conform to the Nisbet rules for talking about evolution [Is Dawkins Re-Framing His Position on Science & Religion?]. Chris Mooney—who hasn't completely abandoned the bizarre views of his former colleague (Nisbet)—is also jumping on the bandwagon [Richard Dawkins, Accommodationist].

Sheesh! Come on guys, get a life.

Dawkins wasn't very careful about what he said in that interview but to assume that he's all-of-a-sudden become an accommodationist is really stupid of you.

Now we have the makings of a really Alice-in-Wonderland (or Woody Allen) scenario. Jerry Coyne is currently in Los Angeles at a meeting with Richard Dawkins. He (Coyne) showed the Josh, Matt, and Chris postings to Richard and here's what Coyne wrote on his blog [Richard Dawkins is not an accommodationist].

Well, I know Richard Dawkins. I am at a meeting with Richard Dawkins. I just discussed these accusations of accommodationism with Richard Dawkins. And I can tell you, Chris, Sheril, and Josh, that Richard is not one of you.

Right now I feel like Woody Allen in Annie Hall. If you’ve seen the movie, you’ll remember that in one scene Allen is in a movie line with Diane Keaton, and becomes annoyed by some pompous guy trying to impress his date by nattering on about the work of Marshall McLuhan. Allen goes behind a movie sign and pulls out McLuhan himself, taking him over to confront Mr. Pomposity. McLuhan coldly eyes him and says, “Excuse me, but I am Marshall McLuhan, and I couldn’t help overhearing what you said. I have to tell you that you know nothing of my work!” Allen turns to the camera and comments, “Don’t you wish life could be like this?”

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Jonathan Wells Is a Winner!

 
This week's Egregiously stupid remark of the week by an IDiot goes to Jonathan Wells for his comment about HOX genes.

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A Julia Child Recipe

 
Posting a video of Julia Child preparing a delicious dish is something you're more likely to find on other blogs. But this is a recipe for "Primordial Soup" so it's appropriate to let Sandwalk readers know about it.

You should definitely try this at home in your own kitchen. But don't eat it.

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[Hat Tip: Martin Brazeau on The Lancelet]

Good Science? Bad Science Journalism?

It was inevitable that science writers all over the world would screw up the story of Ardipithicus ramidus as reported in a series of papers published in Science [see the special Science webpage: Ardipithicus ramidus].

Everyone will have their favorite example. Mine comes from today's issue of The Toronto Star in an article by Joseph Hall titled Did apes descend from us?

Man didn't descend from apes.

What is closer to the truth is that our knuckle-dragging cousins descended from us.

That's one of the shocking new theories being drawn from a series of anthropology papers published Friday in a special edition of the journal Science.

Scientists say a 4.4-million-year-old fossil called Ardi – short for ardipithecus ramidus – is descended from the "missing link," or the last common ancestor between humans and apes.

The 4-foot, 110-pound female's skeleton and physiological characteristics bear a closer resemblance to modern-day humans than to contemporary apes, meaning they evolved from humanlike creatures – not the other way around.

We did not descend from apes—humans are apes. Modern humans and other modern apes share a common ancestor. It's silly to say that humans descend from monkeys, or apes, and it's just as silly to say that chimpanzees descend from humans.

The second part of the quotation is pretty accurate but it's overshadowed by the unnecessary hype in the first few sentences. There are no "shocking new theories" being promoted.

C. Owen Lovejoy is one of the authors on several of the papers just published (e.g. White et al. 2009; Suwa et al. 2009). He is quoted in the Star article, presumably from a 'phone interview by the author.

"It's transformative. This is a lot closer to anything that you'd call the missing link than anything that's ever been found," says Lovejoy, a biological anthropologist at Ohio's Kent State University.

Among other things, research on Ardi suggests humans are far more primitive in an evolutionary sense than today's great apes – like chimps and gorillas – which have continued to evolve from the missing link.

"In a way we're saying that the old idea that we evolved from a chimpanzee is totally incorrect," he says. "It's more proper to say that chimpanzees evolved from us."

Can you blame the reporter when this is what one of the authors says? Yes you can, because, as Carl Zimmer points out, it's up to science reporters to do a bit of digging to find out the real story behind the scientific papers and the press releases.

But we also need to blame scientists for the sorry state of scientific literacy. That was a remarkably stupid thing for C. Owen Lovejoy to have said to a science journalist. As a scientist he should have known that the "old idea" (we evolved from a chimpanzee) is wrong and the "new idea" (chimpanzees evolved from us) is also wrong for the same reasons.

Maybe Lovejoy was misquoted? After all, he's a member of the National Academy of Sciences so he must know what he's talking about. Let's look at the Kent State University press release [Kent State University Professor C. Owen Lovejoy helps unveil oldest hominid skeleton].

KENT, Ohio -- Oct. 1, 2009 -- Throw out all those posters and books that depict an ape evolving into a human being, says Kent State University Professor of Anthropology Dr. C. Owen Lovejoy. An internationally recognized biological anthropologist who specializes in the study of human origins, Lovejoy is one of the primary authors who revealed their research findings today on Ardipithecus ramidus, a hominid species that lived 4.4 million years ago in what is now Ethiopia.

"People often think we evolved from apes, but no, apes in many ways evolved from us," Lovejoy said. "It has been a popular idea to think humans are modified chimpanzees. From studying Ardipithecus ramidus, or 'Ardi,' we learn that we cannot understand or model human evolution from chimps and gorillas."

Not much better, although Loverjoy does emphasize the fact that "people often think we evolved from apes." However, he doesn't do much to dispel this way of thinking when he says, "apes in many ways evolved from us."

I don't think we can blame our reporter for this one.

What about the scientific papers? What do they say? Remarkably, the papers actually address the idea that humans might have evolved from chimpanzees as though this was a real scientific belief held by real scientists. Here's the conclusion of the White et al. (2009) paper.

Conclusions. Besides hominids, the only apes to escape post-Miocene extinction persist today as relict species, their modern distributions centered in forested refugia. The markedly primitive Ar. ramidus indicates that no modern ape is a realistic proxy for characterizing early hominid evolution—whether social or locomotor—as appreciated by Huxley. Rather, Ar. ramidus reveals that the last common ancestor that we share with chimpanzees (CLCA) was probably a palmigrade quadrupedal arboreal climber/clamberer that lacked specializations for suspension, vertical climbing, or knuckle-walking (24–27). It probably retained a generalized incisal/postcanine dentition associated with an omnivorous/frugivorous diet less specialized than that of extant great apes (22, 23). The CLCA probably also combined moderate canine dimorphism with minimal skull and body size dimorphism (22, 23), most likely associated with relatively weak male-male agonism in a male philopatric social system (22, 23, 31).

Ardipithecus reveals the first hominid adaptive plateau after the CLCA. It combined facultative terrestrial bipedality (25, 26) in a woodland habitat (28–30) with retained arboreal capabilities inherited from the CLCA (24–27). This knowledge of Ar. ramidus provides us, for the first time, with the paleobiological substrate for the emergence of the subsequent Australopithecus and Homo adaptive phases of human evolution. Perhaps the most critical single implication of Ar. ramidus is its reaffirmation of Darwin’s appreciation: Humans did not evolve from chimpanzees but rather through a series of progenitors starting from a distant common ancestor that once occupied the ancient forests of the African Miocene.

Hmmm ... I'm not that familiar with the scientific beliefs of anthropologists. Maybe they really did think that humans evolved from chimpanzees! That's pretty scary.

Owen Lovejoy has a single author paper where he makes the case for just such a mistaken view of human evolution (Lovejoy 2009). It's a good read. He might be right that his colleagues tended toward a ladder-like view of evolution.

Not all of the reporting is bad. Yesterday I linked to the article by Carl Zimmer [Ardipithecus: We Meet At Last] and today we get to see the reports in Science. One of these reports, A New Kind of Ancestor: Ardipithecus Unveiled by Ann Gibbons, is particularly good. It contains important bits of information like this ...

But not everyone agrees with the team’s interpretations about how Ar. ramidus walked upright and what it reveals about our ancestors. “The authors … are framing the debate that will inevitably follow,” because the description and interpretation of the finds are entwined, says Pilbeam. “My first reaction is to be skeptical about some of the conclusions,” including that human ancestors never went through a chimpanzee-like phase. Other researchers are focusing intently on the lower skeleton, where some of the anatomy is so primitive that they are beginning to argue over just what it means to be “bipedal.” The pelvis, for example, offers only “circumstantial” evidence for upright walking, says Walker. But however the debate about Ardi’s locomotion and identity evolves, she provides the first hard evidence that will inform and constrain future ideas about the ancient hominin bauplan.

It's important to remember that the scientific papers are promoting a particular view of human evolution and the importance of the very fossils that the authors have been working on for many years. They have a big stake in this. There will be biases that creep into the conclusions. It would be wrong to conclude that everything we today hear about Ardipithicus ramidus will stand up to subsequent scrutiny.

If I had to guess, I'd say that the most significant finding is the evidence that Ardipithicus lived in a woodland environment and not on a savanna [see Habitat for Humanity]. This could change the way we think about how humans evolved. If early humans were more likely to lived in wooded areas than in open savanna, then many adaptationist explanations for certain characters will have to be revised. (See the Lovejoy (2009) paper.)

Such a result will make it difficult to explain our supposed instinctual preference for savanna-like terrains, for example [E.O. Wilson in New York]. Why would our ancestral population have fixed alleles making us admire savanna when our ancestors lived in the woods?

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[Image Credit: The map of the Afar Rift is form The View from Afar]

Lovejoy, C. O. (2009) Reexamining Human Origins in Light of Ardipithecus ramidus. Science 326:74e1-74e8. [doi: 10.1126/science.1175834]

Suwa, G., Asfaw, B., Kono, R.T., Kubo, D., Lovejoy, C.O., and White, T.D. (2009) The Ardipithecus ramidus Skull and Its Implications for Hominid Origins. Science 326:68e1-68e7. [doi: 10.1126/science.1175825]

White, T.D., Asfaw, B., Beyene, Y., Haile-Selassie, Y., Lovejoy, C.O., Suwa, G., and WoldeGabriel, G. (2009) Ardipithecus ramidus and the Paleobiology of Early Hominids. Science 326:75-86. [doi: 10.1126/science.1175802]

Creation Astronomy

 
I'm sometimes accused of a bias against creationism and other forms of stupidity. So, in the interests of diversity and political correctness, I present one of the better examples of creationist logic.

This is from The 4th Day Alliance. Don't ever say that I haven't been fair to creationists. This is an accurate, unedited, copy of what's on their website (click on 'Start a Local Chapter"). I'm not making this up. I'm not quote mining.

We are in the midst of a major culture war and we need your help! As you know, one of the foundations upon which great negative change has taken place in our world is the false belief in evolution (naturalism).

While most people are familiar with Charles Darwin’s theory, few realize that an even greater fight is being waged in the area of astronomy. This is because evolution, as it pertains to astronomy, doesn’t just deal with the origin of life, but with the origin of EVERYTHING! If belief in evolution is defeated in the area of cosmology and astronomy, then other forms of evolutionary belief don’t have a leg to stand on. This is why evolutionary astronomers are some of the most dogmatic philosophers in existence today. Their ENTIRE WORLDVIEW rests on the foundation of evolutionary cosmology and astronomy. This is why evolutionists oftentimes feel most threatened by Creation Astronomy and wage the most virulent attacks against Creation Astronomers.

We are requesting your help to combat this problem on a grassroots level. Please consider this opportunity prayerfully.

There are literally hundreds of astronomy clubs around the country, but to our knowledge there is only ONE that is unapologetically Christian and that believes in the absolute truth of the Bible – the 4th Day Alliance. Astronomy clubs are responsible for teaching and introducing the public to astronomy. Unfortunately, 99.99% of the time they are teaching the myth of “billions of years” and false theories like the Big Bang.

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Emma Hale Is My (Distant) Cousin

 
You're probably wondering who the heck is Emma Hale? Up until a few days ago I couldn't have helped you, but now I know a great deal more. She was born in Harmony Township, Susquehanna County, Pennsylvania. This is in the northern part of the state not too far from Binghampton, New York. She died in Nauvoo, Illinois in 1879.

Emma was the wife of Prophet Joseph Smith, founder of the Mormon religion (The Church of Jesus Christ of Latter-Day Saints). The religion is based on the Book of Mormon, which is a translation of the inscriptions on some gold plates that Joseph discovered. The inscriptions tell of a visit by Jesus to the natives of North America.

The following description of Emma Hale's marriage is from the Wikipedia article on Emma Smith.

Emma was born July 10, 1804, in Harmony Township, Susquehanna County, Pennsylvania, as the seventh child of Isaac Hale and Elizabeth Lewis Hale. Emma first met her future husband, Joseph Smith, Jr. in 1825. Smith lived near Palmyra, New York, but boarded with the Hales in Harmony while he was employed in a company of men hoping to unearth buried treasure (specifically a silver mine for Josiah Stowell, a farmer whose farm home still stands on the north side of the Susquehanna River on New York State Route 7 in Ninevah, New York, Just West of Afton). Although the company found no treasure, Smith returned to Harmony several times seeking the hand of Emma. Isaac Hale refused to allow the marriage because he considered Smith's occupation disreputable. Finally, on January 17, 1827, Smith and Emma eloped across the state line to South Bainbridge (Afton), New York, where they were married the following day. The site of the marriage is on the site of the present day Afton Fairgrounds located on New York State Route 41 within the Village of Afton, in the Town of Afton. The Afton Fairgrounds is located on the East side of the Susquehanna River and a New York State Historical Marker commemorates the location. The couple moved to the home of Smith's parents on the edge of Manchester Township near Palmyra.

While there, on September 22, 1827, Joseph and Emma took a horse and carriage belonging to Joseph Knight, Sr. and went to a hill now known as the Hill Cumorah where Joseph claimed to receive a set of Golden Plates. This created a great deal of excitement in the area. In December 1827, the couple decided to move to be with Emma's parents' in Harmony where they reconciled to an extent with Isaac and Elizabeth Hale, who helped Emma and Joseph obtain a house and a small farm. While living there, Joseph began work on the Book of Mormon, and for a time, Emma acted as a scribe. She became a physical witness of the plates, reporting that she felt them through a cloth, traced the pages through the cloth with her fingers, heard the metallic sound they made as she moved them, and felt their weight. She later wrote in an interview with her son, Joseph Smith III: "In writing for your father I frequently wrote day after day, often sitting at the table close by him, he sitting with his face buried in his hat, with the stone in it, and dictating hour after hour with nothing between us."[3]

While in Harmony on June 15, 1828, Emma gave birth to her first child—a son named Alvin—who lived only a few hours.

In May 1829, Emma and Joseph left Harmony and went to live with David Whitmer in Fayette, New York. While there, Joseph finished work on the Book of Mormon, which was published by March 1830.

Emma's father was Issac Hale (1763-1839) and his mother (Emma's grandmother) was Diantha Ward (1741-1771). She is the daughter of Arah Ward (1718-1780) and Arah's father is William Ward (1678-1768). William is the son of Andrew Ward Jr. (1645-1691) who is the son of Andrew Ward Sr. (1597-1660) [Ancestors of Joseph Smith and Emma Hale].

Andrew Ward Sr. is Emma Hale's great⁴-grandfather and my great⁹-grandfather. So Emma Hale and I are distant cousins (very distant). The Ward family is from the New Haven area of Connecticut. It was Emma's father, Issac, who first moved to northern Pennsylvania near the New York state border.

Think about it. I am a Mormon in some alternate universe that isn't very different than this one. Only a few minor changes are required.

Contingency is scary.

UPDATE: Turns out I am not related to Andrew Ward so I'm not related to Emma Hale.

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Why People Believe Weird Things

 

WHY PEOPLE BELIEVE WEIRD THINGS

FEATURING DR. MICHAEL SHERMER

Friday, October 2, 7pm
J.J.R. MacLeod Auditorium
Medical Sciences Building
University of Toronto (1 King's College Circle)

Ever wonder why people believe in UFO abductions, mind-reading, reincarnation, urban legends, not to mention "scientific creationism" and the pernicious myth that the Holocaust never happened?

Dr. Michael Shermer, the Founding Publisher of Skeptic magazine, is a genuine ghost-buster, a relentless crusader against superstition and pseudoscience. Based on his bestselling book, Why People Believe Weird Things, Dr Shermer^Òs lecture will debunk junk science, bad science, voodoo science, pathological science, pseudoscience, and plain old nonsense. The event will be filled with humour,insight, and personal anecdotes - a highly entertaining wake-up call that has proved a hit on college campuses.

Dr. Michael Shermer is the Founding Publisher of Skeptic magazine, the Executive Director of the Skeptics Society, a monthly columnist for Scientific American, the host of the Skeptics Distinguished Science Lecture Series at Caltech, and Adjunct Professor of Economics at Claremont Graduate University.

ADMISSION
$8 regular
$5 students and Centre for Inquiry Members.
This event is FREE to New and Renewing Centre for Inquiry members and one guest.

CONTACT
Visit the event webpage at http://tinyurl.com/ntssw7 or contact
416-971-5676 or jtrottier@centerforinquiry.net

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IDiots, Epigenetics, and Jean-Baptiste Lamarck

 
What do IDiots, epigenetics, and Jean-Baptiste Lamarck have in common? Nothing much, actually, but that never stopped the Intelligent Design Creationists before.

For the latest attempt by IDiots to connect epigenetics and Lamarck see: A Bogey Moment with PZ Myers by Cornelius Hunter.

It is interesting to see how evolutionists respond to failures of their theory. For all their talk of following the evidence and adjusting to new data, evolutionists find all kinds of ways to resist learning from their failures. Consider one of the major failures of evolution, its view of the very nature of biological change. Twentieth century evolutionary theory held that biological change is a rather simple process that is blind to the needs of the organism. As Julian Huxley, grandson of Darwin confidant T. H. Huxley, put it, mutations "occur without reference to their possible consequences or biological uses."

Observations have long since been made to the contrary, but evolutionists cast it as the Lamarckian heresy. Researchers knew they should not suggest a correlation between environmental pressure and biological response, as the careers of those who did were ruined.

Now, you might be asking yourself what this has to do with supporting creationism.

Good question. It means you're starting to think critically.

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Nobel Prize Predictions

 
My colleague, Alex Palazzo, has just posted his annual list of potential Nobel Prize winners in the biological sciences [Gaze into the crystal ball - Nobel Prize Predictions].

I'm hoping for Ernest McCulloch and James Till for their discovery of stem cells. My second choice would be Harry Noller and some combination of others for their work on ribosome structure and function.

Post your prediction on Alex's new blog Transcription and Translation.

If you have time, you might want to correct his misguided views about scientific facts [Science - Building Models, Not Facts].

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Questions for Bill Maher and Richard Dawkins

 

Sometime tomorrow Richard Dawkins will be presenting the Richard Dawkins Award to Bill Maher at the Atheist Alliance International convention in Los Angeles.

Why is this a problem? It's a problem because Bill Maher is a kook. He believes in all kinds of strange things about alternative medicine, cancer, and immunizations.

Orac has the documentation at Respectful Insolence: Some "inconvenient questions" for Bill Maher and Richard Dawkins tomorrow. He also has a list of question for Bill Maher and Richard Dawkins.

PZ Myers will be at the convention. His attempt to defend Maher and Dawkins isn't working, in my opinion. Orac takes him on and exposes the hyprocrisy of the whole sorry episode. Maybe there will be fireworks at the convention tomorrow? I sure hope so. Giving the Richard Dawkins Award to Bill Maher is a travesty.

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What's on American Television?

 
One of the things I see on American television is Glenn Beck. PZ Myers says that Glenn Beck is completely insane.

It certainly seems that way to me but one can't help but wonder why he's given a show on a major cable news network. Surely he represents a substantial number of Americans?

Watch the video. Keep in mind that the song "Battle Hymn of the Republic" was originally "Canaan's Happy Shore" then transformed into "John Brown's Body." The significance of the changing lyrics to this memorable tune will become important near the end of the video.

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Ardipithecus ramidus

 
A (relatively) new hominid named Ardipithecus ramidus is described in several papers that appear in the Oct 2 issue of Science.

Carl Zimmer is ahead of the curve on his one¹ and I urge you to read his blog and learn about this important new ancestor of ours [Ardipithecus: We Meet At Last]. The main point is that this represents the earliest well-described species in our lineage. Ardipithecus ramidus lived in what is now Ethiopia about 4.4 million years ago.

The publicity surrounding these papers gives me an opportunity to raise a related issue. Here at the University of Toronto we are about to reorganize our first year biology courses. One of the required half courses will be BIO130H: Molecular and Cell Biology and the other will be BIO120H: Adaptation and Biodiversity.

The stated goal in the second course is to teach evolution, recognizing that "All science students require an understanding of evolutionary and ecological principles so they can make informed decisions on pressing societal issues ...."

I know what you're thinking ... you're thinking that Moran will be upset about the adaptationist slant in that course. You're right, I'm angry about that, but that's not what I want to talk about today.

The course will not mention fossils and it will not describe the history of life as determined by the fossil record. I think this is a mistake. I think that in order to understand evolution you need to examine all of the evidence that supports it and learn to appreciate that many different disciplines converge on the same conclusion; namely, that living things evolved over hundreds of millions of years.

Not only that, there are many fascinating parts of the fossil record that provide good opportunities for learning about evolution and for critical thinking. Hominid evolution and our relationship to the other apes is only one of them. There's also the Cambrian explosion, mass extinctions, the relationship between birds and dinosaurs, and punctuated equilibria.

It's true that you can't cover everything in a first year half course but the fossil record is too important to leave out, in my opinion. We also have a proposed new required second year course that's supposed to teach evolution. It's called BIO220H: From Genomes to Ecosystems in a Changing World. The fossil record isn't going to be taught in that course either.

What do Sandwalk readers think? Should we be graduating students with a life sciences degree when they've never heard of the fossil record in class?

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1. Where does he find the time to write so many excellent articles and books? Has he been cloned?

[Reconstructions: Copyright 2009, J.H. Matternes.]

The College Student’s Back to School Guide to Intelligent Design Creationism

 
The Evolution News website is run by the Discovery Institute in Seattle, Washington USA. In spite of the title, their goal is not to inform you about evolution. Instead, their goal is to promote anti-evolution thinking and Intelligent Design Creationism.

I'm in the middle of teaching a course about evolution and creationism so the latest posting on their website caught my eye. I urge my students to read the latest posting: Introducing The College Student’s Back to School Guide to Intelligent Design. They have lots of helpful hints about how to deal with evil Professors who oppose intelligent design. Not only that, they have a book for sale called "The College Student’s Back to School Guide to Intelligent Design." It's sort of like "Evolution for Dummies."

The main part of the book is about dealing with your Professor's "misinformed" opinions about Intelligent Design Creationism. Here's a list of nine such opinions. I better read up on how students are going to refute these arguments—at least the ones that aren't farcical or obvious strawmen.

1. Intelligent Design Is Not Science
2. Intelligent Design Rejects All of Evolutionary Biology
3. Intelligent Design Has Been Banned From Public Schools by the Federal Courts
4. Intelligent Design Is Just Politics
5. Intelligent Design Is a Science Stopper
6. Intelligent Design Is “Creationism” and Based on Religion
7. Intelligent Design Is Religiously Motivated
8. Intelligent Design Proponents Don’t Conduct or Publish Scientific
   Research
9. Intelligent Design Has Been Refuted by the Overwhelming Evidence for Neo-Darwinian Evolution

Hmmm ... on second thought, I hope my students don't see this. It looks like a pretty devastating attack on everything I've been saying in class. I'm shaking in my boots.

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Monday's Molecule #138: Winner

 
The purple molecule is cyclin bound to phospho-cyclin-dependent kinase 2 (CDK2) (yellow) and kinase-associated phosphatase (KAP) (blue). The Nobel Laureate is Tim Hunt.

There were lots of correct answers from Asia and Europe this time around but also a few from North America.

This week's winner is Joshua Johnson of Victoria University in Australia. The posting time was convenient for Australians since his email message was sent at 2 o'clock in the afternoon. There wasn't an undergraduate winner this week so I'll carry over the undergraduate prize for next week's molecule.

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This is the earliest posting of a Monday's Molecule. It should make the contest open to a whole new category of Sandwalk readers, especially those in Europe who will see it long before the readers in North America are awake.

It will also work for Asian readers and a few North and South Americans who are up very late at night. (Note to the latter group: get a life! )

The molecule is a compex of three different proteins. One of them—the yellow one—has already been featured as a Monday's Molecule last April. This time I want you to identify the purple molecule. It was first identified and characterized in the organism shown below then subsequently found in lots of other species.

The Nobel Laureate from last April shared the prize with the person who discovered today's molecule. Name that Nobel Laureate.

The first person to identify the molecule and name the Nobel Laureate wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only three ineligible candidates for this week's reward: Philip Johnson of the University of Toronto, Ben Morgan of the University of North Carolina at Chapel Hill and Frank Schmidt of the University of Missouri.

Frank has agreed to donate his free lunch to a deserving undergraduate. Consequently, I have an extra free lunch for a deserving undergraduate so I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours. Comments are now open.

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You Can't Go Home Again

This is a resurrected version of a steroid hormone receptor. It was derived from the modern glucocorticoid receptor (GR) gene by mutating various codons to make them like the predicted ancestral gene. When all of the mutations were introduced, the protein was expressed and its structure was determined.

Glucocorticoid receptor specifically binds cortisol but the ancient protein binds other steroids as well as cortisol. This is pretty much what you might expect. Various gene duplication events lead to a family of proteins and each family member evolved to recognize a single ligand. The fact that you can reconstruct the presumed ancestral protein and show that it bound to multiple ligands is pretty amazing. The work comes out of Joseph Thornton's lab (Ortlund et al. 2007).

Altogether there were about 60 amino acid substitutions along the lineage leading from the ancestral broad-specificity receptor to the cortisol-specific receptor but only two of these turned out to be ones that shifted the specificity. Most of the rest probably had little effect of the function or specificity of the protein. This is the expected result. Most amino acid substitutions during evolution are neutral.

If there are really only two key amino acid substitutions that change specificity then it should be possible to convert a modern glucocorticoid receptor into one that recognizes a broad range of hormones by merely changing two amino acids. In other words, you could revert to the ancient form by reversing evolution and only a few mutations should do it.

Can you go back in time this easily? Apparently not, according to a recent paper from the same lab (Bridgham et al. 2009). Carl Zimmer is on top of this story in a article he published in yesterday's issue of the New York Times "Can Evolution Run in Reverse? A Study Says It’s a One-Way Street."

There's no conceptual advances in this paper, at least for those scientists who have a proper understanding of evolution. Some of the neutral changes along the pathway prepared the way for additional changes that were not possible in the ancestor protein. In other words, strictly neutral changes can add up to significant differences in structural stability making it possible for some adaptive change to occur that could not have otherwise occurred.

This isn't a breakthrough, it's an excellent study that confirms what was predicted on the basis of what we know about evolution. Here's how the authors describe their result in the abstract ...

Using ancestral gene reconstruction, protein engineering and X-ray crystallography, we demonstrate that five subsequent ‘restrictive’ mutations, which optimized the new specificity of the glucocorticoid receptor, also destabilized elements of the protein structure that were required to support the ancestral conformation. Unless these ratchet-like epistatic substitutions are restored to their ancestral states, reversing the key functionswitching mutations yields a non-functional protein. Reversing the restrictive substitutions first, however, does nothing to enhance the ancestral function. Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution.

Because of "historical contingency" you can't reverse evolution. The path that lineages follow as they evolve is determined, in part, by chance and accident and not by natural selection alone.

You can't go home again.

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Bridgham, J.T., Ortlund, E.A., and Thornton, J.W. (2009) An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461:515-519. [PDF]

Ortlund, E.A., Bridgham, J.T., Redinbo, M.R., and Thornton, J.W. (2007) Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317:1544-1548. [PDF]