What Does James Shapiro Think?

James Shapiro is one of those scientist who think that evolutionary theory is due for a "paradigm shift." His schtick is that mutations often involve genome rearrangements and that reorganization of the genome may be a sort of "natural genetic engineering" that cells use to direct evolution. It's hard to figure out what Shapiro actually means and even harder to figure out his motives. I posted an earlier comment from him that suggests he is looking for a middle ground between science and Intelligent Design Creationism. Here's part of that earlier post: The Mind of James Shapiro

What is wrong with "dancing in the DMZ" between intelligent design (as articulated by Michael Behe and others) and neo-Darwinism? Are these two positions the only alternatives? I doubt it. That is why my 1997 article in Boston Review on evolution debates was called "A Third Way." What Dembski calls the "DMZ" (i.e. a zone free of futile conflict) is the place where the real evolutionary science is taking place. I am proud to be there, and I see that an increasing number of people are joining me when they realize that natural genetic engineering, horizontal DNA transfer, interspecific hybridization, genome doubling and symbiogenesis provide solutions to problems recognized to be intractable under the limitations of conventional evolutionary thinking.

Now Susan Mazur has gotten into the game of trying to figure out James Shapiro. You may recall that Susan Mazur has made a minor career out of touting the upcoming revolution in evolutionary theory. Here are some excerpts from her interview with James Shapiro on a website called Counterpunch: The Evolution Paradigm Shift.

Suzan Mazur:... Are Coyne and his pal Richard Dawkins, by not publicly recognizing that a sea change has occurred, milking lucrative performances and book deals? And if so, isn’t this a disservice to science?

James Shapiro: Well that’s a loaded question.

I’ve gone on record in my blog as saying that I thought that Dawkins and his ill-conceived atheist crusade hurts science education and hurts evolutionary science. I’ve criticized Jerry Coyne for making statements that he can’t support. Both Coyne and Dawkins have been characterized as having a neo-atheist agenda in attacking religion. And it is true that many of the comments on my blog reflect a deep reservoir of anti-religious sentiment. I’ve noted in the blog that we should get out of the business of attacking supernaturalists. It’s not in science’s interest to make a war with religion or religious belief.

Suzan Mazur: And get on to the science.

James Shapiro: And get on with the science. And also to have a little bit of humility. Science never provides ultimate answers.

Both Coyne and Dawkins are doing well for themselves by being vitriolic and vehement in their campaign against religious belief and against some of the more foolish things that religious fundamentalists do. But I suspect ego gratification is the major driver more than financial gain. Obviously it’s nice if you make money at the same time.

This appears to be a typical accommodationist position, assuming that Shapiro is an atheist. I just wish he'd be a little more up front about his stance.

James Shapiro: ...The moth cover was ultimately chosen because the kind of exquisite mimicry it represents is an evolutionary puzzle.

How does that come about? I think gradualist explanations are difficult to sustain in the case of mimicry. Recently it’s been discovered that there are master control regions, sort of like Hox complexes but more complicated, that control wing patterns in butterflies. I suspect as people analyze those we’ll know more about how the mimetic patterns evolved.

The book hasn’t been reviewed by any of the major journals yet. Nature and Science have not reviewed it. The National Center for Science Education is reviewing it in June. I’m interested to see whether they want to show that evolution science is alive and doing novel and controversial things.

As I said in my blog, science is not doing very well in this evolution vs. religion dispute. I think part of the reason why we’re doing poorly is that the most recent and exciting science is not being presented to the public. Clearly, the issues are not being presented in a way that shows evolution science isn’t stuck in ideas from the last century and the last century before that.

I wrote the review that will soon appear on the NCSE site. I can assure him that I'm well aware of many exciting developments in evolutionary theory. The ones that are important (population genetics, random genetic drift, Neutral Theory, punctuated equilibria, speciation) are ones that Shapiro doesn't understand or mention in his book. (Gould isn't even in the index!) The ones that are trivial and were dismissed as minor embellishments decades ago are the ones that, in his mind, are going to cause a paradigm shift.

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Monday's Molecule #169

This is going to be an easy one since there have been some complaints. The molecule is quite simple and it isn't found in living organisms although a very similar molecule is quite abundant. Be sure to provide a complete unambiguous name.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is D-serine and the winner is undergraduate Matt McFarlane. Matt, appears to live in lotusland so I'm guessing he won't be able to make it for lunch.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout

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The Problem with Philosophy: Elliott Sober

Elliott Sober is an important philosopher who appears to be widely respected in the philosophy community. So when he comes up with a really silly position on the compatibility of science and religion, we should all take notice. What does this say about the discipline?

Jerry Coyne comments on a recent talk by Sober at the University of Chicago [Can God create mutations? Eliott Sober says we can’t rule that out]. Unfortunately Jerry wasn't able to attend but here's a link to a video of the presentation : "Naturalism and Evolutionary Theory."

Naturalism and Evolutionary Theory

I urge you to read the comments on Jerry Coyne's blog website and join the discussion over there. There are two important questions: (1) Does Sober's argument make any sense to a scientist?, and (2) What does this say about the state of philosophy of science?

With respect to the first question, it's easy to paraphrase Sober's argument ...

Imagine that there are evil aliens who want to destroy human life on this planet and take it over for themselves. These are very patient evil aliens and, furthermore, they don't want us to recognize what they're up to.

They have chosen to manipulate evolution by gradually introducing mutations into our genome that will lead to destructive behavior and by inserting mutations that cause diseases. They do this in a very subtle manner so that we can't distinguish between random mutations and a very small number of directed mutations. The bad alleles are indistinguishable from those that are occasionally fixed by random genetic drift so that, over the course of millions of years, we don't notice anything unusual.

Since science is incapable of detecting the actions of these evil aliens, it follows that science is perfectly compatible with the existence of evil aliens who want to destroy us by manipulating our genome.

We all recognize, I hope, that the argument is silly. It's just as silly if you substitute some kind of God in place of evil aliens.

The second question is more of a challenge. I can see why philosophers want to rule out unprovable claims such as "I know for certain that there are no evil aliens." You can't prove a negative and maybe there are some people out there who need reminding. However, the same logic applies to all kinds of claims including the existence of Santa Claus and the tooth fairy. It even applies to homeopathy and weapons of mass destruction. You can't prove conclusively that homeopathic remedies will never, under any circumstances, cure someone of asthma. You can't prove, beyond a shadow of doubt, that there were never any weapons of mass destruction in Iraq.

Philosophers can make an important contribution by explaining why, and how, we make decisions based on probability and not on mathematical proofs. They could explain why nobody really believes in the existence of evil aliens, tooth fairies, and Santa Claus, in spite of the fact that you can't conclusively prove their non-existence.

This is where science comes in. The scientific way of knowing operates on the quaint notion that extraordinary claims (e.g. evil aliens) require extraordinary evidence—with the emphasis on evidence. Beliefs that are held in the absence of any favorable evidence are not beliefs that are worth holding, especially if those beliefs are going to rule your life. What if you encountered a cult that was building a large spaceport in Saskatchewan in order to welcome the aliens after we have all died in a nuclear holocaust? What would you think of their sanity? Would it help to know that philosophers think their core belief is rational?

I think we need a pragmatic philosophy for the 21st century. One that can actually help us make rational decisions without focusing on sophistry or on pedantic issues that are only of interest to a handful of naive philosophers who are way out of touch with reality. Science and the existence of "evil aliens" are incompatible because there's no need for the "evil alien" hypothesis to explain the world as we see it. There's no evidence for evil aliens. They appear, to all intents and purposes, to be delusions. We don't need to prove their non-existence in order to recognize the incompatibility.

Same thing for gods.

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I'm Paying for This Cross

The Province of Ontario funds two school systems, each of which has a division for French-speaking children. The public school system is open to everyone regardless of religion etc. The Roman Catholic School board is restricted to Roman Catholic students, with some exceptions. Funding comes from general revenue so, in effect, everyone is paying for the dual system.

Here's what my province is supporting as described by The Toronto Catholic District School Board.

For the year of Witness, the students at Neil McNeil Catholic Secondary School have created a travelling cross, which will journey across the school system throughout the year, with each school having an opportunity to spend a day with the cross.

Schools will be able to submit photographs from their day with the cross, including pictures from their prayer services and Masses which will be documented on this website.

The Board hopes that these moments with the travelling cross will provide an opportunity for our students, staff and families to reflect on what it means to bear witness to our Catholic faith. Faith development is integral to every part of Catholic education, as students are called to respect the dignity of all human persons in a caring community. Our journey with the Year of Witness cross will bring this message to our young people in a very tangible way.

I'm not a big fan of the American system of government but there's something to be said for separation of church and state. We do an excellent job of keeping religion out of politics but every now and then I am reminded of government support for religious schools. That's why I've come around to the position of supporting One School System.

OneSchoolSystem.org is a non-governmental human rights organization and education advocacy group seeking the amalgamation of Ontario, Canada's public and Catholic school systems into a single, secular school system for each official language.

The Ontario government currently funds four overlapping school systems: English public, English Catholic, French public, and French Catholic. Not only is this wasteful and inefficient, but the exclusivity of funding for Catholic religious schools gives rise to significant inequities between citizens of different faiths. Ontario's truly public school systems are open to all students and teachers without discrimination, while the publicly funded Catholic systems often deny admission to non-Catholic students and are essentially closed to non-Catholic teachers. We seek to eliminate religious discrimination in admissions and employment in all of Ontario's publicly funded schools while simultaneously ensuring better stewardship of the financial resources committed to the education of our children. A move to a single school system for each official language would achieve both aims.

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[Hat Tip: Veronica at Canadian Atheist: A Gift from Ontario Taxpayers]

Carnival of Evolution #47

This month's Carnival of Evolution (47th version) is hosted by an Australian philosopher named John Wilkins of Evolving Thoughts: Carnival of Evolution 47: All the Evolution News that’s Fit to Blog

Welcome to the 47th edition of the Carnival of Evolution. We have had our science reporters out in force hunting down the best of the blogosphere on evolution and related subjects, and here they are for your delectation and delight and other d-words.

The next Carnival of Evolution (June) will be hosted by a developmental biologist from Minnesota. He has a blog called Pharyngula. You can send articles directly to him (Paul Zachary Myers) or you can submit your articles at Carnival of Evolution. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before. Contact him at the Carnival of Evolution blog.

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Monday's Molecule #168

This molecule is present in most (all?) species. Your mission for today, should you choose to accept it,¹ is to: (a) name this molecule, (b) identify the most important enzyme that uses it as a substrate, and (c) name an important competitive inhibitor of this enzyme.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answers wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is HMG-CoA or 3-hydroxy-3-methylglutaryl Coenzyme A. The enzyme is HMG-CoA reductase, a key enzyme in the pathway leading to synthesis of cholesterol. Competitive inhibitors of this enzyme are used to reduce blood cholesterol levels by blocking synthesis of endogenous cholesterol. The most common inhibitors are the statins such as atorvastin (Lipitor) and lovastatin (Mevacor). The winner is undergraduate Sean Ridout.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout

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1. I watched Mission: Impossible - Ghost Protocol on a recent flight from San Diego to Toronto. You should only do this when you've exhausted all other options.

CFI Canada Sues a Major Drug Store Chain for Selling Homeopathic Product

This video explains it all.

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San Diego Bay

Here's some photos of the area along the bay beside the convention center where Experimental Biology 2012 was held. The convention center is between the two large hotels (Marriot and Hilton) in the first picture. You can see that some people own some very large and expensive boats.

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Communicating Science

Most of you won't be interested in the sessions I've been attending at Experimenatl Biology 2012. They're mostly about science education.

However, there was one session yesterday that attracted some attention and generated a lot of discussion afterward, and in the evening over a few beers. The contributions from the two science journalists were quite predicable. Basically they want scientists to help them do their jobs. They want us to feed them good stories but only if they can be spun as ways of helping their readers. Apparently they only way we can communicate science is to convince the general public that there's something in it for them.

Cara Santa Maria writes for the Huffington Post. Many of her stories involve videos and she wants science stories to be more personal. She says that scientists should not be reluctant to talk about themselves because that what the public wants to hear. That prompted a comment from Paul Berg who says that self-promotion is not dignified and he is opposed to Cara's objective.

Berg also criticized NPR for misquoting all the scientist they interviewed on a recent show about H1N1. Apparently, Berg was interviewed at some length but the bits that were included in the radio broadcast were not representative of his view. Joe Palca of NPR defended science journalism in the standard way. (We're sorry. We're very busy doing multiple stories on short deadlines. And no, we won't let you review our work before it's published.)

I'm a bit tired of going to these meetings and being lectured by science journalists on how to effectively communicate science. It would be one thing if their profession was doing an outstanding job—in that case their advice would be meaningful. But science journalists are not remarkably good at communicating science correctly. So why should we listen to them?

I was reminded of this this morning when I picked up my copy of USA Today from the floor outside my hotel room door. There on the front page was a story about telomeres: Violence ages children's DNA, shortens their chromosomes. I doubt very much whether this study will ever be reproduced. It's almost certainly wrong, in my opinion, or, at the very least, highly misleading. There wasn't even a hint of skepticism in the article. The work was presented as fact.

I will start to be impressed with science journalist when they recognize that this is bad science writing and when they start to do something to police their own profession. When they show me that they (i.e the profession) can distinguish between good science communication and bad science communication then, and only then, can they lecture me on how to effectively communicate my science.

We had a good time debating these issues in the evening. I got to meet scicurious who blogs at Scicurious/Neurotic Physiology. She is, to put it mildly, a force of nature. One of those people who always seems too busy to have a serious conversation. While I was talking to her, she was constantly looking around to see whether she was missing something more exciting elsewhere. Scicurious claims to be the "Official Blogger" of Experimental Biology 2012 because the organizers give her permission to blog about the meeting. (I did not ask for permission, in case anyone is interested.)

I also met Brian Switek of LAELAPS for the very first time. He is actually smarter and even more knowledgeable than his blog suggests. It was delightful talking to him.

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Monday's Molecule #167

I'm in a hotel room in San Diego overlooking the Pacific ocean. I see several small frigates and an aircraft carrier—not a large fleet carrier, unfortunately. The Pacific ocean makes me think of this molecule. What is it and why is it important?

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answers wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is tetrodotoxin, the main toxin in pufferfish (Fugu, named after one of the many species). This week's winners are Dima Klenchin and Deena Allan. Deena needs to get in touch. Dima has won more contests than any other person. (Bill Chaney is a very close second.) I'm glad he doesn't live in Toronto. Unfortunately, I'm going to be in Madison Wisconsin (his home) in a few weeks and he might demand that I pay up. I've decided not to tell him I'm coming.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan

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Happy "Day of Dialogue"

I didn't know about this until I read about it on Friendly Atheist but today is the "Day of Dialogue." Here's how it's described on Day of Dialogue.

As a high school or college student, do you wish your classmates could hear more of the story—like the truth about God’s deep love for us and what the Bible really says about His redemptive design for marriage and sexuality? Wouldn’t it be nice if a deeper and freer conversation could happen when controversial sexual topics are brought up in your school?

The good news is, it can—and that’s where Day of Dialogue® comes in.

In contrast to the whole idea of silence, this is a day that encourages open dialogue.

Because Focus on the Family firmly believes that the truth will rise to the surface when honest conversations are allowed to happen. And that’s why we’re so excited to announce that we’ve become the sponsor for this event.

The Day of Dialogue gives you, as a student, the opportunity to express the true model presented by Jesus Christ in the Bible—who didn’t back away from speaking truth, but neither held back in pouring out His incredible, compassionate love for hurting and vulnerable people. His example calls us to stand up for those being harmed or bullied while offering the light of what God’s Word says.

And the event gives you a chance to express this balanced perspective in a loving and peaceful way. So be sure to mark your calendars for the 2012 Day of Dialogue—Thursday, April 19, 2012—and make plans to participate in your school or college. Register today! And then join us on our Facebook page for updates & info

The Bible shows us that God honored humans by making us in his own image, male and female. God designed men and women to be different and to complement one another. Our masculinity and femininity reflects things about God’s character. Justice and mercy. Strength and beauty. Nurture and Protection. So being male or female isn’t just about biology or cultural stereotypes. Masculine and feminine characteristics reflect something much deeper—attributes of God that resonate in the core being of our souls and personalities.

Some groups have even made out cards they can give to gays and lesbians inviting them to have a conversation about Jesus and their sexuality. That promoted this cartoon on Friendly Atheist [A Response to the Day of Dialogue].

Looking forward to seeing how this plays out on my campus. I'm afraid the Christians might be in for a bit of bullying for being such idiots.

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Going to San Diego

I'll be in San Diego from Saturday, April 21, 'till Wednesday, April 25, attending Experimental Biology 2012.

This is the most important meeting for biochemistry teachers and, in addition, I'm looking forward to meeting with the other members of the editorial board of BAMBED (Biochemistry and Molecular Biology Education). Judy Voet has planned a wild party for Tuesday night!

Let me know if you're going to be there. Maybe I can get you a free copy of my book! (Or at least a signed copy of one that you buy.)

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The Problem of Evolution in America

Once again, Jerry Coyne gets it right.¹ He is about to publish an article in the journal Evolution on Science, Religion, and Society: The Problem of Evolution in America. There's a link from his blog [My paper on religious and social factors affecting American acceptance of evolution] where he notes that the manuscript isn't quite ready for publication and most of you can't see it because it's behind a paywall.

Here's the abstract ...

American resistance to accepting evolution is uniquely high among First World countries. This is due largely to the extreme religiosity of the U.S., which is much higher than that of comparably advanced nations, and to the resistance of many religious people to the facts and implications of evolution. The prevalence of religious belief in the U.S. suggests that outreach by scientists alone will not have a huge effect in increasing the acceptance of evolution, nor will the strategy of trying to convince the faithful that evolution is compatible with their religion. Since creationism is a symptom of religion, another strategy to promote evolution involves loosening the grip of faith on America. This is easier said than done, for recent sociological surveys show that religion is highly correlated with the dysfunctionality of a society, and various measures of societal health show that the U.S. is one of the most socially dysfunctional First World countries. Widespread acceptance of evolution in America, then, may have to await profound social change.

Sandwalk readers will be familiar with Coyne's attack on accommodationism because he's absolutely correct. You will also understand that the problem is not evolution vs creationism but science vs religion. You can't ever solve the problem of creationism without dealing directly with the false doctrines of religion.

But Coyne goes one step further. How do you make America into a more secular society like those in other Western industrialized nations? Coyne argues that the popularity of religion in America is due to the fact that America is a dysfunctional society and religion may represent the only hope most people have in such a society. Therefore ...

Creationism in America, then, may be a symptom of religion, but religion in the modern world may itself be a symptom of unhealthy societies. Ultimately, the best strategy to make Americans more receptive to evolution might require loosening the grip of religion on our country. This may sound not only invidious but untenable, yet data from other countries suggest that such secularism is possible and, indeed, is occurring in the United States right now. But weakening religion may itself require other, more profound changes: creating a society that is more just, more caring, more egalitarian. Regardless of how you feel about religion, that is surely a goal most of us can endorse.

I think he's right about this. You can remove the need for religion by creating a more just society. But I don't think it will be easy. Looking at it from the outside, it appears to me that there are millions of Americans who don't accept the just society² as a desirable goal. They call themselves "Republicans" and they vote for people like Rick Santorum.

I think it's also going to be very difficult to convince most Americans that their society is less than perfect. In other words, most of the rest of American society accepts the concept of a just society but firmly believes that America is the only country that has achieved it.

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1. That doesn't mean that he's right all the time. It just means that his batting average is way above average for an evolution defender.

2. Canadians will be familiar with the term since the just society was the goal of Prime Minister Pierre Elliot Trudeau who named his son, and political heir, "Justin."

Dysfunctional Science

Carl Zimmer, one of the top science writers in the world, has written an article for the New York Times with the following provocative title: A Sharp Rise in Retractions Prompts Calls for Reform. It's partly about the rise in the rate of retractions¹ in scientific journals. This is a serious problem and it's hard to figure out the underlying cause, in spite of the fact that many of the people who comment think they know the answer.

But there's much more to this story as Carl explains on his blog [Dysfunctional science: My story in tomorrow’s New York Times].

In tomorrow’s New York Times, I’ve got a long story about a growing sense among scientists that science itself is getting dysfunctional. For them, the clearest sign of this dysfunction is the growing rate of retractions of scientific papers, either due to errors or due to misconduct. But retractions represent just the most obvious symptom of deep institutional problems with how science is done these days–how projects get funded, how scientists find jobs, and how they keep labs up and running.

As usual, Carl's got it right. There's something wrong with science, or perhaps I should say there's something wrong with the biological sciences since Sean Carroll doesn't see the same problem in physics [Is Physics Among the Dysfunctional Sciences?].

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1. The rate is about 0.04%. Compare this to the rate of fraudulent creationist publications, which is close to 100%.

Monday's Molecule #166

This is another one of those molecules where you have to pay close attention to the structure. There are many similar molecules and you won't win unless you are very specific. You don't need the full IUPAC name. You do need to identify the function of this molecule.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answers wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is heme a, a component of cytochrome a and cytochrome a3. The cytochromes are cofactors in oxidation-reduction reactions where the heme group serves as an electron donor or acceptor. Today's winner is Raul A. Félix de Sousa. Several anonymous/pseudoanonymous respondants were also correct.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa

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