On the Difference Between "Evolutionary Theory" and Scientific Fact

There's been a lot of discussion about Elliott Sober's talk at the University of Chicago. You can watch the entire talk and the questions & answers at [The Problem with Philosophy: Elliott Sober].

Most of the debate is taking place on Jerry Coyne's site [Can God create mutations? Elliott Sober says we can’t rule that out.] and on Jason Rosenhouse's blog [The Reason For the Ambivalence Towards the Philosophy of Science]. Things aren't going well for Elliott Sober and, by implication, for the philosophy of science.

I want to discuss another troubling aspect of Sober's talk. Throughout the talk he refers frequently to "evolutionary theory" or "the theory of evolution." This is consistent with the introduction by Robert Richards where he says they are considering "... the application of evolutionary theory to the humanities and social sciences" (27 sec). The title of Sober's talk is "Naturalism and Evolutionary Theory."

What do they mean by "evolutionary theory"? To me, evolutionary theory means the kinds of things that are discussed in Stephen Jay Gould book "The Structure of Evolutionary Theory." It includes things like population genetics and the potential influence of genome size on the fixation of alleles. It includes things like species sorting and punctuated equilibria. It even includes speculation about selfish genes and the level of selection.

Evolutionary theory does NOT include whether birds and dinosaurs share a recent common ancestor, the age of the Earth, the amount of junk DNA in our genome, or the causes of mutation. Those are interesting questions that bear on evolution but the answers to those questions are not a fundamental part of evolutionary theory. The are questions of scientific fact, in my opinion.

Do philosophers like Elliott Sober agree with this distinction? I don't think so. The main point of Sober's talk is whether evolutionary theory can show that mutations are random. He concludes that evolutionary theory cannot conclusively prove that all mutations arose by chance; therefore, there's room for God-directed mutations as long as their frequency is indistinguishable from randomness.

Sober has a paper that discusses this issue [Evolution without Naturalism]. Here's the part that describes "evolutionary theory" (page 5).

What is this thing called “evolutionary theory,” which theistic evolutionism is able to encompass consistently? It includes the origin of life from nonliving materials by physical processes, the branching genealogical process whose upshot is that current organisms are connected to each other by relations of common ancestry, the random origin of new mutations, and the processes that govern trait evolution within lineages, such as selection and drift. Among these several propositions, the idea that mutations are “random” may seem to be a sticking point.

This is not what I think of when I use the term "evolutionary theory." I don't think the origin of life is a part of evolutionary theory. I don't think that the random origin of new mutations is part of evolutionary theory. As far as I'm concerned, the discovery that mutations occurred preferentially in hotspots or that there was a base composition bias—which there is—would not refute evolutionary theory. I think my understanding of evolutionary theory is closer to that of the majority of evolutionary biologists and it's troubling to me that philosophers seem to use a different definition.

Here's another example from that same paper (page 4) ...

Although evolutionary theory is silent on the question of whether there is a God, it is not neutral with respect to logically stronger hypotheses about God. Consider, for example, the statement

Life appeared on earth about 10,000 years ago due to divine intervention.

This statement is inconsistent with evolutionary theory.

The Young Earth Creationist statement is inconsistent with all available scientific evidence on the age of the Earth. This evidence is so overwhelming that it is a scientific fact (sensu Gould) that the Earth is billions of years old. Why does Sober think that "evolutionary theory" plays a role here?

This is not just a semantic quibble. By confusing "evolutionary theory" with scientific facts Sober makes it much more difficult to follow his line of reasoning.

Is it true that the majority of philosophers of science use "evolutionary theory" when they should frequently be referring to scientific facts? Is it true that most philosophers think that the age of the Earth is a "theory"? Do they also think that evolution is only a theory?

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The Burden of Proof

Hemant Mehta of Friendly Atheist posted this video a few weeks ago: When It Comes to God’s Existence, Who Has the Burden of Proof.

It's quite good. I think it deserves more atrention so I'm reposting it here. It's relevant to the discussions about Elliott Sober and the value of philosophy. Thanks Hemant!

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Look What Just Appeared Right Beside My Office!!!

My next door neighbor used to be the chair of the Immunology Department but Immunology recently moved to another floor of this building. The entire corridor became part of the Department of Biochemistry—or so we thought.

Last week, the old office was renovated and I assumed that the space would become offices for biochemistry students. So did my biochemistry colleague whose office is on the other side.

Surprise! The sign went up yesterday. This room is now a religious chapel, or prayer room, with the rather misleading title of "Multi Faith Room." I assume that its purpose is allow people of all faiths to visit the room from time to time (it's open from 7am to 10pm) and pray behind the screen.

The room has not been transferred to biochemistry, it has been assigned to the Faculty of Medicine. A little island of faculty controlled space in the middle of the Department of Biochemistry.

The Dean knows me. She is well aware of the fact that I'm a prominent defender of evolution in the war against creationism. She also knows that I am an atheist who doesn't shy away from the the conflict between science and religion. She probably doesn't know that I'm a strong supporter of the Centre for Inquiry and adviser to the University of Toronto Secular Alliance.

I put posters and banners on the wall outside my door advertising atheist events and I often post articles promoting evolution over creationism and science over religion.¹ I'll be putting up even more posters in the near future since the Faculty of Medicine has decided to send me the very people who need to hear my message.

Thanks to the Dean for giving me this opportunity to reach out to the other side.

UPDATE: The Multi Faith Room no longer exists. See Multi Faith Room Disappears!!.

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1. I'm looking for more posters. Please let me know if you find something appropriate.

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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The Myth of "Living Fossils"

The general public has been told time and time again that there exist among us certain species that have not evolved for millions of years. These so-called "living fossils" have somehow managed to avoid any changes in the frequencies of alleles in their evolving populations. This is, of course, impossible by any reasonable definition of evolution, a conclusion that was promoted on talk.origins two decades ago [Claim CB930:].

Yet the myth persists. It persists for three reasons:

1. It plays into the popular misconception that natural selection is synonymous with evolution. If a species isn't adapting by obvious changes over time then it isn't evolving. Another way of saying this is that some species can be so perfectly adapted to their environment that all changes are selected against and negative selection prevents evolution.
2. External morphological changes are the only evidence of evolution.
3. The so-called "living fossils" show no evidence of morphological change over millions of years when, in fact, all of the popular examples show plenty of evidence of such change. In other words, the facts are misrepresented.

The last time I blogged about this was just a few months ago when I commented on the first episode of a BBC television documentary called "Survivors." The main topic of the first episode was "Horseshoe crabs are one of nature’s great survivors" and the scientist behind the series is Richard Fortey, a paleontologists at the Natural History Museum in London (UK). I pointed out that some of his statements were misleading and I also explained why horseshoe crabs have evolved according to the scientific evidence [Evolution of Horseshoe crabs].

Why is this important? Because it's wrong to promote incorrect versions of evolutionary theory.

Today's New York Times Book Review has a review of a new book by Richard Fortey called "Horseshoe Crabs and Velvet Worms." The review [Some Things Should Be Dead] praises the writing style and readability of the book but, like most science journalism, does not get into details about the accuracy of the text.¹

While preparing this post, I discovered that Jerry Coyne had also read the review [Two New Biology Books]. Coyne has met Fortey and thinks him a "lovable bear of a man, infectiously excited about biology." However, Coyne wonders what explanation Fortey will offer to support his claim of fossil species.

Fortey has a new book, and it’s about “living fossils,” those plants and animals that have persisted for millions of years without much change in their morphology (think ginkgo tree, coelocanth, and horseshoe crab). To evolutionists, these species are a mystery: why have they remained unchanged so long? One explanation—that they simply lack genetic variation that fuels evolution—is probably wrong: work ages ago by Bob Selander and Dick Lewontin showed that horseshoe crabs are just as genetically variable in their DNA as more malleable species. Another classic explanation is that these species simply live in unchanging environments, so that they arrived at their optimal morphology eons ago and there’s nothing new to adapt to. That’s an appealing but largely untestable explanation, especially because some creatures that live in similar habitats (like the shallow marine habitats of the horseshoe crab) have undergone substantial evolutionary change.

At any rate, Fortey’s new book is "Horseshoe Crabs and Velvet Worms: The Story of the Animals and Plants that Time has Left Behind," and it was reviewed in Thursday’s NYT. Reviewer Dwight Garner gives it two thumbs up, and I’ll be reading it for sure, if for no other reason to see Fortey’s explanation for unchanging species.

I'm not going to buy the book 'cause the only explanation I could accept would be that there's no such thing as a living fossil. I might be interested in a lengthy discussion about the different between natural selection and random genetic drift and/or a discussion about the kinds of morphological changes that have been observed recently among the four living species of horseshoe crabs but I doubt that would be in Fortey's book. Maybe Jerry Coyne will read it and prove me wrong.

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1. This is a pet peeve of mine. The top three most important criteria of good science writing are: accuracy, accuracy, and accuracy. If a review doesn't tell me about the quality of science in a book then the review is completely useless. I don't care if the book wins a Pulitzer Prize (given out by non-scientists) for being an enjoyable read that sounds convincing to most readers. I don't judge science writing by style as the first criterion, nor do I judge it by the personality of the writer.

Teaching Evolution in Tennessee

The state of Tennessee is about to have a new law that impacts the teaching of science in their public schools. Here's how the National Center for Science Education (NCSE) describes the law.

Nicknamed the "monkey bill," HB 368 would, if enacted, encourage teachers to present the "scientific strengths and scientific weaknesses" of topics that arouse "debate and disputation" such as "biological evolution, the chemical origins of life, global warming, and human cloning."

It doesn't take a mental giant to see where the Tennessee legislators are coming from. They want to support teachers who challenge evolution in the classroom. Most of those teachers will, of course, be creationists of one form or another.

But here's the problem. Those ignorant legislators have been very clever to avoid mentioning religion or creationism. On the surface, the new law looks perfectly reasonable.After all, who wouldn't want students to learn both the scientific strengths and weaknesses of current theories of biological evolution?

Winners

Here are three winners having lunch. On the left is David Schuller (Monday's Molecule #156) and that's Joseph Somody (Monday's Molecule #159) on the right.

(Thank-you David for the photo.)

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Monday's Molecule #`165

Name this molecule. You don't need the full IUPAC name but you do need to be specific since there are several different molecules with very similar structures. You also have to tell us why this molecule is important in biochemistry.

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 kanamycin C (not A or B). It binds to the small subunit of the prokaryotic ribosome and inhibits translation. It is/was widely used in cloning experiments since there are several plasmids with kanamycin resistance alleles. I posted all three of the responses that recognized kanamycin but only one named this variant as kanamycin C. That person didn't mention that this was a translation inhibitor so there are no winners this week.

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 10: no winner

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The Toronto Transit Commission Stands for Freedom of Speech

The Toronto Transit Commission (TTC) has resisted attempts to have a controversial ad removed from their buses, streetcars, and subways as reported in The Toronto Star [TTC won’t remove controversial ads].

But a review that is automatically triggered whenever the TTC gets at least five complaints about an ad found there were no grounds to pull either advertisement.

That review was by TTC chair Karen Stintz and TTC commissioner Maria Augimeri.

“Although I would not personally condone the comportment outlined in the advertisement, I feel that I do not have the jurisdiction nor the authority to promote its cancellation; particularly because the TTC would not fare well in a court challenge should the promoter of the advertisement choose to make this issue one of rights and freedoms,” Augimeri said of the ... ad.

“There is nothing that violates any of our policies, and we do have policies around our advertising (based on) the Ontario Human Rights Code, not promoting hate or violence,” said TTC spokesman Brad Ross.

“You don’t have to agree with the message, you don’t have to like the message of the advertiser. Our suggestion would be that if somebody takes issue with the ad they take it up with the advertiser,” he said.

Congratulations TTC! That's exactly right.

It doesn't matter what sort of ad triggered the complaints but just in case you're interested, here it is. The first paragraph says, "Dear Jesus, My mom and dad do drugs at home and it scares me. Will you help them stop? Thank you for hearing my prayer." The second paragraph is, "Don’t worry about anything; instead, pray about everything. Tell God what you need, and thank him for all he has done. If you do this you will experience God’s peace, which is far more wonderful than the human mind can understand." The ad is sponsored by Bus Stop Bible Studies.

Note: Hemant Mehta has a slightly different take on the issue [Christian Bus Ad Advises Child with Druggie Parents to Pray, Not Call for Help].

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[Hat Tip: Canadian Atheist]

Evo Devo and Giants

Anything found to be true of E. coli must also be true of elephants.

-Jacques Monod (1954)While preparing for the last lecture in my molecular evolution course I came across this quotation that explains Evo Devo.

The key to understanding form is development, the process through which a single-celled egg gives rise to a complex, multi-billion-celled animal. This amazing spectacle stood as one of the great unsolved mysteries of biology for nearly two centuries. And development is intimately connected to evolution because it is through changes in embryos that changes in form arise. Over the past two decades, a new revolution has unfolded in biology. Advances in developmental biology and evolutionary developmental biology (dubbed “Evo Devo”) have revealed a great deal about the invisible genes and some simple rules that shape animal form and function. Much of what we have learned has been so stunning and unexpected that it has profoundly reshaped our picture of how evolution works. Not a single biologist, for example, ever anticipated that the same genes that control the making of an insect’s body and organs also control the making of our bodies.

Sean B. Carroll “Endless Forms Most Beautiful: The New Science of Evo Devo” W.W. Norton & Co., New York (2005)

I've already criticized this point of view several times [Things You Didn't Know] [Sean Carroll's View of Evo-Devo] and I won't repeat them here. Read those posts to see what's wrong with Evo Devo.

If I have seen further it is by standing on ye sholders of Giants.

Isaac Newton, 1676I want to emphasize another point. I come from a culture that praised and admired the important work that formed the background to modern discoveries. My mentors were proud of the fact that they stood on the shoulders of giants.

Someone named anthrosciguy commented on my earlier post [Sean Carroll's View of Evo-Devo] by saying ...

No one wants to stand on the shoulders of giants anymore.

That struck me as a profound commentary on much of modern biological science so I thought I'd share it with you. These days it seems like everyone wants to claim credit for discovering something that nobody anticipated. You can't be standing on the shoulders of giants if you're proclaiming a revolution. That would look silly.

I'm pretty sure I know anthrosciguy's real identity but I'll leave it to him to out himself and take credit for a very clever statement.

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Carnival of Evolution #46

 

This month's Carnival of Evolution (46th version) is hosted by Bradly Alicea of Synthetic Daisies: Carnival of Evolution, Number 46 -- The Tree (structures) of Life

Welcome to Carnival of Evolution, Number 46. I am your host, Bradly Alicea. This month's theme is: the Tree (structures) of Life. Since this blog covers a mix of both biological and computational content, it is fitting that we explore this month's submissions in the context of trees (the computational kind) and biological classification (the biological kind). I will indulge in a historical and technical overview of trees used in evolutionary analysis, then present this month's posts.

The next Carnival of Evolution (May) will be hosted by John Wilkins and the one after that by PZ Myers. You can send articles directly to them or you can submit your articles at Carnival of Evolution. Bjørn is looking for someone to host the July edition. He would prefer someone who has not hosted before. Contact him at the Carnival of Evolution blog.

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Monday's Molecule #164

 

What is this structure and what is its significance? You don't need to come up with a chemical name but you do need to be as specific as possible.

Don't forget to tell us why this structure exists.

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 the cap structure on the 5′ end of eukaryotic mRNAs. It's actually a CAP 2 structure with methyl groups at the 2′ positions of the last two nucleotides but that terminology seems to be outdated so I won't insist that you specify. (Thanks to Bill Chaney for getting it right.) The winner is Sean Ridout. (Please contact me by email.)

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

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Food Trucks

 
I love the food trucks. Today was a special day, there were seven new food trucks visiting our campus.

There were so many choices ....

Two of my favorites ...

Bacon poutine and a cinnamon-sugar BeaverTail. Only in Canada!

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The Reason Rally

 
For all of us who weren't there, here's what The Thinking Atheist saw at the Reason Rally last weekend.

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Monday's Molecule #163

 

You blew it last week because you didn't follow instructions. It's not going to get any easier. This week you have to identify the molecule using TWO different common names AND name the Nobel Prize winner most closely associated with this molecule.

Remember, you need THREE answers or you can't win!

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 Vitamin B12, also known as cobalamin. The Nobel Laureate is Dorothy Crowfoot Hodgkin. This week's winners are John Runnels and Raul A. Félix de Sousa. Contact me by email to set up a time.

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

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Human Mutation Rates May Be Lower than We Thought

The predicted mutation rate in humans is thought to be about 130 mutations per generation or 10^-10 per nucleotide per generation [Mutation Rates]. About 120 (>90%)of these new mutations occur in males, mostly during spermatogenesis. Only about 10 mutations are contributed by females. These values are based on what we know about the biochemistry of DNA replication and repair.

The evidence from evolution was consistent with this calculation. Nachman and Crowell (2000), for example, calculated that the accumulation of mutations in 18 pseudogenes from humans and chimpanzees yielded a value of 175 mutations per generation.

Up until recently it wasn't possible to get a direct measurement of the mutation rate but I addressed some of the attempts in November 2010: Human Mutation Rates. In that posting I discussed two experimental results that yielded estimates of the mutation rates in humans.

Recently there have been two attempts to verify this calculation. In one, the Y chromosomes of two men separated by 13 generations in a paternal lineage from a common male ancestor were sequenced. The differences correspond to a mutation rate of 0.75 × 10^-10 per generation, or almost the same as theory predicts. This is based on the fact that if most mutations are nearly neutral (they are) then the rate of fixation by random genetic drift should be the same as the mutation rate.

The other study, by Roach et al. (2010), compared the genome sequences of two offspring and their parents. By adding up all the differences in the offspring they arrived at an estimate of 70 mutations in the offspring instead of the expected 130. This is half the expected value but the study is fraught with potential artifacts and it's best not to make a big deal of this discrepancy.

Now there's another paper that sequenced two sets of parents and a child (Conrad et al., 2011). You might think that the calculation is easy because all you have to do is count the number of new alleles in the child. But this doesn't work because you have to account for somatic mutations that arose in the tissue culture cells lines that are being used as a source of DNA. These can be eliminated by comparing the sequence with fresh DNA samples directly from the parents and child. In addition to false positives, you have to allow for some false negatives.

I don't understand all the mathematical manipulations but they are probably trustworthy. (Some of it was done by Reed Cartwright of Panda's Thumb.) The final estimates are 60 mutations in one of the children and 50 in the other. Both of these values are lower than the calculated rate and when you combine them with earlier results, it's beginning to look like the actual mutation rate is about half of the calculated value based on biochemistry. This could easily be due to a two-fold error in our estimate of repair efficiency. It could be that instead of repairing only 99/100 sites of damage the actual repair machinery fixes 199/200 damaged sites, for example.

The surprising result is that 92% of the new mutations in one of the children comes from the father but in the other family only 32% of the mutations were paternal. We expect that most of the mutations will occur during spermatogenesis so that part is not surprising. What's surprising is that in one case the majority come from the mother.

I suspect that this is an artifact of some kind, or a statistical outlier. The authors, however, take this as evidence of natural variation in male and female mutation rates. I'd like to see the estimates for other children of the same family in order to see if the result is reproducible.

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Conrad, D.F., Keebler, J.E., DePristo, M.A., Lindsay, S.J., Zhang, Y., Casals, F., Idaghdour, Y., Hartl, C.L., Torroja, C., Garimella, K.V., Zilversmit, M., Cartwright, R., Rouleau, G.A., Daly, M., Stone, E.A., Hurles, M.E., Awadalla, P.; 1000 Genomes Project. (2011) Variation in genome-wide mutation rates within and between human families. Nat. Genet. 43:712-714. [doi: 10.1038/ng.862]

Nachman, M.W. and Crowell, S.L. (2000) Estimate of the mutation rate per nucleotide in humans. Genetics: 156:297-304.