Better Biochemistry

This is a "Theme" post where I collect all previous posts on teaching biochemistry and molecular biology.

March 22, 2015
On the handedness of DNA

March 5, 2015
Don't misuse the word "homology"

January 28, 2015
Vision and Change

January 28, 2015
Evidence-based teaching

January 15, 2015
The Nature of Science (NOS)

January 11, 2015
Why can't we teach properly?

January 8, 2015
Evolutionary biochemistry and the importance of random genetic drift

January 3, 2015
Thinking critically about the Central Dogma of Molecular Biology

December 9, 2014
On the meaning of pH optima for enzyme activity

December 9, 2014
On the specificity of enzymes

December 4, 2014
How to revolutionize education

October 20, 2014
How not to teach biochemistry

October 3, 2014
Metabolism first and the origin of life

September 11, 2014
The mystery of Maud Menten

August 8, 2014
Historical contingency and the evolution of the glucocorticoid receptor

July 28, 2014
Finding the "perfect" enzyme

Jun 2, 2014
"Flipping the classroom": what does that mean?

April 25, 2014
ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function

April 24, 2014
ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information

March 21, 2014
ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis

March 5, 2014
The crystal structure of E. coli RNA polymearse σ70 holoenzyme

January 10, 2014
How not to teach biochemistry at memorize.com

December 9, 2013
Monday's Molecule #226

December 6, 2013
Die, selfish gene, die!

December 6, 2013
Do you understand this Nature paper on transcription factor binding in different mouse strains?

December 2, 2013
Monday's Molecule #225

November 12, 2013
David Evans Says, "Teach What the Vast Majority of Scientists Affirm as Settled Science"

November 5, 2013
Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means

October 30, 2013
Time to Re-Write the Textbooks! Nature Publishes a New Version of the Citric Acid Cycle

October 29, 2013
The Khan Academy and AAMC Teach Evolution in Preparation for the MCAT

October 29, 2013
The Khan Academy and AAMC Teach the Central Dogma of Molecular Biology in Preparation for the MCAT

October 29, 2013
The Khan Academy and the Association of American Medical Colleges (AAMC) Team Up to Teach Evolution and Biochemistry for the New MCAT

October 24, 2013
ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation

October 15, 2013
ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution

October 14, 2013
Fundamental Concepts in Biochemistry and Molecular Biology

October 11, 2013
ASBMB Promotes Concept Driven Teaching Strategies in Biochemistry and Molecular Biology

Another curious aspect of the theory of evolution is that everybody thinks he understands it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually, as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology. Jacques Monod (1974)October 8, 2013
On the Importance of Defining Evolution

October 6, 2013
Teaching Biochemistry from an Intelligent Design Creationist Perspective

October 1, 2013
The Many Definitions of Evolution

September 30. 2013
The Problems With The Selfish Gene

September 18, 2013
Breaking News!!! Wikipedia Is Wrong! (about the Central Dogma)

September 13, 2013
Sean Carroll: 'What Is Science?"

September 13, 2013
Better Biochemistry: Teaching ATP Hydrolysis for the MCAT

September 12, 2013
Better Biochemistry: Teaching to the MCAT?

June 27, 2013
The Best Enzyme

April 16, 2013
Where Do Organisms Get Their Energy?

April 10, 2013
Spontaneous Degradation of DNA

March 18, 2013
Estimating the Human Mutation Rate: Biochemical Method

"Reasons to Believe" in ENCODE

Fazale "Fuz" Rana is a biochemist at Reasons to Believe". He and his colleagues are Christian apologists who try to make their faith compatible with science. Fuz was very excited about the ENCODE results when they were first published [One of the Most Significant Days in the History of Biochemistry]. That's because Christians of his ilk were very unhappy about junk DNA and the ENCODE Consortium showed that all of our genome is functional.¹

Fuz is aware of the fact that some people are skeptical about the ENCODE results. He wrote a series of posts defending ENCODE.

1. Do ENCODE Skeptics Protest Too Much? Part 1 (of 3)
2. Do ENCODE Skeptics Protest Too Much? Part 2 (of 3)
3. Do ENCODE Skeptics Protest Too Much? Part 3 (of 3)

The first post is merely a list of the objections many of us raised.

One of the Most Significant Days in the History of Biochemistry

Reasons to Believe is "where science and faith converge." It's the organization founded by creationist Hugh Ross, a graduate of the University of Toronto. One of his leading minions is Fazale ("Fuz") Rana, a biochemist.

Fuz says that "September 5, 2012 marks one of the most significant days in the history of biochemistry."

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Marc Kirschner Defends Basic Science

Marc Kirschner is Chair of the Department of Systems Biology at Harvard Medical School. He's a very smart man and a well-respected scientist.¹ He has an editorial in the June 14th issue of Science: A Perverted View of “Impact” [see also: In search of big breakthroughs: why attempts to predict ‘significant’ research might backfire in The Boston Globe]

Kirschner says that the emphasis on "significance" and "impact" in making funding decisions is "misleading and dangerous." Nobody can really predict how fundamental research will affect the future. He writes ...

Monday's Molecule #206

Last week's molecule was myricyl palmitate, the major component of beeswax [Monday's Molecule #205]. The winner was Bill Chaney. There was no undergraduate winner.

Today's molecule is a very common molecule shown in a somewhat unusual conformation. (It's the conformation of the molecule when it's bound to a certain enzyme.) Identify the molecule (common name only). Can you describe the conformation?

Email your answers to me at: Monday's Molecule #206. I'll hold off posting your answers 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 email message.)

Laurence Hurst Discusses Junk DNA

Laurence Hurst is a Professor of Evolutionary Genetics in the Department of Biology and Biochemistry at The University of Bath (United Kingdom). He did his graduate studies under W.D. Hamilton at Oxford so it's safe to assume that he has adaptationist leanings.

Hurst wrote a comment in BMC Biology where he criticized the logic employed by those of us involved in the junk DNA debate [Open questions: A logic (or lack thereof) of genome organization]. Here's part of what Hurst says about logic ...

As a graduate student I was advised that if you don’t understand why an animal does what at first sight looks like behavior contrary to its best interests, then you should presume that it is you, not the animal, that is stupid. Look harder, the wisdom goes, and you will discover natural selection’s cunning logic.

That's bad advice, as Stephen Jay Gould and Richard Lewontin pointed out 35 years ago [The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme]. But, like many adaptationists, Hurst is willing to concede that this kind of reasoning may not apply at the molecular level.

While this may be good advice to those studying organismic behavior or anatomy, when we approach genomic anatomy and behavior it will not do.

Indeed, typically when thinking about genomes people often make the opposite presumption. Intergenic DNA was dismissed as irrelevant junk and many transcripts are presumed to be just so much noise. Synonymous mutations have been assumed to be neutrally evolving and where in a genome a gene sits is considered to be largely irrelevant. But are these assumptions more witness to a lack of understanding rather than robust statements about how genomes function and evolve? You are, after all, alive reading this, testament to the fact that your genome is doing something right.

So then, what features of our and other genomes are functionally relevant and which just so much noise? More importantly, when selection does act, why is it acting?

Hurst seems to be assuming that we know nothing about most of the genome and he makes the erroneous assumption that junk DNA advocates dismiss all intergenic DNA as junk. These are the hallmarks of someone who is uniformed about the debate over junk DNA. There is strong positive evidence for junk and those arguments need to be addressed (e.g. genetic load, C-Value Paradox). There is also strong evidence for functional intergenic sequences (origins, centromeres. telomeres, SARs, regulatory regions, etc.) and that evidence is part of the debate. None of the advocates of junk DNA claim that all intergenic DNA is junk.

We know that half of our genome is composed of bits and pieces of defective transposons. That's not ignorance. Broken genes are ... broken genes. They don't work. They are junk. We know enough about genes to recognize the difference between active functional transposons and those that carry lethal mutations of are missing large pieces of their coding region. It's logical to conclude that about half of our genome is junk based on those facts alone.

We know enough about transcription to know that spurious transcription and production of junk RNA transcripts are an inevitable consequence of the basic biochemistry of DNA binding proteins. That's not ignorance.

We know enough about nearly neutral mutations and molecular evolution to know the the existence of an approximate molecular clock means that most synonymous mutations and amino acid substitutions are fixed by random genetic drift. That's not due to a lack of understanding. Hurst has published evidence that some of these seemingly neutral mutations affect function but he ignores the evidence that most behave as if they were neutral.

The fact that you are alive does, indeed, mean that your genome is doing something right. It's good enough for survival of our species. It does not mean that all of your genome is functional.

To his credit, Hurst recognizes that the ENCODE scientists were wrong and that the null hypothesis is NOT natural selection.

The challenge is difficult. Assuming that sites involved in interactions are all functional isn’t good enough. By this, the logic employed by ENCODE, following a collision between a car and a pedestrian, a car’s bonnet would be ascribed the 'function' of projecting a pedestrian many meters and the pedestrian would have the 'function' of deforming the car’s bonnet. Similarly, we expect, for example, accidental transcription factor-DNA binding to go on at some rate, so assuming that transcription equals function is not good enough. The null hypothesis after all is that most transcription is spurious and alternative transcripts are a consequence of error-prone splicing. Conversely, assuming unbound sequence, such as nucleosome-free regions, to be lacking in function can mislead, as they can be critical for the proper control of gene expression.

I get the feeling that Hurst is uncomfortable with the idea that most of our genome is junk [see Hacking the Genome] but he's at least on the right track when he recognizes that there's still a legitimate scientific debate.

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Hat Tip: Dan Graur: Laurence Hurst’s Error: The Inability to Distinguish between a Stupid Animal, a Dead Animal, and the Elephant in the Room

Are You an Evolutionist?

Dan Graur has written a post on The Evolution of "Evolutionist". He points out that the term "evolutionist" and "evolutionism" used to refer to those who accept the fact of evolution and support evolutionary theory.

However, he also notes that ...

Since 2000, it is impossible to find the terms “"evolutionist" and "evolutionism" used by anyone except by creation apologists.... I would greatly like to know when exactly was the evolution of "evolutionist" completed and the term acquired its present negative connotation.

I prefer the term "evolutionary biologist" to describe scientists who are experts on evolution. For those non-experts who accept the basic principles of biology, chemistry, physics, geology etc. we don't need a term other than "rational." It's silly to describe them as "gravitationists" or "plate tectonicists" or "thermodynamicists."

Do you ever refer to yourself as an evolutionist?

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Get a Job! ... at NCSE

The National Center for Science Education (NCSE) is looking for a new executive director to replace Eugenie Scott [Help wanted: executive director].

It's gonna be tough filling those shoes.

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More Creationist Stupidity

PZ Myers has discovered an article published in Christian News. The title of the article is: Groundbreaking Genetic Discoveries Challenge Ape to Human Evolutionary Theory. Here's the opening paragraph ...

Fresh findings in the field of genetics have directly challenged yet another key evolutionary hypothesis by showing that the differences between humans and apes cannot be easily accounted for under the theory of evolution.

The paper they are referring to is Farré et al. (2013) and it shows the exact opposite of what the creationists claim. The paper demonstrates reduced recombination rates in those parts of the human and chimp chromosomes where genomic rearrangements have occurred. That's exactly what has been observed for the past 75 years. (See my post on balancer chromosomes, which describes artificial Drosophila chromosomes that were constructed to supress recombination.)

Read PZ's post on the subject to see just how stupid the creationists can be: Do the creationist shuffle and twist!.

I really don't get it. Why does the creationist movement publish material that is blatantly wrong? Even though I mock them repeatedly, I don't really think that every one of them is stupid. Where are the smart ones who review articles like the one published in Christian News? Will we see a retraction or an apology now that their error has been exposed by PZ and by some of the people who commented on the Christian News website?

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Farré, M., Micheletti, D., Ruiz-Herrera, A. (2012) Recombination Rates and Genomic Shuffling in Human and Chimpanzee--A New Twist in the Chromosomal Speciation Theory. Mol. Biol. Evol. 30:853-864.

Name this tree!

There are dozens of trees like this in Venice, California (USA) in the neighborhood where my grandchildren live. Can you name this tree (common name and species name)?

Can you come up with an adaptationist explanation for why this tree is so different from most other trees and bushes?

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RMS Queen Mary

RMS Queen Mary first sailed across the North Atlantic on May 27, 1936. At the time she was one of the largest ocean liners.

Now she lives in "retirement" as a tourist attraction in Long Beach, California (USA) where I took this photo yesterday.

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Naturopathic "Doctors" Graduate from Convocation Hall on the University of Toronto Campus

The Canadian College of Naturopathic Medicine is not affiliated with the University of Toronto but naturopath students do study anatomy in my building (Medical Sciences Building) on the downtown campus. The College rents Convocation Hall for their graduation ceremonies. The latest graduation ceremonies were on May 23, 2013 (see Graduation Day!.

In order to graduate, students at the Canadian College of Naturopathic Medicine need to pass courses in a number of areas. Here are two of the things they study ...

Asian Medicine/Acupuncture

Students learn about the philosophy and principles of Asian medicine: Yin and Yang theory, the meridians and channels system, the five-element theory and the symptoms and signs involving the 12 master meridians. Applying these principles in the context of patient assessment and treatment is emphasized, with acupuncture and therapeutic botanicals being the main approaches.

Homeopathic Medicine

The history, principles and philosophy of homeopathy are discussed in depth. Practical application of homeopathic principles in patient assessment and management is emphasized for acute and constitutional cases. Skills are developed in case analysis, repertorization, materia medica search, remedy differentiation and selection and prescribing the appropriate posology.

This is pseudoscience and quackery. The University of Toronto should not be lending its implicit stamp of approval to such nonsense.

I realize that the university rents out Convocation Hall for all kinds of events but most of them are so detached from the university that no one will mistake the event as an endorsement by the university. This is different. Convocation Hall is where the university's own graduation ceremonies take place (the name is a clue!). The average person will assume that the University of Toronto supports the Canadian College of Naturopathic Medicine and that our faculty has no problem with graduating quack "doctors."

This practice should stop.

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Mutation-Driven Evolution

Back in the late 1980's, I read Molecular Evolutionary Genetics by Masatoshi Nei. He introduced me to the concept that the history of life is driven by mutation and that the old-fashioned view of mutationism needs to be looked at more carefully. A decade later, Arlin Stoltzfus took up the cause and he has published a number of papers on the topic.

If you want to read more about mutationism then you can't find a better source than the series of posts by Arlin on Sandwalk from 2010. The last one, The Mutationism Myth VI: Back to the Future, contains links to all of the others. Be warned, it will be hard to resist the idea of mutationism after you read Arlin's explanation. It will hurt your brain.

I just learned that Masatoshi Nei is about to publish a new book called Mutation-Driven Evolution. Here's the description on Amazon ...
Theme

Mutation

The purpose of this book is to present a new mechanistic theory of mutation-driven evolution based on recent advances in genomics and evolutionary developmental biology. The theory asserts, perhaps somewhat controversially, that the driving force behind evolution is mutation, with natural selection being of only secondary importance. The word 'mutation' is used to describe any kind of change in DNA such as nucleotide substitution, gene duplication/deletion, chromosomal change, and genome duplication. A brief history of the principal evolutionary theories (Darwinism, mutationism, neo-Darwinism, and neo-mutationism) that preceded the theory of mutation-driven evolution is also presented in the context of the last 150 years of research. However, the core of the book is concerned with recent studies of genomics and the molecular basis of phenotypic evolution, and their relevance to mutation-driven evolution. In contrast to neo-Darwinism, mutation-driven evolution is capable of explaining real examples of evolution such as the evolution of olfactory receptors, sex-determination in animals, and the general scheme of hybrid sterility. In this sense the theory proposed is more realistic than its predecessors, and gives a more logical explanation of various evolutionary events.

Mutation-Driven Evolution is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of molecular evolution and population genetics. It assumes that the readers are acquainted with basic knowledge of genetics and molecular biology.

I can't wait to get my hands on a copy of this book. Look for a review in a few months.

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Freedom to Follow the Evidence without Philosophical Restrictions.

Let's look at a recent post on Evolutin News * Views (sic): From Discovering Intelligent Design: Opposition from the Scientific Establishment. As the title suggests, this is an excerpt from one of the books being heavily promoted by the IDiots.

They have a problem. How do the IDiots explain why 99.9% of biologists oppose Intelligent Design Creationism? It's because they all have a materialistic bias that prevents them from following the evidence wherever it may lead. Read this bit ...

ID challenges a reigning scientific paradigm. But as sociologist Steve Fuller says, ID is not anti-science, but rather anti-establishment. ID theorists want more scientific investigation, not less. They simply want the freedom to follow the evidence without harassment or philosophical restrictions.

An ID-based view of science promises to open new avenues of scientific investigation. Without materialist paradigms governing science, perhaps more scientists would have sought function for structures like "junk" DNA and vestigial organs, rather than assuming they were non-functional evolutionary relics.

Let me remind you that the presence of junk DNA in our genome was not anticipated by those who believed in the importance of natural selection. What happened was that the evidence became too substantive to ignore so scientists had to accept the presence of junk DNA in spite of the fact that most of them expected selection to eliminate it.

Now if you insist on believing in an intelligent design paradigm then you simply can't follow the evidence wherever it may lead because junk DNA isn't part of your worldview. In other words, the example used by the IDiots in this post is the exact opposite of the point they are making.

Oops!

Now you know why we call them IDiots.

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Teaching Biochemistry from a Canadian Perspective

I've always been a bit embarrassed to admit that my own department doesn't adopt my textbook in their introductory biochemistry courses. The honors course uses the 4th edition of Voet & Voet but it's only "recommended," not required. The large introductory course for non-specialists recommends several textbooks, including mine.

The arguments against having a required textbook have often focused on the idea that none of the current textbooks covers the material that's being taught—especially in the large course. Our large (1300 students) course tended to emphasize human physiology from a biochemical perspective. Many of the lectures in the metabolism section involved specific case studies.

"The Best Science Book Ever Written"

Some economist named George Gilder has read Darwin's Doubt, the latest IDiot book. Gilder says ...

I spend my life reading science books. I've read many hundreds of them over the years, and in my judgment Darwin's Doubt is the best science book ever written. It is a magnificent work, a true masterpiece that will be read for hundreds of years.

See David Klinghoffer gloat about this at: George Gilder: Darwin's Doubt Is "Best Science Book Ever Written," "Will Be Read for Hundreds of Years".

Are you still wondering why I call them IDiots?

UPDATE: George Gilder is one of the co-founders of the Discovery Institute and the author of the book (Stephen Meyer) works for the Discovery Institute. Just saying .. I'm sure the relationship has no bearing on Gilder's review and I'm sure it's completely above board for someone like George Gilder to be quoted in a blurb on the cover. If there was anything wrong then surely David Klinghoffer would have mentioned it in his blog post. (This is one of those cases where "IDiots" might be too kind.)

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My Visit to High School Biology Classes

Last Monday I went back to my old high school (Nepean High School in Ottawa, Canada) to visit with students in various biology classes. My host was Susanne Gerards who teaches grade 11 biology and grade 12 biology. She's also the lead author on the biology textbook [Biology 12] that the students use in the grade 12 courses.

I was "guest lecturer" in two grade 12 biology classes and one grade 11 biology class. The grade 12 students had just finished the sections on biochemistry and molecular genetics (information flow) so they were up on most things that I blog about. I was surprised at the amount of information they had just leaned—it's comparable to what we teach in our introductory biochemistry course except that there's less emphasis on structures and nothing on enzyme kinetics.

The students were wonderful. Many of them are going to take science courses in university. (They all had their university acceptances.) Only a few of them are interested in medicine.¹

The grade 11 students had finished their section on evolution. Most of them thought that evolution was driven by changes in the environment but they had at least been exposed to random genetic drift. It took a little prompting to that get that out of them. (I think Susanne was a bit embarrassed!). My impression was that the students understood quite a bit about evolution and this was a pleasant surprise.

One of the classes had just finished a discussion about junk DNA when a student raised it in class. He claimed that recent evidence proved that most of our genome has a function. I think the students were still a bit confused about genomes but at least they talked about it. (We didn't talk about it much when I was there.)

I'm pretty sure that the most important thing the students learned was that you actually get paid to be a graduate student! They were also surprised about the relatively high salaries that professors earn when they're hired. I'm hoping that some of them will pursue a career in science.

Susanne Gerards and I had an excellent lunch in Westboro where the restaurants and shops are quite a bit more upscale than they were in the 1960s when I lived there. We also had a lot of fun talking about science after class. With teachers like that I'm confident that Ontario high school students are getting a good science education.

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1. Hardly any of them were going to the University of Toronto in spite of the fact that it's the best university in Canada. I'm not sure why they were avoiding it. The most popular universities were Queen's, McGill, and Waterloo.

What Does the Bladderwort Genome Tell Us about Junk DNA?

The so-called "C-Value Paradox" was described over thirty years ago. Here's how Benjamin Lewin explained it in Genes II (1983).

The C value paradox takes its name from our inability to account for the content of the genome in terms of known function. One puzzling feature is the existence of huge variations in C values between species whose apparent complexity does not vary correspondingly. An extraordinary range of C values is found in amphibians where the smallest genomes are just below 10⁹bp while the largest are almost 10¹¹. It is hard to believe that this could reflect a 100-fold variation in the number of genes needed to specify different amphibians.

Since then we have dozens and dozens of examples of very similar looking species with vastly different genome sizes. These observations require an explanation and the best explanation by far is that most of the genomes of multicellular species is junk. In fact, it's the data on genome sizes that provide the best evidence for junk DNA.

How Do IDiots Define Evolution?

It's not difficult to find a proper definition of evolution. All you have to do is check your basic introductory textbooks on evolution. Google is not your friend in this case 'cause there's a lot of misinformation out there. If you're really interested in a scientific definition of evolution why not go right to the primary source?

Most textbooks use some version of the following for the minimal DEFINITION of evolution [see What IS Evolution?].

Evolution is a process that results in heritable changes in a population spread over many generations.

Now, we all know that Intelligent Design Creationists are keen on real science. They certainly don't want to mislead their flock. Let's see how they define evolution in the latest book they are promoting [From Discovering Intelligent Design: Define Your Terms].

A Concept-Driven Graduate Education

Like most graduate departments, we are constantly evaluating and modifying our graduate program but rarely do we step back and look at the big picture. What are we trying to accomplish?

Graduate education, like undergraduate education, has been subjected to serious study over the past few decades. Guttlerner and Van Vactor (2013) have just published a brief review in Cell that summarizes the goals and how they are trying to achieve them at Havard.

The authors begin by pointing out the importance of a concept-driven curriculum.

The modernization of science education requires a shift from a content-driven curriculum to an interdisciplinary, concept-driven curriculum (Association of American Medical Colleges and Howard Hughes Medical Institute, 2009; American Association for the Advancement of Science, 2009; National Research Council, 2003, 2009). Such a curriculum organizes information around unifying concepts and frees educators from the insurmountable task of presenting the complete breadth of an ever-expanding scientific knowledge base (D’Avanzo, 2008). Concept-driven education is increasingly seen as fundamental for contemporary research scientists and physicians (Association of American Medical Colleges and Howard Hughes Medical Institute, 2009).

Inside Higher Ed Weighs in on the Ball State Academic Freedom Controversy

This is getting more and more interesting. Now there's an article in Inside Higher Ed discussing the controversy over whether Eric Hedin of Ball State University should be teaching a science course that emphasizes Intelligent Design Creationism. [see Science or Religion?]

The article discusses the difference of opinion between Jerry Coyne, on the one hand, and PZ Myers and me, on the other. It's very interesting to read the comments. Jerry Coyne has posted on the Inside Higher Ed article at: Ball State agrees to investigate science course infected with Christianity. His readers have lots to say on the issue of academic freedom.

Let's be clear about one thing. I'm not an American so I'm not terribly concerned about the American Constitution. If Eric Hedin were teaching in Canada, the legal issue would never come up. The part of this that I don't like is outsiders threatening departmental chairs to get them to take action against one of their faculty members. Four Creationists have tried to get the administration of my university to shut down Sandwalk and in all cases my university simply filed the letters in the waste basket.¹ I ban people from Sandwalk if I ever hear of them trying to intimidate someone by complaining to their employer. That's unacceptable behavior in my book.

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1. After sending me a copy.

Earthquake!

Epicentre near Ottawa. Two quakes: 5.2 magnitude at 9:43 am and a 4.1 magnitude aftershock 10 minutes later. I didn't feel either of them. Earthquakes like this happen about 30,000 time a year. We feel one of them every few years in this part of Canada. They are mostly harmless, but exciting.

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[Photo credit: CBC News]

On Teaching Genetics Using Students' and Parents' ABO Blood Types

There are some schools that think it's cool to show examples of simple Mendelian inheritance by collecting and analyzing the blood types of their students and their parents. What could possibly go wrong?

Let me tell you why this is a bad idea. It's true that 99% of the time the blood type of a student is going to be consistent with that of their presumed biological parents. But what if it's not? That could mean that a child is adopted and the child may not know or not want that information to be public. It could also mean that the child's biological father (or mother) is not the same person they call "Mommy" or "Daddy." Is the trauma associated with that discovery worth the benefits of the experiment?

I have a blog post on The Genetics of ABO Blood Types. It's quite popular and every few weeks I get a letter from a distraught parent who has just discovered that the blood type of their children doesn't match the blood type of the parents. Here's the latest example (posted with permission) ...

Dear Professor Moran: I hope you don't mind my writing to you, but I just came across your blog, Sandwalk after doing some research about blood types and wondered if you might have an opinion....

My daughter, in 7th grade is working on a blood type project at school and came home quite upset yesterday after telling the teacher that she was type A+ and both her Dad and I are O+. The teacher (whom I have not yet dragged over hot, burning coals....) told her that that was impossible - that she would either have to have been adopted or have a genetic defect.... It got me thinking that perhaps I had made a mistake somewhere along the way and we spent some time last night digging through info to try to figure it out. I checked with our doctors this morning and our daughter's pediatrician and all blood types have been confirmed. Both my husband and I are O+ and our daughter is A+ She is definitely not adopted and unless she was switched at birth, then there is no doubt as to parentage -- should I be concerned? I do recall that when she was born she had mild jaundice which one doc explained was due to blood type incompatibility.

If high school teachers aren't knowledgeable enough to handle these situations then they should avoid these "experiments."

These "anomalies" are quite frequent and they have simple explanations once you know the real genotype. For example, one parent could be heterozygous for two different O alleles. One with a mutation near the beginning of the gene and the other with a mutation near the end of the gene. Any germ cell recombination event between the two alleles could generate an A allele or a B allele depending on the origin of the O allele.

I think it's also possible for one of the parents to actually be AO or BO but the functional allele is expressed at a very low level giving an O-type phenotype. The A or B allele could, by chance, be much more active in the child. There could be epistatic effects such that splicing or transcription is defective in the parent but compensated for by enhanced activity in the child due to unlinked mutations. (These are known as "suppressors" in bacterial genetics.)

There are many other possibilities. They're rare but it's certain that they will show up in some school class somewhere. It's usually not a good idea to investigate the personal genomics of students because of these problems.

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Jerry Coyne Is at it Again!

Jerry Coyne has discovered that some obscure Professor in some American college is teaching from a Christian viewpoint in his class on "The Boundaries of Science." Jerry thinks that he can stop this Professor from teaching things that he (Coyne) disagrees with by threatening the university with a lawsuit. PZ Myers and I disagreed, pointing out that academic freedom in the universities is an important principle that should not be ignored [see Is It Illegal to Teach Intelligent Design Creationism in American Universities?].

Jerry stands by his position: The Freedom from Religion Foundation to Ball State University: cease and desist your religious indoctrination. Nobody is arguing that Professors shouldn't be criticized for bad teaching and nobody is arguing that the instructor's colleagues and department can't reassign courses to keep a bad teacher away from students. That's not the situation here. The Chair of the department is aware of the situation and doesn't object.

It's dangerous for outsiders to start dictating what a Professor can and can't teach and it's especially dangerous to use legal threats to enforce your own perspective on another university. I strongly disagree with the letter that the Freedom from Religion Foundation sent to the President of Ball State University [see Coyne's blog website]. If this were my university I would expect it to fight such a demand with all the resources at their disposal and I'm certain that my union and the Canadian Association of University Teachers (CAUT) would support my university. So would I.

CAUT actively defends academic freedom as the the right to teach, learn, study and publish free of orthodoxy or threat of reprisal and discrimination. Academic freedom includes the right to criticize the university and the right to participate in its governance. Tenure provides a foundation for academic freedom by ensuring that academic staff cannot be dismissed without just cause and rigorous due process.

I have defended the academic freedom of racists and holocaust deniers in the past. I've even defended the right of an extreme free-market capitalist to indoctrinate business students. In the name of academic freedom, I will even tolerate adaptationists who teach evolution incorrectly.

The purpose of academic freedom is to protect the rights of those who disagree with the majority. Those rights must be protected for everyone, including those who you think are wrong. Otherwise it's not academic freedom.

I teach a course where I promote an atheist view of evolution and the idea that science and religion are incompatible. If the Freedom from Religion Foundation ever wrote a letter to my President demanding that I cease and desist they would be be ignored except, perhaps, for a few laughs over coffee.

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Michael Denton on Junk DNA

I was reading the latest spiel from Sal Cordova (scordova) when I noticed a reference to Michael Denton. Cordova was ranting about how Taxonomic nested hierarchies don’t support Darwinism and he began with ...

Taxonomic nested hierarchies don’t support Darwinism or common descent, actually the opposite. Michael Denton convincingly argued that nested hierarchies can be used to argue against macro evolution. If the fish are always fish, then they will never be birds, reptiles, apes, or humans.

I knew that this was a misrepresentation of Denton's views since he (Denton) supports the idea that nested hierarchies represent the true history of common descent.

Michael Denton thinks that evolution was directed and that explains why fish and mammals are so different even though they contain a common ancestor. He accepts common descent but rejects spontaneous mutation and mechanistic fixation of alleles as the explanation. I checked his latest book Nature's Destiny (1998) to confirm that I was right.

Denton supports a teleological view where God created conditions (first cause) that would lead to humans (final cause) but that the process included evolution from common ancestors. In Denton's case the "design" was inherent in the laws of physics and chemistry and the rules of mutation and gene expression.

While refreshing my memory, I came across this paragraph that I had highlighted in his book fifteen years ago.

If it is true that a vast amount of the DNA in higher organisms is in fact junk, then this would indeed pose a very serious challenge to the idea of directed evolution or any teleological model of evolution. Junk DNA and directed evolution are in the end incompatible concepts. Only if the junk DNA contained information specifying for future evolutionary events, when it would not in a strict sense be junk in any case, could the finding be reconciled with a teleological model of evolution. Indeed, if it were true that the genomes of higher organisms contained vast quantities of junk, then the whole argument of this book would collapse. Teleology would be entirely discredited. On any teleological model of evolution, most, perhaps all, the DNA in a genome of higher organisms should have some function. (pp. 289-290

I wonder what Intelligent Design Creationists think of this argument?

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The Positive Values of a Roman Catholic Education?

The Ontario government funds Roman Catholic Schools but not schools of any other religion. I've just returned from a high school reunion at one of the "public" schools (nonreligious) so I've been thinking about the education I received in an environment that was free of religious indoctrination.

My friends all seem to be pretty moral and they seem to be at least as good at practicing the Golden Rule as any other citizens. When we were students we organized contributions to charity and helped the needy. We made lifelong friends in the public schools.

Most of my high school friends are pretty secular in their outlook and a large percentage are nonbelievers. The percentages aren't much different among my friends who went to Roman Catholic schools.

Here's a bit of propaganda from one who supports government funding of Roman Catholic schools. They need all the support they can get because Roman Catholic values are coming under heavy criticism lately. Roman Catholic students have been bussed to anti-abortion protests and school clubs for gays and lesbians have been banned in the Roman Catholic schools system. "Sex education" is a joke.

What do you think? Does this make you want to continue sending your tax dollars to the Roman Catholic schools?

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Scientific Authority and the Role of Small RNAs

A few weeks ago I criticized Philip Ball for an article he published in Nature: DNA: Nature Celebrates Ignorance. Phil has responded to my comments and he has given me permission to quote from his response. I think this is going to stimulate discussion on some very interesting topics.

The role of small RNAs is one of those topics. There are four types of RNA inside cells: tRNA, ribosomal RNA (rRNA), messenger RNA (mRNA), and a broad category that I call “small RNAs.”

The small RNAs include those required for splicing and those involved in catalyzing specific reactions. Many of them play a role in regulating genes expression. These roles have been known for at least three decades so there haven’t been any conceptual advances in the big picture for at least that long.

What’s new is an emphasis on the abundance and importance of small regulatory RNAs. Some workers believe that the human genomes contains thousands of genes for small RNAs that play an important role in regulating gene expression. That’s a main theme for those interpreting the ENCODE results. Several prominent scientists have written extensively about the importance of this “new information” on the abundance of small RNAs and how it assigns function to most of our genome.

High School Reunion

We attended the Nepean High School 90th Anniversary Celebration in Ottawa (Ontario, Canada) on the weekend. It was wonderful to see old friends, especially those I hadn't seen in almost five decades. (I graduated 49 years ago.)

Here are some friends that I have seen more recently but it was good to get together anyway. Brian (standing) is an old friend—we first met sixty years ago. Chuck (sitting) and his wife Helen (beside him) have been friends since high school. Chuck was best man at my wedding and Brian was also in the bridal party.

Two other members of my bridal party are also high schools friends. Leslie (front) was the bride and Karen (trying to hide on the left) was a bridesmaid.

Ms. Sandwalk has posted a photo of herself as a high school student and cheerleader. One of the other cheerleaders was at the reunion but nobody could convince them to do a cheer.

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[Photo Credit: Sharon took the photo.]

Monday's Molecule #205

Last week's molecule was the lipoamide swinging arm of pyruvate dehydrogenase [Monday's Molecule #204]. The winners were Alex Ling and Michael Florea.

Today's molecule is a major component of something you are all familiar with. Identify the molecule (common name only) and where it's most likely to be found. (Hint: not in humans.)

Email your answers to me at: Monday's Molecule #205. I'll hold off posting your answers 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 email message.)

Almaleea subumbellata

Jerry Coyne says he will post a picture of a plant if he can find a cute one [A vertebrate]. I decided to help him out by pointing you to the latest Botany Photo of the Day.

This is Almaleea subumbellata, or wiry bushpea, from Tasmania, Australia. You can read all about it at the UBC Botanical Garden website. They have a high resolution photo.

Prettier than cats and they don't pee on your rug or scratch your furniture.

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Andyjones Replies

Andyjones has responded to my post on failing to educate him about science. His response is: Failure to Educate? Failure to Persuade. I'm reposting his entire response ....

Larry Moran replied to my latest post with an admission of failure. He thinks he has failed to educate, but I think rather he is confusing the word ‘persuade’ with the word ‘educate’.

He thinks I am rationalising junk DNA with a pile of ‘what-ifs’. But the fact is that most of my ‘what-ifs’ are already known to have some basis in reality. I am not denying any obvious reality. Indeed, the basic machinery of life looks like design, far more than when Paley was around. Yes, there could also be a great deal of junk. That’s why I have said a number of times that ID is not committed to the idea that there is no junk.

Yet, from my point of view, I see a whole pile of Darwinian/post-Darwinian materialists who have only partly explored the genome, working from an assumption that the genome was not designed, and thus are jumping the gun on the evidence. For example, Larry still seems to think that pseudogenes are of themselves ‘solid evidence’ of broken genes despite the fact that we know that at least some pseudogenes influence the rate of translation of real genes by competing with them; a simple design reason why there should be ‘false genes’ = pseudogenes. Who has explored the rest of them?

From his emotive response to my perfectly valid, albeit speculative suggestions (though they were not plucked out of the air either), I don’t trust this guy to think clearly and calmly about the possibility of design. That’s the real problem.

This is all very frustrating. Why do IDiots who have no serious training in biochemistry and molecular biology think they know more than the experts?

And why do they refuse to learn when we attempt to educate them?

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An Example of IDiot "Civility"

Do you remember when Stephen A. Batzer listed several reason why "Darwinists" are so uncivil? [Why Darwinism and Incivility Seem to Go Together] I blogged about it at: Why Are "Darwinists" So Uncivil?. We all had a good chuckle about hypocrisy and stupidity.

You've also seen many IDiots defend their use of "Darwinism" by claiming that it's nothing more than an accurate description of the most important scientific prerspective on evolution.

Here's what David Klinghoffer wrote today in Scientific Anti-Humanism Is Being Refuted by Science Itself.

Scientific anti-humanism refers to the cheapening of human dignity and of the value of human life in the name of science. Among many other pieces of novel information on that theme, the most important point that came out of Michael Medved's discussion with John West just now on the Science and Culture Update is that this corrosive tendency is being refuted by science itself.

Darwin persuasively taught that life is the product of blind, meaningless, purposeless churning, making all life, not just human, hardly anything more special or dignified than cosmic refuse. Indeed in a Darwinian worldview, life is cosmic refuse. While accused abortion butcher Kermit Gosnell may be an outlier, he is an emblematic personality in our Darwin-tutored culture.

How civil of him to link Darwinism with Kermit Gosnell.

Remember, this is Evolution News & Views (sic), sponsored by the Discovery Institute. This is not some backwoods hack operating on his own. It's mainstream civility for the leading Intelligent Design Creationists.

UPDATE Klinghoffer posted the following a short time later in Darwinism Versus Reality: The Painful Divorce. It's just another example of how the IDiots link "Darwinism" with immorality and it puts the lie to the claim that "Darwinism" is just another word for "evolutionary biology."

I wanted to highlight what Josh Youngkin said yesterday in his very perceptive comments about the Jodi Arias verdict. Darwinian materialists like Jerry Coyne end up asserting there's no free will, therefore no such thing as moral responsibility. A murderer may be locked up for everyone else's safety, but not because we're correct to seek to impose retribution. We have no moral right to do so.

As Josh says, this casts the human being who murders as a fundamentally blameless animal, like a man-eating tiger. We would cage or even shoot such a tiger, but we could not blame it for acting as it does.

Profoundly, I thought, Josh's article suggests how remote from human experience a guy like Coyne must travel if he wants to carry his Darwinian materialism to its seemingly logical conclusions.

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Religious Affiliation in Canada

The results of the 2011 Canadian census are beginning to appear. Indi at Canadian Atheist has prepared a nifty pie chart showing that 63.7% of the population identifies themselves as Christians [2011 National Household Survey religion results].

In second place, at 23.9%, are those who say they have no religion. We know that many of the "nones" will not call themselves "atheists" but they might as well be.

The take-home lesson is that almost 24% of Canadians are not religious. That's up from 16.5% in 2001. Times they are a -changin.

The question on the census was ...

22. What is this person’s religion?

Indicate a specific denomination or religion even if this person is
not currently a practising member of that group.

For example, Roman Catholic, Ukrainian Catholic, United Church,
Anglican, Lutheran, Baptist, Greek Orthodox, Jewish, Islam, Buddhist,
Hindu, Sikh, etc.

Specify one denomination or religion only __________

No religion __________

I think you can see why nonbelievers may be somewhat higher than the numbers indicate.

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On My Failure to Educate an Intelligent Design Creationist

A few weeks ago I decided to give Intelligent Design Creationist andyjones the benefit of the doubt and assumed that he really wanted to understand enough biology to have a credible opinion about genomes and junk DNA. I published a series of posts on Educating an Intelligent Design Creationist: Introduction.

Andyjones has replied to my post with: Getting me an Education.

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My first post was: Educating an Intelligent Design Creationist: Pervasive Transcription. I refuted the misconception that nobody ever investigated pervasive transcription and I explained that we know a great deal about the parts of the genome that are being transcribed, and why they are transcribed. I did not claim that this was solid evidence for junk DNA. That wasn't the point. The point was to teach andyjones that there are explanations for pervasive transcription—we don't call it junk just because we have no idea what's going on.

I also pointed out that using pervasive transcription as an argument for function (i.e. against junk) doesn't really cut it unless you don't understand basic biochemistry. Here's how andyjones responded ...

Larry thinks this (especially the situation from the 80s on) amounts to solid evidence for junk DNA, but I honestly don’t see how it does.

Okay. So my attempt to explain the reality of the situation failed miserably.

IDiots Make a Falsifiable Prediction

The Intelligent Design Creationists, otherwise known as IDiots, are getting desperate. They have been relentlessly promoting Stephen Meyer's upcoming book Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design but so far they have pretty much failed to trick evolutionary biologists into trashing the book before it's published.¹ That must be a major disappointment to them.

The baiting continues with an article by David Klinghoffer on the Evolution News & Views (sic) site: What Darwin's Enforcers Will Say About Darwin's Doubt: A Prediction. Here's what he predicts ....

Among possible lines of attack against Stephen Meyer's forthcoming book, Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design, I foresee some critics trying to argue that it's not fair game for Dr. Meyer to invite the general reading public to consider what's going on in peer-reviewed technical literature pertaining to evolution.

After all, biologists should have the opportunity to air their views in a semi-private professional setting without "creationists" barging in and telling the unwashed masses that many scientists have already given up on the Darwinian paradigm and are seeking post-Darwinian alternatives. Even though it's true, still it's wrong to publicize the fact, thereby leading the common folk astray and confirming their prejudice in favor of seeing life and the universe as reflecting some purpose.

This time I will rise to the bait if only for the purpose of preserving this prediction so we can revisit it in the future.

I'd also like to note, for the record, that the IDiots have published a number of books in the past and I don't recall anyone making the argument that Klinghoffer predicts. Can anyone out there point me to an article where scientists criticized the IDiots for pulicizing controversy within the evolutionary biology literature? It would be quite hypocritical for most bloggers to do so since criticizing the scientific literature is what we do.

Is it just my imagination or have evolutionary biologists also published books where they "expose" the controversies within evolution. If scientists do it routinely then why in the world would they criticize an IDiot for doing it? That doesn't make any sense, does it? (Oops, I inadvertently made the false assumption that IDiots are supposed to be rational.)

Finally, Udo Schüklenk alerted me to this creationist article because he is mentioned. Klinghoffer refers to a discussion about the ethics of infanticide and he thinks that his creationist² buddy Wesley Smith is being attacked for exposing a debate within the bioethics community. You should read the papers he links to along with Udo Schüklenk's paper [In defence of academic freedom: bioethics journals under siege] if you want to catch up on that discussion. As usual, the IDiots get it all wrong. Are you surprised?

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1. That's mostly because we don't care. We are not anticipating anything we haven't heard many times before although, I suppose, we could be surprised.

2. Smith is a lawyer and a Senior Fellow at the Discovery Institute. I don't know what kind of creationist he is.

Monday's Molecule #204

The last Monday's Molecule was α-linolenate [Monday's Molecule #203]. It is an omega-3 essential fatty acid. The winner was Anders Ehrnberg.

Today's molecule is actually three different molecules (1,2 and 3). Give the common names for the terminal part of each molecule—the names used in most textbooks. Identify E₂ (enzyme name) and briefly explain what's going on.

Email your answers to me at: Monday's Molecule #204. I'll hold off posting your answers 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 email message.)

Atheism, Skepticism, and Canada's Centre for Inquiry

The Centre for Inquiry logo (above) is from the CFI Canada Facebook page. It's an amazing piece of work because it embodies one of the key features of CFI as an umbrella organization that brings together a number of different groups to unite around common goals.

This is a lot harder than you might think. I think of myself as a skeptic and an atheist but I am not a Humanist. If an organization like CFI were to be taken over by Humanists, I could not be a member. Other people are worried that CFI might be dominated by atheists and an atheist agenda. Some of them have left the organization because they think of themselves as skeptics who are not anti-religion.

Lately the conflict between (some) skeptics and atheists has claimed another victim. PZ Myers is so upset with the narrow view of skepticism promoted by Jamy Ian Swiss [see Skeptics have the amazing superpower of being simultaneously fierce and timid] that he now declares, "I officially divorce myself from the skeptic movement."

What's the problem? It's that some skeptic movements want to concentrate on pseduoscience and pseudomedicine and leave religion alone. They are atheists and accommodationists. Not content with just ignoring vocal atheists, they criticize their tactics as being offensive and inimical to the important skeptical causes. I don't agree with that version of skepticism and neither does PZ Myers. However, unlike PZ, I think the solution is to make it clear that people like Jamy Ian Swiss are wrong to exclude atheism from the skeptical movement.

If the skeptical movement becomes officially accommodationist and anti-atheist then I will have to abandon it just like PZ Myers did.

The advantage of CFI is that it can "accommodate" all these points of view, if we are careful. It can promote an "Extraordinary Claims" campaign that links skepticism about religion and skepticism about pseudoscience and quackery. It can launch a campaign against religion in the schools without antagonizing believers. It can promote charitable causes that bring together freethinkers, humanists, and atheists. It can sponsor Humanist officiants who can preside at weddings and funerals. It can do much to promote what all those groups have in common. All we have to do is tolerate the occasional cause that we might not completely agree with.

It's a bit ironic that PZ Myers is offended by the direction that skepticism is taking yet seems blind to the re-branding of "freethought" that he supports. I'm hoping that in Canada we can avoid the competing conferences that pit freethoughters against skeptics and atheists against humanists. So far, we seem to be on the right track with the Committee for Advancement of Scientific Skepticism (CASS) and CFI events celebrating Dawkins & Krauss and "The Unbelievers" as well as Eschaton 2012, and the upcoming Imagine No Religion.

UPDATE: Jack Scanlan of Young Australian Skeptics says, "A person can be a skeptic and believe in a god." [PZ’s Problem: Does Skepticism Makes An Exemption For Religion?]. I disagree.

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