Monday, September 30, 2013

The Problems With The Selfish Gene

Lots of people fail to understand that the "selfish gene" is a metaphor. They criticize Richard Dawkins for promoting the idea that genes can actually take on the characteristics of selfishness.

Andrew Brown and Mary Midgley are prominent examples of people with this kind of misunderstanding and Jerry Coyne has set them straight in Poor Richard’s Almanac: Andrew Brown and the Pope go after The Selfish Gene and “Selection pressures” are metaphors. So are the “laws of physics.”

However, there are two other problem with the metaphor. The first is rather trivial, it refers to the fact that it's actually alleles, or variants, of a gene that are "selfish." Dawkins knows this. He explains it in his book but I don't think he puts enough emphasis on the concept and in most parts of the book he uses "gene" when he should be saying "allele." I grant that The Selfish Allele is not a catchy title.

Monday's Molecule #217

Last week's molecule was the 5′ cap structure on eukaryotic mRNA. Lot's of people got it right. The winners were Mark Sturtevant and Jacob Toth [Monday's Molecule #216].

As you know, the general public is very gullible. Millions of people have been duped into taking various supplements on the grounds that these supplements will improve their health and/or correct for a deficiency in their diet. These people will freely donate millions of dollars to the quacks who prey on their stupidity. Today's molecule is one of these supplements. Give the common name and the specific name that identifies this particular variant.

Email your answers to me at: Monday's Molecule #217. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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.)

Friday, September 27, 2013

Dark Matter Is Real, Not Just Noise or Junk

UPDATE: The title is facetious. I don't believe for one second that most so-called "dark matter" has a function. In fact, there's no such thing as "dark matter." Most of our genome is junk. I mention this because one of the well-known junk DNA kooks is severely irony-impaired and thought that I had changed my mind.
A few hours ago I asked you to evaluate the conclusion of a paper by Venters and Pugh (2013) [Transcription Initiation Sites: Do You Think This Is Reasonable?].

Now I want you to look at the Press Release and tell me what you think [see Scientists Discover the Origins of Genomic "Dark Matter"].

It seems pretty clear to me that Pugh (and probably Venters) actually think they are on to something. Here's part of the press release quoting Franklin "Frank" Pugh, a Professor in the Department of Molecular Biology at Penn State.
The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.

"These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverage -- making up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.' Of course, the next step is to answer the question, 'what, in fact, do they do?'"

Pugh added that the implications of this research could represent one step towards solving the problem of "missing heritability" -- a concept that describes how most traits, including many diseases, cannot be accounted for by individual genes and seem to have their origins in regions of the genome that do not code for proteins. "It is difficult to pin down the source of a disease when the mutation maps to a region of the genome with no known function," Pugh said. "However, if such regions produce RNA then we are one step closer to understanding that disease."
I'm puzzled by such statements. It's been one year since the ENCODE publicity fiasco and there have been all kinds of blogs and published papers pointing out the importance of junk DNA and the distinct possibility that most pervasive transcription is, in fact, noise.

It's possible that Pugh and his postdoc are not aware of the controversy. That would be shocking. It's also possible that they are aware of the controversy but decided to ignore it and not reference any of the papers that discuss alternate explanations of their data. That would be even more shocking (and unethical).

Are there any other possibilities that you can think of?

And while we're at it. What excuse can you imagine that lets the editors of Nature off the hook?

P.S. The IDiots at Evolution News & Views (sic) just love this stuff: As We Keep Saying, There's Treasure in "Junk DNA".

Venters, B.J. and Pugh, B.F. (2013) Genomic organization of human transcription initiation complexes. Nature Published online 18 September 2013 [doi: 10.1038/nature12535] [PubMed] [Nature]

The Extraordinary Human Epigenome

We learned a lot about genes and gene expression in the second half of the 20th century. We learned that genes are transcribed and we have a pretty good understanding of how transcription initiation complexes are formed and how transcription works.

We learned how transcription is regulated through promoter strength, activators, and repressors. Activators and repressors bind to DNA and those binding sites can lie at some distance from the promoter leading to formation of loops of DNA that bring the regulatory proteins into contact with the transcription complex. Much of our basic understanding of this process was derived from detailed studies of bacteriophage and bacterial genes.


Later on we learned that eukaryotic genes expression was very similar and regulation also required repressors and activators. We discovered that gene expression was associated with chromatin remodeling that opened up regions of the chromosome that were tightly bound to histones in 30nm or higher order structures.

Building on studies in prokaryotes, we learned about temporal gene regulation and differentiation. Much of the work was done in model organisms like Drosophila, yeast, C. elegans, and various mammalian cells in culture.

By the end of the century I was pretty confident that what I wrote in my textbook was a fair representation of the fundamental concepts in gene expression and regulation.

Turns out I was wrong as I just discovered this morning when I read the opening paragraph of a review by Rivera and Ren (2013). Here's what they say ...
More than a decade has passed since the human genome was completely sequenced, but how genomic information directs spatial- and temporal-specific gene expression programs remains to be elucidated (Lander, 2011). The answer to this question is not only essential for understanding the mechanisms of human development, but also key to studying the phenotypic variations among human populations and the etiology of many human diseases. However, a major challenge remains: each of the more than 200 different cell types in the human body contains an identical copy of the genome but expresses a distinct set of genes. How does a genome guide a limited set of genes to be expressed at different levels in distinct cell types?
Wow! The textbooks need to be rewritten! We didn't learn anything in the last century!

It took me the whole first paragraph of this paper to realize that the rest of it was probably going to be worthless unless you were interested in technical details about the field. That's because I'm not as smart as Dan Graur. He only read the title, "Mapping Human Epigenomes" and the abstract before concluding that the authors were speaking in newspeak1 [A “Leading Edge Review” Reminds Me of Orwell (and #ENCODE)].

The Rivera and Ren paper is a "Leading Edge" review in the prestigious journal Cell. It covers all the techniques used to study methylation, histone modification and binding, transcription factor binding, and nucleosome positioning at the genome level. According to the authors, people like me were fooled by studies on individual genes, purified factors, and in vitro binding assays. That didn't really tell us what was going on.

Apparently, the most effective way of learning about the regulation of gene expression in humans is to analyze the entire genome all at once and read off the data from microarrays and computer monitors. (After shoving it through a bunch of code.)
Overwhelming evidence now indicates that the epigenome serves to instruct the unique gene expression program in each cell type together with its genome. The word "epigenetics," coined half a century ago by combining "epigenesis" and "genetics," describes the mechanisms of cell fate commitment and lineage specification during animal development (Holliday, 1990; Waddington, 1959). Today, the "epigenome" is generally used to describe the global, comprehensive view of sequence-independent processes that modulate gene expression patterns in a cell and has been liberally applied in reference to the collection of DNA methylation state and covalent modification of histone proteins along the genome (Bernstein et al., 2007; Bonasio et al., 2010). The epigenome can differ from cell type to cell type, and in each cell it regulates gene expression in a number of ways—by organizing the nuclear architecture of the chromosomes, restricting or facilitating transcription factor access to DNA, and preserving a memory of past transcriptional activities. Thus, the epigenome represents a second dimension of the genomic sequence and is pivotal for maintaining cell-typespecific gene expression patterns.

Not long ago, there were many points of trepidation about the value and utility of mapping epigenomes in human cells (Madhani et al., 2008). At the time, it was suggested that histone modifications simply reflect activities of transcription factors (TFs), so cataloging their patterns would offer little new information. However, some investigators believed in the value of epigenome maps and advocated for concerted efforts to produce such resources (Feinberg, 2007; Henikoff et al., 2008; Jones and Martienssen, 2005). The last five years have shown that epigenome maps can greatly facilitate the identification of potential functional sequences and thereby annotation of the human genome. Now, we appreciate the utility of epigenomic maps in the delineation of thousands of lincRNA genes and hundreds of thousands of cis-regulatory elements (ENCODE Project Consortium et al., 2012; Ernst et al., 2011; Guttman et al., 2009; Heintzman et al., 2009; Xie et al., 2013b; Zhu et al., 2013), all of which were obtained without prior knowledge of cell-type-specific master transcriptional regulators. Interestingly, bioinformatic analysis of tissue-specific cis-regulatory elements has actually uncovered novel TFs regulating specific cellular states.
So, what are all these new discoveries that now elucidate what was previously unknown; namely, "how genomic information directs spatial- and temporal-specific gene expression programs"?

This is a very long review full of technical details so let's skip right to the conclusions.
Six decades ago, Watson and Crick put forward a model of DNA double helix structure to elucidate how genetic information is faithfully copied and propagated during cell division (Watson and Crick, 1953). Several years later, Crick famously proposed the "central dogma" to describe how information in the DNA sequence is relayed to other biomolecules such as RNA and proteins to sustain a cell’s biological activities (Crick, 1970). Now, with the human genome completely mapped, we face the daunting
task to decipher the information contained in this genetic blueprint. Twelve years ago, when the human genome was first sequenced, only 1.5% of the genome could be annotated as protein coding, whereas the rest of the genome was thought to be mostly "junk" (Lander et al., 2001; Venter et al., 2001). Now, with the help of many epigenome maps, nearly half of the genome is predicted to carry specific biochemical activities and potential regulatory functions (ENCODE Project Consortium, et al., 2012). It is conceivable that in the near future the human genome will be completely annotated, with the catalog of transcription units and their transcriptional regulatory sequences fully mapped.
I hope they hurry up. Not only do I have to re-write my description of the Central Dogma2 but I'm going to have to re-write everything I thought I knew about regulation of gene expression and the organization of information in the human genome. That's going to take time so I hope the epigeneticists will publish lots more whole genome studies in the near future so I can understand the new model of gene expression.

Keep in mind that this paper was published in Cell where it was rigorously reviewed by the leading experts in the field. It must be right.

[Image Credit: Moran, L.A., Horton, H.R., Scrimgeour, K.G., and Perry, M.D. (2012) Principles of Biochemistry 5th ed., Pearson Education Inc. page 647 [Pearson: Principles of Biochemistry 5/E] © 2012 Pearson Education Inc.]

1. Newspeak was first described in 1984 proving, once again, that George Orwell (Eric Arthur Blair) was a really smart and prescient guy. For another example see: What Is "Science" According to George Orwell?.

2. Apparently I didn't read the Crick (1970) paper as carefully as they did.

Rivera, C.M. and Ren, B. (2013) Mapping Human Epigenomes. Cell 155:39-55 [doi: 10.1016/j.cell.2013.09.011]

Transcription Initiation Sites: Do You Think This Is Reasonable?

I'm interested in how scientists read the scientific literature and in how they distinguish good science from bad science. I know that when I read a paper I usually make a pretty quick judgement based on my knowledge of the field and my model of how things work. In other words, I look at the conclusions first to see whether they conflict with or agree with my model.

Many of my colleagues do it differently. They focus on the actual experiments and reach a conclusion based on how the perceive the data. If the experiments look good and the data seems reliable then they tentatively accept the conclusions even if they conflict with the model they have in their mind. They are much more likely to revamp their model than I am.

I'm about to give you the conclusions from a recently published paper in Nature. I'd like to hear from all graduate students, postdocs, and scientists on how you react to those conclusions. Do you think the conclusions are reasonable (as long as the experiments are valid) or do you think that the conclusions are unreasonable, indicating that there has to be something wrong somewhere?

The paper is Venters and Pugh (2013). It's title is Genomic organization of human transcription complexes. You don't need to read the paper unless you want to get into a more detailed debate. All I want to hear about is your initial reaction to their final two paragraphs.
Consolidated genomic view of initiation

...The discovery that transcription of the human genome is vastly more pervasive than what produces coding mRNA raises the question as to whether Pol II initiates transcription promiscuously through random collisions with chromatin as biological noise or whether it arises specifically from canonical Pol II initiation complexes in a regulated manner. Our discovery of ~150,000 non-coding promoter initiation complexes in human K562 cells and more in other cell lines suggests that pervasive non-coding transcription is promoter-specific, regulated, and not much different from coding transcription, except that it remains nuclear and non-polyadenylated. An important next question is the extent to which transcription factors regulate production of ncRNA.

We detected promoter transcription initiation complexes at 25% of all ~24,000 human coding genes, and found that there were 18-fold more non-coding complexes than coding. We therefore estimate that the human genome potentially contains as many as 500,000 promoter initiation complexes, corresponding to an average of about one every 3 kilobases (kb) in the non-repetitive portion of the human genome. This number may vary more or less depending on what constitutes a meaningful transcription initiation event. The finding that these initiation complexes are largely limited to locations having well-defined core promoters and measured TSSs indicates that they are functional and specific, but it remains to be determined to what end. Their massive numbers would seem to provide an origin for the so-called dark matter RNA of the genome, and could house a substantial portion of the missing heritability.
Looking forward to hearing from you.

Keep in mind that this is a Nature paper that has been rigorously reviewed by leading experts in the field. Does that influence your opinion?

Venters, B.J. and Pugh, B.F. (2013) Genomic organization of human transcription initiation complexes. Nature Published online 18 September 2013 [doi: 10.1038/nature12535] [PubMed] [Nature]

Thursday, September 26, 2013

Stephen Meyer Says That Constant Mutation Rates Are a "Questionable Assumption"

Stephen Meyer is trying to make the case that the primitive animals of the Cambrian explosion really did arise suddenly as fully formed and distinct species. He says that the evidence points to God(s).

Scientists, on the other hand, have been exploring other possibilities and testing various models. They have shown that the molecular data is not consistent with sudden origins. Instead it shows that all of the major animal phyla are related and that their common ancestors probably lived millions of years before the Cambrian explosion. Thus, the evidence indicates deep divergence and the lack of transitional fossils does not prove the non-existence of these ancestral forms.

In order to support his creationist view, Meyer has to discredit the molecular evidence. We've already seen that he has five arguments against the data [Darwin's Doubt: The Genes Tell the Story?]. The first three were: (1) there are no transitional fossils [The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes]; (2) different molecular phylogenies do not agree in all detail [Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates]; and (3) different genes evolve at different rates [Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different Rates].

None of those arguments are correct and one of them (#3) is just plain silly.

2013 Toronto Science Festival

The University of Toronto is sponsoring a "science" festival with three talks tomorrow and Saturday. You have to buy tickets at: tickets.

There's two technology talks and one science talk. I'm going to the only science talk at the science festival. There are a bunch of other things going on, see the entire program.

Friday, Sept. 27th 7pm– "Human Exploration of Space: 50 Years and Counting": Space Shuttle veteran and first Canadian on board the International Space Station, Julie Payette
“High achiever” barely begins to describe Julie Payette. Masters degree in engineering, pilot, IBM engineer, Officer of the Order of Canada, singer with symphonies in Montreal, Toronto, and Switzerland, conversant in six languages, and now Director of the Montreal Science Centre. Oh, did we mention she was orbiting the Earth, using a giant robot arm to build a space station by the time she was 35? Julie will kick off the festival by sharing her unique insights into the past, present, and future of human space exploration.

Friday, Sept. 27th 8pm– "Brave Genius: Jacques Monod, Chance, and our Place in the Universe": Evolutionary biologist and “evo devo” pioneer, Sean Carroll
Biologist and Nobel Laureate Jacques Monod once remarked that “the most important results of science have been to change the relationship of man to the universe, or the way he sees himself in the universe.” Discoveries in molecular biology, evolutionary biology, and geology over the past half-century have profoundly reshaped our picture of human origins, and revealed the enormous role of chance in the fate of life on Earth. Join evolutionary biologist Sean Carroll as he chronicles some of those discoveries through Monod’s eyes, whose own ascent from struggling graduate student to leader within the French Resistance, co-founder of molecular biology, and emergence as a public figure and leading voice of science involved a great deal of chance, and courage.

Saturday, Sept. 28th 7pm– "Postcards from Mars": Mars rover imaging scientist, Jim Bell
Don’t worry if your application to live on Mars was rejected. You can still visit the Red Planet through the spectacular imagery captured by a trio of Mars Rovers—Spirit, Opportunity and Curiosity. Planetary scientist Jim Bell was instrumental in developing cameras and processing images from the three robotic explorers and in his talk “Postcards from Mars”, he’ll share his favorite vistas of our planetary neighbour with you. Through the beauty of these photographs, you’ll see why Bell can be described as a scientist, an explorer and a nature photographer.

Wednesday, September 25, 2013


Chris DiCarlo talked about fallacies in our class today. We're trying to teach students how to recognize the most important logical fallacies that they are likely to encounter in debates and discussions. He also talked about the importance of consistency and how being caught out as a hypocrite can be devastating to your cause.

Speaking of hypocrisy, the Popular Science website has just banned comments. Apparently they were getting overwhelmed with crackpots and kooks [Why We're Shutting Off Our Comments].
A politically motivated, decades-long war on expertise has eroded the popular consensus on a wide variety of scientifically validated topics. Everything, from evolution to the origins of climate change, is mistakenly up for grabs again. Scientific certainty is just another thing for two people to "debate" on television. And because comments sections tend to be a grotesque reflection of the media culture surrounding them, the cynical work of undermining bedrock scientific doctrine is now being done beneath our own stories, within a website devoted to championing science.

There are plenty of other ways to talk back to us, and to each other: through Twitter, Facebook, Google+, Pinterest, livechats, email, and more.
That's not hypocritical. The hypocrisy comes from Uncommon Descent where someone names "nullasalus" blogged about the Popular Science decisions [Popular Science shuts down comments, citing the presence of dissent from the scientific consensus]. Here's what he/she/it said
Science is not what’s being championed at, nor is ‘bedrock scientific doctrine’ challenged by dissent. Consensus is. Orthodoxy is. Likewise, being ‘politically motivated’ with regards to science is not a problem – it is having political, social and even religious views that PopSci has decided are unacceptable. Dialogue and discussion is welcomed by the self-appointed champions of science – if and only if it results in an outcome they favor. If they suspect it doesn’t, then the dialogue and discussion is over.

Why, it’s almost as if science was never really the concern to begin with.
I was going to make a comment but I can't because I've been banned. Apparently the people at Uncommon Descent have decided that my views are unacceptable. I also can't make any comments over on Evolution News & Views because they don't allow comments.

That's what hypocrisy looks like.

Tuesday, September 24, 2013

An "Atheist" Defends Intelligent Design Creationism

Bradley Monton is a Professor in the Department of Philosophy at the University of Colorado at Boulder. On his website he says he specializes in the philosophy of time, philosophy of religion, philosophy of science (especially physics). He doesn't appear to have any expertise in biology or evolution but he's interested in Intelligent Design Creationism.

A few years ago (2009) he published a book with a provocative title: Seeking God in Science: An Atheist Defends Intelligent Design. Normally I wouldn't pay much attention to such a book but Salvo magazine ("Society, Sex, Science") just published an interview with him [Beyond Belief (or the Lack Thereof)]. It ain't pretty.

Monday, September 23, 2013

Monday's Molecule #216

Last week's molecules were guanine and adenine. Everyone should have known these structures but only undergraduate Zhimeng Yu got it right! [Monday's Molecule #215].

You probably didn't memorize the structure of this week's molecule but you should be able to recognize it and check your answer in a textbook or on the web. What it is it? (I don't know why it has a gray background. Can anyone help? Fixed.)

Email your answers to me at: Monday's Molecule #216. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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.)

Saturday, September 21, 2013

My American Dialect

I finally got to take the quiz at Dialect Quiz & Survey. The server is often overloaded and answering the 140 questions takes more than one hour because of the slow server.

My dialect is most like that of Buffalo NY, which is hardly a surprise since it's the closest American city to Toronto. (I grew up in Ottawa but I don't have much of an Ottawa Valley accent.)

Do the IDiots Really Know What Evidence Looks Like?

I've been dealing with Intelligent Design Creationists for over twenty years. I've spent a lot of time addressing their scientific misconceptions and trying to explain where they've gone wrong. A few years ago, for example, I posted a whole series of article on Jonathan Wells' book The Myth of Junk DNA. A few weeks ago I explained why Jonathan McLatchie was wrong about pseudogenes.

Lately, I been focusing on one of the chapters in Darwin's Doubt—it's the one on molecular evolution and I know something about that subject. It has been pretty easy to show why Mayer is wrong about his conclusions.

That's why it's so frustrating to read what journalist Tom Bethell said the other day on Evolution News & Views (sic) ["What Is the World Really Like?" Darwinism, Materialism, and How They Relate].
The explicit materialism of the Darwinians is the mirror image of creationism. Creationists are easy for scientific materialists to rebut, because the materialists can say, "That is just your belief. We don't have to accept that." In a parallel way, we can say to the materialists: "That is just your belief. We don't have to accept that. And it is the real basis of your evolutionism."

In between the Creationists and the Materialists we encounter the scientific evidence that makes the materialist position increasingly improbable -- the evidence that Stephen Meyer recently presented in Darwin's Doubt: information theory, insufficiency of the fossil record, epigenetics, complexity of life at the molecular level, and so on.

Increasingly, it seems to me, the Darwinians are responding to this science by saying (in effect): "Bah! We won't read that! It's creationism in disguise." They get graduate students like Nick Matzke, or incompetents like John Farrell (in National Review of all places), to do the work for them. All along the Darwinists have found that their materialism has allowed them to lie back and relax without really bothering to study the evidence.

Now that may be changing. They are being put in a position where they just might have to hit the books. I suspect it is not a prospect that they relish.
Keep in mind that this is written by a man who denies that humans cause global warming and denies that HIV causes AIDS.

He has no idea what evidence looks like.

Why Are IDiots So Nasty?

You've probably noticed that in addition to being stupid most IDiots are not very respectful of scientists (i.e. Darwinists). William J Murray1 explains why religious people have to be mean and nasty [Can We Afford To Be Charitable To Darwinists?].
I used to be one that diligently attempted to provide Darwinists charitable interaction. I tried not to ridicule, demean, or use terms that would cause hurt or defensive feelings. My hope was that reason, politely offered, would win the day. My theistic perspective is that returning the bad behavior I received at sites like TSZ would be wrong on my part. I thought I should stick to politely producing logical and evidence-based exchanges, regardless of what Darwinists did. I note that several others here at UD do the same. Lately, however, I’ve come to the conclusion that what I’m attempting to do is the equivalent of bringing a knife to a gun fight; polite reasoning with Darwinists, for the most part, is simply setting up our own failure. It’s like entering a war zone with rules of engagement that effectively undermine a soldier’s capacity to adequately defend themselves, let alone win a war. While pacifism is a laudable idea, it does not win wars. It simply gives the world to the barbarians.

And that’s the problem; a lot of us don’t realize we’re in a war, a war where reason, truth, religion and spirituality is under direct assault by the post-modern equivalent of barbarians. They, for the most part, have no compunction about lying, misleading, dissembling, attacking, blacklisting, ridiculing, bullying and marginalizing; more than that, they have no problem using every resource at their means, legal or not, polite or not, reasonable or not, to destroy theism, and in particular Christianity (as wells as conservative/libertarian values in general). They have infiltrated the media, academia and the entertainment industry and use their influence to generate narratives with complete disregard for the truth, and entirely ignore even the most egregious barbarism against those holding beliefs they disagree with.

Wars are what happen when there is no common ground between those that believe in something worth fighting for. There is no common ground between the universal post-modern acid of materialist Darwinism and virtually any modern theism. There is no common ground between Orwellian statism-as-God and individual libertarianism with freedom of (not “from”) religion. There is only war. One of the unfortunate problems of war is that certain distasteful methods must be employed simply because they are the only way to win. In this war, in a society that is largely a low-information, media-controlled battleground, logic and reason are, for the most part, ineffective. The truth is ineffective because it is drowned out by a concerted cacophony of lies, or simply ignored by the gatekeepers of low-information infotainment. What has been shown effective is the Alinsky arsenal of rhetoric, emotional manipulation, and narrative control.

I would find it distasteful to pick up a gun in a ground war and have to shoot others to defend my family and way of life, but I would do so. Should I not pick up Alinsky’s Rules for Radicals and employ the weapons of my adversaries, if it is the most effective way – perhaps the only way – of winning the cultural war? There comes a point in time where all the high ground offers is one’s back against the precipice as the barbarian horde advances.
I understand where he's coming from. He's a good Christian who advocates "lying, misleading, dissembling, attacking, blacklisting, ridiculing, bullying and marginalizing" because that's what his opponents do. (And because his versions of truth, logic, and reason have proven to be ineffective.)

BTW, did you notice that he forgot to pretend that the Intelligent Design Creationist movement was all about science, not religion? Oops.

Note to William Murray: If you really were trying "not to ridicule, demean, or use terms that would cause hurt or defensive feelings" then why did you call us "Darwinists"?

1. I assumed that he was the Baptist minister but apparently it's a different William J. Murray.

IDiots Love Epigenetics

I read everything posted on Uncommon Descent and Evolution News & Views. These are the most important blogs for learning about Intelligent Design Creationism. The posts on those two blogs represent the very best that Intelligent Design Creationism has to offer. Their best minds are behind the posts.

Here, for example, is Denyse O'Leary in action: Turns out some Texas media DID believe Texas bans discussion of evolution.
... epigenetics is to Darwin’s darlings what relativity and quantum mechanics are to Newtonian physics, only worse, much worse. Newtonian physics was useful within its scale. Darwin’s magical mechanism of natural selection is more like phlogiston, which supposedly produced fire the way Darwinism supposedly produces mind from mud.

And if nothing really happens that way, what becomes of Darwin’s magical mechanism? It’s phogliston, the substance that need not exist!
Seriously, that's the best of the best?

You have to imagine that there are some Intelligent Design Creationists with a modicum of intelligence. Why aren't they speaking up to muzzle people like Denyse O'Leary? She's an embarrassment to their cause.

Friday, September 20, 2013

Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different Rates

Stephen Meyer is promoting the idea that God made all the various types of animals over a short period of time about 530 million years ago. The molecular data refutes that speculation because it shows that the various phyla share common ancestors and many of those ancestors appear long before the Cambrian Explosion.

This data creates a serious problem for the IDiots so they have to discredit it in order to dismiss it. As we've seen in earlier posts, Meyer argues that the molecular data is wrong because: (a) there are no transitional fossils, and (b) different molecular phylogenies do not agree in all detail [see The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes and Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates]. He has five anti-evolution arguments altogether [Darwin's Doubt: The Genes Tell the Story?]. The third one is that different genes evolve at different rates.

On Preparing Students for the 21st Century

Yesterday I attended a meeting organized by the Ontario Ministry of Education. The theme was From Great to Excellent: The Next Phase in Ontario's Education Strategy. The idea was to promote widespread consultation before the Ontario government releases its new plan for education reform next year.

I was attending on behalf of my friend Chris DiCarlo who had to be out of town. He (and I) are promoting the concept of critical thinking; specifically, the idea that it needs to be explicitly taught in a high school philosophy course.

The Minister of Education (Liz Sandals) and several of the senior members of her ministry were there. They told us that today's students are facing unprecedented changes and that the Ontario education system has to change in order to cope. They were mostly thinking about technological change and the possibility that today's students would have new types of jobs and careers.

I'm certain that we can improve our education system but I'm not sure it's helpful, or even correct, to focus on the idea that the next generation will have to cope with situations we never faced in the past. If we could show that our existing education system did a pretty good job of preparing students for change then maybe we should turn our attention to problems other than job training and technological innovation?

Wednesday, September 18, 2013

The Quebec National Assembly Crucifix Belongs in a Museum

I'm indebted to Veronica for telling me about this petition. I stole the title of her post: La Place du Crucifix de l’Assemblée Nationale Est dans un Musée.

Sign this petition if you think the crucifix should be removed from the Quebec National Assembly.

Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates

Stephen C. Meyer believes that the rapid appearance of complex, primitive, animals in the Cambrian cannot be explained without invoking God. The fact that there are no obvious transitional forms in the fossil record means, to him, that those transitional forms don't exist and God must have created all those primitive animals over a short period of time. Presumably, God then let them evolve naturally for the next 530 million years. (Meyer isn't very clear about this.)

Scientists looked at the molecular data in order to test the hypothesis that the Cambrian animals appeared suddenly in a very rapid radiation. The molecular data did not show such a rapid radiation. The overall pattern was consistent with branching evolution spread out over many millions of years. The diagrams that Meyer shows in his book are similar to the figure shown below from Erwin et al. (2007).

Breaking News!!! Wikipedia Is Wrong! (about the Central Dogma)

I shuddered when I spotted Razib's latest post in my aggregator [see The Central Dogma goes YouTube]. "Oh, no!" I thought, "Am I going to have to point him to my post on The Central Dogma of Molecular Biology?

Imagine my surprise when I saw that he has a link to the Wikipedia article on the Central Dogma. I said to myself, "This will set him straight because I wrote some of that article."

Oops! The Wikipedia article on the Central Dogma of Molecular Biology has been changed. Apparently I haven't looked at it for nine years since the important change was made by someone named Kierano back on September 15, 2006. Kierano describes himself (in 2011) as a Ph.D. student in bioinformatics.

Here's the opening paragraphs from before Sept. 15, 2006.
The central dogma of molecular biology was first enunciated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970:
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid.
In other words, 'once information gets into protein, it can't flow back to nucleic acid.'

The central dogma is often misunderstood. It is frequently confused with the standard pathway of information flow from "DNA to RNA to protein". There are notable exceptions to the normal pathway of information flow and these are often mistakenly referred to as exceptions to the central dogma.

The standard information flow pathway can be summarized in a very short and oversimplified manner as "DNA makes RNA makes proteins, which in turn facilitate the previous two steps as well as the replication of DNA", or simply "DNA → RNA → protein". This process is therefore broken down into three steps: transcription, translation, and replication. By new knowledge of the RNA processing, a fourth step must be included: splicing.
This has undergone some edits from what I originally wrote but the main idea is there. Strictly speaking, the Central Dogma of Molecular Biology (Crick version) says only that once information gets into protein it can't flow back to nucleic acid. I thought it was important to explain the main misconception; namely, that the Central Dogma means DNA to RNA to protein. This should be referred to as "the standard information flow pathway" or something similar.

The rest of the Wikipedia article talks about transcription and translation which, strictly speaking, are not part of the Central Dogma. However, the misconception is so widespread that many people expect these to be described under "Central Dogma."

The new version posted on Sept. 15, 2006 says ...
The central dogma of molecular biology was first enunciated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970:
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid.
In other words, 'once information gets into protein, it can't flow back to nucleic acid.'

The dogma is a framework for understanding the transfer of information between information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of information-carrying biopolymers: DNA and RNA (both nucleic acids), and protein. There are 9 possible direct transfers of information that can occur between these. The dogma classes these into 3 general transfers (believed to occur normally in most cells), 3 special transfers (known to occur, but only under abnormal conditions), and 3 unkown transfers (believed to never occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA, (transcription), and proteins can be synthesized using the information in mRNA as a template (translation).

The central dogma is occasionally misunderstood as being a statement of absolute fact. If taken as such, it can be criticised, as there are well-described exceptions. It is also criticised by some systems biologists as being too reductionist.
This is the beginning of a change in emphasis. Kierano removed my statement that the basic meaning of the Central Dogma is often misunderstood. It's clear that he misunderstands it.

On March 10, 2012 someone named Nbauman addd the following statement; "Or, as Marshall Nirenberg said, 'DNA makes RNA makes protein.'" Nbauman cautioned that this was a reliable published source and should not be removed from the Wikipedia article. As far as I can tell Nbauman is not a scientist and has no training in science. In fact, she seems proud of the fact that she is ignorant of the subjects she edits. She does not seem to have noticed that her "authority" (Nirenberg) conflicts with another authority (Francis Crick).

Here's the complete version as of this morning. It's going to change as soon as I get around to it.
The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It was first stated by Francis Crick in 1958[1] and re-stated in a Nature paper published in 1970:
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.
Or, as Marshall Nirenberg said, "DNA makes RNA makes protein."[3]

To appreciate the significance of the concept, note that Crick had misapplied the term "dogma" in ignorance. In evolutionary or molecular biological theory, either then or subsequently, Crick's proposal had nothing to do with the correct meaning of "dogma". He subsequently documented this error in his autobiography.

The dogma is a framework for understanding the transfer of sequence information between sequential information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and protein. There are 3×3 = 9 conceivable direct transfers of information that can occur between these. The dogma classes these into 3 groups of 3: 3 general transfers (believed to occur normally in most cells), 3 special transfers (known to occur, but only under specific conditions in case of some viruses or in a laboratory), and 3 unknown transfers (believed never to occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA (transcription), and proteins can be synthesized using the information in mRNA as a template (translation).

Jesus and Mo

See Jesus and Mo: Sept. 18, 2013

Tuesday, September 17, 2013

The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes

Darwin's Doubt is a book about the problems surrounding the Cambrian Explosion. It's written by a prominent Intelligent Design Creationist and, like most books by IDiots, the main theme is how scientists get everything wrong.

The "problem" is how to account for the very rapid appearance of complex animals about 530 million years ago. Intelligent Design Creationists think that they can ignore all of the evidence for evolution for the following 530 million years and focus on this one problem to discredit naturalistic explanations for the history of life.

You might expect that they would offer an alternative explanation. Like, perhaps, an intelligent being who visited Earth 530 million years ago, created a bunch of different animals with similar body plans, then allowed evolution to proceed for the next half a billion years?

Don't hold your breath waiting for a scientific explanation. They aren't that clever.

23andMe Sponsors a MOOC on Genetics

A private company, 23andMe sponsors a MOOC on genetics in association with UDACITY [Tales from the Genome]. Two of the instructors are employees of 23andMe.
You will learn about fundamental principles of inheritance, gene expression, mutation and variation, development of simple and complex biological traits, human ancestry and evolution, and the acquisition of personal genetic information. By the end of this course, you will be able to read and understand genetic information available from personal genetics services such as 23andMe.

What could possibly go wrong?

[HatTip: an unskeptical Blaine Bettinger: 23andMe and Udacity Partner to Offer A Free Online Genetics Course]

Atheist Freethinkers Support the Quebec Charter of Values ... with Reservations

There's a debate going on in Canada over the so-called "Charter of Values" proposed by the government of Quebec. The fact that the governing party is a separatist party (Parti Québécois) makes the debate much more interesting. (That's Premier Pauline Marois in the photo below.)

The main issue concerns how public servants present themselves to the public. The new law proposes to ban outward signs of religion on the grounds that public servants should represent a secular government. What this means in practice is that Sikh men won't be allowed to wear turbans and kirpas and Muslim women won't be allowed to wear hijabs or niqabs. Christians can't wear large crosses. Atheists can't wear a large red letter "A" on their lapel.

Opinion in Quebec is pretty evenly divided but most of the rest of Canada sees this (mostly incorrectly) as an infringement on fundamental rights and freedoms.

Atheist groups are struggling with this issue. Here's what the Atheist Freethinkers say in today's press release: The Quebec Charter of Values: A major advance towards secularism.
Montreal, 17th September 2013 — Atheist Freethinkers (LPA-AFT), an association which promotes secularism and supports the rights of atheists, welcomes the intention of the government of Quebec to adopt a so-called Charter of Values which would formally establish the secular status of the Quebec state. The project is outlined on its website

The proposed Charter would formally declare separation of religion and state, the religious neutrality of the state and the secular nature of its institutions. It would impose an ethics of restraint and religious neutrality for public servants. It would prohibit obvious religious symbols in the public service. And it would establish clear guidelines for so-called “reasonable” accommodations. Furthermore, it would make it mandatory for any client of public services to have one’s face uncovered in order to be served. All of these measures go in the direction of formalizing the secular nature of the state and assuring the independence and autonomy of the state from religion. This is very good news.

However, like most who support the proposed Charter, we do so with some reservations. Firstly, the title “Quebec Charter of Values” is very badly chosen. What Quebec requires is a Charter of Secularism, a charter which expresses values which have universal, human import, the values of the Enlightenment.

Secondly, it has not been proposed that the large crucifix be removed from the wall of the Quebec National Assembly in Quebec City. This object was installed there in 1936 by the Duplessis government of the day, with the aim of consecrating its alliance with the Catholic Church. If the crucifix is a “Quebec value,” it represents the worst possible value in this context. Its presence in the most important venue of the Quebec state is a blatant violation of secularism, a glaring symbol of non-secularism! The Charter should stipulate its removal – to a museum for instance. To leave it in place would be totally inconsistent and expose the authors of the Charter to charges of hypocrisy. However, it is important to realize that keeping the crucifix in the National Assembly is not explicitly stipulated in the proposed Charter. In fact, this crucifix is not even mentioned there.

Thirdly, the proposed ban on state employees wearing religious symbols while on duty has been poorly formulated. The plan is to include an official dress code in the Charter of Rights and Freedoms. However, this Charter is a quasi-constitutional document and should stipulate only the principle that public servants must exercise restraint – so that public services remains neutral with respect to religion – and establish a mechanism for the implementation of this principle. The dress code and other aspects of the behaviour of public servants belong to the implementation of this principle and should not be included in the Charter of Rights and Freedoms itself. In that way, the details and timing of the implementation would remain open to democratic debate.

The draft Charter was released barely a week ago and we continue to study it. Other aspects of the project may require critical analysis. Moreover, a completely secular charter would include several provisions not included in the announced project – such as cutting public funding to private religious schools; banning prayer at municipal council meetings; banning prayer rooms in government buildings; ending religious accommodations granted for ritual slaughter of animals; prohibiting mutilation of the human body without valid medical reasons and without the consent of the adult concerned; withdrawal of the Ethics and Religious Culture program from public schools; and removal of tax incentives to religious institutions and members of religious orders. These omissions remain to be addressed.

The organization Atheist Freethinkers commends the government for its courage. We note that the government is not responsible for the inflammatory and demagogic excesses of the exaggerated political opposition that arose against its attempt at secularization, even if such excesses could have easily been predicted. This project is not an exercise in identity politics. The numerous accusations of intolerance, xenophobia and even racism are extremely dishonest and even defamatory. Nevertheless, the government could have prevented the worst and minimized the damage by avoiding any measure which the opposition might use as an excuse. Excluding religious symbols is necessary in order to ensure not only the religious neutrality of the public service but also the perception of neutrality. By the same token, the government must not only avoid identity politics but also the perception of such politics. If the proposed Charter had specified the removal of the crucifix from the National Assembly, if its authors had chosen a title with more universal scope, if the plan for gradual removal of religious symbols had been better presented, then the intellectual vacuity of the opposition would have been obvious and that opposition would have been greatly defused.

Despite our reservations, we support the proposed Charter. It could serve as a model for other Canadian provinces and jurisdictions, each adapting the Charter appropriately and provided of course that the model is improved upon – in particular by avoiding the failings discussed above.

As atheists, we greatly value freedom of religion because atheists and apostates are often among the first victims when that freedom is violated. We know that freedom of religion is incomplete or even hollow if it does not include freedom from religion. Thus secularism is important not only for us as atheists but also for believers: it is essential that public institutions, i.e. state institutions, be independent of any religion and, at the same time, that total freedom to practice the religion of one’s choice, or to practice none, be protected in the private sphere and in the public sphere outside of such institutions.

Monday, September 16, 2013

Replacing Textbooks with MOOCs

John Hawks read the article that I discussed in an earlier post [On the High Price of Textbooks]. he outlines his solution to the high cost of textbooks [Textbook troubles].
I'm building the groundwork for a project that will do something about this, at least in the area of biological anthropology. I've been following stories like this for years. Developing the MOOC, I have the tremendous opportunity to make connections with people all over the world. Most of the people signed up are nowhere near the traditional U.S. college textbook market (MOOC international enrollment numbers). I face a problem that can't be solved by textbooks today, and limited-use "rental" text that will go away at the end of the course is not a valid solution.

So I'm doing something about it. The idea has many moving parts, but at its base is the need to supply quality educational content cheaply, with a way to get articles freely outside the usual college system. I'm going to be calling for help, so keep watching this space.
This is refreshingly honest. Of the many claims about MOOCs (Massive Open Online Course), the only one that makes sense to me is to use them as a possible replacement for textbooks. They can be used as a supplemental resources in a student-centered classroom.

MOOCs are good at delivering information—the sort of information you can get from a textbook.

Now I'm waiting to see if anyone creates a MOOC that comes close to the depth and quality of university science textbooks. I imagine that it can be done but it ain't going to be cheap.

John Hawks is an expert on anthropology but I find it difficult to imagine that he's going to be able to create drawings and figures of textbook quality for no cost. I don't see how he's going to ensure high quality editing and reviewing for free. I can't imagine how he's going to mount his course on servers and provide easy access for thousands of students without incurring some costs. He's going to have to pay for permissions to use photos and figures just like the textbooks do. Maybe he'll do all the administrative work himself or maybe somebody will work for him for no salary.

It's possible to overcome all these difficulties and provide free high quality MOOCs that will replace textbooks. So far, nobody has come close in any of the subjects that I'm interested in. Most existing biochemistry MOOCs are horrible.

Holding my breath ....

On the High Price of Textbooks

Once again we have a relatively uninformed journalist writing about the high cost of college textbooks ['Required reading': As textbook prices soar, students try to cope].

I am a textbook author so I'm not totally impartial. However, it's worth pointing out that I don't defend textbooks because I'm a textbook author. Instead, I became a textbook author because I value textbooks. I still have all my college textbooks and I still refer to them from time-to-time. The oldest ones were purchased 50 years ago.

Let's look at what Martha C. White has to say.
Already grappling with skyrocketing tuition and fees, college students also must contend with triple-digit inflation on the price of textbooks. With the average student shelling out $1,200 a year just on books, students, professors and policy groups are searching for ways to circumvent the high cost of traditional textbooks.
It may be true that the average student has to spend $1200 per year on required textbooks but the NBC News Business website didn't do themselves any favors by showing a photo of 21-year-old Priya Shivraj with a stack of textbooks that she presumably had to buy in a single year. She is supposed to be a combined major in biology, Spanish and pre-med and one would guess from her age that she's in her third or fourth year of university.

Here are some of the books in her stack: Introductory Biology, Introductory Chemistry, Organic Chemistry, Introductory Biochemistry, and Immunobiology. Is it possible that a student at NYU would take all those courses in a single year?

But let's not quibble. Many science textbooks cost about $150 and I can easily imagine that a student might have to purchase as many as six of them in a single year.
The College Board found that the average student at a four-year public college spends $1,200 on “books and supplies,” or nearly $1,250 if they go to a private school. On the public policy blog of the American Enterprise Institute, where he is a fellow, University of Michigan-Flint economics professor Mark J. Perry highlighted a chart showing an 812 percent increase in the cost of college textbooks since 1978, a jump even higher than the percentage growth in the cost of health care.
This paragraph says that the "average" includes supplies and it appears to cover four years. What does that mean?

Let's use our critical thinking skills to examine the claim that textbook prices have increased by 812% since 1978. According the the US Bureau of Labor Statistics CPI Inflation Counter there should be a 358% increase in price due to inflation alone. Thus, the real cost has about doubled in 35 years.

I addressed this issue a few years ago in: PZ Rants About Science Textbooks. Here's an updated version of what I said in 2007 ...
So let's understand and agree that the original price of a textbook is not unreasonable. My biochemistry textbook in 1965 was Conn & Stumpf and it cost $9.95. This works out to $73.79 in 2013 dollars using the handy-dandy inflation calculator on the US Dept. of Labor website. The 1965 textbook was much smaller, covered less material, and had no color figures. Modern biochemistry textbooks cost about $150 and they are very much better than the books published 50 years ago.
So the price of biochemistry textbooks has doubled in constant dollars but there's a huge increase in the amount and quality of the material in modern textbooks.

Martha White continues ....
“Students are, in essence, a captive market,” said Ethan Senack, higher education associate at the U.S. Public Interest Research Group. “The publishing industry is dominated by five companies that dominate upwards of 85 percent of the market.”

“I think part of it is the consolidation… There’s less competition now,” Perry said.
This sort of complaint comes up quite often. It suggests that publishers are conspiring to keep the cost of textbooks at least twice as high as they were decades ago. It also assumes that publishers are making outrageous profits at the expense of university students. Let's use our critical thinking skills to ask whether large public companies in the publishing industry are making huge profits. Since these are public companies whose stock is trading on the stock market, it should be possible to test this idea. One of the quickest ways is to simply look at the stock prices, they should be going through the roof if the assumption is correct. They aren't. The textbook publishing industry is making a profit but it's not much different than the profits made by most other companies.

There may be lots of things wrong with making students buy textbooks but it's ridiculous to pretend that the major publishing companies are ripping off students. It's also ridiculous to pretend that the retail price paid by students at their bookstore goes directly to the publisher. The wholesale price of a $150 textbook may be only $100. The bookstores have to make money too. You can buy my book for about $110 on Amazon.

See also: Free/Cheap Textbooks for Students.

Monday's Molecule #215

Last week's molecule was malonate (propanedioic acid). A derivative of malonate called malonyl-CoA is a key intermediate in fatty acid synthesis. Bill Chaney was the first person to identify the molecule and describe its function [Monday's Molecule #214].

Recently I've been having a discussion with the Chair of my department about whether undergraduates in introductory biochemistry courses should memorize structures. He thinks they should. I wondered whether all the professors in my department could draw the structures of some important molecules. Here are a couple of molecules that you might be able to recognize. How many of you can identify them without checking a textbook?

How many of you can identify them even with a textbook? I'll need a fairly exact identification. Be sure to specify "top" and "bottom" molecules.

Email your answers to me at: Monday's Molecule #215. I'll hold off posting your answers for 24 hours. The first one with the correct answer wins. I will only post the names of people with 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.)

Move This Book?

I noticed a couple of books in the Science section of my local bookstore. One was by a guy named Meyer (Stephan C. Meyer) and the other was by someone named Myers (PZ Myers). I bought the one by Myers because I already had the other one.

There are some people who get upset by seeing these books in the Science section. Some of these people even like to move them to other sections, such as religion and/or philosophy. I even did it myself on one or two occasions in the past. Lately, however, I've become somewhat less dogmatic about the creationist books. They are, after all, books about science even though they may try to bring religion into science. That does not mean their view are non-scientific. Many of those books are no worse than some of the other "science" books on the shelf that have nothing to do with religion.

What would you do? Here are the choices ...
  1. Move the Meyer books to another section.
  2. Move the Myers books to another section.
  3. Move both books to other sections.
  4. Leave both books in the Science section.
I'm especially interested in hearing from Jerry Coyne and his supporters who supported Diana MacPherson's successful attempt to get Amazon to reclassify Darwin's Doubt as a religious book [Reader gets ID book moved from science to religion section].

Amazon puts The Happy Atheist in the "Religion and Spirituality" category. Does it belong in the Science section of local bookstores?

Friday, September 13, 2013

Creationist Quotes

"Quote mining" can be fun. Here are some actual quotes taken from online forums. They are spoken by atheist actors.

Someone recently asked me why I mock creationists when I should be giving them more respect.

Sean Carroll: "What Is Science?"

I've been meaning to comment on Sean Carroll's post from last July (July 3, 2013) but there always seems to be something else that commands my attention. The issue is important, in fact I've just finished an entire book on the question (Philosophy of Pseudoscience: Reconsidering the Demarcation Problem edited by M. Pigliucci and M. Boudry).

Sean Carroll (the physicist)1 has a view that's quite similar to my own. Read his post at: What Is Science?. Here are some key points.

Better Biochemistry: Teaching ATP Hydrolysis for the MCAT

I'm digesting the idea that many American biochemistry courses teach to the MCAT exam [see Better Biochemistry: Teaching to the MCAT?]. What this means is that the scientists who teach biochemistry are willing to let the curriculum be established by a group of American medical schools (AAMC). That organization has put up a website to guide faculty members and students in preparation for the 2015 MCAT exam [MCAT2015: Biological and Biochemical Foundations of Living Systems].

One of the links takes you to a chemwiki at the University of California, Davis: Biological Chemistry. From there you can click on several topics. I picked ATP/ADP to see what kind of information the MCAT thinks is appropriate. The information on the ATP website is provided by Tiffany Lui of the University of California, Davis so it's not something that AAMC created. Nevertheless, it is presumably indicative of the sort of thing that might appear on the MCAT exam.

Thursday, September 12, 2013

Humans Are Still Evolving

Sir David Attenborough said something stupid the other day [Sir David Attenborough: Humans have stopped evolving]. (Not for the first time.) He said ...
Because if natural selection, as proposed by Darwin, is the main mechanism of evolution – there may be other things, but it does look as though that’s the case – then we’ve stopped natural selection.

We stopped natural selection as soon as we started being able to rear 95–99 per cent of our babies that are born.

We are the only species to have put a halt to natural selection, of its own free will, as it were.
The headline says that humans have stopped evolving. If that's what he really said then it's easy to prove him wrong by showing that there's a lot more to evolution than natural selection [Have Humans Stopped Evolving?].

But what about his specific claim that natural selection doesn't work on humans any more? I covered that in earlier posts but John Hawks has corrected him today [Humans are still evolving, and soon we'll know a lot more about it]. I love it when I agree with John Hawks! (That's me, visiting him in his lab in Madison, Wisconsin.)

Better Biochemistry: Teaching to the MCAT?


Better Biochemistry
I view science education as a way of teaching students how to think critically. In that sense, it's not any different than education in the arts and humanities. In my opinion, biochemistry should be taught as a bunch of fundamental concepts and principles that will help students understand the basics of life at the molecular level. The course will demonstrate how to think critically and how we come to know what we know—if we teach it correctly. I believe that biochemistry should be taught from an evolutionary perspective since that's the best way to achieve fundamental understanding.

The last thing we should be doing in an undergraduate biochemistry course is to ask students to memorize enzymes, structures, and pathways and regurgitate them on an exam. We should not just be teaching the biochemistry of humans since that does not provide students with a broad view of life and where humans came from. Such an approach also makes biochemistry seem like it's only important because it can contribute to health. We have plenty of evidence that this is the wrong way to teach.

Wednesday, September 11, 2013

The Happiest Countries

Why do the people of these countries think they are happy? Why isn't the USA in the top ten? [World’s Happiest Countries In 2013, According To The UN]

I recently visited #1, #2, #5, #7 and #9 and I can confirm that the citizens of those countries do, indeed, think they are happy. I also visited #17 a few months ago and the citizens of that country do not seem happy. It's probably worse today than it was a few months ago.

Science and Mystery

One of the criticisms of science (narrow definition) is that its reductionist approach is simplistic and materialistic. Here's how Jesus and Mo dealt with that issue last month.

Monday, September 09, 2013

What Is "Science" According to George Orwell?

I'm about to start teaching my course on "Scientific Misconceptions" and one of the most important issues is defining science and dealing with the demarcation problem. Vincent Joseph Torley is also interested in this question—for a different reason—and he discovered an 1945 essay by George Orwell (Eric Arthur Blair (1903-1950)).

It's worth quoting the relevant passages.
Doublethink means the power of holding two contradictory beliefs in one's mind simultaneously and accepting both of them.

George Orwell
In last week’s Tribune, there was an interesting letter from Mr. J. Stewart Cook, in which he suggested that the best way of avoiding the danger of a “scientific hierarchy” would be to see to it that every member of the general public was, as far as possible, scientifically educated. At the same time, scientists should be brought out of their isolation and encouraged to take a greater part in politics and administration.

As a general statement, I think most of us would agree with this, but I notice that, as usual, Mr. Cook does not define Science, and merely implies in passing that it means certain exact sciences whose experiments can be made under laboratory conditions. Thus, adult education tends “to neglect scientific studies in favour of literary, economic and social subjects”, economics and sociology not being regarded as branches of Science, apparently. This point is of great importance. For the word Science is at present used in at least two meanings, and the whole question of scientific education is obscured by the current tendency to dodge from one meaning to the other.

Science is generally taken as meaning either (a) the exact sciences, such as chemistry, physics, etc., or (b) a method of thought which obtains verifiable results by reasoning logically from observed fact.

If you ask any scientist, or indeed almost any educated person, “What is Science?” you are likely to get an answer approximating to (b). In everyday life, however, both in speaking and in writing, when people say “Science” they mean (a). Science means something that happens in a laboratory: the very word calls up a picture of graphs, test-tubes, balances, Bunsen burners, microscopes. A biologist, and astronomer, perhaps a psychologist or a mathematician is described as a “man of Science”: no one would think of applying this term to a statesman, a poet, a journalist or even a philosopher. And those who tell us that the young must be scientifically educated mean, almost invariably, that they should be taught more about radioactivity, or the stars, or the physiology or their own bodies, rather than that they should be taught to think more exactly.
Every war when it comes, or before it comes, is represented not as a war but as an act of self-defense against a homicidal maniac.

George Orwell
I agree with Orwell when he prefers the broad definition of science. I see it as a way of knowing that can be applied to any discipline. I think that everyone should become more scientifically literate but by that I don't mean they should lean more about metabolic pathways or quantum chromodynamics. I mean that they should become more familiar with the scientific approach to acquiring knowledge. That's the fundamental skill that we need to learn.
Clearly, scientific education ought to mean the implanting of a rational, sceptical, experimental habit of mind. It ought to mean acquiring a method – a method that can be used on any problem that one meets – and not simply piling up a lot of facts. Put it in those words, and the apologist of scientific education will usually agree. Press him further, ask him to particularise, and somehow it always turns out that scientific education means more attention to the sciences, in other words – more facts. The idea that Science means a way of looking at the world, and not simply a body of knowledge, is in practice strongly resisted. I think sheer professional jealousy is part of the reason for this. For if Science is simply a method or an attitude, so that anyone whose thought-processes are sufficiently rational can in some sense be described as a scientist – what then becomes of the enormous prestige now enjoyed by the chemist, the physicist, etc. and his claim to be somehow wiser than the rest of us?

A hundred years ago, Charles Kingsley described Science as “making nasty smells in a laboratory”. A year or two ago a young industrial chemist informed me, smugly, that he “could not see what was the use of poetry”. So the pendulum swings to and fro, but it does not seem to me that one attitude is any better than the other. At the moment, Science is on the upgrade, and so we hear, quite rightly, the claim that the masses should be scientifically educated: we do not hear, as we ought, the counter-claim that the scientists themselves would benefit by a little education. Just before writing this, I saw in an American magazine the statement that a number of British and American physicists refused from the start to do research on the atomic bomb, well knowing what use would be made of it. Here you have a group of sane men in the middle of a world of lunatics. And though no names were published, I think it would be a safe guess that all of them were people with some kind of general cultural background, some acquaintance with history or literature or the arts – in short, people whose interests were not, in the current sense of the word, purely scientific.
Where did the George Orwells of this world go? Why don't we have more people like him today? Have they just been drowned out by idiots with access to a microphone?

Irony Upon Irony

For those (few) of you who are interested in the pathology of IDiots, you have to read Irony of the Day. It's posted on Uncommon Descent and the author is Barry Arrington.

This is a satirical summary of his point.
Many skeptics say that the Flying Spaghetti Monster is imaginary. However, it's impossible to prove that the Flying Spaghetti Monster doesn't exist. Even Richard Dawkins says that you can't prove a negative.

Therefore, when you say that the Flying Spaghetti Monster is imaginary, you aren't being a true skeptic. Instead, you are expressing "uncritical arrogant dogmatism that would make the most committed fundamentalist blush. And that, my friends, is the irony of the day."
You can't make this stuff up.

Reviews of Darwin's Doubt: Keeping Score

Several scientists have reviewed Stephen Meyer's latest attack on science [see Slaying Meyer’s Hopeless Monster]. Don't think the IDiots haven't noticed ... they've responded to several specific criticisms (and ignored others).

I know it's hard to keep score so David Klinghoffer has done it for us in: More Evidence of Darwinian Short-Term Memory Loss.
As far as I'm aware, no reviewer has yet genuinely laid a hand on "Darwin's Doubt," not for lack of trying. Well, there's always tomorrow.
The IDiots are learning to master the basic skills of propaganda and they're doing a pretty good job. For example, here's a video promotion of Darwin's Doubt. See if you can recognize the lies, the tricks and the deceptions.