IDiot Irony

Sometimes I really wonder what goes on at the Discovery Institute.

As most of you know by now, Stephen Meyer has written a new anti-evolution book where he criticizes the expert scientific opinion on the Cambrian Explosion. He says that the experts are all wrong and the evidence shows that evolution is impossible. The only reasonable alternative is that god(s) made the primitive animals. Meyer has an undergraduate degree in physics and earth science (1981) and got a Ph.D. in history and philosophy of science ten years later (1991). He is not a scientist and he is not an expert on evolution.

Casey Luskin has a Master's degree in earth sciences but later on he got a law degree and he is primarliy a lawyer. He is not a scientist and he is not an expert on evolution.

David Klinghoffer is a writer. He is not a scientist and he is not an expert on evolution.

Nick Matzke is a graduate student who is finishing up his Ph.D. in evolutionary biology. He is a scientist and he is an expert on evolution. He is also an expert on Intelligent Design Creationism.

Nick Matzke wrote a long review of Darwin's Doubt—a book written by a philosopher [Meyer’s Hopeless Monster, Part II].

Casey Luskin, a lawyer, took it upon himself to critique Matzke's review [How "Sudden" Was the Cambrian Explosion? Nick Matzke Misreads Stephen Meyer and the Paleontological Literature; New Yorker Recycles Misrepresentation]. Luskin says,

Since Matzke published his review, The New Yorker reviewed Meyer's book. Gareth Cook, the science writer who wrote the piece, relied heavily on Matzke's critical evaluation, even though Matzke is a graduate student and not an established Cambrian expert. Cook uncritically recycled Matzke's claim that the Cambrian explosion took "many tens of millions of years," ...

Do you see the irony? Meyer is a philosopher and Luskin is a lawyer but poor old Nick is just a graduate student about to get a Ph.D. in evolutionary biology. Matzke is not an established Cambrian expert. Neither are Meyer or Luskin but that doesn't seem to stop them from criticizing Matzke and all other evolutionary biologists and all paleontologists.¹

David Klinghoffer just can't wait to contribute his two cents. Klinghoffer isn't a scientist and he certainly isn't an expert on paleontology but that doesn't mean he can't have an opinion [Regarding Matzke, Coyne, and Darwin's Doubt, a Reader Asks].

That is a good question. Casey Luskin has already demonstrated what a non-paleontologist Matzke is.

How could non-scientist Klinghoffer possibly know whether lawyer Casey Luskin had made a good case against evolutionary biologist Nick Matzke? Does Klinhoffer realize that Luskin is a lawyer, not a paleontologist?

Do you wonder why we call them IDiots?

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1. My irony meter survived but it was touch-and-go for a minute or two.

Can You Name These Famous People?

I was cleaning up my files and I came across this photo from seven years ago. It's one of those vanity photos¹ where I try to impress you by having my picture taken with famous people.

Can you name all the people in the photo (hint, I'm the one on the right). You're not allowed to guess if you are one of the people in the photo.

Are you impressed? (You should be.)

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1. That's what Jerry Coyne calls them

Speaking of Trees

My friends and colleagues, David Isenman and Jacqueline Segall, used to have a big tree in their back yard. On Monday July 8th it rained ... a lot. The ground became very soggy and the tree tipped over.

So much for the life of this tree. They need a new shed.

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What Is Humanism?

What the heck is humanism? The short answer is ... I have no idea.

If someone tells me they're a humanist then I can guess that they have some kind of ethical standards that have nothing to do with religion but that's about all I can guess. They might as well have told me that they are an atheist and leave it at that.

Are humanists socialists? Do they all favor socialized medicine and support unions? Do they oppose the death penalty? Are they in favor of gun control and abortion on demand? Do humanists oppose the American war in Afghanistan? Did they support the invasion of Iraq?

Are humanists willing to vote for a Republican or a Conservative? How about a Communist? Do all humanists think gay marriage should be legal? Would they legalize prostitution and pornography? Would they legalize drugs like cocaine and marijuana? How do they feel about euthanasia?

Do humanists support a public school system or are some in favor of vouchers and private schools? Do they all have the same position on immigration? on welfare?

I don't know the answer to any of these questions. I don't know what it means to be a humanist.

Hermant Mehta thinks that Humanism tells us what he believes. Watch this video to see what that means.


Still confused? Go to the American Humanist Association website and you'll be even more confused. Read the Humanist Manifesto and the essays by Fred Edwords. They don't answer any of the questions I asked.

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How to Build a Research Institute

The Francis Crick Institute is under construction in London (UK). When I first heard about this I thought that it would be a wonderful place for theoretical biologists—a sort of Institute for Advanced Study for biologists. That would be in keeping with the career of Francis Crick. It's also something that sorely needed in the 21st century because most biology has degenerated into data collection and mining with little attention to ideas and concepts.

Alas, the director, Paul Nurse, had other ideas. He wanted to create "a world-leading centre of biomedical research and innovation." In other words, translation research.

Paul Nurse and two research directors (Richard Treisman and Jim Smith) wrote an editorial in a recent issue of Science [Building Better Institutions]. They take it as a given that what Great Britain needs is a research institute that concentrates on medical research. They also believe that mixing scientists, clinicians, and representatives of the pharmaceutical industry will lead to better results. You better throw in a few physical scientists for good measure because physical scientists have good ideas.

Despite the recent growth in scientific knowledge, conventional discipline-based methods have not been suffi ciently effective at developing new understanding and treatments. Researchers need to be encouraged to identify important questions and tackle them with multidisciplinary approaches. Contemporary biomedical research has to integrate biological, nonbiological, and clinical disciplines, and its application requires interactions with hospital and commercial partners. This can be facilitated by research institutions with an environment that supports strong interdisciplinary interactions between scientists: a place where laboratory biologists are encouraged to collaborate with clinical researchers to understand the medical implications of their work, with pharmaceutical companies for the translation of discoveries into treatments, and with physical scientists to expand their thinking and repertoire of experimental approaches. Such an institution must be continually open to new ideas and permeable to interactions with outside researchers and organizations.

We've been doing exactly that at our hospital research institutes here at the University of Toronto. The industrial relationship has been helped by something we call the MaRS Discovery District. The experiment has been running for over a decade and, as I'm sure you all know, it has been hugely successful. Toronto has been churning out new medical discoveries on a daily basis. (Not!)

The Francis Crick Institute will support young investigators because scientists at the beginning of their career have such a tremendous track record of creativity and originality. (?) In fact, the new institute believes so strongly in young investigator that 80 out of 120 positions will be set aside for them. But what happens when they reach their mid-forties?

These appointments will be of up to 12 years, supported by the Crick's funding partners (the Medical Research Council, Cancer Research UK, and the Wellcome Trust). Group leaders will then leave the institute to establish a research group elsewhere; the aim is to give researchers who are effective and remain in the United Kingdom a transition package to support their moves, creating a thriving network of highly trained researchers.

Science is a risky business so every year there will likely be three or four investigators whose time is up but whose scientific output is just average. What happens when they're tossed out of the institute?

Does anyone think this is a good idea?

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What Should We Teach About the "Tree of Life"?

As most of you already know, I think the Three Domain Hypothesis is dead. The history of life is better explained as a net with rampant transfer of genes between species [The Web of Life]. This idea has been widely promoted by Ford Doolittle.

The debate over the tree of life has implications concerning the distinction between "prokaryote" and "eukaryote." I was checking some recent papers and came across one by Doolittle and Zhaxybayeva (2013) that seems particularly relevant. They discuss the evidence for and against the division of life into three domains and the attempt by Norm Pace to ban the word "prokaryote."

The authors point out, once again, that eukaryotic genes are most closely related to genes from cyanobacteria, proteobacteria, and archaebacteria, in that order. The majority, by far, have their closest homologs in bacteria, not archaebacteria. The most likely explanation is that euakryotes are chimeras resulting from fusion of an archaebacterium and a eubacterium plus genes transferred from mitochondria and chloroplast to the nuclear genome.

The Largest Prokaryotic Genomes

Some bacterial genomes are quite large. A few are larger than the smallest eukaryotic genomes.

Many species of cyanobacteria are complex, multicellular organisms [Multicellular Bacteria]. Those species tend to have large genomes.

Recently Degan et al. (2013) sequenced the genomes of six new cyanobacteria species and one of them turns out to have a large genome.¹ (see Contradictory Phylogenies for Cyanobacteria for more information on that paper.) The species is Scytonema hofmanni and its genome is 12,073,012 bp in size. It has 12,356 potential protein-coding genes. If all of them are correctly identified then the total, counting non-protein-coding genes, is likely to be 12,500 genes. That's a record for prokaryotes.

Half of these genes are only found in Scytonema and that's very strange.

There are bacteria with larger genomes, notably the soil bacterium Ktedonobacter racemifer with a genome size of 13,661,586 bp.

For comparison, the genome of the yeast, Saccharomyces cerevisiae, is 12,156,677 bp in size and it has 6,200 genes.

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Photo Credit: Scytonema hofmanni from cyanobacteria slides.

1. Some of you might be under the impression that I give a shit about Norm Pace and his attempt to banish the word "prokaryote" (Pace, 2009). Don't bother to try and convince me because it requires that I accept the false Three Domain Hypothesis and that ain't gonna happen.

Dagan, T., Roettger, M., Stucken, K., Landan, G., Koch, R., Major, P., Gould, S. B., Goremykin, V.V., Rippka, R., de Marsac, N.T., Gugger, M., Lockhart, P.J., Allen, J.F., Brune, I., Maus, I., Pühler, A. and Martin, W.A. (2013) Genomes of stigonematalean cyanobacteria (Subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome biology and evolution 5:31-44.
[doi: 10.1093/gbe/evs117]

Pace, N.R. (2009) Time for a change. Nature 441:289. [doi:10.1038/441289a]

Contradictory Phylogenies for Cyanobacteria

The cyanobacteria are interesting for a number of reasons. They have a complex photosynthesis pathway with two separate phostosystems and an oxygen evolving complex. That means they can use water as an electron donor and NADP^⊕ as an electron acceptor.

Cyanobacteria probably played an important role in creating an atmosphere with significant levels of oxygen but, contrary to some speculation, they almost certainly arose fairly late in the history of life (i.e. after 500 million years). Cyanobacteria make up a significant proportion of life in the ocean. Primitive cyanobacteria gave rise to chloroplasts in modern plants and algae.

The Shortest Distance ....

I have many pet peeves. One of them concerns the people who build paths and walkways. If you're going to spend a lot of money constructing fancy walkways, then it makes sense to put a little thought into where you're going to put them. As a general rule, you should put the walkway where people are going to walk.

A few years ago (2008), the University of Toronto spent a million dollars on constructing new pathways throughout the downtown campus. The new paths mostly followed the old paths but there were places where that didn't make sense. As I reported back then [If you build it, will they follow?], the old path didn't line up with the new ramp to my building (see photo below). The guys building the path agreed with me that the placement of the walkway made no sense but they were overruled by their supervisor who insisted that the alignment wasn't a problem. People would stay on the new walkway and they would be encouraged to do so by strategic placement of a big rock.



Can you guess what happened? That ramp is now the main entrance to my building for people coming up from the subway exit. Will they follow the path, taking a sharp right turn then a sharp left turn or will they cut straight across the grass making as much of a mess as before the new walkway was constructed?

Here's the result ...

Isn't that ridiculous? Just as predicted, people take the shortest distance between two points and if that means walking over the grass and making an ugly mess, then so be it. What's the point of spending a ton of money to make the campus look nice if this is the result?

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Evidence for Intelligent Design

Remember how the IDiots are always trying to tell us that their movement is scientific? It's all about scientific evidence for design.

The facts say otherwise. Almost all of their arguments are based on "evidence" against evolution and on trashing scientists, especially Darwin. Much of their opposition has nothing to do with scientific evidence of design; instead, it's directed at materialism and atheism and other views that they see as an integral part of something called "Darwinism."

Let's see how bizarre this can get. Friedrich Nietzsche ("God is dead") is hardly someone who the IDiots respect for his philosophical view. But that doesn't matter as long as he said something bad about Charles Darwin [Nietzsche, possibly the Nazis’ favourite well-known philosopher, criticized Darwinism on aesthetic grounds].

But, wait a minute. If Nietzsche was a favorite of the Nazis then Darwin must have been opposed to Nazism because Nazi Neitsche criticized natural selection. I'm confused. What does this have to do with evidence of design?

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How the IDiots View Genome Research

It's safe to say that a majority of knowledgeable scientists now agree that the most of our genome is junk. This is bad news for Intelligent Design Creationism because they have staked their credibility on the idea that if the DNA is present is must be the product of god(s) the intelligent designer and it must be there for a reason.

One of the latest posts on Evolution News & Views (sic) emphasizes this point [More Clues that Intergenic DNA Is Functional]. Its author doesn't identify herself/himself. The point of the post is to cherry-pick a couple of papers from the scientific literature, including the horrible paper by Hangauer et al. (2013) [see How to Make a Scientific Argument ].

Jenny McCarthy Will Be the New Co-Host of The View

You all remember Jenny McCarthy, right? She's the person who urges parents not to vaccinate their children, prompting formation of the Jenny McCarthy body count.

Sandwalk readers might recall that Jenny McCarthy was scheduled to appear at an Ottawa fund raising event last February until CFI Canada and the Ottawa Skeptics forced the organizers to dump her [Jenny McCarthy Dumped].

Now she's been officially named co-host of The View. What in the world was ABC thinking?

I have sent a complaint to ABC. Here's a convenient webpage: contact us.

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Hat Tip: Friendly Atheist.

Monday's Molecule #209

Last week's molecule was depicted on a stamp honoring Gerty Cori. It was supposed to be the "Cori ester" (glucose 1-phosphate) but the image shown on the stamp is not correct. Nobody recognized that so there was no winner last week [Monday's Molecule #208].

Today's molecule is a very famous RNA with secondary structure. Do you recognize it without BLASTing the sequence?

Email your answers to me at: Monday's Molecule #209. 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.)

Happy Bastille Day!

On July 14, 1789 a bunch of French citizens stormed the Bastille and liberated a handful of political prisoners [Bastille Day]. It marks the beginning of the French Revolution.

One of Ms. Sandwalk's ancestors is William Playfair, inventor of pie charts and histograms [Bar Graphs, Pie Charts, and Darwin]. He's famous because he knew Erasmus Darwin. He's also famous because there are stories that he took part in the Storming of the Bastille while living in Paris.

One the other hand, there are plenty of things for which he is less than famous [William Playfair] and there's a a good reason why his children left England and migrated to Canada becoming farmers near Perth, Ontario.

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People I Met in Chicago at SMBE2013

I had a great time at SMBE2013 (Society for Molecular Biology and Evolution) in Chicago. Here are some of the people I met. I apologize for not including everyone—I forgot to take pictures of everyone I talked to.

I went to hear Masatoshi Nei give a talk on Monday morning (July 8) during a special session on "Ideas and Thoughts." The title of his talk was "Darwinism and the Theory of Mutation-Driven Evolution." This was the first time I had seen Nei in person and it was quite a thrill. I've been a huge fan ever since I read Molecular Evolutionary Genetics in 1987. That's when I first became aware of the power of population genetics and the importance of mutation and mutationism.

What Did Dan Graur Say in Chicago?

Dan Graur gave a fantastic and entertaining talk at SMBE2013 [Powerpoint]. He covered a lot of bases, but unfortunately left some out 'cause he had many slides that he didn't get to because of time limitations. Most of the audience enjoyed the talk very much—there was much laughter and enthusiastic head nodding. (I figure that two thirds of the audience agreed with his stance on junk DNA and ENCODE.)

Apparently Cornelius Hunter was in the audience because he blogged about it on Darwin's God: Dan Graur Gave a Great Talk This Week (copied on Uncommon Descent: Dan Graur Gave a Great Talk This Week). It's a shame he didn't make himself known to me or Reed Cartwright or Nick Matzke.

One of the things that Graur said was that if ENCODE is right then evolution is wrong. Now this may be a bit of an exaggeration, but not by much. If the ENCODE leaders are right that 85% of our genome has a biological function then we really do have to rethink the C-value paradox and genetic load. We also have to re-think a lot of biochemistry. I think that's what Dan meant. Cornelius Hunter says that's the one "glaring error" in Graur's presentation.

Theme

Genomes
& Junk DNAGraur said that junk DNA is a "known known" and by that he means that there's plenty of evidence for junk DNA. It's not "dark matter" and we don't use the term "junk" to mask our ignorance. Speaking of ignorance, Cornelius Hunter seems to be completely unaware of any evidence for junk DNA. I guess he didn't stay to hear my presentation.

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How Not to Do Science

Theme
Genomes
& Junk DNAMany reputable scientists are convinced that most of our genome is junk. However, there are still a few holdouts and one of the most prominent is John Mattick. He believes that most of our genome is made up of thousand of genes for regulatory noncoding RNA. These RNAs (about 100 of them for every single protein-coding gene) are mostly involved in subtle controls of the levels of protein in human cells. (I'm not making this up. See: John Mattick on the Importance of Non-coding RNA )

It was a reasonable hypothesis at one point in time.

How do you evaluate a hypothesis in science? Well, one of the things you should always try to do is falsify your hypothesis. Let's see how that works ...

1. The RNAs should be conserved. FALSE
2. The RNAs should be abundant (>1 copy per cell). FALSE
3. There should be dozens of well-studied specific examples. FALSE
4. The hypothesis should account for variations in genome size. FALSE
5. The hypothesis should be consistent with other data, such as that on genetic load. FALSE
6. The hypothesis should be consistent with what we already know about the regulation of gene expression. FALSE
7. You should be able to refute existing hypotheses, such as transcription errors. FALSE

Normally, you would abandon a hypothesis that had such a bad track record but true believers aren't about to do that. So what's next? Maybe these regulatory RNAs don't show sequence conservation but maybe their secondary structures are conserved. In other words, these RNAs originated as functional RNAs with a secondary structure but over the course of time all traces of sequence conservation have been lost and only the "conserved" secondary structure remains.¹ The Mattick lab looked at the "conservation" of secondary structure as an indicator of function using the latest algorithms (Smith et al., 2013). Here's how they describe their attempts to prove their hypothesis in light of conflicting data ...

The majority of the human genome is dynamically transcribed into RNA, most of which does not code for proteins (1–4). The once common presumption that most non–protein-coding sequences are nonfunctional for the organism is being adjusted to the increasing evidence that noncoding RNAs (ncRNAs) represent a previously unappreciated layer of gene expression essential for the epigenetic regulation of differentiation and development (5–8). Yet despite an exponential accumulation of transcriptomic data and the recent dissemination of genome-wide data from the ENCODE consortium (9), limited functional data have fuelled discourse on the amount of functionally pertinent genomic sequence in higher eukaryotes (1, 10–12). What is incontrovertible, however, is that evolutionary conservation of structural components over an adequate evolutionary distance is a direct property of purifying (negative) selection and, consequently, a sufficient indicator of biological function The majority of studies investigating the prevalence of purifying selection in mammalian genomes are predicated on measuring nucleotide substitution rates, which are then rated against a statistical threshold trained from a set of genomic loci arguably qualified as neutrally evolving (13, 14). Conversely, lack of conservation does not impute lack of function, as variation underlies natural selection. Given that the molecular function of ncRNA may at least be partially conveyed through secondary or tertiary structures, mining evolutionary data for evidence of such features promises to increase the resolution of functional genomic annotations.

Here's what they found ..

When applied to consistency-based multiple genome alignments of 35 mammals, our approach confidently identifies >4 million evolutionarily constrained RNA structures using a conservative sensitivity threshold that entails historically low false discovery rates for such analyses (5–22%). These predictions comprise 13.6% of the human genome, 88% of which fall outside any known sequence-constrained element, suggesting that a large proportion of the mammalian genome is functional.

Apparently 13.6% of the human genome is a "large proportion." Taken at face value, however, the Mattick lab has now shown that the vast majority of transcribed sequences don't show any of the characteristics of functional RNA, including conservation of secondary structure. Of course, that's not the conclusion they emphasize in their paper.

Why not?

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1. I can't imagine how this would happen, can you? You'd almost have to have selection AGAINST sequence conservation.

Smith, M.A., Gese, T., Stadler, P.F. and Mattick, J.S. (2013) Widespread purifying selection on RNA structure in mammals. Nucleic Acid Research advance access July 11, 2013 [doi: 10.1093/nar/gkt596]

Where Am I?

How many of you recognize this place? Note that the line-up is not (quite) out the door. How cool is that!?

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Monday's Molecule #208

Last week's molecule was the fatty acid synthase complex [Monday's Molecule #207]. The winner was Matt McFarlane. He should contact me by email to collect his winnings.

Today's molecule was pictured on a US stamp issued in April 2008. Can you identify the molecule? ... Be precise, there's only one correct answer and it may not be the one you think.

Email your answers to me at: Monday's Molecule #207. 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.)

Can You Prove that God(s) Do Not Exist?

Atheists do not believe in any gods. An atheist does not claim to have proof that gods don't exist, although they do claim that most of the evidence for god(s) is wrong.

I really like the way Hemant Mehta explains this on his blog Friendly Atheist.

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Canada and Ontario Will Celebrate Pope John Paul II Day

The House of Commons in Canada has passed a bill declaring that Canada will celebrate Pope John Paul II Day on April 2nd every year [An Act to establish Pope John Paul II Day]. It was a private member's bill introduced by Conservative Wladyslaw Lizon (Mississauga East—Cooksville). Lizon is Polish, which partly explains his admiration for the former Pope. Read what Veronica Abbass has to say about this: Tommy Douglas versus Karol Wojtyła.

Meanwhile, in Ontario, a similar bill was passed by the provincial legislature [see Blindsided on Canadian Atheist].

It's tempting to dismiss both these bills as trivial. After all, nobody really expects either government to make a big fuss about it next April 2nd. Its also tempting make excuses by recognizing that few MPs or MPPs could risk speaking out against them.

I don't think we should settle for that. The facts are revolting. Canada has set aside a special day for a foreign despot whose religious and moral views are despised by a large number of Canadians, and rejected by most Catholics. How in the world could that happen in the 21st century?

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Five Things You Should Know if You Want to Participate in the Junk DNA Debate

Here are five things you should know if you want to engage in a legitimate scientific discussion about the amount of junk DNA in a genome.

1. Genetic Load
   Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk.
2. C-Value Paradox
   A comparison of genomes from closely related species shows that genome size can vary by a factor of ten or more. The only reasonable explanation is that most of the DNA in the larger genomes is junk.
3. Modern Evolutionary Theory
   Nothing in biology makes sense except in the light of population genetics. The modern understanding of evolution is perfectly consistent with the presence of large amounts of junk DNA in a genome.
4. Pseudogenes and broken genes are junk
   More than half of our genomes consists of pseudogenes, including broken transposons and bits and pieces of transposons. A few may have secondarily acquired a function but, to a first approximation, broken genes are junk.
5. Most of the genome is not conserved
   Most of the DNA sequences in large genomes is not conserved. These sequences diverge at a rate consistent with fixation of neutral alleles by random genetic drift. This strongly suggests that it does not have a function although one can't rule out some unknown function that doesn't depend on sequence.

If you want to argue against junk DNA then you need to refute or rationalize all five of these observations.

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How to Make a Scientific Argument

The debate over the amount of junk in our genome is a genuine scientific debate. There are legitimate scientific points of view on both sides although the weight of evidence and logic is tilting heavily in favor of junk DNA. It looks more and more like most (~90%) of our genome is junk.

The problem with the debate is that the scientific literature is full of papers attacking junk DNA while there are very few papers promoting it. This is partly because there haven't been any new discoveries in favor of junk DNA. On the other hand, there have been quite a few discoveries showing that some small part of the genome that was thought to be junk might have a function. Even though these discoveries make an insignificant contribution to the big picture, they are often blown up out of all proportion and promoted as an end to junk DNA.

A recent paper in PLoS Genetics illustrates the problem.

Monday's Molecule #207

Last week's molecule was N-acetylmuramic acid (MurNAc) one of the components of the polysaccharide in bacterial cell walls [Monday's Molecule #206]. The winner was Michael Florea. He should contact me by email to collect his winnings.

Today's (Tuesday's) molecule is a new addition to biochemistry textbooks because its structure was only solved a few years ago. There are plenty of hints in the figure. You have to identify the molecule AND each of the seven activities that are labelled. Bonus points for the PDB identification number and the species.

Email your answers to me at: Monday's Molecule #207. 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.)

Evolution vs God

It's Ray Comfort and he's going to destroy Richard Dawkins. Bet you can hardly wait to see this movie. PZ Myers is in it. Read what he has to say at: Lie harder, little man.

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A Philosopher Trashes Junk DNA

I am one of those scientists who think that the discipline of "philosophy of science" is catering to some pretty stupid philosophers. Dan Graur found one of them, his name is Max Andrews and he's a graduate student in philosophy at the University of Edinburgh, Scotland ["I’ve Got a Little List" & “Let the Punishment Fit the Crime"].

You can read Max Andrews' blog posting at: Junk DNA Isn’t Junk. Be careful, you might find it very difficult to see the connection between this philosophy student's view of biology and anything you might recognize as real science.

It goes without saying that Max Andrews gets the Central Dogma wrong—many scientists make the same mistake. But here's a taste of what else he gets wrong.

The argument from junk DNA suggests that a designer would be maximally efficient in his use of information. There appears to be some information that does not execute or have any meaningful coding. Darwinism takes this issue and uses it as the result of the prediction that there would be left over information not being used due to natural selection and random mutation. However, it doesn’t appear that all junk DNA is actually junk.

Genome organization is patterned to be maximally informative. The overlapping codes observed are known to be evolutionarily costly, because random mutations will likely have a deteriorating effect, not an instructing role So the complex specified information entailed by any genomic region is orders of magnitude higher than previously suspected by, say, Dembski. Any seemingly random aspect of chromosome sequence arrangement is not. A case in point involves endogenous retroviruses (ERV’s). This implies that the taxonomically-specific formatting, indexing, punctuation, etc., of genomes were precisely written. Morphogenetic information is not reducible to the genotype—though it is strongly dependent upon it. Therefore, changes in DNA do not equal changes in the information that structures the body plan.

I wonder who his supervisor is? Maybe Dan or I could be external reviewer on his Ph.D. oral?

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On the Misuse of the Term "Genetic Code"

Dan Graur is fed up with journalists who don't know the difference between the "genetic code" and the sequence of a genome. He's not alone. But, unlike the rest of us, Dan has a solution. It may be a little difficult to enforce ...

See: An Artistic Inspiration for Putting an End to the Misuse of the Term “Genetic Code”.

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Will There Be a Junk DNA Debate in Chicago?

Quite a few people think that there's going to be a serious debate about junk DNA at the SMBE meeting in Chicago next week. One of the sessions has a provocative title, "WHERE DID 'JUNK' GO?", but if you look at actual session titles it doesn't look like there's going to be much of a debate.

It's true than the session organizer, Wojciech Makalowski, advertised the session as a dicussion about junk DNA ....

Keep Calm and Ask About Onions

Nick Matzke is going to the SMBE (Society for Molecular Biology and Evolution) meeting in Chicago next week. He's created a T-shirt for supporters of junk DNA [KEEP CALM and ASK ABOUT ONIONS].

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Get Science Right in Canada

Get Science Right

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John Mattick on the Importance of Non-coding RNA

John Mattick is a Professor and research scientist at the Garvan Institute of Medical Research at the University of New South Wales (Australia). He received an award from the Human Genome Organization for ....

The Award Reviewing Committee commented that Professor Mattick’s “work on long non-coding RNA has dramatically changed our concept of 95% of our genome”, and that he has been a “true visionary in his field; he has demonstrated an extraordinary degree of perseverance and ingenuity in gradually proving his hypothesis over the course of 18 years.”

The Best Enzyme

Theme

Better BiochemistryWhile I was collecting posts on biochemistry, I came across one that I wrote almost five years ago. It was about a new record for catalytic proficiency. As you know, enzymes speed up reactions that occur naturally and spontaneously. The difference between the spontaneous rate and the rate catalyzed by an enzyme is called the catalytic proficiency.

That old post [Enzyme Efficiency: The Best Enzyme] had a nice graphic showing the spontaneous rates of some reactions that take place quickly inside a cell.

Here it is ....

And here's how the information in that 2008 post got incorporated into the latest edition of my textbook.

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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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