Ravel's Bolero at the Copenhagen Central Train Station

 
I love these things!

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An Interview with Maarten Boudry

 

As most of you know already, I've been a big fan of Maarten Boudry ever since I first met him in Toronto a few years ago. Last year I visited him in Gent and he bought me a beer (or three). Maarten's thesis (Here be dragons) has been published on the internet. If you haven't read it by now, you're in for a treat.

Now you can hear him in person in an interview on Think Atheist: Episode 31 Dr. Maarten Boudry OCT 23, 2011.

It almost makes you want to be a philosopher.

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Stephen Meyer Talks About Junk DNA

Stephen C. Meyer has a Ph.D. degree (1991) in the History and Philosophy of Science from Cambridge University in the UK. He is currently Program Director of the Center for Science and Culture at the Discovery Institute in Seattle, Washington, USA.

Meyer's book, Signature in the Cell: DNA and the Evidence for Intelligent Design, is an attempt to present Intelligent Design Creationism as genuine science. I'll have more to say about this later but for now I want to concentrate on one particular aspect of his case.

Mayer claims that one requirement of a genuine scientific theory is the ability to make falsifiable predictions. Does Intelligent Design Creationism make such predictions? Yes, one of the predictions is that genomes will not contain very much junk DNA. It will be instructive to see how Intelligent Design Creationists handle this issue, especialy since I've just finished a thorough review of The Myth of Junk DNA by Jonathan Wells.

Here's what Meyer says about junk DNA.

The Myth of Junk DNA by Jonathan Wells

This is the final installment of my review of The Myth of Junk DNA by Jonathan Wells (Discovery Institute Press, 2011). The other posts are listed at the bottom of this summary and in the theme posting "Genomes & Junk DNA."

Most of the IDiots at the Discovery Institute feel threatened by the existence of large amounts of junk DNA in some eukaryotic genomes, including our own. That's why they are determined to refute this idea by showing that most putative junk DNA actually has a function. Jonathan Wells feels confident enough about his reading of the scientific literature to announce that junk DNA is a "myth" and he's written a book to promote this idea.

Wells never defines "junk DNA" correctly. The correct definition of "junk" is DNA that has no known function. Wells pretends that the original definition of junk DNA was "noncoding" DNA. Thus, all those bits of noncoding DNA that have a function are evidence that refutes the notion of junk DNA.

The truth is that no knowledgeable scientist ever suggested that regulatory regions, origins of replication, centromeres, telomeres, genes that produce functional RNA molecules, and chromatin organizing regions were ever classified as junk DNA. They all knew that there was lots of noncoding DNA that had a well-defined function. Right from the beginning of his book, Wells is attacking a strawman and misleading his readers.

Monday's Molecule #146

 

Give me the complete, unambiguous, name of the molecule to win a free lunch with me.¹ Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

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

Name the molecule shown in the figure. Remember that your name has to be unambiguous. The best way to do this is to use the full IUPAC name but usually there are traditional names that will do.

UPDAYE: The winner is DK.

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1. Or with Johnny Depp or Angelina Jolie, depending on who's available on a given day.

Pray for Peterborough

 
Tomorrow the city council of Peterborough, Ontario will open their meeting with The Lord's Prayer [Agenda].

Saying Christian prayers at public meetings was declared illegal following an Ontario Court of Appeals ruling in 1999. The city council of Peterborough is announcing in advance that it will be performing an illegal act tomorrow at 6:30 PM. I assume the police will be there to arrest the mayor and council members (not).

Veronica will be there.

What's the point of having council members recite a Christian prayer before their meeting? Probably half the council members are not practicing Christians. What's the point of making the audience sit through the Lord's prayer? Many of them are at the meeting to make a presentation. What message does it send if they are not Christian?

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[Photo Credit: Saying prayers at a Durham council meeting [Praying before City Council Meetings]]

Daniel Belden and the Deerfield Massacre

William Beldon (1609-1655) was born in Heptonstall Parish, Yorkshire, England. He settled in Wethersfield in the Colony of Connecticut in 1641. (Wethersfield is just south of Hartford.)

William Beldon married Thomasine Sherwood (1615-1655) and they had the following children.

1. Samuel Beldon (1647-1737)
2. Daniel Belden (Belding) (1648-1732)
3. John Belden (1650-1713)
4. Susannah Beldon (1651-1706)
5. Mary Beldon (1653-1724)
6. Nathaniel Beldon (1654- )

I descend from John Belden (1650-1713) and his wife Ruth (Hale) Hayes (1646-1700). But this is a story about his brother, Daniel Beldon (sometimes known as Daniel Belding).

More than a Blog?

Mainstream scientists and mainstream journals are still trying to figure out what blogging is all about. They aren't alone. Science journalists are also puzzled. Even the bloggers are confused.

The latest contribution from the mainstream has just been published in the journal EMBO Reports: More than a blog. It discusses, among other things, the effect blogging had on the Wolfe-Simon et al. (2010) paper claiming that a strain of bacteria could incorporate arsenic into its DNA in place of phosphorus.

The author of the EMBO Reports article is Howard Wolinsky, an American journalist. I want to address one part of his article. Wolinsky writes,

This incident, like a handful before it and probably more to come, has raised the profile of science blogging and the freedom that the Internet offers to express an opinion and reach a broad audience. Yet it also raises questions about the validity of unfettered opinion and personal bias, and the ability to publish online with little editorial oversight and few checks and balances.

It's true that there's no editorial oversight on science blogs. It's not quite true that there are no checks and balances since most science bloggers read and comment on each other's posts and bad science bloggers are easily exposed (e.g. creationist sites).

But that's not what I want to comment about. Wolinsky's implies that the world of traditional science communication is free of personal bias and regulated by checks and balances. That's not true. The incident he's referring to is the "arsenic affair" and it a good idea to keep in mind what happened last December.

First, most of the fuss arose over the press release where the lead author made claims that were not in the Science paper and were not supported by evidence. Up until the advent of science blogging there were no serious checks and balances on press releases save for the occasional journalist who sometimes expressed a bit of skepticism. Science blogs are actually serving as checks and balances on press releases and irresponsible science journalism. That needs to be stated more often.

Second, it's simply not true that papers published in the scientific literature undergo rigorous editorial/peer review that is subject to checks and balances. It's simply not true that papers in the scientific literature are free of "unfettered opinion and personal bias." We've all known about this for decades. Science bloggers are now bringing that knowledge to the general public and (among other things) exposing bad papers to the critical analysis they should have received before being accepted for publication. There's general agreement that the Wolfe-Simon et al. (2010) paper was not subjected to rigorous peer review before it was published online. Thanks to the bloggers, publication of the print version of the paper was delayed for months and when it appeared it was accompanied by several letters of criticism. That never would have happened without science bloggers.

Science bloggers are providing the checks and balances that have gone missing in the so-called "peer-reviewed" scientific literature. The bloggers are becoming the "peers" that review the papers when the system breaks down.

While it is true that science bloggers may have an agenda and aren't subjected to rigorous peer review before publication, this should not be treated as a new phenomenon that's peculiar to blogs. If you're going to raise these issues in an article about blogging then you should also raise them with respect to the traditional scientific literature.

Third, science journalists are partly responsible for the increased role that science bloggers are playing in exposing bad science. Traditionally it was supposed to be science journalists who acted as a check on bad science and bad press releases. Recent incidents have shown us that we can no longer count on science journalists to act as skeptical reviewers. The "arsenic affair" is a good example (Carl Zimmer is a notable exception).

Today it's more likely that science journalists will follow the lead of science bloggers rather than do the required homework on their own. Many science journalists just publish paraphrased versions of press releases leaving it up to the science bloggers to expose the flaws in the press releases, and in the published paper.

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[HatTip: Jarry Coyne: An EMBO report on science blogging]

Junk & Jonathan: Part 13—Chapter 10

This is part 13 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

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The title of Chapter 10 is "From Junk DNA to a New Understanding of the Genome." It's a very misleading title since the bulk of the chapter is an attempt to refute the arguments of various evolutionary biologists.

In this chapter, we return to the arguments based on junk DNA that we encountered in Chapter 2. Richard Dawkins, Kenneth Miller, Michael Shermer, Francis Collins, Philip Kitcher, Jerry Coyne and John Avise all claimed that most of our DNA is nonfunctional junk, and that this provides evidence for Darwinian evolution and against intelligent design (ID).

Wells' statement is very misleading. He's confusing the argument about conserved pseudogenes with a claim that most of our genome is junk. Several of these authors have pointed out that the presence of similar pseudogenes at the same location in the genomes of different species (e.g. humans and chimps) is powerful evidence of descent from a common ancestor. They also point out that the IDiots have a hard time explaining such observations [Creationist Logic]. (In fact, no IDiot has ever offered a satisfactory explanation.)

Better Biochemistry: Near-Equilibrium Reactions

This is part of a series on important concepts in biochemistry. I'm concentrating on those concepts that may be widely understood and/or not well described in most textbooks. Naturally, I think we do a pretty good job in our book!

Biochemical reactions are characterized by a Gibbs free energy change that describes the amount of energy produced or consumed in the reaction. In order to compare different reactions, chemists have developed a standard Gibbs free energy change that can be used to describe all reactions. The standard Gibbs free energy change in biochemical reactions is the energy produced or consumed when all the reactions and products are at a concentration of 1M, the temperature is 25°C (298 K), the pressure is 1 atm, the pH is 7.0, and the concentration of water is 55M.

Here's an example from the gluconeogenesis/glycolysis pathway (see below). It's the reaction catalyzed by aldolase where a six-carbon molecule (fructose) is cleaved to produce two three-carbon molecules. The reaction shown here is the one in the glycolysis pathway that breaks down glucose.

The standard Gibbs free energy change for this reaction is ...

ΔG'°_reaction = +28 kJ mol^-1
In a chemistry course you might learn that this reaction is NOT spontaneous because the standard Gibbs free energy change is positive. In other words, you need to supply energy—as indicated by the plus sign in the standard Gibbs free energy change—in order to make the reaction go from left to right. The reaction will be "spontaneous" in the opposite direction where ΔG'°_reaction = -28 kJ mol^-1.

The concept of "spontaneous" and "not spontaneous" based on the standard Gibbs free energy change makes no sense in a biochemical context. The aldolase reaction, for example is part of the gluconeogenesis pathway where the two three-carbon molecles are joined to produce fructose-1,6-bisphosphate. This eventually leads to the production of glucose.

The adolase reaction is also part of the glycolysis pathway that runs in the opposite direction (as shown above). Cells can easily switch from making glucose to degrading it. How can this happen if the free energy change is +28 kJ mol^-1.¹

It isn't. The actual Gibbs free energy change inside the cell is very different than the standard Gibbs free energy change. This reaction rapidly reaches equilibrium inside the cell. Under those conditions the rates of the forward and reverse reactions are equal and ΔG = 0.

In the case of the aldolase reaction, the concentrations of the reactants and products at equilibrium will not be equal as the standard Gibbs free energy change requires. Instead, the concentration of fructose-1,6-bisphosphate will be much higher than the concentrations of glyceraldehyde-3-phosphate and dihydroxyacetone phosphate.

In biochemical terms we say that this is a "near-equilibrium" reaction. Most metabolic reactions are near-equilibrium reaction with ΔG = 0 (or close to it).

This is an important concept in biochemistry. You can't understand pathways and flux if you don't know that most of the reactions are near-equilibrium reactions where ΔG = 0.Sup>1 You also can't understand regulated reactions, where ΔG is not zero, unless you've grasped the fundamentals. (Regulated reactions are called "metabolically irreversible reactions.")

Many textbooks do a poor job of explaining near-equilibrium reactions and their importance in metabolic pathways. Some still use standard Gibbs free energy changes as a measure of direction. Fortunately, the teaching of this concept has improved enormously over the past 15 years.³ The bad news is that if you took your last biochemistry course before 1995 you may be hopelessly out-of-date!

Here's an example of bad teaching from a 2003 textbook!

Although the cleavage of fructose-1,6-bisphosphate is frequently unfavorable (ΔG'° = +23.8 kJ/mol), the reaction proceeds because the products are rapidly removed.

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1. You also have to understand the concept of steady-state—the concentrations of intermediates in a pathway don't change very much.
2. Some textbooks use +24 kJ mol^-1.
3. The best textbooks had it right long before that.

Monday's Molecule #145

 

I'm restarting Monday's Molecule. The last one was almost two years ago [Monday's Molecule #144].

The rules have changed a bit. Monday's Molecule will no longer be linked to a Noble Prize because I'm running out of Nobel Prizes that lend themselves to such a linkage. All you have to do is supply the complete, unambiguous, name of the molecule to win a free lunch. Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins.

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

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. Many of them have kindly donated their free lunch to the next contest.

Name the molecule shown in the figure. Remember that your name has to be unambiguous. The best way to do this is to use the full IUPAC name but there are several traditional names that will do.

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Kevin O'Leary Is a Jerk

 

Kevin O'Leary is one of those people who think that the world revolves around entrepreneurs and making money. He's well known in Canada because he's one of the "dragons" on Dragon's Den.

O'Leary recently got in trouble by saying that if he were Prime Minister he would "make unions illegal" and throw union members in jail. He also said; ""Unions are sheer evil." … "Unions themselves are born out of evil. They must be destroyed with evil." … "Look, no one could contain unions in hell. They were so evil they came out of hell and they came upon earth." [NUPGE / OPSEU file complaint with CBC Ombudsman over offensive anti-union comments by Kevin O'Leary].

As you might imagine, Kevin O'Leary is against the "Occupy Wall Street" movement even if he doesn't understand it. To him it must sound like a bunch of "left-wing nutbars" trying to muscle in on his God-given right to exploit the gullible.

Unfortunately he used that expression ("left-wing nutbar") on national television (CBC) and applied it to the guest they were interviewing (Chris Hedges). You can see it for yourself in the video. It's very embarrassing. I'm normally a supporter of the CBC but this makes it look like FOX News.

O'Leary has already been reprimanded by CBC's Ombudsman [CBC ombudsman says O'Leary's 'nutbar' remark violated journalistic standards]. I think it's time he was removed from the "The Lang & O'Leary Exchange."¹

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1. Not because he has a different opinion than I do. Because he's stupid.

Is Intelligent Design Creationism a Scientific Theory?

You should recall that Casey Luskin is one of those "serious science bloggers" who strikes fear into the hearts of evolutionary biologists. In fact, we are so afraid of people like Casey Luskin and Jonathan M that we go out of our way to avoid responding to their posts [see: A Reason to Doubt the IDiots].

Luskin's latest posting on Evolution News & Views (sic) is: How Do We Know Intelligent Design Is a Scientific "Theory"?. Here's the main argument ...

ID is a theory of design detection, and it proposes intelligent agency as a mechanism causing biological change. ID allows us to explain how aspects of observed biological complexity, and other natural complexity, arose. And it uses the scientific method to make its claims.

The scientific method is commonly described as a four-step process involving observations, hypothesis, experiments, and conclusion. ID begins with the observation that intelligent agents produce complex and specified information (CSI). Design theorists hypothesize that if a natural object was designed, it will contain high levels of CSI. Scientists then perform experimental tests upon natural objects to determine if they contain complex and specified information. One easily testable form of CSI is irreducible complexity, which can be tested for by reverse-engineering biological structures through genetic knockout experiments to determine if they require all of their parts to function. When scientists experimentally uncover irreducible complexity in a biological structure, they conclude that it was designed.

A Twofer

A few weeks ago David Klinghoffer criticized science bloggers for only going after "extremely marginal and daffy creationists." He challenged us to take on the "real scientists" like Jonathan M. [A Reason to Doubt the IDiots]

Today you're in for a treat, dear readers, 'cause I'm going to respond to a daffy creationist who happens to be Jonathan M. It's a twofer!

A Reason to Doubt the IDiots

 

David Klinghoffer is one of the most entertaining bloggers at Evolution News & Views. His version of logic never fails to bring a smile to my face.

Klinghoffer's latest posting is: A Reason to Doubt the Real, Rather than Pretended, Confidence of Darwin Advocates.

Much of the debate about Darwinian evolution is conducted in public online forums. If interpreted with some care, these give a convenient way of measuring the real confidence of leading spokesmen on the Darwin side. I don't mean the level of bluster -- they're all full of bluster -- but rather what they really must feel at some level deep down.

If you follow the top Darwin blogs you'll notice how eagerly and often they go in for mocking extremely marginal and daffy creationists. PZ Myers specializes in this. So too, in his books, does Richard Dawkins. How about answering the arguments of a real scientist who advocates intelligent design on scientific rather than Bible-thumping grounds -- a Douglas Axe or Ann Gauger, for example? How about a thoughtful critique of The Myth of Junk DNA or Signature in the Cell? A response to serious science bloggers like ENV's Casey Luskin or Jonathan M.?

Uh, no, thank you!

It's quite a contrast with intelligent-design advocates who, like them or not, wrestle with the top scientists and thinkers on the other side, while ignoring the small timers.

I really don't think this merits further comment by me.¹ I'll let the words stand for themselves. I hope you were as amused as I am.

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1. I assume those "serious scientists" don't read Sandwalk, Why Evolution Is True, Panda;s Thumb, Thoughts from Kansas, or dozens of other blogs and books that refute the nonsense spouted by those "serious scientists."

Image Credit: conservababes