500,000 Visitors

 
Sometime on Wednesday night Sandwalk notched up 500,000 visitors. To put this in perspective, after 16 months of blogging the total number of visitors is less than half the number who visit Pharyngula in one month.

This is depressing. We need to do something about it. Is there any way we can shut down Pharyngula?

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Fractal Wrongness

 

From Kuenwoo Lee (may not be original) ...

Fractal Wrongness

The state of being wrong at every conceivable scale of resolution. That is, from a distance, a fractally wrong person's worldview is incorrect; and furthermore, if you zoom in on any small part of that person's worldview, that part is just as wrong as the whole worldview.

Debating with a person who is fractally wrong leads to infinite regress, as every refutation you make of that person's opinions will lead to a rejoinder, full of half-truths, leaps of logic, and outright lies, that requires just as much refutation to debunk as the first one. It is as impossible to convince a fractally wrong person of anything as it is to walk around the edge of the Mandelbrot set in finite time.

If you ever get embroiled in a discussion with a fractally wrong person on the Internet--in mailing lists, newsgroups, or website forums--your best bet is to say your piece once and ignore any replies, thus saving yourself time.

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The image is "borrowed" from Jeffrey Shallit's blog Recursivity [Fractal Wrongness]

Examples of Protein Structure

Here's a slideshow of figures from Horton et al. (2006) showing cartoons of various proteins. At first it seems as though every protein is completely different but after a while you begin to notice that there are recurring motifs—especially β sheets in the hydrophobic core of a domain.



Click here to see a full-screen version of the slideshow. More adventuresome readers might want to visit the actual structures on the Protein Data Base (PDB). Here are the links to each PDB record. References to the people who solved the structure can be found in the PDB record.

• Human (Homo sapiens) serum albumin [PDB 1BJ5] (class: all-α). This protein has several domains consisting of layered α helices and helix bundles.
• Escherichia coli cytochrome b₅₆₂ [PDB 1QPU] (class: all-α). This is a heme-binding protein consisting of a single four-helix bundle domain.
• Escherichia coli UDP N-acetylglucosamine acyl transferase [PDB 1LXA] (class: all-β). The structure of this enzyme shows a classic example of a β-helix domain.
• Jack bean (Canavalia ensiformis) concanavalin A [PDB 1CON] (class: all-β). This carbohydrate-binding protein (lectin) is a single-domain protein made up of a large β-sandwich fold.
• Human (Homo sapiens)peptidylprolyl cis/trans isomerase [PDB 1VBS] (class: all-β). The dominant feature of the structure is a β-sandwich fold.
• Cow (Bos taurus) γ crystallin [PDB 1A45] (class: all-β) This protein contains β-barrel two domains.
• Jellyfish (Aequorea victoria) green fluorescent protein [PDB
  1GFL] (class: all-β). This is a β-barrel structure with a central α helix. The strands of the sheet are antiparallel.
• Pig (Sus scrofa) retinol-binding
  protein [PDB 1AQB] (class: all-β). Retinol binds in the interior of a β-barrel fold.
• Brewer’s yeast (Saccharomyces carlsburgensis) old yellow enzyme
  (FMN oxidoreductase) [PDB 1OYA] (class: α/β). The central fold is an α/β barrel with parallel β strands connected by α helices. Two of the connecting regions are highlighted in yellow.
• Escherichia coli enzyme required for tryptophan biosynthesis [PDB 1PII] (class: α/β). This is a bifunctional enzyme containing two distinct domains. Each domain is an example of an α/β barrel. The left-hand domain contains the indolglycerol phosphate synthetase activity, and the right-hand domain contains the phosphoribosylanthranilate isomerase activity.
• Pig (Sus scrofa) adenylyl kinase [PDB 3ADK] (class: α/β). This single-domain protein consists of a five-stranded parallel β sheet with layers of α helices above and below the sheet. The substrate binds in the prominent groove between helices.
• Escherichia coli flavodoxin [PDB 1AHN] (class: α). The fold
  is a five-stranded parallel twisted sheet surrounded by α helices.
• Human (Homo sapiens) thioredoxin [PDB 1ERU] (class: ). The structure of this protein is very similar to that of E. coli flavodoxin except that the five-stranded twisted sheet in the thioredoxin fold contains a single antiparallel strand.
• Escherichia coli L-arabinose-binding protein [PDB 1ABE] (class: α/β). This is a two-domain protein where each domain is similar to
  that in E. coli flavodoxin. The sugar L-arabinose binds in the cavity between the two domains.
• Escherichia coli DsbA (thiol-disulfide oxidoreductase/disulfide isomerase) [PDB 1A23] (class: α/β). The predominant feature of this structure is a (mostly) antiparallel β sheet sandwiched between α helices. Cysteine side chains at the end of one of the α helices are shown (sulfur atoms are yellow).
• Neisseria gonorrhea pilin [PDB 2PIL] (class: α + β). This polypeptide is one of the subunits of the pili on the surface of the bacteria responsible for gonorrhea. There are two distinct regions of the structure: a β sheet and a long α helix.
• Chicken (Gallus gallus) triose phosphate isomerase [PDB 1TIM]. This protein has two identical subunits with α/β barrel folds.
• HIV-1 aspartic protease [PDB 1DIF]. This protein has two identical all-β subunits that bind symmetrically. HIV protease is the target of many new drugs designed to treat AIDS patients.
• Streptomyces lividans potassium channel protein [PDB 1BL8]. This membrane-bound protein has four identical subunits, each of which contributes to a membrane-spanning eight-helix bundle.
• Bacteriophage MS2 capsid protein [PDB 2MS2]. The basic unit of the MS2 capsid is a trimer of identical subunits with a large β sheet.
• Human (Homo sapiens) hypoxanthine-guanine phosphoribosyl transferase (HGPRT) [PDB 1BZY]. HGPRT is a tetrameric protein containing two different types of subunit.
• Rhodopseudomonas viridis photosystem [PDB 1PRC]. This complex, membrane-bound protein has two identical subunits (orange, blue) and two other subunits (purple, green) bound to several molecules of photosynthetic pigments.

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Horton, H.R., Moran, L.A., Scrimgeour, K.G., perry, M.D. and Rawn, J.D. (2006) Principles of Biochemisty. Pearson/Prentice Hall, Upper Saddle River N.J. (USA)

Levels of Protein Structure

There are four levels of protein structure. The primary structure refers to the sequence of amino acid residues in the polypeptide chain written left-to-right from the N-terminus to the C-terminus.

Secondary structures are ordered structures formed by internal hydrogen bonding between amino acid residues. The common secondary structures are the α helix, the β strand, and various loops and turns. The β sheet is often counted as secondary structure although, strictly speaking, it is a motif (see below).


The tertiary structure of a polypeptide is the three-dimensional conformation. Typical proteins contain α helices, β strands, and turns, although there are some proteins that only have α helices and turns, and others that have only β sheets and turns. In many cases, the final structure consists of distinct, independently folded regions called domains.

An example of a protein with multiple domains is shown on the left. This protein is the enzyme pyruvate kinase from cat (Felix domesticus). There are three separate domains indicated by the square brackets on the side. Note that each of the domains is connected to another by a short stretch of unordered polypeptide chain.

In some cases, a particular domain is shared by several proteins suggesting that different proteins can be formed by combining various domains that evolved separately. In other cases, similar domain structures might arise independently by convergent evolution.

Quaternary structure only applies to proteins that are composed of more than one polypeptide chain. Each of the polypeptides is called a subunit. The subunits might be identical, as in the example shown above, or they might be very different as in my favorite enzyme ubiquinone:cytochrome c oxidoreductase (complex III).

There are certain motifs that occur over and over again in different proteins. The helix-loop-helix motif, for example, consists of two α helices joined by a reverse turn. The Greek key motif consists of four antiparallel β strands in a β sheet where the order of the strands along the polypeptide chain is 4, 1, 2, 3. The β sandwich is two layers of β sheet [see β Strands and β Sheets].

The vast majority of motifs do not have a common evolutionary origin in spite of many claims to the contrary. They arise independently and converge on a common stable structure. The fact that these same motifs occur in hundreds of different proteins indicates that there are a limited number of possible folds in the universe of protein structures. The original primitive protein may have been relatively unstructured but over time there will be selection for more and more stable structures. This selection will favor the common motifs.

Larger motifs are often called domain folds because they make up the core of a domain. The parallel twisted sheet is found in many domains that have no obvious relationship other than the fact that they share this very stable core structure. The β barrel structure is found in many membrane proteins. There are dozens of enzymes that have adapted to an α/β barrel. These enzymes are not evolutionarily related. (The β helix is much less common.)

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[Figure Credit: The figures are from Horton et al. (2006)]

Horton, H.R., Moran, L.A., Scrimgeour, K.G., perry, M.D. and Rawn, J.D. (2006) Principles of Biochemisty. Pearson/Prentice Hall, Upper Saddle River N.J. (USA)

Loops and Turns

In addition to α helices and β strands, a folded polypeptide chain contains two other types of secondary structure called loops and turns. (There are also regions of unordered structure, often called coils.)

Loops and turns connect α helices and β strands. The most common types cause a change in direction of the polypeptide chain allowing it to fold back on itself to create a more compact structure.

Loops are not well defined. They generally have hydrophilic residues and they are found on the surface of the protein. Loops that have only 4 or 5 amino acid residues are called turns when they have internal hydrogen bonds. Reverse turns are a form of tight turn where the polypeptide chain makes a 180° change in direction. Reverse turns are also called β turns because they usually connect adjacent β strands in a β sheet.

Reverse turns. (left) Type I β turn. The structure is stabilized by a hydrogen bond between the carbonyl oxygen of the first N-terminal residue (Phe) and the amide hydrogen of the fourth residue (Gly). Note the proline residue at position n + 1 (right) Type II β turn. This turn is also stabilized by a hydrogen bond between the carbonyl oxygen of the first N-terminal residue (Val) and the amide hydrogen of the fourth residue (Asn). Note the glycine residue at position n + 2 [PDB 1AHL (giant sea anemone neurotoxin)]. (Horton et al. 2006)

The two most common common types of β turn are the type I and type II turns shown above. The key point about turns is that they are highly ordered structures stabilized by internal hydrogen bonds. This is why they are counted as the third form of secondary structure (along with the α helix and β strand).

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Horton, H.R., Moran, L.A., Scrimgeour, K.G., perry, M.D. and Rawn, J.D. (2006) Principles of Biochemisty. Pearson/Prentice Hall, Upper Saddle River N.J. (USA)

Nobel Laureates: Sir William Henry Bragg and Lawrence Bragg

 

The Nobel Prize in Physics 1915.

"for their services in the analysis of crystal structure by means of X-rays"


In 1915, Sir William Henry Bragg (1862 - 1942) and William Lawrence Bragg (1890 - 1971) were awarded the Nobel Prize in Physics for their work on the structure of crystals as determined by X-ray crystallography. The Physics prize in 1914 had been awarded to Max von Laue for his discovery of the diffraction of X-rays by crystals.

In order to solve the structure of a crystal, two advances were necessary. First, the senior Bragg developed an X-ray spectrometer that produced a monochromatic (single frequency) beam of X-rays of the desired strength. Second, his son Lawrence, worked out the mathematics of the diffraction in order to relate the pattern of diffraction images to the underlying structure. Part of this solution is the Bragg Equation or Bragg's Law.

After World War II, William Lawrence Bragg (then Sir Lawrence Bragg) became head of the Cavendish Laboratory in Cambridge. He rapidly transformed the laboratory into a center or the study of biological molecules. Bragg was responsible for hiring several future Nobel laureates including Max Perutz, John Kendrew, and Fred Sanger. Francis Crick and Jim Watson were also part of this group [see The Storyof DNA: Part 1].

The Braggs were the first Australians to win Nobel Prizes. Lawrence Bragg was the youngest person to win a Nobel Prize (he was 25 years old in 1915). The Braggs are the only father and son team to share a Nobel Prize. (Can anyone name the other parent/sibling pair(s) to win separate Nobel Prizes?)

The presentation speech was delivered by Professor G. Granqvist, Chairman of the Nobel Committee for Physics of the Royal Swedish Academy of Sciences.
THEME:

Nobel Laureates

Von Laue's epoch-making discovery of the diffraction of the X-rays in crystals, on the one hand established wave motion as the essential quality of those rays and, on the other, afforded the experimental proof of the existence of molecular gratings in the crystals. The problem, however, of calculating the crystal structures from von Laue's formulae was an exceedingly complicated one, in as much as not only the space lattices, but also the wavelengths and the intensity-distribution over the various wavelengths in the spectra of the X-rays, were unknown quantities. It was consequently a discovery of epoch-making significance when W.L. Bragg found out that the phenomenon could be treated mathematically as a reflection by the successive parallel planes that may be placed so as to pass through the lattice points, and that in this way the ratio between the wavelengths and the distances of the said planes from each other can be calculated by a simple formula from the angle of reflection.

It was only by means of that simplification of the mathematical method that it became possible to attack the problem of the crystal structures, but to attain the end in view it was further necessary that the photographic method employed by von Laue should be replaced by an experimental one, based on the reflection principle, which admitted of a definite, even though at first unknown, wavelength being made use of. The instrument requisite for the said purpose, the so-called X-ray spectrometer, was constructed by Professor W.H. Bragg, W.L. Bragg's father, and it has been with the aid of that instrument that father and son have carried out, in part conjointly, in part each on his own account, a series of extremely important investigations respecting the structure of crystals.

If a number of cubes are laid on and beside each other in such a way that one cube face coincides in every case with the face of an adjoining cube, whereby consequently eight vertices always meet in one point, those angular points give a visual picture of the lattice points in the so-called simple cubic lattice. If again a lattice point is placed so as to coincide with the central point of each cube face, the so-called face-centred cubic lattice is obtained, whereas the centred cubic lattice has one lattice point in every cube-centre. With the exception of these three cases there is no cubic lattice that fulfils the condition that parallel planes placed in any direction whatever so as to pass through all the lattice points, shall also be at a constant distance from each other. The space lattice in the regular or cubic system must therefore coincide with one of those three, or constitute combinations of them. In such lattice combinations, on the other hand, in which the condition just mentioned is not fulfilled, where consequently parallel planes placed to pass through all the lattice points in certain directions are not equidistant, that circumstance is revealed by an abnormal intensity distribution among spectra of different orders, when the reflection takes place by those planes.

From crystallographical data it is always known how the face of a cube is situated in any given regular crystal, and there is consequently no difficulty in fixing the crystal on the spectrometer table in such a way that the reflection shall take place by planes with any prescribed orientation.

The rays falling on the crystal were produced by X-ray tubes, platinum being at first used for the anticathode. The characteristic X-radiation of the metals consists, as is well known, of a few strong lines or narrow bands, and the very first experiments with the spectrometer revealed the X-radiation that is characteristic of platinum. However, in the research undertaken to find out the nature of complicated space lattices, in which an abnormal intensity distribution among spectra of varying orders constitutes one of the most important of the results observed, it soon proved desirable to have available an X-radiation of approximately half the wavelength of the strongest platinum-line. From theoretical considerations W.H. Bragg regarded it as probable that a metal whose atomic weight was somewhere near the figure 100, would give a characteristic radiation of the desired wavelength. Accordingly anticathodes of palladium and rhodium were produced, which fully answered the purpose in view, so that spectra ev en of the fifth order could be obtained and measured. In order to take practical advantage, however, of those results, it was essential to have a method for calculating the intensity in the case of a complicated space lattice, that would prove simpler than the one given by von Laue's theory, and W.L. Bragg developed one.

The above is a brief sketch of the methods discovered by the two Braggs for investigating crystal structures. The results of their investigations embrace a large number of crystals belonging to various systems and can only be cursorily summarized in this place.

To begin with, the two investigators applied themselves to the simplest types of the regular system, represented by the alkaline haloid salts. It then proved that potassium bromide and potassium iodide showed the spectra that are characteristic of a face-centred cubic lattice, while the spectra of potassium chloride represented a simple cubic lattice, sodium chloride occupying an intermediate position. As it must be assumed, on the strength of the analogy of these salts, both in a chemical and a crystallographical sense, that they are possessed of a corresponding space lattice, which could also be corroborated in another way, it was proved by those researchers that the lattice of the crystals in question consists of two face-centred cubic lattices corresponding to the two atoms, which interpenetrate in such a way that they together constitute one single cubic lattice.

From these investigations it follows that a metal atom in the crystals of the alkaloid salts is situated at one and the same distance from the six haloid atoms nearest to it, and vice versa - a relationship that was found to prevail, mutatis mutandis, in all the crystals examined. That means the exceedingly important discovery, both for molecular physics and chemistry, that the crystals consist of atomic lattices and not, as has been always imagined, of molecular ones.

Two face-centred cubic lattices can also interpenetrate in such a way that every point belonging to the one lattice is at the centre of gravity of a tetrahedron whose vertices are points belonging to the other lattice. That structure was found by the two Braggs in the diamond, and afforded an experimental support for the tetrahedral arrangement that chemists postulate for the four-coordinate carbon. On the other hand, the explanation became evident of why crystallographers have not been able to agree regarding the class in the regular system to which the diamond should be referred.

It would carry us too far and be quite too complicated a proceeding to give an account here of the further investigations into the space lattices of the crystals. It will suffice to add that, in the course of their investigations, the two Braggs have also discovered important relations between the amplitude and the phase difference of the diffracted rays on the one hand and the atomic weights on the other, and have also shown experimentally the influence of heat on the space lattice.

Finally it may be mentioned that the two investigators have also determined the wavelengths of the X-rays and the distances between the successive planes placed to pass through the lattice points with such exactitude, that the error, if any, is probably a t most some few units per cent and is more due to the general physical constant entering into the calculations than to the measurements themselves.

Thanks to the methods that the Braggs, father and son, have devised for investigating crystal structures, an entirely new world has been opened and has already in part been explored with marvellous exactitude. The significance of these methods, and of the results attained by their means, cannot as yet be gauged in its entirety, however imposing its dimensions already appear to be. In consideration of the great importance that these methods possess for research in the realm of physics, the Swedish Royal Academy of Sciences decided that the 1915 Nobel Prize in Physics should be divided between Professor W.H. Bragg and his son W.L. Bragg, in recognition of their services in promoting the investigation of crystal structures by means of X-rays.

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β Strands and β Sheets

 
The &alpha helix is one form of secondary structure in proteins. When a polypeptide chain contains the right sequence of amino acids it can adopt a helical conformation.

There are other conformations commonly found in proteins. One of them is the β structure, which is characterized by long extended polpeptide chains in contrast to the compact helix of the α helix. Single β strands are rarely found in proteins because the structure is not that much more stable than a random coil. However, when two adjacent β strands line up they can from bridges of hydrogen bonds. This creates a very stable structure known as a β sheet. In the example shown (left) three parallel β strands line up edge to edge to form a highly stable sheet with multiple hydrogen bond (shown in yellow).

β sheets can also be formed when antiparallel β strands align edge to edge. As a matter of fact, the antiparallel conformation is more stable, and more common, than the parallel conformation.

β strands are usually drawn as wide arrows with the tip of the arrow head representing the C-terminal end of the polypeptide chain. As shown in the cartoon on the right, the strands are often twisted and the amino acid side chains project above and below the plane of the β strand.

The amino acid composition of β strands tends to favor hydrophobic (water fearing) amino acid residues. The side chains of these residues tend to be less soluble in water than those of more hydrophilic (water loving) residues. As you might imagine, β structures tend to be found inside the core structure of proteins where the hydrogen bonds between strands are protected from competition with water molecules.

One of the common motifs in proteins is the β sandwich, formed when two β sheets are stacked on top of one another. The example shown below is the coat protein of grass pollen grains [PDB 1BMW]. For those people who are allergic to grass pollen, this protein is the main culprit. This example is the simplest form of a β sandwich since each sheet consists of only two β strands.



In order to appreciate why this is such a stable (and common) motif we need to add in the amino acid side chains. (They are usually ignored in the kinds of structures shown above so we can trace the polypeptide backbone.) In the figure on the right I've drawn the hydrophobic side chains in blue so you can see how they cluster together to form the interior "filling" of the sandwhich. You can think of these hydrophobic regions as being like the oil in a mixture of oil and water. The oil droplets tend to come together to exclude the water molecules. Similarly, the hydrophobic residues tend to come together in the middle of the protein and exclude water molecules. This is called hydrophobic interaction and it's one of the dominent weak forces n biochemistry.

Most proteins are made up of combinations of α helices and β strands. The third kind of secondary structure is turns.

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[Figures are from Horton et al. (2006) © Laurence A. Moran, Pearson/Prentice Hall]

Horton, H.R., Moran, L.A., Scrimgeour, K.G., perry, M.D. and Rawn, J.D. (2006) Principles of Biochemisty. Pearson/Prentice Hall, Upper Saddle River N.J. (USA)

Monday's Molecule #64

 
Today's molecule isn't really a molecule. It's an indirect representation of a molecule. It would be amazing if one of you could guess the molecule by looking at the figure but that's probably beyond the ability of most Sandwalk readers. (I know I can't do it.) Your task is to identify what that strange picture is all about and how is it generated.

There's a direct connection between this image and Wednesday's Nobel Laureate(s). Your second task is to figure out the significance of today's photograph and identify the Nobel Laureate(s) who is associated with discovering the technique. (Be sure to check previous Laureates.)

The reward goes to the person who correctly identifies the technique and the Nobel Laureate(s). In addition, you must identify what is unique about this particular Nobel Prize.

Previous winners are ineligible for one month from the time they first collected the prize. There is only one ineligible candidate for this week's reward. The prize is a free lunch at the Faculty Club.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the structure and the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: We have a winner! There were several dozen readers who knew that this was a photograph of an X-ray diffraction pattern. Several of them knew that the crystal was sodium chloride. Many of them guessed correctly that the Nobel Laureates were the Braggs—the first, and only, father and son team to win a Nobel Prize together. The first person to send all of this information in an email message was Andre Macphail. He wins a free lunch at the Faculty Club. Unfortunately, he lives in France so he won't be able to make it anytime soon. He's taking a rain check.

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My God Delusion Index Is Zero, What's Yours?

 

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[Hat Tip: Muse in vivo]

The Austrian Evolution Summit: The Invitation and Outline

Susan Mazur has followed up on her previous article about the upcoming conference on evolution [see Don't Throw the Baby Out with the Bathwater]. She has now published the original invitation to the conference and the first outline of the program [The Invite -- "Altenberg 16" Evolution Summit]. If you're interested in what needs to be in a new extended evolutionary theory, then get on over to Scoop and read the invitation.

Here's what the Alternberg 16 are going to talk about ...

SELECTION AND ADAPTATION REFORMED
* Drift: John Beatty, University of British Columbia
* Neutralism: Sergey Gavrilets, University of Tennessee
* Multilevel selection: David Sloan Wilson, Binghamton University

NEW VIEWS ON GENOMES AND INHERITANCE
* Gene regulatory networks: Greg Wray, Duke University
* Genomes and post-genomes: Michael Purugganan, New York University
* Epigenetic inheritance: Eva Jablonka, Tel-Aviv University
* Niche inheritance: John Odling-Smee, Oxford University

UNDERSTANDING THE PHENOTYPE
* Dynamics of macroevolution: David Jablonski, University of Chicago
* Phenotypic plasticity: Massimo Pigliucci, Stony Brook University
* Origins of form: Stuart Newman, New York Medical College

CONTRIBUTIONS FROM EVO-DEVO
* Innovation: Gerd Müller, University of Vienna
* Modularity: Günter Wagner, Yale University
* Evolvability: Marc Kirschner, Harvard University

CHARACTERISTICS OF EXTENDED SYNTHESIS
* Non-centrality of the gene: Werner Callebaut, Hasselt University
* Principles of transition: Eörs Szathmary, Collegium Budapest
* Conceptual differences in the two syntheses: Alan Love, University of Minnesota

It looks pretty interesting. Some, but not all, of these topics need to be incorporated into modern evolutionary theory. It's too bad they're missing some other topics that should be there (group selection, species sorting, speciation). This conference would be much better if Stephen Jay Gould were still alive and could attend.

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Speaking of cheating ....

 
The Face book controversy [Is it cheating to discuss an assignment in a Facebook study group?] has spread to lots of other blogs. On some of them, support for the students is getting bloggers in all kinds of hot water (e.g., A Blog Around the Clock).

Meanwhile, PZ Myers exposes another kind of cheating. This time it's the Intelligent Design Creationists () who are caught with their pants down. Read how Casey Luskin completely misrepresents the National Academy of Sciences with some very creative quote mining [Why do newspapers continue to publish Discovery Institute press releases?].

This is clearly dishonest behavior and it's about time for the general public to take notice. It will be interesting to see if any Intelligent Design Creationist tries to distance themselves from Casey Luskin. It would be a shock if any of them actually criticize Luskin for his dishonesty. If you know of a single example of a honest Intelligent Design Creationist who admits that Luskin was dishonest then please let me know. I'd like to praise them in a separate posting. Let's see if Denyse O'Leary, Bill Dembski or Micheal Behe can step up to the plate.

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Happy Birthday PZ Myers

 

Today is PZ's 51st birthday. Here's a photo¹ of him sitting in the cafeteria of the Natural History Museum in London.

That's a famous guy sitting next to him but PZ doesn't seem to have noticed.

Bora is collecting all the birthday postings here.

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1. The photo is a bit grainy because my camera was on movie mode. Trust me, you don't want to see the complete movie.

Paris Slideshow

 
Here are some picture from Paris. I'm experimenting with slideshows.




Paris Slideshow

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How the National Academy of Sciences Framed their Book on Evolution

 

The National Academy of Science (USA) recently published a book on the evolution/creationism controversy. You can download it for free on their website [Science, Evolution and Creationism].

In an earlier posting I complained about one part of that book. I think the NAS made a mistake by claiming that science and religion are entirely compatible. They mislead the public by focusing on those scientist who were religious rather than state the truth, which is that the majority of scientists are not religious [see National Academies: Science, Evolution and Creationism].

We know why they did this. It was to appease the average religious American and make evolution less threatening. I don't agree with this sort of framing because it distorts the truth. As far as I'm concerned, accuracy is the number one goal of any publication by scientists and it should never be compromised.

Two of the authors of the booklet have published an article in CBE: Life Sciences Education where they explain how they developed their frame (Labov and Pope, 2008).

However, unlike its predecessors, this new edition was shaped to a large extent by a careful program of audience research. This research was initiated to bring about a better understanding of the frame of reference that the intended audiences bring to this issue. The committee decided early in the revision process that its goal was to successfully inform opinion leaders and influentials who could then use this information to help reframe discussions about the evolution "controversy." By presenting authoritative scientific information in ways that address the questions and concerns of those who are unsure about teaching evolution in science classrooms, the authoring committee would provide opinion leaders and influentials (scientists, business leaders, clergy, teachers, members of school boards, policy makers, judges, lawyers, and others) with the tools needed to change the understanding and decisions of other people who comprise the "wobbly middle." They defined the wobbly middle as the large percentage of citizens that various national polls have shown to be undecided about whether or not evolution, creationism, or some combination should be taught in public school science classrooms.

This opens a can of worms. It is very difficult walk the thin line between "presenting authoritative information" and framing that information so that it makes everyone comfortable. I'm not sure that it can be done.

As a result of discussions with non-scientists, surveys of the general public, and selected focus groups, the authors decided to place more emphasis on the compatibility of science and religion. And they decided to take the position that religion was a valid way of knowing. (In spite of the fact that most scientists disagree.)

Compared with the previous two versions, there is more discussion in SE&C about how science and religion differ as ways of knowing and how, for many scientists and other people, acceptance of the evidence for evolution can be reconciled with personal faith. Published statements are provided from various religious denominations and from prominent living scientists declaring that acceptance of the evidence for evolution is compatible with the tenets of their faith.

I'm sure Matt Nisbet and Chris Mooney are very pleased about this.

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Labov, J.B. and Pope, B.K. (2008) Understanding Our Audiences: The Design and Evolution of Science, Evolution, and Creationism. CBE Life Sci Educ 7: 20-24. [CBE Life Sciences] [DOI:10.1187/cbe.07-12-0103]

Polymerase Chain Reaction

 
The other day I was talking with several colleagues about PCR, or the polymerase chain reaction. We first started to hear about it in the mid-1980's and I was not very impressed. It was a cool reaction but what the heck was it good for? I didn't think I would ever have a need to learn about PCR.

Today's citation classic on The Evilutionary Biologist proves just how wrong I was about PCR [This Week's Citation Classic]. John Dennehy talks about it's inventor Kary Mullis, an "interesting guy" (one of the understatements of the year). Mullis is by far the most embarrassing Noble Laureate.

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