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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Uncommon Descent holds that...

 
The mission of Uncommon Descent is clearly stated at the top of the sidebar on the blog. It says ...

Materialistic ideology has subverted the study of biological and cosmological origins so that the actual content of these sciences has become corrupted. The problem, therefore, is not merely that science is being used illegitimately to promote a materialistic worldview, but that this worldview is actively undermining scientific inquiry, leading to incorrect and unsupported conclusions about biological and cosmological origins. At the same time, intelligent design (ID) offers a promising scientific alternative to materialistic theories of biological and cosmological evolution -- an alternative that is finding increasing theoretical and empirical support. Hence, ID needs to be vigorously developed as a scientific, intellectual, and cultural project.

The Intelligent Design Creationists make a big deal of this whenever they get around to defending their worldview. They claim that Intelligent Design Creationism is a "promising scientific alternative" that deserves respect. They say that Intelligent Design Creationism is not just anti-evolutionism.

There're lying, of course, but what else is new. Here's the latest posting on Uncommon Deescent as posted by that well-known scientist and intellectual DaveScot [Speaking of T-Shirts - this is reputedly by the same designer].

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DARWIN: The Evolution Revolution

 
Today is the opening day of the Darwin exhibit at the Royal Ontario Museum in Toronto (Canada). The exhibit runs from now to Aug. 4, 2008 [The Evolution Revolution].

Discover the extraordinary story of Charles Darwin in Darwin: The Evolution Revolution, the most comprehensive exhibition ever mounted on the man whose revolutionary theory changed the world. This extraordinary exhibition traces Darwin’s life from his early years of curious observation and scientific study to his uninspired days at boarding school. Relive his five-year voyage aboard the HMS Beagle that brought him to the Galapagos Islands, and discover some of the unique animals he encountered, including African spur-thighed tortoises, an iguana and live frogs.

Walk through his historic study where he developed his ground-breaking Theory of Evolution. Intimate letters, photographs and personal artifacts give insight into aspects of Darwin’s life that are rarely seen. Discover why it took so long for Darwin to publish his findings, and how his daughter’s untimely death in 1851 may have contributed to his decision to eventually publish On The Origin of Species.

Interactive media and videos help bring Darwin and his ideas to life, and contemporary scientists explain how Darwin’s theories have held their relevance in so many areas of modern biology and science.

Darwin is organized by the American Museum of Natural History, New York in collaboration with The Field Museum, Chicago; the Museum of Science, Boston; the Royal Ontario Museum, Toronto, Canada; and the Natural History Museum, London, United Kingdom.

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[Photo Credit: David McKay, ©ROM: A first edition of Charles Darwin’s On the Origin of Species, published in 1859, on loan to the ROM from the Thomas Fisher Rare Book Library, University of Toronto. (The Origin of Species)]

Is it cheating to discuss an assignment in a Facebook study group?

 
A student at Ryerson University in Toronto faces expulsion from the university for setting up a Facebook study group that discussed chemistry assignments.

This is a complicated issue that's made the newspapers here in Toronto. One of the undergraduate bloggers at the University of Toronto explains the situation and offers an opinion. Check out Expelled for cheating on Facebook?.

Unethical conduct in general, and cheating in particular, has become a major problem at universities around the world. Part of the problem is due to the availability of resources and contacts on the internet. This opens up new possibilities for circumventing the intent of assignments and essays—possibilities that weren't available a decade ago. Nobody knows how to deal with the new realities.

In this particular case, the Professor explicitly required that students complete the assignment individually without help from anyone else. That's a very reasonable requirement, in my opinion, and there probably were times the past when almost all students were honorable enough to obey this rule. Today, that sense of "honor" seems horribly old-fashioned. To most students it will not seem like cheating if they ask their friends for help with the assignments and share information. That's what happened on the Facebook study group.

Ironically, the public nature of Facebook is what brings the chemistry students together in the first place but it is also what revealed that they are violating the rules.

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[Photo Credit: The Toronto Star: Student faces Facebook consequences]

Science, Religion, and Framing

 
There was a conference on framing at the AAAS meeting last month [How Matt Nisbet Conned AAAS]. When the meeting was first being organized I wrote to the moderator, David Goldston, to complian about the lack of balance and fairness. He replied that he had nothing to do with inviting the speakers. He told me that, as moderator, he intended to play "devil's advocate" to ensure fairness.

Goldston has written up a summary of the meeting for Nature (Goldston, 2008). In that article he cautions us that the public may not be as hostile to science as we think. With that in mind, it is wise, acording to Goldston, to develop ways to make science more appealing to a religious public.

Recognizing the complexity of public attitudes, a number of scientists and other scholars are trying to develop language to discuss evolution in ways that might build bridges to the religious. These efforts were the subject of a well-attended panel I moderated at last month's annual meeting of the American Association for the Advancement of Science in Boston, Massachusetts. Some panellists, in effect, advocated co-opting the language of religion. For example, Kenneth Miller of Brown University in Providence, Rhode Island, the author of a leading textbook on evolution and a practising Catholic, talked about embracing the notion of life having a design, but explaining it as the result and embodiment of evolution. Others, such as Matthew Nisbet, a communications scholar at American University in Washington DC who organized the panel, suggested moving the discussion away from scientific theory and talking about the medical and other benefits that have resulted from understanding evolution.

No doubt all these approaches are worth trying, and the general message of the panel — that scientists should address the public with respect rather than contempt — is well taken. But the panel failed to grapple with two important facets of the way science and religious attitudes intersect.

What are those two facets? The first is the fact that the fight is not about science alone. It's about a whole range of social issues that upset the religious right.

The second point is more interesting ...

Second, the panellists tiptoed around the fact that scientific discovery can genuinely undermine religious beliefs. The focus of the panel was on teaching evolution, but discoveries in genetics and neuroscience are likely to be far more problematic in the long run. The two fields are verging on drawing the ultimate materialist picture of human nature — humans as nothing more than proteins and electrical impulses, all machine and no ghost, to play off Descartes' formulation. This view will challenge not only fundamentalist views about the soul, but more widely held notions about what it means to be a person. That will further complicate age-old questions about the nature of individual responsibility and morality.

That's a good point. What does it have to do with the conference and with the views advocated by people like Miller and Nisbet? Would using the language of religion and talking about design—as Miller suggests—make believers more comfortable about becoming materialists? Will advertising the medical benefits of science—as Nisbet sugggests— relieve the angst of learning that God has no role to play in the universe? I don't think so. Framing science isn't going to hide the fact that it is antithetical to many of the core beliefs of the religious.

So far, so good. At least Goldston dropped a little hint to suggest that he wasn't completely taken in by the Nisbet propaganda.

But wait. In his last paragraph Goldston goes completely off the rails revealing why he was chosen as moderator.

Responding to these issues will be difficult for scientists and non-scientists alike. New discoveries about the human genome and neuroscience will no doubt be clearly linked to potential medical advances, but they may also raise new questions about what kinds of interventions are appropriate. The conundrums may leave even atheists longing for some theological guidance on how to decide what is moral. And wandering about this uncharted territory may make the well-rehearsed battles over evolution seem like the good old days.

What nonsense. Atheists don't need "theological guidance" to work through these problems. As a matter of fact, atheists are well placed to deal with the issues once the stranglehold of religion is broken. That's because atheists have long been deciding what's "moral" in the absence of God. We're good at it.

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Goldston, D. (2008) The Scientist Delusion. Nature 462:17. [Nature] [doi:10.1038/452017a]
[HatTip: Pete Dunkelberg]

Name This Building

 
How many of you can identify this Parisian building? I know I couldn't before I came across it two weeks ago.

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Michael Egnor Is an IDiot

 
Michael Egnor rises to the defense of Jonathan Wells. Readers may recall that Wells made a really stupid claim that studying antibiotic resistance in bacteria had nothing to do with evolution.

When the authors of the paper in question rejected this silly claim, Wells bent over backwards to justify his stupidity. Now Michael Egnor joins him [Dr. Wells’ Observation about the King’s Clothes].

There's one small part of that posting that really caught my eye.

The viscous personal attacks on Dr. Wells are an example. If you were a scientist, how candid about questioning the relevance of Darwinism would you be if your livelihood depended on Darwinist professors like Dr. Myers and Dr. Moran?

Anyone with an IQ above 50 knows that neither PZ or I are Darwinists [Why I'm Not a Darwinist]. We have both posted numerous articles attacking adaptationism and the emphasis on natural selection as the only mechanism of evolution. We have questioned all kinds of things about the modern orthodoxy from punctuated equilibria to evo-devo.

In other words, both of us have as much of a reputation for questioning fellow evolutionists as for challenging IDiots like Wells and Egnor.

The fact that Michael Egnor cannot see this speaks volumes.

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John Doesn't Like Richard

 
John Wilkins went to hear Richard Dawkins last night in Pheonix, Arizona. I'll leave it to you readers to figure out why John and Richard were together in such a strange place. (Hint: It's not because John got lost.)

I'm sure it will come as a surprise to no one that Wilkins took exception to some of the things Dawkins said [Dawkins' Lecture in Poenix]. As you might imagine, Wilkins really got annoyed when Dawkins talked about those who choose to overlook the silliness of belief in the supernatural. Here's what John writes ...

In particular I was annoyed that those of us who do not condemn someone for holding religious beliefs were caricatured as "feeling good that someone has religion somewhere". Bullshit. That is not why we dislike the Us'n'Themism of TGD. We dislike it because no matter what other beliefs an intelligent person may hold, so long as they accept the importance of science and the need for a secular society, we simply do not care if they also like the taste of ear wax, having sex with trees, or believing in a deity or two. Way to go, Richard. Good bit of framing and parodying the opposition. Real rational.

John, it's you who aren't being rational about this topic. Somewhere on this planet there may be a true believer in God who resembles your hypothetical caricature but they are very rare.

Most people who are willing to believe in imaginary deities are willing to believe all sorts of other things as well. They do NOT accept science with all of it's implications, You need only think of Ken Miller, Francis Collins, Michael Denton, and Simon Conway Morris to see how religious beliefs corrupt science. It's also a bit of a stretch to imply that their version of a "secular society" is the same as that of atheists.

Wake up and smell the roses. I don't care if some people like the taste of ear wax because that preference does not impinge on their understanding of science. You just can't make a similar valid claim about believers in the supernatural no matter how many times you say it. Your logic fails because there are very few believers whose faith doesn't conflict with science in one way or another.

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Do You Trust Homeopathic Medicine?

 
tkindoll at Skeptchick analyzes an international poll were respondents were asked whether they trust homeopathic medicne [Hot Off the Press - New Data on Homeopathy Usage Around the World]. Read her comments. Here's the bottom line—citizens of India are the most ignorant of science on this issue but the French are way up there as well. This is something I observed while I was in France a few weeks ago. There are frequent favorable references to pseudoscientific medicine on French television.

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Vaccines Don't Cause Autism

 
David Kirby is one of the most prominent proponents of the claim that autism is really mercury poisoning and it's caused by childhood vaccines. This isn't my field but I can recognize woo when I see it. Fortunately for the side of rationality, there are some smart people who know how to deal with the purveyors of ignorance. One of these is Orac at Respectful Insolence.

The US government recently settled a court case that appears to concede a role for vaccines in autism. Orac dissects that claim in a really excellent posting, David Kirby and the government "concession that vaccines cause autism": The incredible shrinking causation claim. Here's the bottom line ...
Orac is the nom de blog of a humble pseudonymous surgeon/scientist with an ego just big enough to delude himself that someone, somewhere might actually give a rodent's posterior about his miscellaneous verbal meanderings, but just barely small enough to admit to himself that few will. (Continued here, along with a DISCLAIMER that you should read before reading any medical discussions here.)¹

One thing that you should remember about Kirby's pretty rhetorical flourishes and speculation. It's all there to distract you from the utter failure of science to support the original claims of the mercury militia, namely that mercury in vaccines was the cause for most cases of autism, or, as Generation Rescue puts it, that autism is a "misdiagnosis for mercury poisoning." Multiple large and well-designed epidemiological studies have utterly failed to find a link between mercury in vaccines or vaccines in general and autism. Indeed, the idea that vaccines cause autism is the incredible shrinking hypothesis. It's gone from confident claims that mercury or vaccines cause nearly all cases of autism to a lot of handwaving based on one case conceded by the government in which the plaintiff had a rare mitochondrial disease which may have been aggravated by vaccines plus multiple bouts of inflammation due to otitis media, a far cry from previous cries blaming vaccines for an "autism tsunami." Is it possible that in rare cases vaccines can aggravate a preexisting condition and lead to injury that resembles autism or ASD? Despite all the studies cited by Kirby in is speculations, what we really have is one documented case of a child in which childhood vaccines probably exacerbated a preexisting mitochondrial disease who later went on to meet the diagnostic criteria for mild autism; so it's possible. It's also a far cry from the original claims of the mercury militia. Don't forget that. Also don't forget that, no matter what new physiologic alterations or abnormalities are found in autistic children, antivaccinationists always--and I mean always--manage to find a rationale to link it to vaccines, no matter how tortured that rationale is.

This is a serious issue. It's part of a much bigger picture including the attack on science by creationists. The issue is not only science vs. religion: it's rationalism vs. superstition. David Kirby is just as dangerous to the cause of science as Jonathan Wells of any or the other creationists.

Other Links: Rebecca on Skepchick: Vaccines don’t cause autism. Okay?

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1. This is one of those times when I refer to an anonymous blogger because, as Orac himself admits, his identity is an open secret.

Hybrid Plants Colonize New Environments

 
Today's Botany Photo of the Day shows Helianthus anomalus, a hybrid species of sunflower that grows in the sand dunes of Utah.

This species arose about 50,000 years ago as a hybrid of Helianthus annuus and Helianthus petiolaris. The Botany Photo of the Day website describes experiments that reproduced this hybridization event showing that hybrids can be more fit—in certain environments—than either parent. [see Jane Harris Zsovan Doesn't Understand Speciation]

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To My American Friends

 
Be careful. here's a great deal at stake here.

The world can't afford another eight years of the Bush doctrine.

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Lunch with the Winners

 
I just got back from lunch with the winners of the Monday Molecule/Nobel Laureate quiz. The two winners were Alex Ling and Dave Schuller. Alex is a student at the University of Toronto. Unfortunately he had to rush off to a class before I could get my camera ready. Maybe I can borrow the photo that Dave took and post it later on.

Dave Schuller is an X-ray crystallographer from Cornell working in the group that manages the synchrotron [MacCHESS]. He decided to drive up from Cornell this morning to have lunch with us. Right now he's on his way back with a stop at McMaster University in Hamilton. Maybe that's why he looks a little dazed in the picture.  

Dave brought me a mastodon from the Natural History Museum at Cornell. He also brought me some Bible Flash Cards so I can practice memorizing my Bible Stories. Here's an example ....

Q: Where did God ask Abraham to go?
A: Isreal, but it took 25 years of traveling to get there.

Some of the other questions were much more difficult. How many of you can remember how Ruth cared for Naomi or where the Last Supper was held? I didn't know the answer to those ones but thanks to Dave Schuller I do now.

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Tangled Bank #100

 
The latest issue of Tangled Bank is #100. It's hosted at AECHAEOPORN [Tangled Bank #100, Bad Flu Edition].

PZ Myers, in his link to this clears up a numbering error, and it turns out this is the 100th edition of Tangled Bank. Congratulation to Dr. Myers in such a long term and well run blog carnival, and thanks to all the other hosts who put time and energy to 1 through 99!

I’ve come down with a terrible flu right in time for Tangled Bank #100. This is making it quite difficult to even sit at my computer and type. Luckily, we have a volunteer to put together this issue in my absence. A famous movie star and producer and great mind of evolutionary biology. His most recent work will include the likes of Dr. Richard Dawkins and Dr. PZ Myers.

Because of various publicity concerns, he wishes to remain nameless. However, he promised that his work will be fair an unbiased, offering no cherry picking or quote mining at all.

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If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

The Humanist Globe

 
I just found a new website called the The Humanist Globe. It was created by Mark Robinson who I met at the opening of the Centre for Inquiry (Toronto) last year.

Check it out. It's full of all kinds of interesting things.

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The α Helix

 
Monday's molecule #63 is an α helix. This conformation of amino acids was first discovered by Linus Pauling who received the Nobel Prize in 1954, partly for his work on the α helix.

The following description of the α helix is taken from Horton et al. (2006) Principles of Biochemistry.

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Figure 4.10
α Helix. A region of α-helical secondary structure is shown with the N-terminus at the bottom and the C-terminus at the top of the figure. Each carbonyl oxygen forms a hydrogen bond with the amide hydrogen of the fourth residue further toward the C-terminus of the polypeptide chain. The hydrogen bonds are approximately parallel to the long axis of the helix. Note that all the carbonyl groups point toward the C-terminus. In an ideal α helix, equivalent positions recur every 0.54 nm (the pitch of the helix), each amino acid residue advances the helix by 0.15 nm along the long axis of the helix (the rise), and there are 3.6 amino acid residues per turn. In a right-handed helix, the backbone turns in a clockwise direction when viewed along the axis from its N-terminus. If you imagine that the right-handed helix is a spiral staircase, you will be turning to the right as you walk down the staircase.

The α-helical conformation was proposed in 1950 by Linus Pauling and Robert Corey. They considered the dimensions of peptide groups, possible steric constraints, and opportunities for stabilization by formation of hydrogen bonds. Their model accounted for the major repeat observed in the structure of the fibrous protein α-keratin. This repeat of 0.50 to 0.55 nm turned out to be the pitch (the axial distance per turn) of the α helix. Max Perutz added additional support for the structure when he observed a secondary repeating unit of 0.15 nm in the X-ray diffraction pattern of α-keratin. The 0.15 nm repeat corresponds to the rise of the helix (the distance each residue advances the helix along its axis). Perutz also showed that the α helix was present in hemoglobin, confirming that this conformation was present in more complex globular proteins.

In theory, an α helix can be either a right- or a left-handed screw. The α helices found in proteins are almost always right-handed, as shown in Figure 4.10. In an ideal α helix, the pitch is 0.54 nm, the rise is 0.15 nm, and the number of amino acid residues required for one complete turn is 3.6 (i.e., approximately 3 2/3 residues:one carbonyl group, three N—Cα—C units, and one nitrogen). Most α helices are slightly distorted in proteins but they generally have between 3.5 and 3.7 residues per turn.

Within an α helix, each carbonyl oxygen (residue n) of the polypeptide backbone is hydrogen-bonded to the backbone amide hydrogen of the fourth residue further toward the C-terminus (residue n + 4). (The three amino groups at one end of the helix and the three carbonyl groups at the other end lack hydrogenbonding partners within the helix.) Each hydrogen bond closes a loop containing 13 atoms—the carbonyl oxygen, 11 backbone atoms, and the amide hydrogen. This α helix can also be called a 3.6₁₃ helix, based on its pitch and hydrogen-bonded loop size. The hydrogen bonds that stabilize the helix are nearly parallel to the long axis of the helix.

Figure 4.11
View of a right-handed α helix. The blue ribbon indicates the shape of the polypeptide backbone. All the side chains, shown as ball-and-stick models, project outward from the helix axis. This example is from residues Ile-355 (bottom) to Gly-365 (top) of horse liver alcohol dehydrogenase. Some hydrogen atoms are not shown. [PDB 1ADF].

A single intrahelical hydrogen bond would not provide appreciable structural stability but the cumulative effect of many hydrogen bonds within an α helix stabilizes this conformation. Hydrogen bonds between amino acid residues are especially stable in the hydrophobic interior of a protein where water molecules do not enter and therefore cannot compete for hydrogen bonding. In an α helix, all the carbonyl groups point toward the C-terminus. Since each peptide group is polar and all the hydrogen bonds point in the same direction, the entire helix is a dipole with a positive N-terminus and a negative C-terminus.

The side chains of the amino acids in an α helix point outward from the cylinder of the helix (Figure 4.11). The stability of an helix is affected by the identity of the side chains. Some amino acid residues are found in conformations more often than others. For example, alanine has a small, uncharged side chain and fits well into the α-helical conformation. Alanine residues are prevalent in the α helices of all classes of proteins. In contrast, tyrosine and asparagine with their bulky side chains are less common in α helices. Glycine, whose side chain is a single hydrogen atom, destabilizes α-helical structures since rotation around its α-carbon is so unconstrained. For this reason, many helices begin or end with glycine residues. Proline is the least common residue in an α helix because its rigid cyclic side chain disrupts the right-handed helical conformation by occupying space that a neighboring residue of the helix would otherwise occupy. In addition, because it lacks a hydrogen atom on its amide nitrogen, proline cannot fully participate in intrahelical hydrogen bonding. For these reasons, proline residues are found more often at the ends of α helices than in the interior.

Proteins vary in their α-helical content. In some, most of the residues are in helices. Other proteins contain very little structure. The average content of helix in the proteins that have been examined is 26%. The length of a helix in a protein can range from about 4 or 5 residues to more than 40, but the average is about 12.

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©Laurence A. Moran and Pearson Prentice Hall

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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 Laureate: Linus Pauling

 

The Nobel Prize in Chemistry 1954.

"for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances"


In 1954, Linus Carl Pauling (1901 - 1994) was awarded the Nobel Prize in Chemistry for his work on the nature of chemical bonds and the structures of complex molecules. In the field of biochemistry he is best known for working out the form of the α helix in 1948 (published in 1950). The α helix is a stretch of secondary structure in proteins where the polypeptide chain forms a helix. The theoretical model was quickly confirmed by Perutz's group at Cambridge where Francis Crick was working at the time [see The Storyof DNA: Part 1].

The presentation speech was delivered by Professor G. Hägg, member of the Nobel Committee for Chemistry of the Royal Academy of Sciences.
THEME:

Nobel Laureates

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen.

When, in the early nineteenth century, Dalton had produced experimental proofs that matter consists of atoms it was not long before an explanation was sought of the forces that bind the atoms together. Berzelius was of the opinion that this chemical bond was caused by electrostatic attraction between the atoms; according to this belief, a bond was established between two atoms if one of the atoms was positively, and the other negatively charged. In 1819 when Berzelius presented his theory he could apply it almost exclusively to inorganic substances; only few organic substances were known as pure compounds, and the study of these was difficult due to their complicated and often insufficiently known composition. Berzelius, however, contrived to explain, with the help of the new theory, the bond conditions for a great number of inorganic substances, and could in this wav contribute in a high degree to a greater clarity in this field.

Even in inorganic chemistry, however, certain difficulties arose. How should one explain, for instance, how two hydrogen atoms unite to become a hydrogen molecule? In order to obtain attraction between atoms, one of the atoms must be positive and the other negative; but why should two atoms of the same kind possess charges with opposite sign? And when the knowledge of organic compounds increased, new difficulties arose. Berzelius, for example, found it necessary to assume that the hydrogen atom was always positive and the chlorine atom always negative. Now it was also found that in organic molecules a hydrogen atom could often be exchanged for a chlorine atom, which should be impossible if one was positive and the other negative.

With increased knowledge, problems that could not be explained by Berzelius' theory became more and more numerous, and the theory became discredited.

After the atomic theory had been accepted, it soon became apparent that another important object in the field of chemistry must be to determine not only the nature of the chemical bond but also how the atoms are arranged geometrically when they unite to form larger groups, such as molecules. Permit me to quote from a book, remarkable in its day, Die Chemie der Jetztzeit written in 1869 by the Swedish chemist Blomstrand:

"It is the important task of the chemist to imitate faithfully in his own way the elaborate constructions which we call chemical compounds, and in the erection of which the atoms have served as building stones, to determine as to number and relative position the points of attack at which one or the other of the atoms attaches itself to the other, in short, to determine the distribution in space of the atoms."

Blomstrand makes it the aim, therefore, to find the geometrical construction of substances, or what is nowadays called their structure.

At the end of the last century it became obvious that one had to consider several different kinds of chemical bond. Thus, the difficulties of the Berzelius theory were also explained. Berzelius' interpretation was in principle correct as regards a very important type of bond, but he had made the mistake of applying it also to bonds of a different type. After Bohr had introduced his atomic theory one could moreover with its help give a fairly satisfactory explanation of the Berzelius bond. As this bond occurs between electrically charged atoms, so-called ions, this bond type has often been called the ionic bond. The most typical ionic bonds unite the atoms in the crystals of simple salts.

The bond which above all others had prevented a general application of the Berzelius theory is now commonly known as the covalent bond. It occurs commonly when atoms unite to form a molecule and was once characterized by the famous American chemist Gilbert Newton Lewis as "the chemical bond". The bond between the two hydrogen atoms in a hydrogen molecule, which, as was said before, could not be explained by Berzelius' theory, is covalent.

For a long time it was difficult to explain the nature of the covalent bond. Lewis, however, succeeded in 1916 in showing that it is brought about by electrons - generally two - which are shared in common by two neighbouring atoms, thereby uniting them. Eleven years later Heitler and London were able to give a quantum-mechanical explanation of the phenomenon. An exact mathematical treatment of the covalent bond, however, was possible only in the simple case where only one electron unites the two atoms, and when these do not contain additional electrons outside the atomic nuclei. Even for the hydrogen molecule, which contains two electrons, the treatment cannot be absolutely exact, and in still more complicated cases the mathematical difficulties increase rapidly. It has, therefore, been necessary to use approximate methods, and the results depend to a large extent on the choice of suitable methods and the manner of their application.

Linus Pauling has actively contributed towards the development of these methods, and he has applied them with extreme skill. The results have been such as to be easily usable by chemists. Pauling has also eagerly sought to apply his views to a number of structures which have been experimentally determined during the last decades, both in his own laboratory in Pasadena and elsewhere. It is hardly necessary to mention that we have nowadays great possibilities of reaching Blomstrand's objective of determining the distribution of atoms in space. This is principally done by methods of X-ray crystallography involving an examination of how a crystal influences X-rays in certain respects, and then out of the effect seeking to determine how the atoms are placed in the crystal. Pauling's methods have been very successful and have led to observations which have further advanced the theoretical treatment.

But if the structure of a substance is too complicated it may become impossible to make a more direct determination of the structure with X-rays. In such cases it may be possible, from a knowledge of bond types, atomic distances and bond directions, to predict the structure and then examine whether the prediction is supported by the experiments. Pauling has tried this method in his studies of the structure of proteins with which he has been occupied during recent years. To make a direct determination of the structure of a protein by X-ray methods is out of the question for the present, owing to the enormous number of atoms in the molecule. A molecule of the coloured blood constituent hemoglobin, which is a protein, contains for example more than 8,000 atoms.

In the late nineteen thirties Pauling and his colleagues had already begun to determine with X-rays the structure of amino acids and dipeptides, that is to say, compounds of relatively simple structure containing what may be called fragments of proteins. From this were obtained valuable information - about atomic distances and bond directions. These values were supplemented by the determination of the probable limits of variation for distances and directions.

On this basis Pauling deduced some possible structures of the fundamental units in proteins, and the problem was then to examine whether these could explain the X-ray data obtained. It has thus become apparent that one of these structures, the so-called alpha-helix, probably exists in several proteins.

How far Pauling is right in detail still remains to be proved, but he has surely found an important principle in the structure of proteins. His method is sure to prove most productive in continued studies.

It is hardly necessary to question the practical use of the knowledge of the nature of chemical bonds and of the structure of substances. It is obvious that the properties of a substance must largely depend on the strength with which its atoms are united and the nature of the resulting structure. This I does not only apply to the physical properties of the substance, for instance hardness and melting point, but also to its chemical properties, that is to say how it participates in chemical reactions. If we know how certain atoms or groups of atoms are placed in a molecule we can often predict how the molecule should react under given conditions. And as every reaction results in the breaking of some bonds and the formation of others the result will largely depend on the relative strength of the different bonds.

Professor Pauling. Since you began your scientific career more than thirty years ago you have covered a diversity of subjects ranging over wide fields of chemistry, physics, and even medicine. It has been said of you that you have chosen to live "on the frontiers of science" and we chemists are keenly aware of the influence and the stimulative effect of your pioneer work.

Wide though your field of activity may be, you have devoted the greater part of your energy to the study of the nature of the chemical bond and the determination of the structure of molecules and crystals.

It is with great satisfaction, therefore, that the Royal Swedish Academy of Sciences has decided to award to you this year's Nobel Prize for Chemistry for your brilliant achievements in this fundamental field of chemistry.

On behalf of the Academy I wish to extend to you our heartiest congratulations, and now ask you to receive from the hands of His Majesty the King, the Nobel Prize for Chemistry for the year 1954.

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Defining Evolution

 
PZ Myers has started a thread on the definition of evolution [An exercise for the readers]. Here is PZ's choice ...

Evolution is a well-confirmed process of biological change that produces diversity and coherent functionality by a variety of natural mechanisms.

And here's what I posted in the comments on his blog.

The minimal definition of evolution is ..

Evolution is a process that results in heritable changes in a population spread over many generations. [What Is Evolution?]

The truly shocking thing is how many believers in evolution get it wrong. Unfortunately, that includes you PZ. Two of the absolutely essential features of any definition of evolution are: (1) it requires permanent genetic changes and (2) it is populations, not individuals, that evolve. Both of these restrictions are missing from your definition.

What this means is that there are lots of things covered by your definition that do not fit into the scientific definition of evolution. I'll leave it to your readers to come up with a list of such changes.

This is always an interesting discussion and the comments on Pharyngula make some good points. What do Sandwalk readers think of my definition?

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THE SECULAR CONSCIENCE: Why Belief Belongs in Public Life

 
The Centre for Inquiry Ontario is sponsoring a talk by Austin Dacey (photo below) on Friday night March 7th at the Beverley St. location [THE SECULAR CONSCIENCE: Why Belief Belongs in Public Life]. The talk starts at 7:30 pm and there's a reception for Friends of the Centre at 6pm.

I don't like the sound of this. It could be an interesting night.

Austin Dacey, Center for Inquiry's representative to the United Nations will speak in Toronto as one of the first stops on his book release tour.

Secularism has lost its soul. From Washington to the Vatican to Tehran, religion is a public matter as never before, and secular values-personal autonomy, toleration, separation of religion and state, and freedom of conscience-are attacked on all sides and defended by few. The godly claim a monopoly on the language of morality in public debate, while secular liberals stand accused of standing for nothing. Secular liberals have undone themselves. For generations, too many have insisted that questions of conscience-religion, ethics, and values-are "private matters" that have no place in public debate. Ironically, this ideology prevents them from subjecting religion to due scrutiny when it encroaches on individual rights, and from unabashedly advocating their own moral vision in politics for fear of "imposing" their beliefs on others.

In this incisive book, philosopher Austin Dacey calls for a bold rethinking of the nature of conscience and its role in public life. Inspired by an earlier liberal tradition he traces to Spinoza and John Stuart Mill, Dacey urges liberals to lift their self-imposed gag order and
defend a renewed secularism based on the objective moral value of conscience. He likens conscience to the free press in an open society: it is protected from coercion and control, not because it is private, but because it has a vital role in the public sphere. Conscience is free, but not liberated from shared standards of truth and right.

The Secular Conscience will be published by Prometheus Books in March 2008. In spring 2008, the author will bring his timely message directly to secularists, humanists, and skeptics. One of his first stops will be at the Centre for Inquiry Ontario in Toronto.

Austin Dacey, Ph.D., is a philosopher with the Center for Inquiry in New York City, where he serves as United Nations representative and a contributing editor at Skeptical Inquirer and Free Inquiry magazines. He teaches philosophy, ethics, and science education at Polytechnic University and State University of New York. He is the author of articles in numerous publications including the New York Times. His website is www.austindacey.com.

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[Photo Credit: austindacey.com]