Human Genes Involved in the Signal Hypothesis Pathway

 
The Signal Hypothesis describes the mechanism whereby proteins that are destined to cross a membrane are synthesized. One of the key components of this pathway is Signal Recognition Particle or SRP. The structure of SRP is shown below from a paper by Maity and Weeks (2007)

Most of SRP is composed of an RNA molecule called 7SL RNA. It is shown as red and yellow helices in the bottom figure. The secondary structure is depicted in the top right-hand corner of the figure. There are six different proteins in SRP. All of them are bound to the RNA in one way or another. The six proteins are SRP9, SRP14, SRP54, SRP68, and SRP72. The numbers refer to the molecular mass in kilodaltons.


There are three genes for 7SL RNA. They are all found on chromosome 14 (above). Two of them are closely linked and the third one is somewhat farther away.

• RN7SL1: Entrez Gene 6029. Chromosome 14q22.1
• RN7SL2: Entrez Gene 378706. Chromosome 14
• RN7SL3: Entrez Gene 378707. Chromosome 14

The genes for the protein components are:

• SRP9: Entrez Gene 6726. Chromosome 1q42.12
• SRP14: Entreez Gene 6727. Chromosome 15q22
• SRP54: Entrez Gene 6729. Chromosome 14q13.2
• SRP68: Entrez Gene 6730. Chromosome 17q25.1
• SRP72: Entrez Gene 6731. Chromosome 4q11

The three membrane components are the SRP receptor, the translocon (formerly known as ribophorin), and the signal peptidase. There are two subunits in the SRP receptor, α (docking protein) and β. The human genome contains a single gene for SRP receptor α subunit called SSPR (SSPRα). The genome has two separate genes for the β subunit called SSRB and SSR2.

• SSPR (Docking protein) (SSRα): Entrez Gene 6734. Chromosome 11q24.3
• SRPRB: Entrez Gene 58447. Chromosome 3q22.1
• SSR2: Entrez Gene 6746. Chromosome 1q21-q23

The translocon is composed of three proteins; SEC61, SEC62, and SEC63. The SEC61 protein has three subunits; α (genes SEC61A1 and SEC61A2), β (gene SEC61B), and γ (gene SEC61G).

• SEC61A1: Entrez Gene 29927. Chromosome 3q21.3
• SEC61A2: Entrez Gene 55176. Chromosome 10p14
• SEC61B: Entrez Gene 10952. Chromosome 9q22.32-q31.3
• SEC61G: Entrez Gene 23480. Chromosome 7p11.2
• TLOC1 (SEC62): Entrez Gene 7095. Chromosome 3q26.2
• SEC63: Entrez Gene 11231. Chromosome 6q21

Finally, there are three subunits of the signal peptidase complex encoded by SPCS1 (signal peptidase complex, subunit 1), SPCS2, and SPCS3.

• SPCS1: Entrez Gene 28972. Chromosome 3q22.1
• SPCS2: Entrez Gene 9789. Chromosome 1q21-q23
• SPCS3: Entrez Gene 60559. Chromosome 11q24.3

There are 20 genes required for effective translocation of proteins with a signal sequence (only the SRP are shown on the chromosome maps). Additional proteins are required to assist in the translocation (chaperones) and in glycosylation of the protein once it enters the lumen of the endoplasmic reticulum.

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Maity, T.S. and Weeks, K.M. (2007) A threefold RNA-protein interface in the signal recognition particle gates native complex assembly. J. Mol. Biol. 369:512-24 [PubMed]

Iranian Army Is a Terrorist Organization - What's This All About?

 
The New York Times reports on a recent US Senate resolution.

The Senate approved a resolution today urging the Bush administration to designate Iran’s Islamic Revolutionary Guard Corps as a foreign terrorist organization, and lawmakers briefly set aside partisan differences to approve a measure calling for stepped-up diplomacy to forge a political solution in Iraq.

Since last month, the White House has been weighing whether to deem the entire Revolutionary Guard as a terrorist group or to take a narrower step focused only on the Quds Force, an elite unit of the corps. Either approach would signal a more confrontational posture by declaring a segment of the Iranian military to be a terrorist organization.

Saying that it's "confrontational" is putting it mildly. Is there a logical reason for doing this? Here's what General Petraeus says,

It quoted General Petraeus as saying it is “increasingly apparent to both coalition and Iraqi leaders that Iran, through the use of the Iranian Republican Guard Corps Quds Force, seeks to turn the Shiite militia extremists into a Hezbollah-like force to serve its interests and fight a proxy war against the Iraqi state and coalition forces in Iraq.”

Ahhh .... now I get it. We have a case where foreign soldiers in Iraq might be helping certain militia groups in order to serve its own interests and fight a proxy war against its perceived enemies. All soldiers who do that are terrorists, right?

Makes a lot of sense to me.

As an aside, I note that the US Congress is a lot more confident about military intelligence these days. I guess the fiasco of Colin Powell's UN Presentation on February 6, 2003 has been forgotten in light of a vastly improved intelligence gathering network. We can now be confident that all pronouncements about the evil axis countries are accurate, right?

[Photo Link: U.S. Special Forces Secure Tribal Sheikhs Meeting In Diyala Google.]

Conservative Think Tanks

 
Conservative think tanks have been wrong about so many things in the recent past it's a wonder anybody still pays attention. Bill Maher gets it in a show that aired last winter.



[Hat Tip: Canadian Cynic.]

Plants, not Fungi, Are Most Closely Related to Animals?

 
The American Society for Biochemistry & Molecular Biology has drawn up guidelines for a new curriculum in undergraduate education. The complete recommendation can be found at Recommended Curriculum for a Program in Biochemistry and Molecular Biology in the Journal Biochemistry and Molecular Biology Education (BAMBED).

Under the list of "Skills that biochemistry and molecular biology students should obtain by the time they have finished their undergraduate program," there are a number of motherhood type statements. One of them is "Ability to assess primary papers critically." We've been discussing these required skills for the past few months. I've questioned the wisdom of teaching undergraduates how to critically evaluate the scientific literature because I think it's a skill that only comes after a lot of experience in the discipline.

There are many confusing papers out there and it's difficult to decide what's right and what's wrong. We can give students our opinion but that's not the same as teaching them how to critically evaluate a paper.

Here's an example of how difficult it is to read the scientific literature. A recent paper by John Stiller (2007) promotes the idea that plants are more closely related to animals than fungi. Here's the abstract.

Evolutionary relationships among complex, multicellular eukaryotes are generally interpreted within the framework of molecular sequence-based phylogenies that suggest green plants and animals are only distantly related on the eukaryotic tree. However, important anomalies have been reported in phylogenomic analyses, including several that relate specifically to green plant evolution. In addition, plants and animals share molecular, biochemical and genome-level features that suggest a relatively close relationship between the two groups. This article explores the impacts of plastid endosymbioses on nuclear genomes, how they can explain incongruent phylogenetic signals in molecular data sets and reconcile conflicts among different sources of comparative data. Specifically, I argue that the large influx of plastid DNA into plant and algal nuclear genomes has resulted in tree-building artifacts that obscure a relatively close evolutionary relationship between green plants and animals.

This position is contrary to a whole lot of work that has been published over the past several decades. I don't think very much of this paper and neither do John Logsdon of Sex, Genes & Evolution [Promoting Plants at the Expense of Fungi?] and Ryan Gregory of Genomicron [Discovery wants to "demote" fungi]. Read their blogs to see why we're skeptical about this paper.

How do you explain this to undergraduates? How can you teach them to critically evaluate such a paper when, on the surface, it seems perfectly reasonable and the data seems sound? I submit that most of us work within a model of how we think the history of life has developed over millions of years. That model is based on reading hundreds of papers and getting a "feel" for the data. Some papers are rejected and some are given more credence and this is based on all kinds of intangibles—including the reputation of the authors. Can undergraduates be taught such a thing? I don't think so.

Tangled Bank #89

 

The latest version of the Tangled Bank has been posted on Aardvarchaeology [Tangled Bank #89].

Nobel Laureate: Günter Blobel

 

The Nobel Prize in Physiology or Medicine 1999.

"for the discovery that proteins have intrinsic signals that govern their transport and localization in the cell"

Günter Blobel (1936- ) received the Nobel Prize in Physiology or Medicine for The Signal Hypothesis and Signal Recognition Particle.

The Presentation speech was delivered on Dec. 10, 1999 by Professor Ralf Pettersson of the Nobel Committee at Karolinska Institutet. The drawing depicts the first version of the Signal Hypothesis in 1971 from the Nobel Lecture.

Your Majesties, Your Royal Highness, Ladies and Gentlemen,

Imagine a large factory that manufactures thousands of different items in millions of copies every hour, that promptly packages and ships each of them to waiting customers. Naturally, to avoid chaos, each product requires a clearly labeled address tag. Günter Blobel is being awarded this year's Nobel Prize in Physiology or Medicine for having shown that newly synthesized proteins, analogous to the products manufactured in the factory, contain built-in signals, or address tags, that direct them to their proper cellular destination.

An adult human is comprised of approximately 100,000 billion cells, all of which are structurally similar. A striking feature is that each cell contains small compartments or organelles. Organelles are bounded by impermeant, lipid-rich membranes that ensure the physical and functional separation of vital biochemical processes. This compartmentalization enables cells to be compared to a large city in which each public function is housed in a separate building. The blueprint for all cellular processes is maintained in the genome located in the cell nucleus, the City Hall of the cell. Energy production takes place within mitochondria, the power plant of the cell; the breakdown and recycling of waste takes place in the lysosome etc. The production of new products, proteins in the case of the cell, is carried out by ribosomes in a process resembling an assembly line. There is indeed a feverish amount of activity within cells. Every second, thousands of protein molecules are degraded and replaced by new ones. How does a newly made protein get to its correct intracellular location, and how do proteins enter into and move across the membranes surrounding individual organelles? These two central questions occupied the minds of scientists during the 1960s.

Günter Blobel has provided the answer to both these questions. In 1967 he joined the renowned cell biology laboratory headed by George Palade at the Rockefeller University in New York. Palade, who received the Nobel Prize in 1974, had defined and charted the route that secretory proteins take from their site of synthesis within the cell to the cell surface. Secreted proteins are made in the cell in association with a membrane system called the endoplasmic reticulum.

Blobel began by examining how a newly synthesized secretory protein is targeted to and then translocated across the endoplasmic reticulum membrane. Based on the results from a series of elegant experiments, Blobel put forth the so-called "signal hypothesis," in a preliminary form in 1971 and a mature final form in 1975, to explain how this process takes place. The signal hypothesis postulated that newly made proteins contain built-in signals, address tags or zip codes, that target proteins to the endoplasmic reticulum and that subsequently lead them across the reticulum membrane through a specialized channel. Proteins that are translocated across to the other side are packaged for subsequent transport to the cell surface.

To test this hypothesis, Blobel developed an ingenious experimental test tube system, which enabled him to individually study each step of the process. The system which relied on components obtained from mouse, rabbit, and dog cells, laid the foundation for the development of the field of molecular cell biological research. In the following 20 years, Blobel and his co-workers characterized this complex process in great detail. The original signal hypothesis, in all its essential parts, has stood the test of time and proven to be correct.

Blobel extended his studies and was able to demonstrate that proteins destined to become transported to other organelles, or that become integrated into different cellular membranes, also contain specific address tags and so-called "topogenic" signals. The guiding principles that Blobel has helped to elucidate are universally applicable and highly conserved. They have remained almost unchanged during the course of evolution, functioning in yeast, plant, and animal cells.

Perhaps the most important consequences of Günter Blobel's discoveries is that we now understand the fundamental principles guiding the formation and maintenance of cell and organelle structure. The signal hypothesis provides a framework to understand the mechanisms underlying many hereditary diseases and other disease processes in which specific proteins become mislocalized. In addition, these discoveries have enabled the pharmaceutical industry to turn cultured cells into efficient mini-factories for the production of protein-based drugs, such as insulin, growth hormone, coagulation factors, etc.

Günter Blobel, your discovery that proteins contain built-in signals that direct them to their correct destination within cells and across membranes has had a profound impact on our understanding of how a cell and its organelles are assembled and maintained. Your work has also laid the foundation for modern molecular cell biology. On behalf of the Nobel Assembly at Karolinska Institutet I wish to convey to you my warmest congratulations and I now ask you to step forward to receive your Nobel Prize from the hands of His Majesty the King.

Bayblab Supports MMP

 


Good for Bayblab. Read a short summary of the issue at [Electoral Reform: Referendum 2007].

To be fair, it's only kamel (the smart one ) who supports MMP. We don't know if the other bloggers at Bayblab are onside yet.

Will the IDiots Make the Same Mistake with RNA that They Made with Junk DNA?

 
Robert Crowther (whoever that is) posted a similar question on the Intelligent Design Creationis blog of the Discovery Institute. His question was Will Darwinists Make the Same Mistake with RNA that They Made in Ignoring So-Called "Junk" DNA?.

One interesting thing that leapt out at me when reading this was the fact that, while many scientists now realize that it was a mistake to jump to the conclusion that there were massive amounts of "junk" in DNA (because they were trying to fit the research into a Darwinian model), they are on the verge of committing the same exact mistake all over again, this time with RNA.

In order to understand such a bizarre question you have to put yourself in the shoes of an IDiot. They firmly believe that the concept of junk DNA has been overturned by recent scientific results. According to them, the predictions of Intelligent Design Creationism have been vindicated and all of the junk DNA has a function.

Of course this isn't true but, unfortunately, there are some scientists whose level of intelligence is not much above that of the typical IDiot [Junk DNA in New Scientist] [The Role of Ultraconserved Non-Coding Elements in Mammalian Genomes].

Now the IDiots have turned their attention to RNA. They fell hook line and sinker for the hype about functional sequences in junk DNA and they're falling just as easily for the hype about new RNAs. They believe all those silly papers that attribute function to every concevable RNA molecule that has ever been predicted or detected in some assay.

The IDiots were wrong about junk DNA and they're wrong about RNA. The answer to my question is "yes," the IDiots will make the same mistake. You can practically count on it. The answer to Crowther's question is "no." Most (but not all) scientists did not fall for the spin on junk DNA and they realize that the vast majority of our genome is junk. In the long run, they will not fall for the claim that most of the junk DNA is functional because it encodes essential RNA molecules.

Canada Ranks #9 on the Corruption Scale!

 
According to Transparency International Canada is in 9th place in terms of corruption. I think our dismal showing is because university Professors don't ask for bribes like they do in other countries. We should change that. From now on an "A" is going for $1000 and if you want a "B" it will only cost you $600!



[Hat Tip: Gene Expression]

Signal Recognition Particle

 
The signal recognition particle binds to ribosomes at the site of the exit tunnel and interacts with the N-terminal end of newly synthesized protein. If the protein contains a signal sequence then protein synthesis is temporarily arrested. The complex is directed to the membrane surface and the end of the protein is inserted through a pore in the membrane. Protein synthesis then continues and the newly synthesized protein is inserted into the endoplasmic reticulum in eukaryotes or across the plasma membrane in bacteria [The Signal Hypothesis].

In all species (bacteria and eukaryotes) the signal recognition particle is composed of a conserved ~300 nucleotide RNA molecule (7SL/7S RNA) and several (usually six) proteins. Only one of the proteins is common to both bacteria and eukaryotes (Hainzl et al. 2007). The organization of the mammalian SRP is shown above (Maity and Weeks, 2007).

There are two distinct regions of SRP. The large subunit consists of nucleotides 101-255 of the 7S RNA molecule. The RNA is folded into the secondary structure shown on the left (Mauty and Weeks, 2007). In this diagram, the linear nucleotide sequence is connected by solid lines with arrows and the dashed lines depict hydrogen bond interactions between bases that are brought into proximity by the secondary, and tertiary, structure of the RNA molecule.

Four proteins (SRP19, SRP54, SRP68, SRP72) are bound to the large subunit. SRP54 is the only protein found in all species. The large subunit recognizes the signal peptide and binds to the membrane receptor.

The other subunit is called the Alu subunit. The significance of this name will become clear in another posting. The RNA component consists of nucleotides 1-100 and 256-299 arranged in a single double helical structure. Proteins SRP9 and SRP14 bind to the Alu subunit. The Alu subunit is responsible for arresting protein synthesis.

SRP is an important cellular component and it plays a crucial role in protein synthesis and protein trafficing. It's also a good example of a ribonucleotide particle present in all species. Most people don't appreciate the fact that many small RNAs are an integral part of the cellular machinery. Other examples are the telomerase complex and RNAse P. These small RNAs have been known for a long time. The recent publicity about other types of small RNAs has unfortunately conveyed the impression that this is a new discovery.

The structure of SRP has not been fully worked out but a great deal is known about the various components. A model of the complete mammalian signal recognition particle, incorporating the known structures of the RNA and the various proteins, is shown below (Halic and Beckmann, 2005).

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Hainzl, T., Huang, S. and Sauer-Eriksson, A.E. (2007) Interaction of signal-recognition particle 54 GTPase domain and signal-recognition particle RNA in the free signal-recognition particle.
Proc. Natl. Acad. Sci. (USA) 104:14911-6. [PubMed]

Halic, M. and Beckmann, R. (2005) The signal recognition particle and its interactions during protein targeting. Curr. Opin. Struct. Biol. 15(1:116-125. Review. [PubMed]

Maity, T.S. and Weeks, K.M. (2007) A threefold RNA-protein interface in the signal recognition particle gates native complex assembly. J. Mol. Biol. 369:512-24 [PubMed]

A Synthetic Anticoagulant Related to Heparin

 
Heparin (left) is an oligosaccharide bound to a very specific protein to form heparin proteoglycan. The physiologically important oligosaccharide is called heparan sulfate. It is found on the surface of normal endothelial cells and it is this molecule that binds antithrombin III. The interaction of heparan sulfate and antithrombin III inhibits blood clotting [Inhibiting Blood Clots: Anticoagulants].

It is very difficult to synthesize heparan sulfate so the synthetic drug is quite expensive. The results of a number of studies indicated that the exact structure of each of the sugar residues (rings) was very important for proper anticoagulant activity as was the position of the sulfate groups (those with "S" that are bound to the rings).

Theme

Blood Clotting
A recent paper by Chen et al. (2007) shows that simpler forms of the heparin-like oligosaccharide have significant anticoagulation activity. They started with a compound called N-sulfo heparosan, which is prepared from bacterial oligosaccharides by a combination of enzymatic and chemical steps. This starting material was then modified using various recombinant enzymes to produce a large class of heparin-like molecules. One of these derivatives, recomparin (below left) (Lindhardt and Kim, 2007) had significant anticoagulation activity. (Click on the figure to enlarge.)


The result is significant because recomparin does not have the modified rearranged sugar (iduronic acid, IdoUA)that was previously thought to be essential for anticoagulation activity. The modification of the oligosacchraide to create the iduronic acid residues was complicated an inefficient. Thus, the new recomparin drug will be much cheaper to make.

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Chen, J., Jones, C.L. and Liu, J. (2007) Using an Enzymatic Combinatorial Approach to Identify Anticoagulant Heparan Sulfate Structures. Chemistry & Biology 14: 972-973.

Lindhardt, R.J. and Kim, J-H. (2007) Combinatorial Enzymatic Synthesis of Heparan Sulfate (review of Chen et al. 2007). Chemistry & Biology 14:972-973.

Theme: Blood Clotting

 

Theme

Blood Clotting
March 26, 2007
Monday's Molecule #19. Warfarin—an anticoagulant and a rat poison.

March 27, 2007
Vitamin K. Vitamin K plays an important role in blood clotting.

March 28, 2007
Nobel Laureates: Dam and Doisy. Dam: "for his discovery of vitamin K" Doisy: "for his discovery of the chemical nature of vitamin K"

April 2, 2007
Monday's Molecule #20. Heparin—an anticoagulant.

April 2, 2007
Blood Clotting: The Basics. Fibrinogen and how it forms clots.

April 4, 2007
Nobel Laureate: Arne Tiselius. ""for his research on electrophoresis and adsorption analysis, especially for his discoveries concerning the complex nature of the serum proteins"


April 4, 2007
Blood Clotting: Platelets. What are platelets and how do they form blood clots?

April 4, 2007
Blood Clotting: Extrinsic Activity and Platelet Activation. Description of the activity of thrombin and the activation of blood platelets.

April 5, 2007
Blood Clotting: Intrinsic Activity. The role of factors VIII and IX. Deficiencies in Factor VIII cause hemophilia A an X-linked form of hemophilia that was common in European royal families descending from Queen Victoria.

April 8, 2007
Genes for Hemophilia A & B and von Willebrand disease. Locations of the F8, F9 and vWF genes on human chromosomes X and 12.

April 12, 2007
Inhibiting Blood Clots: Anticoagulants. How does heparin inhibit blood clotting?

April 15, 2007
Human Anticoagulant Genes. Mapping the genes for anticoagulant factors.

April 16, 2007
Dicumarol and Warfarin Inhibit Blood Clotting. The role of vitamin K in blood clotting.

September 26, 2007
A Synthetic Anticoagulant Related to Heparin. Synthesis of a new anticoagulant to replace heparin.

April 26, 2008
Fibrin and Blood Clots. What does a blog clot look like?

May 10, 2008
On the Evolution of the Blood Clotting Pathway.
Ian Musgrave explains Russel Doolittle's latest results.

The Signal Hypothesis

 
Monday's Molecule #44 is signal recognition particle or SRP. The figure is a model of SRP (red) bound to a ribosome at the exit site of the tunnel in the large subunit (white asterisk) (Schaffitzel et al. 2006). In the right-hand version of the model you can see that SRP is made up of an RNA molecule and associated proteins.

Signal recognition particle is an important component of the secretory pathway. The mechanism of secretion in response to a signal on the growing polypeptide is known as the Signal Hypothesis. Here's how we describe it in our textbook Principles of Biochemistry 4/e.

Secreted proteins are synthesized on the surface of the endoplasmic reticulum, and the newly synthesized protein is passed through the membrane into the lumen. In cells that make large amounts of secreted protein, the endoplasmic reticulum membranes are covered with ribosomes.

The clue to the process by which many proteins cross the membrane of the endoplasmic reticulum appears in the first 20 or so residues of the nascent polypeptide chain. In most membrane-bound and secreted proteins, these residues are present only in the nascent polypeptide, not in the mature protein. The N-terminal sequence of residues that is proteolytically removed from the protein precursor is called the signal peptide since it is the portion of the precursor that signals the protein to cross a membrane. Signal peptides vary in length and composition, but they are typically from 16 to 30 residues long and include 4 to 15 hydrophobic residues.

In eukaryotes, many proteins destined for secretion appear to be translocated across the endoplasmic reticulum by the pathway shown in the Figure. In the first step, an 80S initiation complex—including a ribosome, a Met-tRNA_i^Met molecule, and an mRNA molecule—forms in the cytosol. Next, the ribosome begins translating the mRNA and synthesizing the signal peptide at the N-terminus of the precursor. Once the signal peptide has been synthesized and extruded from the ribosome, it binds to a protein-RNA complex called a signal recognition particle (SRP).

SRP is a small ribonucleoprotein containing a 300-nucleotide RNA molecule called 7SL RNA and four proteins. SRP recognizes and binds to the signal peptide as it emerges from the ribosome. When SRP binds, further translation is blocked. The SRP-ribosome complex then binds to an SRP receptor protein (also known as docking protein) on the cytosolic face of the endoplasmic reticulum. The ribosome is anchored to the membrane of the endoplasmic reticulum by ribosome-binding proteins called ribophorins, and the signal peptide is inserted into the membrane at a pore that is part of the complex formed by the endoplasmic reticulum proteins at the docking site.

Once the ribosome-SRP complex is bound to the membrane, the inhibition of translation is relieved and SRP dissociates in a reaction coupled to GTP hydrolysis. Thus, the role of SRP is to recognize nascent polypeptides containing a signal peptide and to target the translation complex to the surface of the endoplasmic reticulum.

Once the translation complex is bound to the membrane, translation resumes and the new polypeptide chain passes through the membrane. The signal peptide is then cleaved from the nascent polypeptide by a signal peptidase, an integral membrane protein associated with the pore complex. The transport of proteins across the membrane is assisted by chaperones in the lumen of the endoplasmic reticulum. In addition to their role in protein folding, chaperones are required for translocation, and their activity requires ATP hydrolysis. When protein synthesis terminates, the ribosome dissociates from the endoplasmic reticulum, and the translation complex disassembles.

©:L.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 Biochemistry, 4th edition. Pearson Prentice Hall, Upper Saddle River NJ (USA)

Schaffitzel, C., Oswald, M., Berger, I., Ishikawa, T., Abrahams, J.P., Koerten, H.K., Koning, R.I. and Ban, N. (2006) Structure of the E. coli signal recognition particle bound to a translating ribosome. Nature 444:503-506.

BPR3 Icon Winner

 
This is the winner in the Bloggers for Peer-Reviewed Research Reporting icon contest [… And the winner is …]. We're not supposed to start using it just yet because the designer, Uriel Klieger, is going to make a few changes based on suggestions from bloggers.

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[Hat Tip: Scienceroll who thinks that there are only two science bloggers who link to references properly. And I'm not one of them. Boo!]

Nobel Prize Gossip

 
Alex Palazzo has a wonderful and very complete list of potential Nobel Prize winners [Gaze into the crystal ball - Nobel Prize Gossip].

What do you think? Get involved in the debate on The Daily Transcript. My vote goes to James Till and Ernest McCulloch, but I may be a bit biased. I hope Alex is also rooting for the Canucks.

The Physiology & Medicine Prize will be announced on Monday, October 8th and the Chemistry Prize will be announced on Wednesday, October 10th.

How to Get Tenure

 
Janet Stemwedel is about to submit her tenure dossier. She describes the process and the dossier on Adventures in Ethics and Science [A postcard from academe: my tenure dossier]. It's worth a read to see how the process works. Note that Janet has included a section on blogging and her department recognizes that as a legitimate academic pursuit.

Good luck, Janet, although I really don't think you'll need it.

Random Genetic Drift and Population Size

One of the most persistent myths of evolutionary biology is that random genetic drift only occurs in small populations. You'll find this myth everywhere you look, even in textbooks that should know better. A few minutes ago I was looking for a simple way to explain this in the comments section of P-ter Accuses Me of Quote Mining when I came across this explanation in Modern Genetic Analysis by Anthony Griffiths, William Gelbart, Jeffrey Miller, and Richard Lewontin (1999 edition). This is the offspring of a textbook that David Suzuki started many years ago [ 17. Population and Evolutionary Genetics].

One result of random sampling is that most new mutations, even if they are not selected against, never succeed in entering the population. Suppose that a single individual is heterozygous for a new mutation. There is some chance that the individual in question will have no offspring at all. Even if it has one offspring, there is a chance of 1/2 that the new mutation will not be transmitted. If the individual has two offspring, the probability that neither offspring will carry the new mutation is 1/4 and so forth. Suppose that the new mutation is successfully transmitted to an offspring. Then the lottery is repeated in the next generation, and again the allele may be lost. In fact, if a population is of size N, the chance that a new mutation is eventually lost by chance is (2N − 1)/2N (For a derivation of this result, which is beyond the scope of this book, see Chapters 2 and 3 of Hartl and Clark, Principles of Population Genetics.) But, if the new mutation is not lost, then the only thing that can happen to it in a finite population is that eventually it will sweep through the population and become fixed. This event has the probability of 1/2N In the absence of selection, then, the history of a population looks like Figure 17-17. For some period of time, it is homozygous; then a new mutation appears. In most cases, the new mutant allele will be lost immediately or very soon after it appears. Occasionally, however, a new mutant allele drifts through the population, and the population becomes homozygous for the new allele. The process then begins again.

Even a new mutation that is slightly favorable selectively will usually be lost in the first few generations after it appears in the population, a victim of genetic drift. If a new mutation has a selective advantage of S in the heterozygote in which it appears, then the chance is only 2S that the mutation will ever succeed in taking over the population. So a mutation that is 1 percent better in fitness than the standard allele in the population will be lost 98 percent of the time by genetic drift.

The fact that occasionally an unselected mutation will, by chance, be incorporated into a population has given rise to a theory of neutral evolution, according to which unselected mutations are being incorporated into populations at a steady rate, which we can calculate. If the mutation rate per locus is μ, and the size of the population is N, so there are 2N copies of each gene, then the absolute number of mutations that will appear in a population per generation at a given locus is 2Nμ. But the probability that any given mutation is eventually incorporated is 1/2N so the absolute number of new mutations that will be incorporated per generation per locus is (2Nµ)(1/2N) = µ If there are k loci mutating, then in each generation there will be kμ newly incorporated mutations in the genome. This is a very powerful result, because it predicts a regular, clocklike rate of evolution that is independent of external circumstances and that depends only on the mutation rate, which we assume to be constant over long periods of time. The total genetic divergence between species should, on this theory, be proportional to the length of time since their separation in evolution. It has been proposed that much of the evolution of amino acid sequences of proteins has been without selection and that evolution of synonymous bases and other DNA that neither encodes proteins nor regulates protein synthesis should behave like a molecular clock with a constant rate over all evolutionary lineages. Different proteins will have different clock rates, depending on what portion of their amino acids is free to be substituted without selection.

This is an important conclusion. It shows that alleles are fixed in large populations by random genetic drift. I'd like it a lot if people would stop saying that drift only occurs in small populations.

Random Genetic Drift Simulation

 
We often talk about Random Genetic Drift on Sandwalk. Here's a handy-dandy simulator to help you understand the concept [Genetic Drift].

P-ter Accuses Me of Quote Mining

 
There are many adaptationists who recognize that random genetic drift exists. They will, when pressed, admit that neutral alleles can be fixed in a population. However, these adapationists pften maintain that visible phenotypes cannot be neutral with respect to survivability. Thus all visible phenotypes, with rare exceptions, are adaptations.

Several people have expressed this point of view in the comments on Sandwalk but the most prominent proponent is Richard Dawkins. I often use a quotation from The Extended Phenotype to demonstrate how Dawkins thinks about this issue. It comes from a chapter titled Constraints on Perfection. Here's the complete paragraph; I often use just the part that begins "The biochemical controversy ....[Richard Dawkins on Visible Changes and Adaptationism].

I have tried to show that adapatationism can have virtues as well as faults. But this chapter's main purpose is to list and classify constraints on perfection, to list the main reasons why a student of adaptation should proceed with caution. Before coming to my list of six constraints on perfection, I should deal with three others that have been proposed, but which I find less persuasive. Taking first, the modern controversy among biochemical geneticists about "neutral mutations", repeatedly cited in critiques of adaptationism, it is simply irrelevant. If there are neutral mutations in the biochemist's sense, what this means is that any change in polypeptide structure which they induce has no effect on the enzymatic activity of the protein. This means that the neutral mutations will not change the course of embryonic development, will have no phenotypic effect at all, as a whole-organism biologist would understand phenotypic effect. The biochemical controversy over neutralism is concerned with the interesting and important question of whether all gene substitutions have phenotypic effects. The adaptationism controversy is quite different. It is concerned with whether, given that we are dealing with a phenotypic effect big enough to see and ask questions about, we should assume that it is the product of natural selection. The biochemist's 'neutral mutations' are more than neutral. As far as those of us who look at gross morphology, physiology and behaviour are concerned, they are not mutations at all. It was in this spirit that Maynard Smith (1976b) wrote: "I interpret 'rate of evolution' as a rate of adaptive change. In this sense, the substitution of a neutral allele would not constitute evolution ..." If a whole-organism biologist sees a genetically determined difference among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists.

Natural selection is the only explanation we know for the functional beauty and apparently "designed" complexity of living things. But if there are any changes that have no visible effect—changes that pass right under natural selection's radar—they can accumulate in the gene pool with impunity and may supply just what we need for an evolutionary clock.

Richard Dawkins
The Extended Phenotype (2005)I have discussed this quotation with Richard Dawkins and I am convinced that it fairly represents his viewpoint. The only quibble would be that Dawkins would probably admit of one or two exceptions where neutral alleles might produce a phenotypic effect. In other words, his statement above is perhaps an example of hyperbole but that's how I always read it anyway. Almost all popular science writers make generalizations of this sort and it's not a great crime.

The bottom line is that Dawkins thinks that neutral mutations cannot have an effect on embryonic development; therefore, they cannot result in a visible phenotype. Dawkins believes that almost all visible mutations will have either a beneficial or a detrimental effect on the survivability of an organism and that neutral mutations are a phenomenon that's confined to the molecular level where they may not even count as evolution.

P-ter thinks that I misrepresent Dawkins by quote mining [Larry Moran caught quote mining]. Here's what P-ter says,

This certainly seems to place Dawkins as an "adaptationist", one who thinks that all differences in phenotypes are adaptations. I was a little surprised by this, but the quote seemed clear, and I wasn't going to take the time to find my original.

Luckily, another commenter pointed out that The Extended Phenotype is searchable at Google Books [The Extended Phenotype]. And funny, the very next line after Moran stops quoting is possibly relevant:

The next lines P-ter is referring to is the beginning of a new paragraph ...

He might, nevertheless, be dealing with a neutral character in the sense of an earlier controversy (Fisher & Ford 1950; Wright 1951). A genetic difference could show itself at the phenotypic level, yet still be selectively neutral.

P-ter then continues with ...

Dawkins goes on to express some skepticism about some arguments for evolution by drift, but he's certainly not an "adaptationist" in the Moran sense.

I suppose I'm somewhat naive: distorting someone's argument through selective quotation is a classic creationist tactic, and Moran has written a bit about the propaganda techniques used by that crowd. Little did I know his familiarity is not of an entirely academic sort.

[1] As opposed to "pluralists", as he likes to call himself. For someone who (rightfully, in my opinion) is disdainful of "framing" (the view that scientists need to spin their results in order to resonate better with the public), he certainly knows how to frame.

This is a very serious charge. I'm accused of deliberately distorting Dawkins' position by selective quotation. According to P-ter, Dawkins does not believe what he says in the quoted paragraph. (And elswhere, I might add.) According to P-ter Dawkins believes that mutations with a visible phenotype can be neutral. (We're not talking about one or two exceptions here, we're talking about the generality that applies to a significant percentage of mutations.)

P-ter's evidence of the crime of quote mining is the first two sentences of a paragraph that appears on the bottom of page 32. You can read it for yourself but it seems obvious to me that Dawkins is raising a possible objection to his claim and then dismissing it. Here are the first few (not just two) sentences of that paragraph: I think they convey the correct intent.

He might, nevertheless, be dealing with a neutral character in the sense of an earlier controversy (Fisher & Ford 1950; Wright 1951). A genetic difference could show itself at the phenotypic level, yet still be selectively neutral. But mathematical calculations such as those of Fisher (1930b) and Haldane (1932a) show how unreliable human subjective judgement can be on the "obviously trivial" nature of some biological characters. Haldane, for example, showed that, with plausible assumptions about a typical population, a selection pressure as weak as 1 in a 1000 would take only a few thousand generations to push an initially rare mutation to fixation, a small time by geological standards. It appears that in the controversy referred to above, Wright was misunderstood (see below) ...

A careful reading of Dawkins shows that the objection to his claim doesn't stand because people misunderstood Wright. Thus, according to Dawkins, characters that appear to be neutral really aren't.

I maintain that my original characterization of the Dawkins' position is accurate and his words reflect his true beliefs. I resent P-ter's accusation that I deliberately tried to misrepresent Dawkins by quoting that passage.

Incidentally, P-ter puts words in my mouth. I recognize several different kinds of adaptationist. The worst of them are those who think every visible phenotype is an adaptation of some sort but there are many who do not hold this extreme position. It's simply not true that I say every adaptationist must deny the fixation of neutral alleles with a visible phenotype. Some are easier to mock than others, but it's pretty easy to get most of them going whenever I point out that Dawkins is an adaptationist.

Gene Genie #16

 

The 15th edition of Gene Genie has just been published on Neurophilosophy [Gene Genie #16].

There are several articles on personal genomics and the genomes of Craig Venter and Jim Watson.

Monday's Molecule #44

 
UPDATE: We have a winner. See comments.

Today's molecule (in red) is part of a larger complex. There are two view of this complex in the figure. You have to supply the common name of this molecule—the one colored red in the complex. There's a direct connection between this molecule and Wednesday's Nobel Laureate(s).

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are no ineligible candidates for this Wednesday's reward. The prize is a free lunch at the Faculty Club.

Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right.

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

Iranian President Mahmoud Ahmadinejad Speaks at Columbia University

 
Tomorrow President Mahmoud Ahmadinejad of Iran will speak at Columbia University. There are some who argue that universities should not invite controversial speakers. There are some who argue that Iran is the "enemy"—a member of the axis of evil—and once an enemy has been identified, and vilified, you must never allow them to speak in their own defense. It's especially horrible, according to these people, to allow a publicly-funded university to sponsor such a person.

Those people are dead wrong. Fortunately, the President of Columbia University has the gumption to stand up to those who would destroy the universities and free society [President Bollinger's Statement About President Ahmadinejad's Scheduled Appearance].

I would like to add a few comments on the principles that underlie this event. Columbia, as a community dedicated to learning and scholarship, is committed to confronting ideas—to understand the world as it is and as it might be. To fulfill this mission we must respect and defend the rights of our schools, our deans and our faculty to create programming for academic purposes. Necessarily, on occasion this will bring us into contact with beliefs many, most or even all of us will find offensive and even odious. We trust our community, including our students, to be fully capable of dealing with these occasions, through the powers of dialogue and reason.

I would also like to invoke a major theme in the development of freedom of speech as a central value in our society. It should never be thought that merely to listen to ideas we deplore in any way implies our endorsement of those ideas, or the weakness of our resolve to resist those ideas or our naiveté about the very real dangers inherent in such ideas. It is a critical premise of freedom of speech that we do not honor the dishonorable when we open the public forum to their voices. To hold otherwise would make vigorous debate impossible.

That such a forum could not take place on a university campus in Iran today sharpens the point of what we do here. To commit oneself to a life—and a civil society—prepared to examine critically all ideas arises from a deep faith in the myriad benefits of a long-term process of meeting bad beliefs with better beliefs and hateful words with wiser words. That faith in freedom has always been and remains today our nation’s most potent weapon against repressive regimes everywhere in the world. This is America at its best.

If you don't understand this then you don't understand anything about the purpose of a university and the importance of listening to the other side.

What Happens When Alternative Medicine Doesn't Work?

 
Skeptico reports that Merck has just pulled a new AIDs drig because tests were showing that it didn't work [When will CAM do this?]. That's the way the system is supposed to work.

The sound, effective kind of medicine is based on science and evidence. Medicine that is not evidence-based is called "alternative." "complementary" or "traditional" medicine. Don't be fooled by these terms. They all mean the same thing; namely, that the medicine doesn't pass the test of evidence-based.

Skepico asks when was the last time that an alternative treatment was canceled because it wasn't working? There are lots of examples in the posting.

Homeopaths pulling (say) Belladonna for the treatment of urinary tract infections, because they determined it doesn’t work for that.

Astronomy Picture of the Day: Sept. 22, 2007

 
Today's Astronomy Picture of the Day is a bit unusual. It shows a time in the distant future when I'll be able to drive from Toronto to Cape Town in just a few days. Unfortunately, Cape Town will no longer be on the cape.

Jena, Louisiana

 
Jena is a small town in Louisiana. It was named for Jena in Germany, the site of a famous victory by Napoleon in 1806. I'm a (very amateur) student of military history so I'm familiar with this battle [Battle of Jena-Auerstedt].

The American town is in the news because of allegations of racism at the local high school. The local prosecutor seems to have been motivated by less than honorable motives in charging six young black men with attempted murder in a schoolyard fight.

While watching coverage on television, I was struck by the modern name of the town. It's pronounced "Geena" in Louisiana. There's nothing wrong with this. They can call pronounce the name of the town however they want. But just for the record, the name of the German city, and the battle, is pronounced "yaene." You can hear it here: Jena.

The Dangers of Creationism in Education

 
The Committee on Culture, Science and Education of the Parliamentary Assembly, Council of Europe has issued a report on The dangers of creationism in education. One of the most interesting parts of this report is that the committee does not back away from labeling Intelligent Design as a form of creationism. For example, in the opening paragraphs the report says,

Creationism in any of its forms, such as “intelligent design”, is not based on facts, does not use any scientific reasoning and its contents are definitely inappropriate for science classes.

However, some people call for creationist theories to be taught in European schools alongside or even in place of the theory of evolution. From a scientific view point, there is absolutely no doubt that evolution is a central theory for our understanding of life on Earth.

The Assembly calls on education authorities in member states to promote scientific knowledge and the teaching of evolution and to oppose firmly any attempts at teaching creationism as a scientific discipline.

Later on they define creationism using a great deal of common sense.

Creationists question the scientific character of certain items of knowledge and argue that the theory of evolution is only one interpretation among others. They accuse scientists of not providing enough evidence to establish the theory of evolution as scientifically valid. On the contrary, they defend their own statements as scientific. None of this stands up to objective analysis. ...

Creationism has many contradictory aspects. The “intelligent design” idea, which is the latest, more refined version of creationism, does not deny a certain degree of evolution but claims that this is the work of a superior intelligence. Though more subtle in its presentation, the doctrine of intelligent design is no less dangerous.

I will continue to refer to Intelligent Design Creationism as an accurate representation of the views of people like Dembski, Behe, Phillips etc. Their allies, like Denyse O'Leary, are also creationists by my definition. They aren't Young Earth Creationists, they are Intelligent Design Creationists.

Readers might recall that I have been accused of inventing a new definition of "creationism" [Creationism Continuum]. Some people, even evolutionists, think that the only creationists are those who believe in the literal truth of Genesis. They maintain that it is wrong to refer to intelligent design proponents as creationists. Obviously, I disagree and I'm not alone. In fact, I'd go one step farther than the Committee on Culture, Science and Education, I'd say that Theistic Evolutionists are also creationists because they believe in a creator.

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[Hat Tip: Panda's Thumb]

MMP: The Belgium Connection

 
I've encountered many critics of the Mixed Member Proportional system who are uttering the same mantra. It includes the phrase "Belgium has 33 parties." I think this is meant to be a criticism of the MMP system. Those who mention the mantra often associate it with the fact that Belgian politicans have had trouble forming an effective government since the June 10, 2007 election.

I suspect there's a common source for this Belgian story. Does anyone know where it comes from?

Here are the facts as I know them. True, there were 33 parties contesting the last election in Belgium. But only 11 of them won seats in parliament (see below). In Canada there were 5 parties with seats in parliament for most of the 1990's and that was with a First-Past-the-Post system. In the last federal election in Canada there were 21 parties seeking election [Canadian Political Parties]. This includes my favorite, the Rhinoceros Party of Canada. The Green Party didn't win a single seat in spite of the fact that it got 4.5% of the vote. The Bloc got 51 seats with 10.5% of the vote. We have a minority government in Ottawa.

Belgium has a full Proportional Representation system. In Ontario we're being asked to consider a Mixed Member Proportional system. They aren't the same thing. The Belgian example doesn't seem to be particularly relevant to the Ontario debate.

Life in Modern Iraq.

 
Maclean's magazine has the story by Patrick Graham [How George Bush became the new Saddam].

It was embarrassing putting my flak jacket on backwards and sideways, but in the darkness of the Baghdad airport car park I couldn’t see anything. “Peterik, put the flak jacket on,” the South African security contractor was saying politely, impatiently. “You know the procedure if we are attacked.”

I didn’t. He explained. One of the chase vehicles would pull up beside us and someone would drag me out of the armoured car, away from the firing. If both drivers were unconscious—nice euphemism—he said I should try to run to the nearest army checkpoint. If the checkpoint was American, things might work out if they didn’t shoot first. If it was Iraqi . . . he didn’t elaborate.

Arriving in Baghdad has always been a little weird. Under Saddam Hussein it was like going into an orderly morgue; when he ran off after the U.S.-led invasion of March 2003 put an end to his Baathist party regime, the city became a chaotic mess. I lived in Iraq for almost two years, but after three years away I wasn’t quite ready for just how deserted and worn down the place seemed in the early evening. It was as if some kind of mildew was slowly rotting away at the edges of things, breaking down the city into urban compost.

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[Hat Tip: Jennifer smith Best Cover. Ever]

Street Art

 

BigHeathenMike says this is the coolest street art he's ever seen[Wow]. Who could argue with that? Go to Mike's Weekly Skeptic Rant to find out where this drawing came from.

Avery, MacLeod and McCarty (1944)

 

This weeks classic on John Dennehy's blog is the famous Avery, MacLeod and McCarty (1944) paper [This Week's Citation Classic]. If you already know about this paper then wander on over to The Evolutionary Biologist whenever you get a chance and refresh your memory. If you don't know what the heck we're talking about then get your butt over there immediately and correct this major deficiency in your education!

Not only was Oswald Avery one of the greatest scientists of the modern era, he was also a Canadian!

What's She Holding in her Hand?

 
Check out Eva's blog easternblot for a cartoon she just posted [Scientist Illustration]. What is the scientist holding in her hand? Try and figure it out for yourself before reading Eva's answer.

Vote for MMP

 


I'm voting for the Mixed Member Proportional (MMP) electoral system on October 10th [Vote for MMP] [Mixed Member Proportional Electoral System].

See Bloggers for MMP for a complete list.

Canadian Dollar = American Dollar

 
Today, for the first time in 30 years the value of the Canadian dollar (loonie) reached parity with the American dollar. It's big news in Canada. Most people think it's a good thing but it's not necessarily a good thing at all. A falling (collapsing?) US currency may be good for America and bad for Canada. [Click on the chart to enlarge.]

If you want to see one reason why this isn't good for Canadians see Jennifer Smith's posting The Parity Blues.

New Panda's Thumb

 
Check it out at Panda's Thumb.

A lot of people put a great deal of work into the upgrade but the person who deserves the most praise is Reed Cartwright of De Rurum Natura (and Panda's Thumb). You can thank him by going to Upgrade Starts Today.

In case you didn't know. The unofficial mascot at the Panda's Thumb is Prof. Steve Steve. Isn't he a handsome fellow? I think he's a biochemist—or possibly a paleontologist. I always get them mixed up.

Reed Cartwright is the father of Prof. Steve Steve. He's also the father of Prof. Steve Steve and Prof. Steve Steve. They have left home to gallivant around the world but they can often be found in North Carolina or Oakland CA.

There are quite a few bloggers on Panda's Thumb. I don't have a complete list but they include most of the leading lights in the fight against creationism in the USA. Some of them are adaptationists but don't let that deter you. It's good to hear what the other side has to say from time to time. (The adaptationists usually refer to the blog as Mt. Improbable. The unofficial mascot of the adaptationists is Prof. Dick Dick. )

If you aren't reading Panda's Thumb on a regular basis, now is a good time to start. There should be lots of postings as soon as the site is ready.