Wednesday, October 31, 2007

Nobel Laureate: Arthur Kornberg

 

The Nobel Prize in Physiology or Medicine 1959.
"for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid"


Arthur Kornberg (1918-2007) received the Nobel Prize in Physiology or Medicine for discovering an enzyme that replicates DNA. The enzyme, now known as DNA polymerase I, plays a key role in joining Okazaki fragments on the lagging strand and in DNA repair [DNA Polymerase I and the Synthesis of Okazaki Fragments] [Biochemist Arthur Kornberg (1918 - 2007)]. Kornberg shared the prize with Severo Ochoa.

The presentation speech was delivered by by Professor H. Theorell of the Royal Caroline Institute.

In the lessons I have learned from the enzymology of DNA replication, I depended at every turn on colleagues near and far for orientation and guidance. Most of all, I learned from the efforts and contributions of my students, too numerous to be mentioned individually. Without them there would be no story for me to tell.

Arthur Kornberg (2000)
Your Majesties, Your Royal Highnesses, Ladies and Gentlemen.

To maa man vaere hvis livet skal lykkes, «There must be two if life shall succeed», is the theme of a sentimental old Danish song. The author had in mind man and woman, but she probably did not know how right she was from a more elementary biological viewpoint. Two principles are necessary so that «life» shall «succeed». One consists of proteins, the other of nucleic acids. The analogy is more than just a play upon words. Just as man and woman are responsible for the regeneration of mankind, likewise is the interplay between proteins and nucleic acids the only, and universally repeated basic mechanism of life. In the long series of substances which build up viruses, bacteria, plants, and animals, everything else might vary, but the proteins and nucleic acids are always present as the life-supporting elements. These both show certain principal characteristics. Their molecules are very large, and are built up from thousands of smaller units linked together in chains - just like a string of pearls - which have a tendency to form helices. Single helices join together in complicated threads which can contain proteins or nucleic acids or both. In the mixed «super molecules», the reactions of life proceed in the subtle pattern of the intimately associated strands.

The proteins contain amino acids as their elementary part. In the whole of Nature on this earth, there are found only some twenty amino acids in proteins. The elementary parts of the nucleic acids, the nucleotides, consist of nitrogenous bases, sugar, and phosphoric acid. There are found in Nature practically no more than eight of these most important nucleotides, all of which contain phosphoric acid, but in which the nitrogenous base may be one of five different kinds. The sugar can be of two different kinds, one of which, «ribose», contains one more oxygen atom than the other, «deoxyribose». This seemingly insignificant difference in a single atom produces a remarkably great effect. Nucleic acids are divided into two different series because of this characteristic. These series have widely different functions, so widely different in fact, that this is the reason why we have two Prize Winners on the stage today.

«Deoxyribonucleic acids», which Arthur Kornberg has now synthesized, are mainly present as the hereditary substance in chromosomes. The «ribonucleic acids», which Severo Ochoa has synthesized, have other functions, such as to assist in the synthesis of proteins. The Swedish scientist Torbjörn Caspersson has played an important role in demonstrating this last fact. From his and other research-workers' discoveries, it has been possible to conclude that nucleic acids assist in the synthesis of protein. The exact chemical mechanism, however, is as yet unknown. Inasmuch as nucleic acids and proteins are the two main principles of life, it seemed highly probable that, vice versa, the proteins should take part in the rebuilding of nucleic acids. This seems so much the more probable when we realize that proteins, in the form of enzymes, take part in practically every chemical reaction in the biological world. It is to the everlasting credit of Ochoa and Kornberg to have clarified this fundamental mechanism by preparing proteins that build up nucleic acids in test tubes.

For proteins it has been proved, and for the nucleic acids it is highly probable, that the order of the different building blocks in the chains is by no means left to chance, but on the contrary is planned in detail for each kind of molecule and for each kind of living organism.

It is this regulated order between the building blocks that always makes human children grow up to be human beings, and the serpent's offspring grow up to be serpents. It is disturbances in this regulated order which change the hereditary factors and allows the variations of species over thousands of years. The almost infinite possibilities to combine the building blocks in different ways makes it possible to vary the form in which life appears on our earth. Let me give a comparable example. By different combinations of the 28 letters in our alphabet, we can write everything that can be expressed in our own language, as well as in all other languages. The building blocks of the proteins, the amino acids, are approximately equal in number to the letters of the alphabet. The protein molecules can be compared with words with 100, 1,000, or even 10,000 letters. It is clear that Nature here has been generous with the possibility to make different combinations amounting to astronomical figures. But here, another factor might be brought up. The differences between the amino acids are necessary not only to produce the possibilities for variation, but also to enable the proteins, by their enzymatic activity, to regulate the different aspects of metabolism. Even the two types of nucleic acids with 4 different nucleotides in each, when made up from 100 to 10,000 nucleotide units in each molecule, give a fantastic number of possible combinations. Thus it would seem as if it were too heroic an enterprise to try to find out the procedure whereby Nature forms such complicated substances as nucleic acids with such an unerring accuracy in placing each building block.

A few years ago, Ochoa and Kornberg, each in his own laboratory, started to investigate the problem. The development turned for Ochoa's part in a direction that made him work with systems that produced ribonucleic acids, while for Kornberg it led him to investigate the formation of deoxyribonucleic acids. They have both, in a series of outstanding investigations, without direct cooperation, but nevertheless, as personal friends probably profiting from each other's results, reached the goal at the same time. As everyone else, they were able to make use of results obtained by preceding research workers, among whom I can only mention a few. It might be of interest to mention that uric acid, the first representative of the purines (a class of nitrogenous bases that form part of the nucleic acids) was discovered in Sweden in 1776 simultaneously by both Carl Wilhelm Scheele and Torbern Bergman. It is a curious parallel to the shared Nobel Award of today, and a reminder of Sweden's great era in the science of chemistry. The German scientist Albrecht Kossel received the Nobel Prize in 1910 for his elucidation of the chemistry of the nitrogenous bases of the nucleic acids, whereas the English scientist Alexander Todd clarified in detail the chemical properties of the nucleic acids, and received the Nobel Prize for Chemistry in 1957. But what really enabled Ochoa and Kornberg to succeed was their own excellent previous work in related fields. Both have worked with bacteria from which they have made preparations of a high degree of purity, Ochoa from an acetic acid bacterium, and Kornberg from the coli bacterium. Ochoa's enzyme produces ribonucleic acids from ribonucleotides having twice the ratio of phosphoric acid residues as that contained in ribonucleic acid. The ribonucleic acid is formed by splitting out half of the phosphoric acid residues, and linking the nucleotides together to form large molecules, which, as far as we can prove today, do not differ in any way from natural nucleic acids. Kornberg's enzyme produces deoxyribonucleic acids in a similar, but not identical fashion. Both have arrived at the same, principally important result that in order to make the reaction start, it is necessary to add in the beginning a small amount of nucleic acid to act as a template. Otherwise the enzymes do not «know» which kind of nucleic acid they are to produce. As soon as they get a template to act as a guide, they start, just like a skilled type-setter, to copy the «manuscript» they have received. Here one recognizes life's own principle that like creates like. Even though several research workers had earlier suspected that such a mechanism was involved, the actual experimental proof is of greatest importance. Furthermore, Ochoa's enzyme has given us the possibility of enzymatically synthesizing simplified nucleic acids of great interest.

To give an idea of where the discoveries that are being honored today may lead to in the near future, I want to mention one example. Other scientists, especially S. S. Cohen in the U.S.A., have shown that the nucleic acid of a certain bacteriophage, T2, which is a kind of bacterial virus, contains a somewhat chemically different nitrogenous base. If bacteria are infected with T2 phage, this different nucleic acid is soon produced in the bacteria. Kornberg succeeded in explaining the mechanism in detail. T2 phage behaves like the worst kind of usurper. Within four minutes it produces a number of enzymes which destroy a nucleotide necessary for the bacterium's normal production of nucleic acids, and rebuilds it to the different nucleotide of the T2 phage, and thereby destroys the bacteria.

We are sure to witness in the near future several important discoveries in biochemistry, virus research, genetics, and cancer research as a consequence of the work of Ochoa and Kornberg. They have helped us to advance quite some distance on the road to understanding the mechanism of life.

Professor Severo Ochoa, Professor Arthur Kornberg, dear friends and colleagues. Some 130 years ago, Friedrich Wöhler, in the laboratory of Berzelius, synthesized urea from inorganic matter. This event occurred in the heart of this city of Stockholm, less than half a mile from where we are now standing. He thus overbridged the first gap between living and dead material. You have now made the second fundamental discovery on this pathway, the synthesis in test tubes of one of the two basic principles of life.

On behalf of the Caroline Institute, I extend to you our warm congratulations, and ask you to receive this year's Nobel Prize for Physiology or Medicine from the hands of His Majesty the King.


DNA Polymerase I and the Synthesis of Okazaki Fragments

 
Slightly modified from Horton et al. (2006) ...


During DNA replication, a molecular machine called a replisome forms at the replication fork where the two strands of DNA are separating. The replisome contains activities that separate the strands and hold them apart for synthesis by the replisome version of DNA polymerase, called DNA polymerase III in bacteria. The complex has two sliding clamps that bind the complex to the strands of DNA so that DNA replication is highly processive.

DNA polymerases catalyze chain elongation exclusively in the 5′ → 3′ direction. Since the two strands of DNA are antiparallel, synthesis using one template strand occurs in the same direction as fork movement, but synthesis using the other template strand occurs in the direction opposite fork movement. The new strand formed by polymerization in the same direction as fork movement is called the leading strand. The new strand formed by polymerization in the opposite direction is called the lagging strand.

THEME

Deoxyribonucleic Acid (DNA)
Recall that the replisome contains a DNA polymerase III holoenzyme dimer with two core complexes that can catalyze polymerization. One of these is responsible for synthesis of the leading strand, and the other is responsible for synthesis of the lagging strand.

Here's a video showing the entire process (source unknown, please contact me if you know who made this video). The details of one of the important steps are presented below the fold.



A. Lagging-Strand Synthesis Is Discontinuous

The leading strand is synthesized as one continuous polynucleotide, beginning at the origin and ending at the termination site. In contrast, the lagging strand is synthesized discontinuously in short pieces in the direction opposite fork movement. These pieces of lagging strand are then joined by a separate reaction.

The short pieces of lagging-strand DNA are named Okazaki fragments in honor of their discoverer, Reiji Okazaki. The overall mechanism of DNA replication is called semidiscontinuous to emphasize the different mechanisms for replicating each strand.

B. Each Okazaki Fragment Begins with an RNA Primer

It is clear that lagging-strand synthesis is discontinuous, but it is not obvious how synthesis of each Okazaki fragment is initiated. The problem is that no DNA polymerase can begin polymerization de novo; it can only add nucleotides to existing polymers. This limitation presents no difficulty for leading-strand synthesis since once DNA synthesis is under way nucleotides are continuously added to a growing chain. However, on the lagging strand, the synthesis of each Okazaki fragment requires a new initiation event. This is accomplished by making short pieces of RNA at the replication fork. These RNA primers are complementary to the lagging strand template. Each primer is extended from its 3′ end by DNA polymerase I to form an Okazaki fragment, as shown in the Figure. (Synthesis of the leading strand also begins with an RNA primer, but only one primer is required to initiate synthesis of the entire strand.)

The use of short RNA primers gets around the limitation imposed by the mechanism of DNA polymerase, namely, that it cannot initiate DNA synthesis de novo. The primers are synthesized by a DNA dependent RNA polymerase enzyme called primase—the product of the dnaG gene in E. coli. The three-dimensional crystal structure of the DnaG catalytic domain revealed its folding and active site are distinct from the well studied polymerases, suggesting that it may employ a novel enzyme mechanism. Primase is part of a larger complex called the primosome that contains many other polypeptides in addition to primase. The primosome, along with DNA polymerase III, is part of the replisome.

As the replication fork progresses, the parental DNA is unwound, and more and more single-stranded DNA becomes exposed. About once every second, primase catalyzes the synthesis of a short RNA primer using this single-stranded DNA as a template. The primers are only a few nucleotides in length. Since the replication fork advances at a rate of about 1000 nucleotides per second, one primer is synthesized for approximately every 1000 nucleotides that are incorporated. DNA polymerase III catalyzes synthesis of DNA in the 5′ → 3′ direction by extending each short RNA primer.

C. Okazaki Fragments Are Joined by the Action of DNA Polymerase I and DNA Ligase

Okazaki fragments are eventually joined to produce a continuous strand of DNA. The reaction proceeds in three steps: removal of the RNA primer, synthesis of replacement DNA, and sealing of the adjacent DNA fragments. The steps are carried out by the combined action of DNA polymerase I and DNA ligase.

DNA polymerase I of E. coli was discovered by Arthur Kornberg about 45 years ago. It was the first enzyme to be found that could catalyze DNA synthesis using a template strand. In a single polypeptide, DNA polymerase I contains the activities found in the DNA polymerase III holoenzyme: 5′ → 3′ polymerase activity and 3′ → 5′ proofreading exonuclease activity. In addition, DNA polymerase I has 5′ → 3′ exonuclease activity, an activity not found in DNA polymerase III.

DNA polymerase I can be cleaved with certain proteolytic enzymes to generate a small fragment that contains the 5′ → 3′ exonuclease activity and a larger fragment that retains the polymerization and proofreading activities. The larger fragment consists of the C-terminal 605 amino acid residues, and the smaller fragment contains the remaining N-terminal 323 residues. The large fragment, known as the Klenow fragment, is widely used for DNA sequencing and many other techniques that require DNA synthesis without 5′ → 3′ degradation. In addition, many studies of the mechanisms of DNA synthesis and proofreading use the Klenow fragment as a model for more complicated DNA polymerases.

The Figure (right) shows the structure of the Klenow fragment complexed with a fragment of DNA containing a mismatched terminal base pair. The 3′ end of the nascent strand is positioned at the 3′ → 5′ exonuclease site of the enzyme. During polymerization, the template strand occupies the groove at the top of the structure and at least 10 bp of double-stranded DNA are bound by the enzyme, as shown in the figure. Many of the amino acid residues involved in binding DNA are similar in all DNA polymerases, although the enzymes may be otherwise quite different in three-dimensional structure and amino acid sequence.

The unique 5′ → 3′ exonuclease activity of DNA polymerase I removes the RNA primer at the beginning of each Okazaki fragment. (Since it is not part of the Klenow fragment, the 5′ → 3′ exonuclease is not shown in the Figure above, but it would be located at the top of the structure, next to the groove that accommodates the template strand.) As the primer is removed, the polymerase synthesizes DNA to fill in the region between Okazaki fragments, a process called nick translation (see Figure below). In nick translation, DNA polymerase I recognizes and binds to the DNA chain. In this way, the enzyme moves the nick along the lagging strand. After completing 10 or 12 cycles of hydrolysis and polymerization, DNA polymerase I dissociates from the DNA, leaving behind two Okazaki fragments that are separated by a nick in the phosphodiester backbone. The removal of RNA primers by
DNA polymerase I is an essential part of DNA replication because the final product must consist entirely of double-stranded DNA.





The last step in the synthesis of the lagging strand of DNA is the formation of a phosphodiester linkage between the 3′-hydroxyl group at the end of one Okazaki fragment and the 5′-phosphate group of an adjacent Okazaki fragment. This step is catalyzed by DNA ligase. The DNA ligases in eukaryotic cells and in bacteriophage-infected cells require ATP as a cosubstrate. In contrast, E. coli DNA ligase uses NAD+ as a cosubstrate. NAD+ is the source of the nucleotidyl group that is transferred, first to the enzyme and then to the DNA, to create an ADP-DNA intermediate.


[©Laurence A. Moran and Pearson/Prentice Hall]

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

Polyphosphate

 
Monday's Molecule was polyphosphate [Monday's Molecule #49]. Polyphosphate is a string of phosphate groups joined together by phosphoanhydride linkages. The polymer serves as a convenient storehouse for phosphorus but it also has significantt roles in regulating metabolic activity. It is present in all cells, although the specifics of its synthesis and degradation have been more intensely studied in bacteria than in eukaryotes.

One of the definitive reviews is by Arthur Kornberg et al. (1999). Here's the abstract—it pretty much describes the importance of polyphosphate.
Inorganic polyphosphate (poly P) is a chain of tens or many hundreds of phosphate (Pi) residues linked by high-energy phosphoanhydride bonds. Despite inorganic polyphosphate's ubiquity--found in every cell in nature and likely conserved from prebiotic times--this polymer has been given scant attention. Among the reasons for this neglect of poly P have been the lack of sensitive, definitive, and facile analytical methods to assess its concentration in biological sources and the consequent lack of demonstrably important physiological functions. This review focuses on recent advances made possible by the introduction of novel, enzymatically based assays. The isolation and ready availability of Escherichia coli polyphosphate kinase (PPK) that can convert poly P and ADP to ATP and of a yeast exopolyphosphatase that can hydrolyze poly P to Pi, provide highly specific, sensitive, and facile assays adaptable to a high-throughput format. Beyond the reagents afforded by the use of these enzymes, their genes, when identified, mutated, and overexpressed, have offered insights into the physiological functions of poly P. Most notably, studies in E. coli reveal large accumulations of poly P in cellular responses to deficiencies in an amino acid, Pi, or nitrogen or to the stresses of a nutrient downshift or high salt. The ppk mutant, lacking PPK and thus severely deficient in poly P, also fails to express RpoS (a sigma factor for RNA polymerase), the regulatory protein that governs > or = 50 genes responsible for stationary-phase adaptations to resist starvation, heat and oxidant stresses, UV irradiation, etc. Most dramatically, ppk mutants die after only a few days in stationary phase. The high degree of homology of the PPK sequence in many bacteria, including some of the major pathogenic species (e.g. Mycobacterium tuberculosis, Neisseria meningitidis, Helicobacter pylori, Vibrio cholerae, Salmonella typhimurium, Shigella flexneri, Pseudomonas aeruginosa, Bordetella pertussis, and Yersinia pestis), has prompted the knockout of their ppk gene to determine the dependence of virulence on poly P and the potential of PPK as a target for antimicrobial drugs. In yeast and mammalian cells, exo- and endopolyphosphatases have been identified and isolated, but little is known about the synthesis of poly P or its physiologic functions. Whether microbe or human, all species depend on adaptations in the stationary phase, which is truly a dynamic phase of life. Most research is focused on the early and reproductive phases of organisms, which are rather brief intervals of rapid growth. More attention needs to be given to the extensive period of maturity. Survival of microbial species depends on being able to manage in the stationary phase. In view of the universality and complexity of basic biochemical mechanisms, it would be surprising if some of the variety of poly P functions observed in microorganisms did not apply to aspects of human growth and development, to aging, and to the aberrations of disease. Of theoretical interest regarding poly P is its antiquity in prebiotic evolution, which along with its high energy and phosphate content, make it a plausible precursor to RNA, DNA, and proteins. Practical interest in poly P includes many industrial applications, among which is the microbial removal of Pi in aquatic environments.
Much work has been done since this review was published in 1999 but the basic concepts haven't changed. Arthur Kornberg [Biochemist Arthur Kornberg (1918 - 2007)] was very interested in polyphosphates and he is responsible bringing it to the attention of the biochemistry community. His lab worked on polyphosphates for the past 25 years. As you know, Kornberg died last Friday but one of his papers on polyphosphate was just published two weeks ago (Zhang et al. 2007). That paper describes the enzyme polyphosphate kinase 1 in slime mold Dictyostelium discoideum, one of the few eukaryotes to have the enzyme that makes and degrades polyphosphate. The paper shows that polyphosphate regulates cell division in Dictyostelium.

In a paper published earlier this year Kornberg's lab showed that E. coli ppk mutant cells do not support lytic infection by bacteriophage P1 (Li et al. 2007). The mutant cells lack polyphosphate. P1 growth is inhibited because the transcriptional activator for late gene synthesis is not activate in the absence of polyphophate.


Kornberg, A., Rao, N.N. and Ault-Riché, D. (1999) Inorganic polyphosphate: a molecule of many functions. Annu. Rev. Biochem. 68:89-125. [PubMed]

Li, L., Rao, N.N. and Kornberg, A. (2007) Inorganic polyphosphate essential for lytic growth of phages P1 and fd. Proc. Natl. Acad. Sci. (USA) 104(6):1794-1799. [PubMed]

Zhang, H., Gómez-García, M.R., Shi, X., Rao, N.N. and Kornberg, A. (2007) Polyphosphate kinase 1, a conserved bacterial enzyme, in a eukaryote, Dictyostelium discoideum, with a role in cytokinesis. Proc. Natl. Acad. Sci. (USA) 104:16486-16491. [PNAS] [PubMed]

Tuesday, October 30, 2007

Wealth and Religiosity

 
One of the most interesting results from the PEW Global Attitudes Survey is the correlation between wealth and belief in God. As a general rule, the wealthier the nation the lower the religiosity—with two major outliers. Here's the chart that's invading the blogosphere.


Canada is the blue square that falls right on the line above Western Europe. As usual, Canadians are more religious than Western Europeans but less religious than Americans. The key question is why is America so different?

Many people have argued that there's no point in challenging religion in America because you are never going to change people's minds. According to them, Americans will always be religious and the "aggressive atheists" are wasting their time. I don't agree with this pessimistic outlook and, when I see charts like the one above, I tend to think that Americans may be near a tipping point where there might be large scale abandonment of religion with just a little nudge in the right direction.

On the other hand, maybe the poll results are deceptive. Maybe the US value for religiosity and wealth is an average of two distinct classes. One class could be economically disadvantaged (poor) but very religious. This would put them on the curve at the same place as, say, Mexico. The other class could be wealthy and less religious, ranking them closer to Western Europeans. Is that possible? If so, it may be harder to change the minds of the religious groups since they aren't seeing the benefits of American per capita GDP.


Do You Have to Believe in God to Be Moral?

 
From the [PEW Global Attitudes Survey].
Is Faith Necessary for Morality?

Throughout most of Africa, Asia, and the Middle East, there is widespread agreement that faith in God is a prerequisite for morality. For example, in all 10 African countries included in the study, at least seven-in-ten respondents agree with the statement “It is necessary to believe in God in order to be moral and have good values.” In Egypt, no one in the sample of 1,000 people disagrees. Out of the 1,000 Jordanians interviewed, only one person suggests it is possible to not believe in God and still be a moral person.

In the four predominantly Muslim Asian countries – Indonesia, Bangladesh, Pakistan and Malaysia – huge majorities also believe morality requires faith in God. Elsewhere in Asia, however, opinions are a bit more mixed. Majorities in Japan and China, as well as substantial minorities of Indians and South Koreans, reject the notion that believing in God is required for morality.

In Arab countries there is a strong consensus that faith is necessary, although in Lebanon there are substantial differences among the country’s three major religious communities – Shia Muslims (81% agree), Christians (65%), and Sunni Muslims (54%). In neighboring Israel, a slim majority (55%) think faith in God is not necessary for moral values.

In Europe, the consensus view is just the opposite: throughout Western and Eastern Europe, majorities say faith in God is not a precondition for morality. This is true across Europe, regardless of whether a country’s primary religious tradition is Protestant, Catholic or Eastern Orthodox. And it is true regardless of which side of the Iron Curtain a country was on.

Still, even within Europe there is some variability – Swedes, Czechs, and the French emerge as the most likely to reject the necessity of religion, while Ukrainians, Germans, and Slovaks are the least likely.

Meanwhile, in the Americas there are considerable differences among countries. While Brazilians, Venezuelans, Bolivians, and Peruvians tend to believe faith is a necessary foundation for moral values, Mexicans, Chileans, and Argentines are more divided on this issue. Only 30% of Canadians suggest morality is impossible without faith, compared to nearly six-in-ten Americans (57%).
What's interesting about these surveys is the difference between opinions in American and in Western Europe. Canada almost always falls somewhere between these two extremes.


What Scientific Instrument Enhances the Quality of Life for People Around the World?

 
Eva, one of our own graduate students, asks this question on her blog easternblot [Quality of Life]. It's a multiple choice question. How hard can it be?

I mean, there can't be all that many scientific instruments that enhance the quality of life for people all around the world, right? Before checking her list, see if you can think of a few possibilities.


What Could Possibly Go Wrong if Everybody Has a Gun?

 
The title of this article is a rip-off of Canadian Cynic [ I mean, what could possibly go wrong?]. That article, in turn, is a response to a provocative article on Halls of Macadamia titled "In Canada, you have to run and hide...".

The story is about certain laws in the USA covered in "Stand Your Ground" bills. Here's a description of the issue from Feb. 2006 in The Christian Science Monitor [Is self-defense law vigilante justice?].
Instead of embracing a citizen's "duty to retreat" in the face of a physical attack, states may be taking cues from the days of lawless frontier towns, where non-deputized Americans were within their rights to hold the bad guys at bay with the threat of deadly force.

First enacted in Florida last year, "Stand Your Ground" bills are now being considered in 21 states including Georgia, according to the National Rifle Association and the Brady Campaign to Prevent Gun Violence. The South Dakota senate approved one just last week.

These new measures would push the boundaries beyond the self-defense measures already on the books. Twelve states already allow citizens to shoot intruders in their homes, and 38 states permit concealed weapons in public places. The "Stand Your Ground" laws would allow people to defend themselves with deadly force even in public places when they perceive a life-threatening situation for themselves or others, and they would not be held accountable in criminal or civil court even if bystanders are injured.

Laws putting more judgment in an individual's hands stem from people's increased concern about crime in their communities. Proponents say it helps shift the debate from gun control to crime control, and that these laws are part of the rugged individualism of Americans.
Yes, folks. This is not a joke. There really are people out there who think that Dodge City was crime free because everyone was armed to the teeth before restrictions on carrying guns were imposed [Only in America] [Should Christians Be Armed?]. After all, what could possible go wrong when you give everyone a hand gun and expect them to serve up vigilante justice?

"These laws send a more general message to society that public spaces belong to the public - and the public will protect [public places] rather than trying to run into the bathroom of the nearest Starbucks and hope the police show up," says David Kopel, director of the Independence Institute in Golden, Colo.

Some critics say such "Wild West" laws are vigilante justice, and commonplace confrontations and more likely turn to violence.
Well, one thing that could go wrong is that innocent people could possibly get hurt. Canadian Cynic points us to this example from the New York Times in 1994 [Judge Awards Damages In Japanese Youth's Death].
A judge today awarded more than $650,000 in damages and funeral costs to the parents of a Japanese exchange student, saying there was "no justification whatsoever" for the killing of the 16-year-old boy who approached a suburban homeowner's door in a Halloween costume almost two years ago....

Mr. Peairs was at home with his family in October of 1992 when the student, Yoshihiro Hattori, and an American companion mistakenly rang his doorbell in search of a Halloween party. Mr. Peairs's wife, Bonnie, answered and, frightened, yelled to her husband to get his gun. Mr. Peairs shot Mr. Hattori dead after warning him to "freeze," a phrase the young man apparently did not understand.
This isn't the only case of this type. The problem with encouraging people to take the law into their own hands is that they tend to act aggressively instead of just running away (or slamming the door). We shouldn't encourage people to use guns to act out their paranoia.


Diversity and the Major Histocompatibility Complex

 
A number of authors have applied this test [for homozygosity] to protein polymorphism data. In most cases, either no selection or purifying selection was indicated. In the case of human HLA (MHC) loci, however, Hedrick and Thomson (1983) found a significant reduction in homozygosity. It is, therefore, likely that the high polymorphism at these loci is maintained by some sort of balancing selection.

Masatoshi Nei (1987)
The adaptationist/pluralist debate really began in earnest with the discovery that there was much more genetic diversity in a population than expected if natural selection was the major mechanism of evolution [The Cause of Variation in a Population]. This lead to Neutral Theory and the recognition—by all but a few stubborn holdouts—that random genetic drift was responsible for most of evolution at the molecular level [Silent Mutations and Neutral Theory].

However, there are adaptationist explanations for diversity. They usually involve some form of balancing selection as is the case with sickle cell alleles in those parts of the world where malaria is a problem. Other versions of balancing selection are more complicated, especially those where the goal is to maintain multiple alleles that benefit the population as a whole.

The classic example is the major histocompatibility (MHC) locus that contains multiple alleles at the same genetic locus as well as multiple alleles segregating in the population. The case for selecting diversity seems strong.

In spite of the fact that this is an important concept I'm not going to touch this particular example since it's much too complicated. Fortunately for us, we have an immunologist blogger at Mystery Rays from Outer Space who works on antigen presentation. He bravely goes where Sandwalk fears to tread.

Read "Heavyweight championship: Overdominance vs. frequency-dependent selection" to see what the controversy is all about. If you need a refresher course on MHC class I molecules then "iayork" has that base covered as well [ It was twenty years ago today] [ MHC molecules: The sitcom].


DriPs and the Inefficiency of Translation

 
There's been a lot of talk recently about junk DNA and the possibility that large parts of it may, after all, have a function. Some of this speculation revolves around reports that most of the junk DNA is transcribed [Junk RNA] [Transcription of the 7SL Gene].

I believe that a great deal of this transcription is accidental and artifact. It's consistent with the idea that DNA replication, transcription, and translation are complex processes that are error-prone. Not every transcript, for example, has to be functional.

Iayork over on Mystery Rays from Outer Space has picked up on this theme in order to discuss mistakes in translation and the Drips hypothesis [RNA, protein, and information]. Check it out. There's more coming.

Students need to be aware of the fact that biology is messy. Some things just happen by mistake and we shouldn't fall into the trap of assuming that every peptide and every bit of RNA is made for a purpose. Life isn't as well-designed as some people think.


Monday, October 29, 2007

Teach the Controversy

 
The latest issue of the McGill Journal of Education is devoted to the Evolution/Creationism debate. There are several interesting articles but one that caught Greg Laden's eye was by Eugenie Scott on teaching the controversy [WHAT’S WRONG WITH THE “TEACH THE CONTROVERSY” SLOGAN?]. Greg agrees with her that we should not address the evoluton/creationism controversy in shools [How To Get Away With Teaching The Controversy].

I'm on the opposite side on this one. In Canadian schools I think we should teach the controversy—even in biology class. Here's my reasoning. You'd have to be some kind of idiot not to recognize that there's a conflict between evolution and many religious beliefs. Pretending that it's not there is no way to educate students.

If we really want to educate then we should address this issue head on and explain why the religious point of view contradicts science. One clear example is the age of the Earth. Students need to hear about the scientific evidence and why it isn't compatible with a 6000 year old Earth as described in the Bible. Another obvious example is the evidence for evolution and how it conflicts with most religious myths.

My children heard about this in their public high school and the biology teacher even organized debates between the two sides (creationists vs. evolutionists). He made an effort to keep everyone honest and avoid insults but there was no attempt to disguise the fact that a controversy existed.

Other Ontario schools did this too. On three occasions I was invited to other high schools to explain the evolution/creationism controversy. One one of these occasions I debated a Christian fundamentalist creationist in a Roman Catholic school. What's wrong with that?

There's nothing wrong with that. Teaching the controversy is a good idea. It's good when teachers explain what's wrong with astrology and it's good when they explain what's wrong with Young Earth Creationism.

The reason this won't work in the USA has nothing to do with whether we should address public controversies that involve science. I assume that students will be allowed to debate the pros and cons of global warming and they might even get lessons on what's wrong with holocaust deniers. The reason the evolution/creation controversy is banned is because religion is involved and that's a taboo subject in American schools.

How does Eugenie Scott deal with the position I advocate?
An argument that has been persuasive in both the United States and Canada is the claim that having students decide between ID and evolution, or to have students “critically analyze” evolution, is pedagogically sound critical thinking instruction from which students would benefit. Of course, all teachers want students to be critical thinkers! It might be a useful critical thinking exercise for students to debate actual scientific disputes about patterns and processes of evolution, as long as they have a solid grounding in the basic science required. (For further discussion, see Alters & Alters, 2001; Scott & Branch, 2003; Dawkins & Coyne, 2005.) It would, however, not be a good critical thinking exercise to teach students that scientists are debating whether evolution takes place: on the contrary, it would be gross mis-education to instruct students that the validity of one of the strongest scientific theories is being questioned. It would, therefore, be gross mis-education to teach students the inaccurate science presented in Icons of Evolution, and other Intelligent Design literature.
I think she's making an incorrect assumption here. We can "teach the controversy" by dealing directly with the conflict between religion and science and by explaining that scientists do not question evolution. The whole idea behind teaching, as far as I'm concerned, is to teach the truth and not some made-up stories that the Intelligent Design Creationists are pushing. Scott is assuming that in order to teach the controversy we have to present the IDC side as if it were true. That's nonsense. It makes about as much sense as assuming that you have to pretend that astrology is true in order to demonstrate that it isn't. (Everyone agrees that there's a controversy over the validity of horoscopes, right? Should we teach about it in school?)

I just finished teaching a section on the evolution/creation controversy to second year students. We used Icons of Evolution as our textbook and the students each picked a single chapter and wrote an essay explaining why Wells is wrong. You could easily do the same thing in high school and that would be a real contribution to education. As it is, by ignoring those arguments you allow them to stand unchallenged.

Now, we all know that there's an additional problem that isn't being mentioned. It's the quality of teachers. I think many people want to avoid teaching the controversy in American schools because it would give teachers the opportunity to promote creationism. That's the point that Greg Laden mentions on his blog. If that's the problem then we should fix it. If teachers don't understand the material they're supposed to be teaching then educate them, or fire them. (I know, it's not that easy.)

We want our students to be critical thinkers and this issue is a perfect one for them to put that critical thinking into practice. If you dare not go there because; (a) you don't want religion in the school, or (b) you don't trust the teachers, then, please, state those reasons up front and don't pussy foot around the issue by pretending that there's something else involved.

Here's the essay that should have been written.
We can't educate our students about the conflicts between science and religion because that would require teachers to bring up religion in school. It is forbidden to discuss religion in public schools in America and that's why we can't allow teaching the controversy. This is too bad because otherwise it might be a good vehicle for teaching critical thinking. It's better to allow the local churches to undermine everything we teach in school because the alternative violates the constitution. (Of course, this argument might become moot with one more appointment to the supreme court.)

Furthermore, even if we could mention religion in school, it wouldn't be a good idea to debate evolution vs. creationism because there are too many "science" teachers who reject evolution in favor of Biblical creationism. We prefer the status quo where neither evolution nor creationism is being taught. Teaching the controversy under these circumstances just opens the door to teaching creationism instead of evolution.


Another Dr. Moran!!!

 
From UNC PHYSICS AND ASTRONOMY WEEKLY CALENDAR:

Monday, October 29
12:20 p.,m. Room 258, Phillips Hall (UNC-CH)

Ph.D. Defense

Jane Moran (Physics and Astronomy, UNC-CH)


Investigating the Circumstellar Environments of Young Stars with the PROMPT Polarimeter

Abstract: We have designed and built a prototype imaging polarimeter for use on the PROMPT robotic telescopes located at Cerro Tololo International Observatory. The polarimeter uses a Fresnel rhomb and wollaston prism to image two orthogonal polarization states onto a single CCD chip, with an image field of view of 10 x 4.5 arcmin. Using the polarimeter, we have investigated the circumstellar regions of 11 Herbig Ae/Be stars, and done extensive follow-up observations on 3 stars of interest: KK Oph, a well-studied star with previously limited polarimetric data; NX Pup, a star known to vary photometrically but with previously unknown polarimetric variability; and SS73 44, a star with very limited previous photometric data and no prior polarimetric data. We have found polarimetric and photometric variations in KK Oph and NX Pup that are consistent with models of dust obscuration. Both KK Oph and NX Pup show an increase in polarization accompanied by a decrease in visual magnitude and a reddening. However, neither star shows the "blueing" at deep photometric minima and maximum polarization characteristic of the UXor classification of stars. We have demonstrated that SS73 44 has an intrinsic polarization component, but does not display the photometric and polarimetric variations expected from a young star with an evolving circumstellar environment, indicating that this object either has a disk seen in an orientation that has little inclination, or one with no appreciable puffed-up inner rim.

My daughter just called. She's now Dr. Moran!


[Photo Credit: (top) PROMPT telescopes in Chile today. (bottom) Jane at the beginning of construction.]

Why Do Leaves Turn Red in the Fall?

 
In the Northern Hemisphere this is the time of year when the leaves of deciduous plants turn color and fall off. Why do they change color and why are some leaves so red?

There are two different answers to the question. The first one deals with the trigger for leaf senescence. It's the shortening of daylight hours that starts the process and from the time it is triggered by photoperiod the process proceeds in a manner that is not influenced very much by the environment, including whether the weather is cold or hot (Keskitalo et al. 2005). What this means is that the leaves all fall off at about the same time each year. The intensity of leaf color, on the other hand, is affected by the weather. Warm weather tends to produce a less spectacular display of fall colors.

The second answer addresses the reason for leaf color. It has to do with senescence. In the autumn the leaves of deciduous trees fall off the tree to prepare for winter. As the leaves die, the tree attempts to salvage as much nitrogen and carbohydrate as it can. While the photosynthetic apparatus is winding down it is more likely to produce free radicals and oxidative damage [Superoxide Dismutase Is a Really Fast Enzyme]. To prevent excess damage the leaves produce pigment molecules that block some of the light and reduce levels of photosynthesis. Red pigments, such as anthocyanins are especially effective (Feild et al. 2002).

Anthocyanins are only produced in the autumn. They are not found in leaves during the summer and their main role is to block sunlight from the photosynthesis machinery during leaf senescence. Other leaf colors are due to the unmasking of accessory pigments as chlorophyll breaks down. The regular pigments such as carotenoids (orange) [Vitamin A (retinol)] and xanthophylls (yellow) become more prominent because their breakdown is delayed [Why Leaves Change Color].

The intensity of the color is influenced by the composition of the soil. When the soil is deficient in nitrogen the tree needs to recover more nitrogen from the leaves before they fall off. This leads to increased production of anthocyanins in order to prolong the period when the leaf cells can remain metabolically active to export nitrogen and carbohydrates [Why do autumn leaves bother to turn red?].


Feild, T.S., Lee, D.W. and Holbrook, N.M. (2002) Why leaves turn red in autumn. The role of anthocyanins in senescing leaves of red-osier dogwood. Plant Physiol. 127:566-574. [PubMed]

Keskitalo, J., Bergquist, G., Gardeström, P. and Jansson, S. (2005) A cellular timetable of autumn senescence. Plant Physiol. 139:1635-48. [PubMed]

Monday's Molecule #49

 
Today's molecule is very simple. You don't get any credit for just naming the molecule.

There's an indirect connection between this molecule and Wednesday's Nobel Laureate(s). Let's see who knows and loves biochemistry!

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous winners are ineligible for one month from the time they first collected the prize. There are three ineligible candidates for this week'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. This one is easy. Get your response in quickly.

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

UPDATE: The molecule is polyphosphate. We have a winner!


Sunday, October 28, 2007

Where Was I?

 

Today I was not too far from this place. Unfortunately I didn't have time to stop and see the drawings. Where was I?


Where Was I?

 
Today I was near this place. Where was I?



Help Build The Beagle

 
A replica of HMS Beagle is being built as part of the 2009 celebrations surrounding the 150th anniversary of the publishing of On Origins of Species, and the 200th anniversary of Darwin's birth. The ship will sail around the world stopping at all the places Darwin stopped at on his famous voyage.

You can help build the Beagle. Check out The Beagle Project Blog.


Saturday, October 27, 2007

Biochemist Arthur Kornberg (1918 - 2007)

 
Arthur Kornberg died yesterday of respiratory failure. He was 89 [Arthur Kornberg, Biochemist, Dies at 89.

Kornberg won the Nobel Prize in 1959 for his discovery of DNA polymerase (now known as DNA polymerase I). His son, Roger Kornberg was awarded the Nobel Prize last year for working out the structure of RNA polymerase [Nobel Laureate: Roger Kornberg]. Another son, Tom, was co-discoverer of the DNA replication enzymes DNA polymnerase II, and DNA polymerase III. Tom and I were graduate students together in the early 1970's and the lab I was in (B. Alberts) worked on the same problems as Arthur Kornberg's lab at Stanford. Bruce Alberts and Arthur Kornberg received the Gairdner Award here in Toronto in 1995.

Kornberg was proud to be known as a biochemist and he always defended the principles of biochemistry. His autobiography For the Love of Enzymes extolled the virtues of purifying and characterizing enzymes as a way to understanding how life works at the molecular level.

One of his most famous defenses of biochemistry is Kornberg (2004).
Fashions prevail in science as in all human affairs. In recent years, biochemistry has become less fashionable, but there is no doubt that the discipline is important for the full understanding of biology.
Biochemists also know him for creating the Ten Commandments of Enzymology. Unlike the author of the original ten commandments, Kornberg was able to modify and amend his commandments as new developments came along (Kornberg, 2003).
Thou shalt…
  • I. Rely on enzymology to resolve and reconstitute biologic events
  • II. Trust the universality of biochemistry and the power of microbiology
  • III. Not believe something just because you can explain it
  • IV. Not waste clean thinking on dirty enzymes
  • V. Not waste clean enzymes on dirty substrates
  • VI. Use genetics and genomics
  • VII. Be aware that cells are molecularly crowded
  • VIII. Depend on viruses to open windows
  • IX. Remain mindful of the power of radioactive tracers
  • X. Employ enzymes as unique reagents
My condolences to the family.


[Photo Credit: University of Rochester Medical Center]

Kornberg, A. (2004) Biochemistry matters. Nature Structural & Molecular Biology 11:493. [PubMed]

Kornberg, A. (2003) Ten commandments of enzymology, amended. Trends Biochem Sci. 28:515-7. [PubMed]

Reconstituting a Virus

 
This week's citation classic from John Dennehy is
Fraenkel-Conrat and Williams (1955) [This Week's Citation Classic].
This week's citation classic is probably the coolest experiment you've never heard of.


This Is so Sad!

 
Over the past several days Sandwalk has been spammed with hundreds of comments linking to sites like those listed below. Because I can't keep up with deleting them all, I've had to introduce word verification into the comments posting section of the blog. I'm really, really sad about this.

Why do people behave this way? What ever happened to common decency?

Is there anything I can do to get even?

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Where Am I?

 



Wednesday, October 24, 2007

Nobel Laureate: James Batcheller Sumner

 

The Nobel Prize in Chemistry 1946.

"for his discovery that enzymes can be crystallized"



In 1946, James Batcheller Sumner (1887-1955) won the Nobel Prize in Chemistry for crystallizing the enzyme urease from jack bean [see: Dealing with Uric Acid and Monday's Molecule #48]. This was definitive proof that enzymes were proteins, something that was still controversial back when the work was done in the early 1920's.

The Presentation Speech was given by previous Nobel Prize winner Professor A. Tiselius, member of the Nobel Committee for Chemistry of the Royal Swedish Academy of Sciences.
Your Majesty, Royal Highnesses, Ladies and Gentlemen.

In 1897 Eduard Buchner, the German research worker, discovered that sugar can be made to ferment, not only with ordinary yeast, but also with the help of the expressed juices of yeast which contain none of the cells of the Saccharomyces. The discovery was considered so important that in 1907 Buchner was awarded the Nobel Prize for Chemistry.

Why was this apparently somewhat trivial experiment considered to be of such significance? The answer to this question is self-evident, if the development within the research work directed on the elucidation of the chemical nature of the vital processes is followed. Here, as in other fields of research, progress has taken place step by step, and the conquest of new fields has often been very laborious. But there, more than in most fields, a tendency has showed itself to consider the unexplained as inexplicable - which is actually not strange where problems of life and the vital processes are concerned. Thus ordinary yeast consists of living cells, and fermentation was considered by the majority of research workers - among them Pasteur - to be a manifestation of life, i.e. to be inextricably associated with the vital processes in these cells. Buchner's discovery showed that this was not the case. It may be said that thereby, at a blow, an important class of vital processes was removed from the cells into the chemists' laboratories, to be studied there by the chemists' methods. It proved, too, that, apart from fermentation, combustion and respiration, the splitting up of protein substances, fats and carbohydrates, and many other similar reactions which characterise the living cell, could be imitated in the test tube without any cooperation at all from the cells, and that on the whole the same laws held for these reactions as for ordinary chemical processes. But - and this is a very important reservation - this was only possible if extracts or expressed juices of such cells were added to the solution in the test tube. It was then natural to assume that these cell juices or cell extracts contained some substance which had the capacity of initiating and maintaining the reactions and guiding them into the paths they follow in the cell. These unknown active substances were called enzymes or ferments, and the investigation of their effects became one of the principal problems of chemistry during the first decades of this century, which for the rest it still is.

The important question of the nature of the enzymes remained unsolved, however, in spite of the energetic efforts of the research workers. It is manifestly a question of substances of complicated structures, which are present in such extremely small amounts that they, so to speak, slip through the fingers when one tries to grasp them. It is really remarkable to see how far it was possible to get in the study of the effects of the enzymes and the course of the enzymatic reactions, without knowing anything definite about the nature of these very active substances, nay, even without even being quite clear that they were substances which could be isolated in the pure form at all.

In 1926, however, in connection with his studies of a special enzyme "urease", James B. Sumner of Cornell University, Ithaca, U.S.A. succeeded in producing crystals which exhibited strikingly great activity. The basic material was the bean of a South American plant, Canavalia ensiformis, in America called the "jack bean", and the crystals had an activity that was about 700 times as great as that of bean flour. What was still more important was that it was possible to dissolve the substance and re-crystallize it several times without its activity being affected. The crystals proved to consist of a protein substance. Sumner expressed the opinion that in reality this protein substance was the pure enzyme.

As is so often the case with important discoveries, this result will probably to a certain degree have "been in the air", in that at the time it had been assumed in many quarters that the enzymes were protein substances of quite a special nature. On the other hand, Willstätter, the German chemist and Nobel Prize winner, had carried out far-reaching purifying experiments with enzymes and had arrived at results which caused him to doubt whether it was a question of protein substances or carbohydrates at all. We know now that this was due to the fact that Willstätter's purifying methods yielded solutions which were all too weak for it to be possible for chemical reactions to give a definite result.

For the chemist crystallization is the final goal in the preparation of a substance in pure form. Even though crystallizability is not such a reliable criterion of purity in the case of protein substances as in that of simpler substances, nevertheless Sumner's results have now been accepted as verified and thus also accepted as the pioneer work which first convinced research workers that the enzymes are substances which can be purified and isolated in tangible quantities. Thereby the foundation was laid for a more detailed penetration of the chemical nature of these substances, on which an understanding of the reactions taking place in living cells must finally depend.


[Photo Credit: The photograph of urease crystals is from Sumner (1926) (urease crystals)]

Sumner, J.B. (1926) The Isolation and Crystallization of the Enzyme Urease. J. Biol. Chem. 69:435-441.

I Rank Number One on Google

 
David Ng at The World's Fair has invented a new blogging meme [The World's Fair exceptional "I rank number one on google" meme!!]. The rules are:
I'd like to suggest a meme, where the premise is that you will attempt to find 5 statements, which if you were to type into google (preferably google.com, but we'll take the other country specific ones if need be), you'll find that you are returned with your blog as the number one hit.
Here are my 5 statements ....
  • Larry Moran
  • Sandwalk
  • Three Domain Hypothesis
  • adaptationist-pluralist
  • is there a genetic component to intelligence


[Hat Tip: PZ Myers at Pharyngula (#1 on Google!)]

Tangled Bank #91

 
The latest version of the Tangled Bank has been posted on The Radula [Tangled Bank #91].

This one is remarkable because I finally figured out how to submit an article. The people who run this carnival don't make it easy.



Tuesday, October 23, 2007

Dealing with Uric Acid

Most animals have to deal with excess nitrogen, which they get from food. One of the common sources is the nitrogen in purines such as adenosine, guanosine, deoxyadenosine, and deoxyguanosine. These nucleosides are broken down into the bases adenine and guanine plus the sugars, ribose and deoxyribose.

Adenine and guanine are converted to uric acid, via xanthine. Uric acid cannot be further metabolized in birds, some reptiles, and primates. These species excrete uric acid in their urine. They also excrete urea but this is derived from the breakdown of amino acids.

All other species convert uric acid to allantoin. This is the end product for most mammals, turtles, some insects, and gastropods. The remaining species can break down allantoin to allantoate and this product is excreted in some bony fishes.

The next step in the degradation pathway is the splitting of allantoate to two molecules of urea. Urea derived from purines is excreted by most fishes, amphibians, and freshwater mollusks. The remaining animal species degrade urea to ammonia and carbon dioxide using the enzyme urease.

In some cases the free bases adenine and guanine are salvaged to be used in synthesizing ATP, RNA, and DNA. The salvage pathways require special enzymes to recover the bases. Adenosine phosphoribosyltransferease converts adenine back to AMP and hypoxanthine-guanine phosphoribosyltransferase (HGPRT) salvages hypoxantinine and guanine.


Lesch-Nyhan Syndrome and Gout

As with other pathways, defects in purine metabolism can have devastating effects. In 1964 Michael Lesch and William Nyhan described a severe metabolic disease characterized by mental retardation, palsylike spasticity, and a bizarre tendency toward self-mutilation. Individuals afflicted with this disease, called Lesch–Nyhan syndrome, rarely survive past childhood. Prominent biochemical features of the disease are the excretion of up to six times the normal amount of uric acid and a greatly increased rate of purine biosynthesis. The disease is caused by a hereditary deficiency of the activity of the enzyme hypoxanthine–guanine phosphoribosyltransferase ((HGPRT) [OMIM 300322]. The disease is usually restricted to males because the mutation is recessive and the gene for this enzyme is on the X chromosome (Xq26-27.2). Lesch–Nyhan patients usually have less than 1% of the normal activity of the enzyme and most show a complete absence of activity. In the absence of hypoxanthine–guanine phosphoribosyltransferase, hypoxanthine and guanine are degraded to uric acid instead of being converted to IMP and GMP, respectively. The PRPP normally used for the salvage of hypoxanthine and guanine contributes to the synthesis of excessive amounts of IMP, and the surplus IMP is degraded to uric acid. It is not known how this single enzyme defect causes the various behavioral symptoms. The catastrophic effects of the deficiency indicate that in some cells the purine salvage pathway in humans is not just an energy-saving addendum to the central pathways of purine nucleotide metabolism.

Gout is a disease caused by the overproduction or inadequate excretion of uric acid. Sodium urate is relatively insoluble, and when its concentration in blood is elevated, it can crystallize (sometimes along with uric acid) in soft tissues, especially the kidney, and in toes and joints. Gout has several causes, including a deficiency of hypoxanthine–guanine phosphoribosyltransferase activity, which results in less salvage of purines and more catabolic production of uric acid. The difference between gout and Lesch–Nyhan syndrome is due to the fact that gout patients retain up to 10% enzyme activity. Gout can also be caused by defective regulation of purine biosynthesis.

Gout can be treated by giving patients allopurinol, a synthetic C-7, N-8 positional isomer of hypoxanthine. Allopurinol is converted in cells to oxypurinol, a powerful inhibitor of xanthine dehydrogenase. (Xanthine dehydrogenase is the enzyme responsible for synthesis of uric acid.) Administration of allopurinol prevents the formation of abnormally high levels of uric acid. Hypoxanthine and xanthine are more soluble than sodium urate and uric acid, and when they are not reused by salvage reactions, they are excreted.

Allopurinol and oxypurinol. Xanthine dehydrogenase catalyzes the oxidation of allopurinol, an isomer of hypoxanthine. The product, oxypurinol, binds tightly to xanthine dehydrogenase, inhibiting the enzyme.

[The text and figures in the box are from Horton et al. (2006) Principles of Biochemistry ©L.A. Moran and Pearson/Prentice Hall]

[The gout cartoon is by James Gillray 1799]

No Intelligence Allowed

 
Ben Stein is the star of a new film that's about to be released. It's called Expelled: No Intelligence Allowed and it's supposed to document the behavior of the evil atheist Darwinists who are suppressing the truth about how life began. (It was God that did it, dummy.)

Stein is interviewed by Bill O'Reilly, providing us with an excellent example of the intelligence that's being expelled from scientific debate. Why in the world should we have any respect for the opinion of Ben Stein?



One of the things that constantly amazes me about this issue is how people like Bill O'Reilly can survive on a major TV network. I guess intelligence isn't a requirement.


[Hat Tip: PZ Myers at Pharyngula (Two people vying to out-stupid each other)]

Why Five Fingers?

 
Josh Rosenau is settling into his new job at the National Center for Science Education (NCSE). Part of his mission is to educate us in the ways of evolution and so far he's doing a great job. NCSE has always had a correct perspective on evolution, as far as I'm concerned, even though some of the people who used to work there tended to favor adaptationism.

Here's Josh's latest from his blog Traveling from Kansas [The Panglossian Paradigm, or as science moves forward, creationists move back]. Note that the opinions on his blog do not necessarily reflect those of NCSE.
For really confused students, I draw on a point Stephen Jay Gould made in Eight Little Piggies (in the essay by the same name), that the number of fingers we have is entirely contingent on history. While one can try to construct an explanation for the superiority of 5 fingers, paleontological history shows that there were potential ancestors of the tetrapod clade (which we are part of) which had as many as eight rays per fin. If they had succeeded, 8 fingers would be the norm, and the Simpsons would look very odd with only 4. As Gould says of historical contingency: "Other configurations would have worked and might have evolved, but they didn't--and five works well enough."

In the essay, Gould is building on a point he made most forcefully in an essay he wrote with Richard Lewontin, "The Spandrels of San Marcos and the Panglossian Paradigm: A Critique of the Adaptationist Program." The point was that biologists were too quick to insist that every feature was adaptive and a result of natural selection. Spandrels are triangular structures produced when two round arches meet. They are necessary byproducts of joining rounded and flat surfaces. Nonetheless, in many churches they are richly decorated and the entire artistic vision for a space can be shaped by the spandrels. One might, Gould points out, be lead to think that the spandrels are there in order to be used for paintings, and not that they are necessary by-products nicely dressed up. The worldview he criticizes treats anything, whether spandrels or five fingers, as the product of intense selection, a perfect solution to the problems it faces.
There's lot more where that came from so get on over to Travelling from Kansas for more information on the "correct" worldview.

By coincidence, today's Scientific American question is Why do most species have five digits on their hands and feet?. While there's a bit of catering to an adaptationist perspective the answer to the question is ...
Is there really any good evidence that five, rather than, say, four or six, digits was biomechanically preferable for the common ancestor of modern tetrapods? The answer has to be "No," in part because a whole range of tetrapods have reduced their numbers of digits further still. In addition, we lack any six-digit examples to investigate. This leads to the second part of the answer, which is to note that although digit numbers can be reduced, they very rarely increase. In a general sense this trait reflects the developmental-evolutionary rule that it is easier to lose something than it is to regain it. Even so, given the immensity of evolutionary time and the extraordinary variety of vertebrate bodies, the striking absence of truly six-digit limbs in today's fauna highlights some sort of constraint.
Remember the take-home lesson (mostly from Josh's article). Living organisms are not well designed in spite of what the creationists and the adaptationists would have you believe.



Monday, October 22, 2007

Monday's Molecule #48

 
Today's molecule is several molecules and a reaction. You have to identify all the molecules in the reaction and name the common enzyme that catalyzes the reaction.

There's connection between this reaction and Wednesday's Nobel Laureate(s).

The reward goes to the person who correctly identifies the molecules, the enzyme, and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are only two 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 molecules, the enzyme, 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. This one is easy. Get your response in quickly.

Comments will be blocked for 24 hours. Comments are not open.

UPDATE: We have a winner!


Gene Genie #18

 

The 18th edition of Gene Genie has just been published on Eye on DNA [Gene Genie #18 with the PG Tips Chimp].



Saturday, October 20, 2007

Is There a Genetic Component to "Intelligence"?

 
This is not my field and, quite frankly, I don't really care about any differences or similarities in intelligence between different human demes. However, the recent kerfuffle over the intemperate remarks of a Jim Watson have raised a number of interesting issues. One of these is whether there is a genetic component to intelligence.

I have always thought there was. I remember reading Richard Dawkins' take on this subject some years ago. He pointed out that if the average "intelligence" of humans has increased over the past million years by evolution then it follows logically that there were genes (alleles) for differences in intelligence that were selected. It seems unreasonable to imagine that all the alleles have reached fixation so that in today's 7 billion members of the Homo sapiens species there is no genetic variation for "intelligence." (I'm putting "intelligence" in quotation marks because I don't want to get into protracted battles about how to measure it or even how to define it. Let's just agree that there's something called intelligence that exists.)

Up until now I have been under the impression that certain genetic defects resulted in lowered intelligence. For example, Down's Syndrome is strongly correlated with low scores on an IQ test suggesting that the presence of extra chromosome 21 genes affects intelligence. That's a genetic component of intelligence by most reasonable definitions.

In spite of evidence to the contrary, there seem to be a number of people who deny that there's a genetic component to intelligence. One of these is Greg Laden, whose opinion I greatly respect. In a recent posting [Watson’s Lecture Canceled] he even disputes the twin studies that show a strong correlation between intelligence and heritability.
Heritability does not distinguish in and of itself between traits passed on with genes from traits passed on via culture, learning, environment, and so on. For instance, which language a person speaks has a very high heritability value, but this “trait” is entirely, 100% learned with absolutely no genetic component whatsoever. Twin studies have been used to suggest that IQ has a component of heritability that is genetic since it is more correlated in twins than in, say, full sibs. However, non-genetic traits can follow the same pattern. Non-genetic traits can show this pattern because, with respect to environments, full sibs who are not twins do not share the same environment as twins. (And for other reasons.)
It seems to me that Greg is arguing against a genetic component to intelligence. He seems to be going out of his way to discredit any studies that suggest otherwise. I'm not sure where he's coming from on this and that's the reason for posing the question in this posting.

Later on in the comments section of Greg's article he says the following.
We have, on this site anyway, not discussed the fact that neural development in humans does not really allow for much influence from genetics in the way that is asserted by the Rushtonian race argument; we have seen some discussion that the allegations that intelligence = g = IQ = something measurable in a simple way = something that varies across individuals because of allelic differences in some set of genes. But there are a LOT of reasons to not accept this idea, aside from the major disconnect between the genome and the functioning of the brain owing to the actual way real brains actually develop in real life. There has been very little discussion regarding the disconnect between the concept of heritability and the concept of subspecies in animals (race is simply another term for subspecies).

There are so many levels at which this is so wrong that I can’t help but feel … and I’ve said this already … that the Race Concept and the intelligence piece of this are simply not valid scientific arguments, and are almost always either political arguments or arguments being made from ignorance. They are political in their motivation, because the science here is simply operating in a totally different place (a little place I call reality).
Clear as mud. I fully sympathize with the mixture of politics and science that confuses this issue. There are people who want there to be differences in intelligence between races because it fits with their political agenda.

I wonder if there aren't people who believe the opposite because it fits with their political agenda? I wonder if there aren't people who go out of their way to construct pseudo-scientific arguments denying that there can be a genetic component to intelligence. Why would they do this? Because if there's no genetic component to intelligence then there can be no differences between demes and this avoids a messy political debate.

Frankly, I'm not sure if Greg Laden is doing this so I'd like to see some clarification. Is there a genetic component to intelligence? Are there "intelligence" alleles segregating within the human population such that some people are smarter than others because of their parents and not just because of socioeconomic environment? Or, are all differences in intelligence due to environment?

Please, let's not let this thread degenerate into a discussion about racism. Let's talk about the science and stick to the question.