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.

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DNA Polymerase I and the Synthesis of Okazaki Fragments

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

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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.

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[©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.

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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]

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.

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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.

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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.

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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.

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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].

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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.

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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.

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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!

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[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?].

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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!

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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?

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Where Was I?

 
Today I was near this place. Where was I?

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