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Michael Yon is a (very) freelance reporter in Iraq. He has a blog where he solicits support for his mission in Iraq. The mission is to bring the "truth" to the American public. Why does he do it?I do it because we need to see this clearly: what happens in and to Iraq is a defining moment for our nation, and the world. This enemy is smart and they are deadly, but they are also losing. Iraq can become a strong and free nation. But it will take the constant application of pressure over time to stem the flow of blood. If we back off too soon, they will rebound. If we cut our losses and run, they will follow us home. Peace can prevail here, if we can use our strength to maintain our progress.It's sort of refreshing to see a "journalist" who lays his cards on the table. At least he doesn't pretend to be objective, like many other journalists.
At a meeting today in Baqubah one Iraqi official I spoke with framed the al Qaeda infiltration and influence in the province. Although he spoke freely before a group of Iraqi and American commanders, including Staff Major General Abdul Kareem al Robai who commands Iraqi forces in Diyala, and LTC Fred Johnson, the deputy commander of 3-2 Stryker Brigade Combat Team, the Iraqi official asked that I withhold his identity from publication. His opinion, shared by others present, is that al Qaeda came to Baqubah and united many of the otherwise independent criminal gangs.We're used to thinking of propaganda as something that's just made up by a disinformation committee whose job it is to discredit and demonize the enemy. But that's not how effective propaganda works. The best kinds of stories are those that can be attributed to an apparently reliable but unnamed source such as an "Iraqi official." That way you can repeat it ad nauseum without invoking any of the normal skepticism that a journalist should use. This is how we learned about rape rooms [Rape Rooms: A Chronology] and weapons of mass destruction. In some cases the source is identified but later exposed a liar (e.g. the Kuwait incubator story [ The Lie]). It doesn't seem to matter if a story turns out to be untrue once it has served its purpose.
Speaking through an American interpreter, Lieutenant David Wallach who is a native Arabic speaker, the Iraqi official related how al Qaeda united these gangs who then became absorbed into “al Qaeda.” They recruited boys born during the years 1991, 92 and 93 who were each given weapons, including pistols, a bicycle and a phone (with phone cards paid) and a salary of $100 per month, all courtesy of al Qaeda. These boys were used for kidnapping, torturing and murdering people.
At first, he said, they would only target Shia, but over time the new al Qaeda directed attacks against Sunni, and then anyone who thought differently. The official reported that on a couple of occasions in Baqubah, al Qaeda invited to lunch families they wanted to convert to their way of thinking. In each instance, the family had a boy, he said, who was about 11 years old. As LT David Wallach interpreted the man’s words, I saw Wallach go blank and silent. He stopped interpreting for a moment. I asked Wallach, “What did he say?” Wallach said that at these luncheons, the families were sat down to eat. And then their boy was brought in with his mouth stuffed. The boy had been baked. Al Qaeda served the boy to his family.
A few days ago I posted pictures of the telegram notifying Francis Crick that he had won the Nobel Prize [Wellcome Trust Images]. The photos were from the Wellcome Images website.
If you need some practice making up just-so stories then get on over to Pharyngula and join the party. The commenters are having a gay old time making up adaptationist explanations for homosexuality [Gay roundup]. If you don't want to make up your own stories then you can vote for your favorite on seyd [Evolution and Homosexuality]. All the tired old standards are there including ...Likewise, removing a portion of the population from breeding relieves the breeders of some of these costs either directly by assisting with child rearing, or indirectly by taking over other costly activities (like food collection) so that t he parents can spend more resources on their progeny.Naturally, PZ is not joining in. He doesn't believe that an adaptationist explanation is required. I agree. In fact, I'm not even sure that an evolutionary explanation is needed since the evidence for a heterosexual gene is practically nonexistent. (Note that if there's a gay and/or lesbian allele then there has to be a heterosexual one as well.)
On Not Getting with the Adaptationist Program
The appreciable release of fixed CO2 and the consumption of energy—with no apparent benefit to the plants—arise because of the lack of absolute substrate specificity of Rubisco. This side reaction can greatly limit crop yields. It looks very much as though Rubisco is just an inefficient enzyme that's incapable of distinguishing between two very similar substrates, CO2 and O2. It appears to be an example of a badly "designed" enzyme*, not unlike many others that have significant error rates. 
The Calvin Cycle is the primary conduit for the fixation of carbon dioxide into the biosphere; ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the rate-limiting fixation step. Our goal is to direct the evolution of RuBisCO variants with improved kinetic and biophysical properties. The Calvin Cycle was partially reconstructed in Escherichia coli; the engineered strain requires the Synechococcus PCC6301 RuBisCO for growth in minimal media supplemented with a pentose. We randomly mutated the gene encoding the large subunit of RuBisCO (rbcL), co-expressed the resulting library with the small subunit (rbcS) and the Synechococcus PCC7492 phosphoribulokinase (prkA), and selected hypermorphic variants. The RuBisCO variants that evolved during three rounds of random mutagenesis and selection were over-expressed, and exhibited 5-fold improvement in specific activity relative to the wild-type enzyme. These results demonstrate a new strategy for the artificial selection of RuBisCO and other non-native metabolic enzymes.©Laurence A. Moran and Pearson Prentice Hall 2007
Andrews, J. T. and Whitney, S. M. (2003) Manipulating ribulose bisphosphate carboxylase/oxygenase in the chloroplasts of higher plants. Arch. Biochem. Biophys. 414:159–169.
Parikh, M.R., Greene, D.N., Woods, K.K., Matsumura, I. (2006) Directed evolution of RuBisCO hypermorphs through genetic selection in engineered E.coli. Protein Eng Des Sel. 19(3):113-9.
I think there are incorrect ways of doing science and I think that much of today's scientific literature is an example of bad science. This isn't news. Back in 1963 Peter Medawar felt the same way and he expressed this viewpoint on a BBC radio show. The transcript, Is the scientific paper a fraud, is published in Medawar's collection of essays called "The Strange Case of the Spotted Mice" (Medawar, 1996). (The title of the book refers to a scientific fraud in immunology that Medawar uncovered in the early 1970's.) ... the scientific paper may be a fraud because it misrepresents the processes of thought that accompanied or gave rise to the work that is described in the paper.Janet Stemwedel discuses this paper on her blog Adventures in Ethics and Science [Why does Medawar hate the scientific paper?]. Janet uses the paper as a way of introducing some key concepts in epistemology—loosely defined as "the investigation of the origin, nature, methods, and limits of knowldege." (Burr and Goldinger, 1980). Read Janet's blog and the comments in order to see this perspective.
What induction implies in its cruder form is roughly speaking this: scientific discovery, or the formulation of scientific theory, starts with the unvarnished and unembroidered evidence of the senses. It starts with simple observation—simple, unbiased, unprejudiced, naïve, or innocent observation—and out of this sensory evidence, embroidered in the form of simple propositions or declarations of fact, generalizations will grow up and take shape, almost as if some process of crystallization or condensation were taking place. Out of a disorderly array of facts, an orderly theory, an orderly general statement, will somehow emerge.Now, nobody has ever accused Peter Medawar of being stupid so before you start to quibble about this sort of generalization, be aware that Medawar does not apply it to all of science and every scientific paper. He's talking about common, but not exclusive, practice.
... the starting point of induction, naïve observation, innocent observation, is a mere philosophic fiction. There is no such thing as unprejudiced observation. Every act of observation we make is biased. What we see or otherwise sense is a function of what we have seen or sensed n the past.This seems like something that's so obvious that it hardly deserves mentioning. But it does deserve mentioning. Medawar was right to have brought it out into the open and it's something we always need to keep in mind.
We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme,The debate between the adaptationists and the pluralists is often dismissed—usually by the adaptationists—as mere quibbling about scientific data. After all, they argue, all we need to do is collect data on each characteristic under discussion in order to resolve the question; is it an adaptation or an accident?
or the Panglossian paradigm.
Gould and Lewontin (1979)What is wrong with the traditional form of the scientific paper is simply this: that all scientific work of an experimental or exploratory character starts with some expectation about the outcome of the inquiry. This expectation one starts with, this hypothesis one formulates, provides the initiative and incentive for the inquiry and governs its actual form. It is in the light of this expectation that some observations are held relevant and others not; that some methods are chosen, others discarded; that some experiments are done rather than others. It is only in the light of this prior expectation that the activities the scientist reports in his scientific papers really have any meaning at all.
Burr, John, R. and Goldinger, Milton (1980) Philosophy and Contemporary Issues Macmillan Publishing Co., New York
Gould, S.J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc. R. Soc. Lond. B 205:581-598.
P. B. Medawar (1996) "Is the Scientific Paper Fradulent?" in THE STRANGE CASE OF THE SPOTTED MICE, Oxford University Press, Oxford.
The Nobel Prize in Chemistry 1961.
Melvin Calvin (1911-1997) won the Nobel Prize in 1961 for his discovery of the Calvin Cycle—the pathway of carbon fixation in photosynthetic organisms, especially plants.Your Majesties, Your Royal Highnesses, Ladies and Gentlemen.
In order to grow and to perform its various activities, every living organism needs a supply of energy in some suitable form. In this respect the organisms existing on this planet can be divided into two fundamentally different groups. All animals, including man, and also some lower organisms, require a supply of energy-rich organic material, food-stuffs that "contain calories", to use a popular expression. The energy contained in the food-stuffs is made available by a biological oxidation ("combustion") of carbohydrates, fats, etc. Obviously, these types of organisms, the so-called heterotrophic organisms, are absolutely dependent on supplies of organic material, occurring outside themselves.
As opposed to the heterotrophic organisms, the organisms belonging to the second group, the so-called autotrophic organisms, i.e. the green plants and certain bacteria, do not require organic material supplied from without. They synthesize organic compounds, primarily carbohydrates, from simple substances, carbon dioxide and water, substances that, in themselves, do not contain any calories. The energy needed for the synthesis is supplied by light which is absorbed by the organisms and subsequently converted by them from light energy into chemical energy. The sequence of reactions by which carbon dioxide and water are converted to carbohydrate is called carbon dioxide assimilation or, taking into account the role of light energy, photosynthesis.
It becomes obvious that photosynthesis not only provides an explanation for the existence of the autotrophic organisms but also furnishes food for man and animals. In other words, photosynthesis is the absolute prerequisite for all life on earth and the most fundamental of all biochemical reactions. It has been estimated that plants and microorganisms on earth transform about 6,000 tons of carbon from carbon dioxide to carbohydrate per second, with at least four-fifths of this amount contributed by organisms in the oceans.
It is understandable that a reaction of such importance and such dimensions should attract the interest of science at an early stage. For more than a century, however, progress in the understanding of the chemistry of photosynthesis was very slow, partly for want of suitable experimental methods.
More than fifty years ago it was recognized that photosynthesis comprised two distinct phases, light reactions and dark reactions. The Nobel Laureate today, Dr. Melvin Calvin, has spent many years of research work on the chemistry of both phases of photosynthesis and, in the case of the second phase, that is to say the reactions leading from carbon dioxide to the assimilation products - to quote Calvin, "the path of carbon in photosynthesis" his work has resulted in the complete clarification of an extremely intricate problem.
Success was achieved as a result of sharp-witted, skilful and persistent work, to some degree facilitated by the availability of certain modern experimental methods that allow investigations which, in older times, were simply impossible. Two such methods may be mentioned: the method of the isotopic labeling of molecules, introduced by de Hevesy, and the chromatographic methods, developed by Martin and Synge, which permit the separation of minute quantities of compounds in complicated mixtures. By an ingenious combination of these and many other methods, Calvin succeeded in tracking the path of the carbon atom from carbon dioxide, taken up by the plant, to the finished assimilation products. The radioactive carbon isotope, 14C well-known also in other connections, has played a particularly important role in Calvin's work.
Most of Calvin's experiments have been performed using a microscopic green alga, Chlorella pyrerloidosa, but parallel experiments with higher plants have shown that the mechanism of carbon dioxide assimilation is the same in all plants.
A question that had occupied scientists for more than a century, was: "What is the primary product of the assimilation; what first happens to the carbon dioxide taken up by the plant?" Calvin demonstrated that the primary reaction is not, as had been assumed previously, a reduction of carbon dioxide as such, but a fixation of carbon dioxide to a substance, the carbon dioxide acceptor, occurring in the plant. Calvin was able to show that the product formed in this fixation reaction is an organic compound known as phosphoglyceric acid.
This discovery was of fundamental importance for the development that followed. The primary product of assimilation was recognized as being a compound, well-known from earlier work as an intermediary product of the biological degradation of carbohydrates, and not some previously unknown compound; phosphoglyceric acid had been identified as a breakdown product of sugar as early as 1929 by Ragnar Nilsson here in Stockholm. Calvin's identification of the primary assimilation product with phosphoglyceric acid led to the very important conclusion that there is an intimate connection between photosynthesis and carbohydrate metabolism as a whole.
Calvin's subsequent investigations mapped out the path between the primary product and the end products of assimilation, the various carbohydrates.What had formerly been assumed to be a reduction of carbon dioxide was shown to be a reduction of phosphoglyceric acid. For a reduction of phosphoglyceric acid to the carbohydrate level, the plant has to supply both a reducing agent and a so-called energy-rich phosphate. It is for the production of these co-factors that plants utilize light energy. This means that light energy is not directly involved in the reactions of assimilation; light energy is used for regeneration of co-factors which are consumed in the assimilation reactions.
As mentioned above, the primary reaction in the assimilation is a fixation of carbon dioxide to an acceptor, the chemical nature of which has been established by Calvin. Rather unexpectedly, this acceptor was found to be a derivative of a sugar, ribulose, to which nobody had paid much attention previously. When carbon dioxide is fixed to the ribulose derivative, phosphoglyceric acid is formed.
As the acceptor is consumed during the fixation reaction it must obviously be regenerated from the assimilation products. Calvin has elucidated the very complicated mechanism of this regeneration. Between the primary product and the acceptor there are no less than ten intermediary products and the reactions between these products are catalyzed by eleven different enzymes.
Professor Melvin Calvin. Your investigations on plant photosynthesis have shed light on a field of biochemistry which was, until recently, veiled in obscurity. You have tracked the various steps of the path of carbon in photosynthesis and created a clear picture of this complicated sequence of reactions, reactions of immense importance for life on our planet.
On behalf of the Royal Academy of Sciences, I extend to you our warm congratulations, and I ask you to receive this year's Nobel Prize for Chemistry from the hands of His Majesty the King.
Come have all the spaghetti and salad you can eat in honor of his noodly goodness. Afterwards we will be showing some great films and documentaries that will be bound to spark a great conversation.SUMMARY (from what the bleep.com):WHAT THE BLEEP DO WE KNOW?! is a new type of film. It is part documentary, part story, and part elaborate and inspiring visual effects and animations. The protagonist, Amanda, played by Marlee Matlin, finds herself in a fantastic Alice in Wonderland experience when her daily, uninspired life literally begins to unravel, revealing the uncertain world of the quantum field hidden behind what we consider to be our normal, waking reality…The chorus members act as hosts who live outside of the story, and from this Olympian view, comment on the actions of the characters below. They are also there to introduce the Great Questions framed by both science and religion, which divides the film into a series of acts. Through the course of the film, the distinction between science and religion becomes increasingly blurred, since we realize that, in essence, both science and religion describe the same phenomena.THE FRIDAY, JULY 13TH SUPERSTITION BASH
- Featuring our "in house" physics Ph.D candidate Eddie Ackad to critically examine the documentary.
Jennie Fiddes is a recent graduate of U of T, earning a BA in Anthropology and Archaeology. She is currently employed as a field archaeologist in the GTA and is an amateur close-up magician. She recently completed an undergraduate thesis project on magic and magician culture in Toronto and is interested in all things magic related.
Jennie will be discussing why magic appeals to people and how this can be both entertaining and dangerous. By demonstrating a few tricks, she will take you through different styles of magic and show the effects they can have on the average thinker and how people can be readily fooled and the impact this can have on their emotions.
As a highlight of the event, we are proud to present the world famous Dr. Joe Nickell. Joe Nickell, Ph.D., is Senior Research Fellow of the Committee for Skeptical Inquiry and investigative columnist for Skeptical Inquirer magazine. A former professional stage magician and private investigator for a world-famous detective agency, Dr. Nickell utilizes his varied background as an investigator of myths and mysteries, frauds, forgeries, and hoaxes. He has been called "the modern Sherlock Holmes," "the original ghost buster," and "the real-life Scully”. He has investigated scores of haunted-house cases, including the Amityville Horror and the Mackenzie House in Toronto, Canada.The Obstacle Course
Dr. Nickell will be discussing his long history of skeptical inquiry including investigating superstitious claims, alien encounters, haunting, and the like. Dr. Nickell stories always entertain.
Thirteen interactive superstition stations will be setup for your enjoyment and educational enrichment:
- Station 1: The Ladder
- Station 2: Lucky Charms
- Station 3: Mirrors
- Station 4: Horseshoes
- Station 5: Black Cats
- Station 6: Cracks
- Station 7: Touch Wood
- Station 8: Four-Leaf Clover
- Station 9: Split Milk
- Station 10: The Salt Bowl
- Station 11: Pennies
- Station 12: Umbrellas
- Station 13: Hats
Life as we know it is based on carbon. All organisms need to have a source of carbon in order to grow and multiply. Animals, such as humans, get their carbon from eating other living things but there are many other species that can assimilate carbon directly from inorganic sources. This process is known as carbon fixation. 
Mechanism of Rubisco-catalyzed carboxylation of ribulose 1,5-bisphosphate to form two molecules of 3-phosphoglycerate. A proton is abstracted from C-3 of ribulose 1,5 -bisphosphate to create a 2,3 -enediolate intermediate. The nucleophilic enediolate attacks producing 2-carboxy-3-ketoarabinitol 1,5 -bisphosphate, which is hydrated to an unstable gem diol intermediate. The C-2-C-3 bond of the intermediate is immediately cleaved, generating a carbanion and one molecule of 3-phosphoglycerate. Stereospecific protonation of the carbanion yields a second molecule of 3-phosphoglycerate. This step completes the carbon fixation stage of the Calvin cycle—two molecules of 3-phosphoglycerate are formed from CO2 and the five-carbon sugar ribulose 1,5-bisphosphate.
I have complained about misuse of the term "Darwinism" by the Intelligent Design Creationists. They seem to be unable to grasp the fact that not all evolutionary biologists are Darwinists.Darwinian logic often contends that because a given proportion of ID proponents are creationists, ID must therefore be creationism. It's a twist on the genetic fallacy, one I like to call the Darwinist "Genesis Genetic Argument." As noted, it implies that each any and every argument made by a creationist must be equivalent to arguing for full-blooded creationism. This fallacious argument is easy to defeat on logical grounds by pointing out that some ID proponents are not creationists, and in fact have been persuaded to support ID in the absence of religion. Thus something other than creationism or religion must be fundamental to the set of views underlying ID (big hint: it's the scientific data indicating real design in nature)!First off, it's ridiculous to pretend that some IDiots view the intelligent designer as anyone other than God. While I've no doubt that they might dig someone like this out of the woodwork, the fact remains that 99.999% of all intelligent design advocates see God as the designer. The term "creationist" refers to someone who postulates a role for a Creator (i.e., God) in creating life. Any IDiot who says they were persuaded to support intelligent design in the absence of belief in a Creator is, well, an idiot. But I repeat myself.
Dembski chides me for never using the term "intelligent design" without conjoining it to "creationism." He implies (though never explicitly asserts) that he and others in his movement are not creationists and that it is incorrect to discuss them in such terms, suggesting that doing so is merely a rhetorical ploy to "rally the troops." Am I (and the many others who see Dembski's movement in the same way) misrepresenting their position? The basic notion of creationism is the rejection of biological evolution in favor of special creation, where the latter is understood to be supernatural. Beyond this there is considerable variability. Some creationists think the world is young while a fewer number accept that it is ancient.Pennock then goes on to show that Dembski is a creationist and so are most (all?) of his followers.
