Gene Genie #11

 
The 11th edition of Gene Genie has been published at Med Journal Watch [Gene Genie #11].

Get on over there to find out where this photograph comes from.

Banned in China

 
Back on March 3, 2007 Sandwalk was not blocked on Chinese servers [Not Banned in China]. Today it is blocked. Test your own site at Great Firewall of China.

Personality Quiz

 
I wonder what the common personalities look like? Has anyone posted one of those?

Your Personality is Very Rare (INTP)

Your personality type is goofy, imaginative, relaxed, and brilliant. Only about 4% of all people have your personality, including 2% of all women and 6% of all men You are Introverted, Intuitive, Thinking, and Perceiving.

How Rare Is Your Personality?

[Hat Tip: GrrlScientist]

Friday the 13th in Port Dover

 
More than 100,000 people and 10,000 motorcycles are expected to descend on Port Dover, Ontario today [Port Dover hogs Friday 13th fame]. It happens every Friday the 13th but the crowd is much larger when the date falls in the summer months. Todays entertainment will include Steppenwolf and the Jeff Healey Band [PD13 News]. I'm told that beer is sometimes served at these events. Go figure.

Sandwalk Resists

 

Afer considerable debate, and much agonizing, I've decided not to join ScienceBorg ScienceBlogs at this time.

When I first started Sandwalk, I was anxious to be part of that group but now, seven months later, there doesn't seem to be a good reason to give up this site for one in the SEED consortium. There are very few advantages to joining ScienceBlogs. They do not come close to outweighing the one major disadvantage—you have to give up a great deal of independence in order to become part of the SEED site.

At one time it seemed as though ScienceBlogs was cornering the market on good science blogging so it was desirable to be associated with a group that had a reputation for quality blogging. That time has past. Now there are lots of good science blogs that have resisted assimilation so it's not so bad to remain on the outside.

[The image is from Borg trioM copyright Paramount Pictures and CBS Television. Its use is consistent with fair use laws in many jurisdictions throughout the world.]

Can You Recognize Propaganda When You See it?

 
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.

But, having declared his intentions, it falls upon his readers to interpret his writings with a great deal of skepticism. That doesn't seem to have happened recently when his story about "baked Iraqi boys" attracted the attention of the right-wing warmongers in the USA and elsewhere. It spread like wildfire.

Here's what Michael Yon wrote on July 5, 2007 [Baqubah Update: 05 July 2007].

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.

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.

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.

Remember that the point of propaganda is to make your enemy look as evil as possible. That's how you justify killing them and sacrificing the lives of your troops. Both sides do it. In the case of the insurgents, the propaganda consists of endless stories about the brutality of the occupying forces and this includes stories that are just as horrible as the one quoted above.

The key for rational people is to recognize that the "good guys" aren't all that "good" and the "bad" guys aren't all bad. War is hell.

[Hat Tip: Canadian Cynic]

Francis Crick Isn't Always Right

 
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.

Since then, a number of bloggers have commented on a brief note that Crick wrote on the back of a letter in 1989. I deliberately skipped that image last week because I thought it was embarrassing. I still do, in spite of the fact that the famous PZ Myers has declared it a nice quote [That's a nice quote].

What's so nice about it? It looks pretty stupid to me. What is there about DNA that gives support to evolution by natural selection—or even just "evolution" for that matter? Are my fellow bloggers just mesmorized by the juxtaposition of Francis Crick's name with the words "evolution" and "natural selection"?

Remember that 1989 corresponds to Crick's dotty period in La Jolla.

[Some people will argue that the sequences of various DNA's from different species lend support to evolution. Of course that's true but it's not what Crick wrote and I doubt very much it's what he meant. He was probably thinking about the beauty of the DNA molecule and it's appearance of "design" by natural selection.]

Calling All Adaptationists

 
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.)

Fixing Carbon: Building a Better Rubisco

On Not Getting with the Adaptationist Program

As its complete name indicates, ribulose 1,5- bisphosphate carboxylase– oxygenase (Rubisco) catalyzes not only the carboxylation but also the oxygenation of ribulose 1,5-bisphosphate [Fixing Carbon: the Rubisco Reaction]. The two reactions are competitive—CO₂ and O₂ compete for the same active sites on the Rubisco molecule [Fixing Carbon: the Structure of Rubisco]. The oxygenation reaction produces one molecule of 3-phosphoglycerate and one molecule of 2-phosphoglycolate.

Oxygenation consumes significant amounts of ribulose 1,5- bisphosphate in vivo. Under normal growth conditions, the rate of carboxylation is only about three to four times the rate of the oxygenation reaction. The oxidative pathway consumes NADH and ATP because the products have to be converted back into ribulose 1,5- bisphosphate in order to continue carbon fixation. The light-dependent uptake of O₂ catalyzed by Rubisco, followed by the release of CO₂ during the subsequent metabolism of 2-phosphoglycolate, is called photorespiration.

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 inefficiency of Rubisco, both in terms or its low reaction rate and its propensity for errors, is why massive amounts of the enzyme are needed in plants. The result is that Rubisco is probably the most abundant enzyme on Earth.

But if nature has done such a bad job of design, can scientists do better? That's the goal of many research labs since improving the efficiency of Rubisco can greatly enhance crop yields, and, incidentally, makes lots of money for the inventors of the genetically modified crops.

Several labs are attempting to genetically modify plants to enhance the carboxylation reaction and suppress the oxygenation reaction. The “perfect” enzyme would have very low oxygenase activity and very efficient carboxylase activity. The kinetic parameters of the carboxylase activity of Rubisco enzymes from several species are listed in the table below (Andrews and Whitney, 2003).


The low catalytic proficiency of the enzyme is indicated by the k_cat/K_M values. These values should be compared to those of typical enzymes that have values from ten to one thousand times greater. It seems likely that the carboxylase efficiency can be improved 1000-fold by modifying the amino acid side chains in the active site.

The difficult part of the genetic modification is choosing the appropriate amino acid changes. The choice is made easier by a detailed knowledge of the structures of several Rubisco enzymes from different species and by examination of the contacts between amino acid side chains and substrate molecules. Models of the presumed transition states are also important. Additional key residues can be identified by comparing the conservation of amino acid sequences in enzymes from a wide variety of species.

The underlying strategy assumes that evolution has not yet selected for the most well–designed enzyme. This assumption seems reasonable since there are many examples of ongoing evolution in biochemistry. Nevertheless, progress has been slow in spite of the enormous financial rewards.

In addition to intelligently-directed genetic engineering to improve on nature, some groups have relied on a form of artificial evolution to do the job. Here's the abstract of a recent paper (Parikh et al. 2006).

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

^*As you might imagine from our discussion of the adaptationist program, there are many biochemists who are very uncomfortable with the notion of a function that has no adaptive explanation. Textbooks are full of adaptive just-so stories that try to justify the oxygenation reaction. None of them hold up to close scrutiny. The Voet and Voet textbook (Biochemisty) avoids the worst just-so stories by saying, "Although photorespiration has no known metabolic function, the RuBisCOs from a great variety of photosynthetic organisms so far tested all exhibit oxygenase activity. Yet, over the eons, the forces of evolution must have optimized the function of this important enzyme." They then go on to describe two unlikely adaptive explanations of the oxygenation reaction. Note that Don and Judy Voet assume that the very existence of the oxygenation reaction demands an optimization assumption and, consequently, an adaptationist explanation. Accident is not a possibility in their minds.

---

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.

Is There a Correct Way to Do Science?

 
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.)

Medawar says,

... 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.

I want to take the discussion in another direction. Medawar's complaint is that the scientific paper distorts the real process of science by misrepresenting the steps that are actually followed in a scientific investigation. In particular, the typical paper suggests that induction is the main mechanism of scientific discovery. Here's how Medawar describes the naive scientific method,

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.

One of the reasons why pure inductive reasoning is misleading is because we never start an investigation with a clean slate.

... 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.

Now we get to a famous quotation from Medawar's talk. Janet Stemwedel discusses it in the context of Popper and falsification—conveniently ignoring Kuhn, who is far more relevant—but I want to use it to talk about adaptationism.

We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme,
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.

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?

They are wrong. This is not a debate about facts at all. It's a debate about the the prior expectations that one has before any data is collected. Criticism of the adaptationist program focuses on the state of mind that researchers posses when they are designing experiments and formulating hypotheses to test. In other words, it's what Medawar refers to when he says that scientists start with "some expectation of the outcome of the enquiry." It's their bias or prejudice that's being questioned and not just whether the horns of an Indian rhinoceros are adaptations or not [Visible Mutations and Evolution by Natural Selection].

One of the main arguments of the Intelligent Design Creationists is that modern scientists adopt a naturalist assumption whenever they do science. This rules out creationism by definition. Some scientists attempt to deny that scientists have any pre-conceived notions at all. They promote the myth of pure inductive reasoning driven only by facts and evidence. It would be wise to drop this form of argument since it is obviously false. Scientists do have prejudices and biases. We need to recognize them and try to deal with them. The essence of skepticism is to always question your assumptions and discard them if they cease to become useful. That's what distinguishes the scientist from the preacher.

---

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.

Nobel Laureate: Melvin Calvin

 
The Nobel Prize in Chemistry 1961.

"for his research on the carbon dioxide assimilation in plants"


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.

Calvin did most of his work with Chlorella, a green algae. The complex pathway was worked out using ¹⁴C labelled compounds to trace the various reactions inside the cell.

The presentation speech was delivered by Professor K. Myrbäck, member of the Nobel Committee for Chemistry of the Royal Swedish Academy of Sciences.

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.

Difficult Science Question

 


I think you can figure out the question. Does this make a perpetual motion machine?

[Hat Tip: LolCat Builder via Monado]

Summer Skeptics Bash July 12 & 13th

 
Come to the Center for Inquiry, 216 Beverley Street at College, just south of the University of Toronto, in the heart of downtown.

In honour of Barry Beyerstein (1947-2007), author, Professor of Psychology at Simon Frasier University, Chair of the Society of B.C. Skeptics and Fellow of the CFI Committee for Skeptical Inquiry (formerly CSICOP).

1. FLYING SPAGHETTI MONSTER DINNER $5 (FREE for Friends of the Centre) Thurs, July 12, 7pm
   
   Featuring screening & debunking of the paranormal-plugging What the Bleep do We Know? with physics PhD candidate Edward Ackad.
   
   
2. SUPERSTITION BASH, Friday, July 13
   
   Featuring a full day of activities, including a presentation by world famous skeptical investigator Joe Nickell at 6pm and a haunted walk at 8:30pm
   
   $5 (Joe Nickell talk), $15 (Full Day, with haunted walk) - $10 full day for Friends of the Centre.

FLYING SPAGHETTI MONSTER DINNER–Thurs, July 12

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.

Film: What the Bleep do we Know??

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.

- Featuring our "in house" physics Ph.D candidate Eddie Ackad to critically examine the documentary.

THE FRIDAY, JULY 13TH SUPERSTITION BASH

A day long event, featuring 3 components

1. The morning (9:00am - 12:30pm), with a Superstition obstacle course and related activities designed for children aged 7-9.
2. The afternoon (2:00pm - 5:00pm), with similar interactive activities designed for an older audience.
3. The evening (5:00pm - 9:30pm), with presentations and a haunted walk!

1. The morning (9:00am - 12:30pm)

• 9:00am: Introductions
• 9:15 – 10:15: Superstition Obstacle Course - 13 stations with interactive activities and educational information
• 10:15am – 10:45am: Jeopardy-style trivia game
• 10:45 – 11:00 minutes “Failed prediction listing” and snack
• 11:00 – 11:30: Fake séance (sceptics)
• 11:30 – 12:00: "Magic for sceptics", with Jennie Fiddes (see info below on this program)
• 12:00: Concluding Mirror smash, featuring Joe Nickell

2. The Afternoon (2:00pm - 5:00pm)
Similar activities as above, but with the following additional activities:

1. "Misfortune" telling
2. Homeopathic beer chugging contest
3. Voodoo Doll activity
4. Open mike setting for people to tell their own superstitions and ghost stories and for debunking opportunities
5. Evening Presentations and Events (5:00pm - 9:30pm)
• 5:00pm - 6:00pm: "Superstitions: A Critical Look" - presentation by Justin Trottier
• 6:00pm - 7:30pm: "Investigating Paranormal Claims" with Joe Nickell (see info below)
• 8:30pm: University of Toronto haunted walk, with Muddy York Walking Tours, the longest running haunted walk group in Toronto

Cost
The cost for participating in the July 13 Superstition Bash, which includes all activities, is $15. The cost for Dr. Nickell's talk only is $5. Friends of the Centre get in to all activities for $10

SPECIAL OFFER: Join now as a CFI Friend of the Centre and get into all two day Summer Skeptics Bash activities entirely free of charge!

Contact Information: Email: justin.trottier@gmail.com Phone: 416-971-5676

"Magic for Skeptics", with Jennie Fiddes

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.

"Investigating Paranormal Claims", with Joe Nickell

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.

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.

The Obstacle Course

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

Fixing Carbon: the Structure of Rubisco

Rubisco (ribulose 1,5-bisphosphate carboxylase–oxygenase) is the key enzyme of the Calvin cycle. It catalyzes the fixation of atmospheric CO₂ into carbon compounds. This reaction involves the carboxylation of the five-carbon sugar ribulose 1,5 -bisphosphate by CO₂ with the eventual release of two three-carbon molecules of 3-phosphoglycerate. The reaction mechanism of Rubisco is shown in [Fixing Carbon: the Rubisco Reaction].

Rubisco makes up about 50% of the soluble protein in plant leaves making it one of the most abundant enzymes on Earth. Interestingly, its status as an abundant enzyme is due partly to the fact that it is not very efficient—the low turnover number of ~3 s^-1 (three reactions per second) means that large amounts of the enzyme are required to support CO₂ fixation!

The Rubisco of plants, algae, and cyanobacteria is composed of eight large (L) subunits and eight small (S) subunits as shown above in top (a) and side (b) views of the enzyme from spinach (Spinacia oleracea). The large subunits are shown as alternately yellow and blue and the small subunits are purple.

There are eight active sites located in the eight large subunits. Four additional small subunits are located at each end of the core formed by the large subunits. The Rubisco molecules in other photosynthetic bacteria have only the large subunits containing the active sites. For example, in the purple bacterium Rhodospirillum rubrum, Rubisco consists of a simple dimer of large subunits.

The purple bacterium version of Rubisco has a much lower affinity for than the more complex multisubunit enzymes in other species but it catalyzes the same reaction. In a spectacular demonstration of this functional similarity, tobacco plants were genetically engineered by replacing the normal plant gene with the one from the purple bacterium Rhodospirillum rubrum. The modified plants contained only the dimeric bacterial form of the enzyme. The plants grew normally and reproduced as long as they were kept in an atmosphere of high CO₂ concentration.

©Laurence A. Moran and Pearson Prentice Hall 2007

Fixing Carbon: the Rubisco Reaction

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.

In most cases, carbon is derived from carbon dioxide in the atmosphere or dissolved in water. There are dozens of different chemical reactions in which carbon dioxide is taken up and attached to another organic molecule. Humans can do this to limited extent but not enough to support all of our carbon needs. Bacteria, protists, plants and fungi are much better at efficiently incorporating carbon from carbon dioxide.

The reactions of carbon fixation are often expensive because they require an input of energy to drive the assimilation of the newly-fixed carbon into metabolic pathways that are operating inside the cell. Photosynthetic organisms often have an abundant supply of energy so they can take up large amounts of carbon to make organic molecules. In fact, the association between carbon fixation and photosynthesis is so obvious that it's often assumed that the processes are directly coupled.

They aren't. There are many non-photosynthetic species that can efficiently fix carbon from carbon dioxide and there are many organisms that can carry out photosynthesis but they don't fix huge amounts of carbon using the standard pathways.

Nevertheless, there is one major carbon-fixing pathway that is present in most photosynthesizing bacteria, protists, fungi, and especially plants. It's called the Calvin Cycle after its discoverer Melvin Calvin (see photo) [Nobel Laureate 1961]. In modern biochemistry courses we discuss this pathway in the photosynthesis chapter but it's no longer considered to be part of photosynthesis. Photosynthesis ends with the light-driven synthesis of the energy molecules ATP and NADPH.

The first step in this pathway is the most important; it's the step where a carbon dioxide molecule is attached to a five carbon compound and the resulting 6-carbon intermediate is split into two 3-carbon molecules. The 3-carbon molecules then enter various metabolic pathways, including a pathway that recreates the 5-carbon precursor—hence the name "cycle."

The initial reaction is shown in the schematic below where each ball represents a carbon atom. The substrate for the reaction is the 5-carbon compound with the green balls and the blue ball represents the carbon atom in carbon dioxide (CO₂). As you can see, the reaction takes place in two steps. The first step is the actual fixation reaction; it creates a 6-carbon molecule with the incorporated carbon atom from CO₂. In the second step this 6-carbon molecule is cleaved producing two 3-carbon molecules.


The 5-carbon substrate is called ribulose 1,5-bisphosphate [Monday's Molecule #34]. It's related to the ribose in ribonucleic acid (RNA) except that it's the keto form of ribose and it has two phosphate groups attached to the 1 and 5 positions. The final products are called 3-phosphoglycerate. They are common intermediates in many metabolic pathways.

Here's the complete reaction. The enzyme that catalyzes this reaction is the most abundant enzyme on the entire planet. It's called ribulose 1,5-bisphosphate carboxylase-oxygenase, or Rubisco for short.

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.

©Laurence A. Moran and Pearson Prentice Hall 2007