Homeschooling and Creationism

 
Not all homeschoolers are Creationists but for strong Biblical literalists homeschooling does offer an easy way of "protecting" children from evil ideas in the real world. Such ideas may cause them to doubt their religion.

If you are a Young Earth Creationist there are some problems associated with the anti-science approach to education. If would be nice to have some helpful advice in case your children ever have to deal with the real world outside the home.

The current issue of Home School Enrichment magazine comes to the rescue. They have an article called Creation and You that's available for free download. (You have to give them an email address.)

The main part of the article extols the virtues of the Answers in Genesis Creation Museum; "600,000 visitors have gone through its doors into an amazing experience demonstrating the power, creativity, and love of the Creator God." I suppose this is a good thing if you're into brainwashing. We just spent yesterday with two young girls in the Royal Ontario Museum in Toronto and there was very little evidence of the "power, creativity, and love of a Creator God." On the other hand, there was quite a bit of good science. Our two friends might have got a bad impression of Biblical literalism. If their parents had been Young Earth Creationists we would have been in big trouble for leading them astray.

Anti-science homeschoolers are right to keep their children away from real museums.

But that's not the only problem they face. What to do if your kids want to have a career in Creation Science? Hmmm ... that's a tough one, isn't it? Here's the answer ....

Preparing for a Career in Creation Science

Answers in Genesis content developers Gary Vaterlaus and Roger Patterson agree that more researchers are needed in Creation Science, but warn that the path may not be easy. Several Christian colleges across the country offer science courses taught from a Young-Earth Creationist perspective, but few research positions are available to those with anything less than a Master’s degree in their field; more likely a Ph.D. And, Roger says, getting those degrees will likely require spending some time in a secular university.

Furthermore, Gary explains that the evolutionary teachings at these secular universities are only part of the problem—there is also a very real prejudice against Creationists who attempt to embark upon a career in any of the relevant branches of science. Aside from the strong possibility of a known-Creationist student receiving failing grades merely for believing God created the universe, Gary cited a case where evolutionists actually petitioned a university to revoke a graduate’s Ph.D. when it was discovered he was a Creationist.

There is a need for young, up-and-coming students to enter the realm of Creation Science, but Gary and Roger emphasize that a student must have an unshakable foundation on the reliability and truthfulness of the Bible, and then be ready, willing, and able to face unbelievably strong opposition while pursuing a degree that will qualify them for the research positions they wish to obtain.

While none of this should dissuade students from choosing such a career, it is important for students and their parents to recognize the potential difficulties and take steps early to ensure a successful and victorious outcome.

For students wishing to be involved in the area of Creation Evangelism, such as speaking at churches or writing about creation related topics, Roger believes a Bachelor’s degree in some branch of science is important for establishing credibility. Several Christian colleges offer science programs, taught from a Young-Earth Creationist perspective, in which students can earn their Bachelor’s degrees. However, many Christian colleges have compromised in the area of origins and evolution, so this is something that should be carefully investigated when researching options for collegebound Creationist students.

Life is tough if you are anti-science but want a career in science. Not only are the secular universities trying to persuade you that truth is important in science but even some of the Christian colleges are "compromised."

But you can succeed if you resist education and maintain "unshakable foundation on the reliability and truthfulness of the Bible." Incredible.

What about average students who venture out into the secular world? What happens if they happen to pick up a book written by a (gasp!) real scientist, or if they mistakenly enter a real museum?

Roger Patterson of Answers in Genesis has some advice.

Homeschool parents often wonder how to protect their children from evolutionary ideas. We brought this up to Roger Patterson, a former biology teacher in a public school who is now one of the main content-developers at Answers in Genesis, and were impressed by his answer:

“As a ministry in general,” Roger explains, “we don’t say, ‘keep your kids isolated from evolutionary ideas.’We think that’s kind of a bad philosophy because when they do go out on their own, they’re going to face those things every day. Case in point: [my wife and I recently] got this space-age ant colony gel material. Flip open the book, and you’re reading through the instructions and all these fun facts about ants, [then] ‘Fossil ants have been found a hundred million years old.’ What we would hope parents can do through homeschooling is teach their kids how to spot those things, and then what the biblical response is for those things. Not to isolate them from those things, but to insulate them to some degree and then help them understand what the problems are there.

“Okay, this is a fun ant gel colony, [but] they didn’t need to throw that little tidbit [about millions of years] in there; it adds nothing to the product or your ability to enjoy and watch the ants. And when you look at it from the perspective that God created these creatures to do what they do, and it’s an amazing thing, it even gives an opportunity to give praise to God when you run across the idea of evolution. [We can say] ‘We know that’s not true. Praise God He did create us, that He is the one who’s sustaining all this.’ Rather than running away and hiding from all those things, let’s face up to it. And then if you’re with your friend, you can tell them about it if they don’t understand those things.

“So my encouragement is not to be afraid of going and getting the dinosaur book from the library, but [be sure to] teach your children as they go through it to understand that some parts [evolutionary statements] are made up, based on the idea of rejecting God in science, and other parts are facts—such as when it tells us what shape the egg was, what size it was, what food they probably ate. Those types of things, we can trust those; those are solid scientific ideas. It’s when we start adding our own assumptions into those things, and telling stories, that we run into trouble.”

Roger explains that there are certain “code words” that parents can teach their children to watch out for. Among these would be “millions or billions of years,” statements about kinds of animals changing into other kinds of animals, and questionable statements of what scientists “know.” Above all, Roger says, it’s important to make sure our children have a solid biblical foundation for
their education, and to help them stand firm on the full authority of scripture.

I can't imagine what it must be like to be constantly on the lookout for sneaky remarks about evolution and other scientific facts that challenge your religion. I can't imagine what it must be like to brainwash your kids into responding with, "We know that’s not true. Praise God He did create us, that He is the one who’s sustaining all this."

I not a huge fan of the idea that teaching your children to be Young Earth Creationists is a form of child abuse but there are times, like today, when Dennet and Dawkins seem to have a strong case.

Home schooling isn't always a good thing for children.

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A Shocking Discovery

 
Almost all proteins in Escherichia coli begin with the amino acid N-formylmethionine (f-met), a modified version of methionine.

N-formylmethionine is inserted at AUG codons at the beginning of the open reading frame in mRNA. The initiation mechanism requires a specific initiator tRNA called f-Met-tRNA (right).

Internal AUG codons are recognized by another tRNA and normal methionine is inserted at these positions. The observation that a single codon (AUG) can serve as the codeword for two different amino acids depending on their position was made over thirty-five years ago and it has been incorporated into the textbooks for decades.

You can imagine how surprised I was to read this in a press release written by Haley Stephenson of ScienceNOW Daily News. You can read it yourself on the Science website: Genetic Code Sees Double.

Call it the genetic version of a double-entendre. Scientific dogma dictates that various three-letter combinations of our genetic sequence each "mean" exactly one thing--each codes for a particular amino acid, the building block of proteins. But a protozoan named Euplotes crassus appears to be more versatile: One of its three-letter combinations has two meanings, coding for two different amino acids. Although the find may seem trivial, it poses a major challenge to more than 4 decades of scientific thinking.

The idea that a protozoan might use UGA to encode both cysteine and a modified form of serine called selenocysteine is quite interesting. It has long been known that UGA is a normal stop codon that is also used to encode selenocysteine. It has also been known for a long time that some organisms can use UGA to encode cysteine.

But the idea that scientific dogma has been overturned by the discovery of a single codon that can encode two different amino acids is just plain silly. It doesn't pose a "major challenge to more than 4 decades of scientific thinking" unless your scientific thinking is flawed to begin with.

This must be an example of hyperbole. Such a claim would never make it into a scientific publication, especially in a prestigious journal like Science. Or so I thought.

Here's the opening sentence in the paper by Turanov et al. (2009).

Although codons can be recoded to specify other amino acids or to have ambiguous meanings (1, 2), and stop codons can be suppressed to insert amino acids (3), insertion of different amino acids into separate positions within nascent polypeptides by the same codeword is believed to be inconsistent with ribosome-based protein synthesis.

It's enough to make me give up writing biochemistry textbooks. Apparently nobody reads them.

We seem to be producing a generation of scientists who don't know about the fundamentals of biochemistry and molecular biology that were elucidated in bacteria and bacteriophage in the mid-20th century. Doesn't anyone teach this stuff any more?

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Turanov, A.A., Lobanov, A.V., Fomenko, D.E., Morrison, H.G., Sogin, M.L., Klobutcher, L.A., Hatfield, D.L., and Gladyshev. V.N. (2009) Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon. Science 323:259-261. [DOI: 10.1126/science.1164748]

John Pieret Issues a Challenge

 
John Pieret took the American Civil Liberties Literacy Quiz.

In his posting, Flunking At Being American, he reports that he scored 32/33 or 96.97%. Impressive.

He then asks, "I would be interested to know how non-US citizens score on the test."

Ask, and you shall receive. Here's my result.

You answered 30 out of 33 correctly — 90.91 %

Average score for this quiz during January: 74.2%
Average score: 74.2%

You can take the quiz as often as you like, however, your score will only count once toward the monthly average.

I didn't know which amendment was which, and what the Bill of Rights specifically prohibited. I'm too embarrassed to reveal the third question I got wrong.

Here's one I got right.

27) Free markets typically secure more economic prosperity than government’s centralized planning because:

A. the price system utilizes more local knowledge of means and ends
B. markets rely upon coercion, whereas government relies upon voluntary compliance with the law
C. more tax revenue can be generated from free enterprise
D. property rights and contracts are best enforced by the market system
E. government planners are too cautious in spending taxpayers’ money

I got it right by thinking like an American! (Ouch!)     ;-)

It's a very strange "civil liberties literacy" question. Is it un-American to advocate socialist policies?

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What Could Be More Scary than the Flying Spaghetti Monster?

 
From the BBC News: Church removes 'scary crucifix'.

A large sculpture of Christ on the cross has been removed from outside a church in West Sussex after its vicar said it was "scaring young children".

The Reverend Ewen Souter said the 10ft crucifix was "a horrifying depiction of pain and suffering" which was also "putting people off".

The sculpture, located at the side of St John's Church in Broadbridge Heath, has now been given to Horsham Museum.

It will be replaced with a new stainless steel cross.

Stainless steel crosses are also pretty scary.

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[Hat Tip: RichardDawkins.net]

Africans Need Jesus?

 
From RichardDawkins.net: Matthew Parris: As an atheist, I truly believe Africa needs God.

Now a confirmed atheist, I've become convinced of the enormous contribution that Christian evangelism makes in Africa: sharply distinct from the work of secular NGOs, government projects and international aid efforts. These alone will not do. Education and training alone will not do. In Africa Christianity changes people's hearts. It brings a spiritual transformation. The rebirth is real. The change is good.

Read the comments. Some people aren't convinced that Christianity is the only way to change people's hearts for the better. Some people think it might be a wee bit condescending to imply that rationalism might be fine among Caucasians but Africans need superstition.

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Changing Your Mind About Evolutionary Psychology

 
Every year John Brockman collects essay from his friends (I want to be one) and published them on his website and in a little book [The Edge Annual Question - 2009].

This year's question was, "What game-changing scientific ideas and developments do you expect to live to see?" Last year's question was, "What Have You Changed Your Mind About? Why?" The book is now out.

There are far too many answers to these questions. I usually look at a few of them but it soon becomes boring.

Sharon Begley feels the same way but she has picked out a few interesting mind changes from the 2008 question. She writes in the Jan. 3, 2009 issue of Newsweek [On Second Thought ...].

The most fascinating backpedaling is by scientists who have long pushed evolutionary psychology. This field holds that we all carry genes that led to reproductive success in the Stone Age, and that as a result men are genetically driven to be promiscuous and women to be coy, that men have a biological disposition to rape and to kill mates who cheat on them, and that every human behavior is "adaptive"—that is, helpful to reproduction. But as Harvard biologist Marc Hauser now concedes, evidence is "sorely missing" that language, morals and many other human behaviors exist because they help us mate and reproduce. And Steven Pinker, one of evo-psych's most prominent popularizers, now admits that many human genes are changing more quickly than anyone imagined. If genes that affect brain function and therefore behavior are also evolving quickly, then we do not have the Stone Age brains that evo-psych supposes, and the field "may have to reconsider the simplifying assumption that biological evolution was pretty much over" 50,000 years ago, Pinker says. How has the view that reproduction is all, and that humans are just cavemen with better haircuts, hung on so long? "Even in science," says neuroscientist Roger Bingham of the University of California, San Diego, "a seductive story will sometimes … outpace the data." And withstand it, too.

There are many reasons for changing your mind about the validity of evolutionary psychology but the idea that "human genes are changing more quickly than anyone imagined" isn't one of them.

As you might have guessed, John Hawks is really happy to encourage that kind of thinking. Hawks is a proponent of the idea that genes can be fixed in the entire human population by natural selection in only a few thousand years [Recent evolution in Newsweek].

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An Unnecessary War?

 
Read what Jimmy Carter has to say about the current situation in Gaza [An Unnecessary War].

I wish Canadian politicians would be as rational as Carter and appreciate that this is a complex situation where nobody is totally right.

The one thing we can be sure about is that war is wrong.¹

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1. Firing rockets at your neighbors is war.

[Hat Tip: Runesmith's Canadian Content]

Testing Natural Selection: Part 2

 
There are several interesting articles about evolution in the Januray 2009 issue of Scientific American. One of the most interesting is an article by H. Allen Orr of the University of Rochester (NY, USA). The magazine title is "Testing Natural Selection"¹ and, as the title implies, the focus is on evolution by natural selection.

Orr's article gives us an opportunity to compare and contrast the views of an adaptationist (Orr) and a pluralistic approach to evolution.

In Testing Natural Selection: Part 1 we discussed two of Orr's opinions: (1) random genetic drift is not as common as most people think, and (2) most (if not all) visible phenotypic change is driven by natural selection.

Here, we discuss Orr's ideas about speciation.

When we say "speciation" we're talking about the biological species concept. Speciation occurs when two formerly compatible populations evolve to the point at which they can no longer interbreed. The key question is what causes this reproductive isolation and how does it evolve?

To contemporary biologists, then, the question of whether natural selection drives the origin of species reduces to the question of whether natural selection drives the origin of reproductive isolation.

For much of the 20th century, many evolutionists thought the answer was no. Instead they believed that genetic drift was the critical factor in speciation. One of the most intriguing findings from recent research on the origin of species is that the genetic drift hypothesis about the origin of species is probably wrong. Rather natural selection plays a major role in speciation.

Orr is correct to point out that random genetic drift is important in speciation. It's the mechanism described in many evolutionary biology textbooks, though it's not the mechanism that most people think about when they think about speciation.

Many biologists have always believed that natural selection plays a much more important role in speciation than random genetic drift. They aren't happy with the textbook description. Orr is one of these biologists. He now claims that the drift explanation is "probably wrong."

Let's think about what has to happen when two species become reproductively isolated. We'll use allopatric speciation as an example.²

We begin with a situation where two populations (races, subspecies) are geographically separated. There is very little gene flow between them so they evolve independently of each other. Over time, they may come to be different because each is adapting to different environments or they may just drift apart by accident. With respect to the actual speciation event, these differences don't matter.

From time to time, individuals from the two subspecies will interbreed to produce fertile offspring. This is responsible for limited gene flow between the subspecies and it proves that speciation has not occurred. If the barrier between the two populations breaks down they will merge back into a single population.

But if the two species have been separated for a long period of time, mutations that prevent interbreeding will accumulate and hybrids will become less and less viable until eventually no fertile hybrids are produced and speciation is complete. There are many ways that this can happen but a common hypothesis involves the build-up of post-zygotic genetic incompatibilities called Dobzhansky-Muller (D-M) incompatibilities.

How are D-M incompatibilites fixed in the population? If they interfere with the matings of individuals from the two populations then how come they don't contribute to infertility when individuals from the same population mate with each other? When the mutation first arises it seems to have a very strange property. It doesn't affect matings between an individual carrying the D-M allele and an individual not carrying that allele from the same population but it does affect matings between the individual carrying the new D-M allele and and an individual from the other population.

In order for this to happen there must already be some genetic differences between the two populations in terms of mating and reproduction. Those differences have accumulated in each of the populations but they must not have an effect on hybrid crosses. Presumably, the new D-M allele is not harmful in one genetic background but it is in the other.

Are these pre-existing potentiators neutral within a population, in which case they become fixed by random genetic drift? Or, are they beneficial in one of the populations, and not in the other, in which case they are fixed by natural selection? The general consensus has been that they are neutral within a population and they accumulate by accident. When enough of them become fixed the cumulative effect is to prevent hybridization. The last allele to arise, the D-M incompatibility allele, is the straw that breaks the camel's back.

Orr believes that the alleles are beneficial in one of the populations. Thus, according to him, reproductive isolation is driven by natural selection. He gives two examples.

The first one is the incomplete speciation in monkeyflower subspecies. I described this in an earlier posting [Speciation in Monkeyflowers], where I pointed out that the role of natural selection was not clear. The differences in flower color and pollinators could have arisen by selection if one postulates changes in the bee population but they could also be due to chance.

For an adaptationist like Allen Orr there's no doubt about what happened.

A good example is the evolutionary history of the two monkeyflower species mentioned earlier. Because their pollinators seldom visit the “wrong” species of monkeyflower, the two species are almost completely isolated reproductively. Even though both species sometimes occur in the same locations in North America, a bumblebee that visits M. lewisii almost never visits M. cardinalis, and a hummingbird that visits M. cardinalis almost never visits M. lewisii. Thus, pollen is rarely transferred between the two species. In fact, Schemske and his colleagues showed that pollinator differences alone account for 98 percent of the total blockage in gene flow between the two species. In this case, then, there can be no doubt that natural selection shaped the plants’ adaptations to distinct pollinators and gave rise to strong reproductive isolation.

This is not a good example of speciation by natural selection. We simply don't know if the flower color mutation spread in one of the populations because it conferred a selective advantage on individuals within that population.

Besides, these two "species" will still form viable hybrids so they're not really species in the first place.

The other example of presumed speciation by natural selection comes from studies on Drosophila There are several example of D-M incompatibility alleles that have been identified. In some of them, there is evidence at the sequence level for rapid fixation. If correct, this is a good indication that the alleles have become fixed by natural selection. The resulting reproductive isolation is an epiphenomenon.³

One example is OdsH in Drosophila mauritiana. It appears to result in an increase in sperm production so it may have been selected in the early population of this species, before it became a species. Presumably, the allele was beneficial in the genetic background that had evolved up to that point and presumably it was detrimental in the genetic background of whatever subspecies it was related to.

The genetic background is obviously part of the speciation event. I suppose that if even one of the D-M alleles is selected then it's fair to say that speciation by natural selection took place.

The question is whether this is common or not. Shucker et al. (2005) looked at post-zygotic reproduction isolation in two populations of grasshopper and provided evidence that all the D-M incompatibilities could be adequately explained by random genetic drift. We'll need to have many more examples in order to decide whether natural selection explains most speciation events.

Personally, I find it easier to understand how reproductive isolation could arise by accidental accumulation of many neutral alleles that eventually lead to reproductive isolation. It's harder to envisage alleles that confer a selective advantage within one population but are extremely detrimental in the other.

Orr doesn't agree.

The studies of the monkeyflower and of hybrid sterility in fruit flies only begin to scratch the surface of a large and growing literature that reveals the hand of natural selection in speciation. Indeed, most biologists now agree that natural selection is the key evolutionary force that drives not only evolutionary change within species but also the origin of new species. Although some laypeople continue to question the cogency or adequacy of natural selection, its status among evolutionary biologists in the past few decades has, perhaps ironically, only grown more secure.

I'm not an expert on speciation and I don't hang out with people who work in the field. However, my general impression from reading the scientific literature is that Orr's statements may be somewhat exaggerated. From what I can see, there are a great many evolutionary biologists who question the hegemony of natural selection. Their numbers seem to be growing, not shrinking.

I don't know where Orr is coming from when he implies that laypeople question the adequacy of natural selection. In my experience laypeople only think about natural selection. They have no idea that there are any other mechanisms of evolution.

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1. The website title is "Testing Natural Selection with Genetics."

2. In allopatric speciation the two diverging populations are geographically separated. That's what makes them distinct populations. In sympatric speciation the two populations may exist in the same geographical and restricted gene flow between them is due to other factors. It's easier to visualize what's happening during allopatric speciation but the logic can apply to sympatric speciation as well.

3. I don't think Orr is actually proposing that there would be selection for reproductive isolation. How would that work?

Shuker, D.M., Underwood, K., King, T.M., and Butlin, R.K. (2005) Patterns of male sterility in a grasshopper hybrid zone imply accumulation of hybrid incompatibilities without selection. Proc. Roy. Soc. B 272:2491-2497. [DOI: 10.1098/rspb.2005.3242]

Buy a Dinosaur

 
Today's the day you can buy a dinosaur fossil. Maynards, in Vancouver, is auctioning off the complete collection of dinosaur fossils from the Seibu Museum in Tokyo, Japan [Auction Details: Dinosaurs].

The collection includes ...

* Eusthenopteron foordi
* Bothriolepis
* Aspidorhynchus
* Araripichthys castilhoi
* Crinoids
* Tyrannosaurus rex
* Ankylosaur
* Dinosaur eggs
* Stegosaurus
* Edmontosaurus annectens
* Triceratops
* Whiteia
* Platecarpus
* Araucarites mirabilis
* Alethopteris
* ...and More

Haven't you always wanted a Stegosaurus in your living room? I think I'll bid on the T. rex. It would look great in my office. Do you think my students might be intimidated?

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Nobel Laureate: Elias Corey

 

The Nobel Prize in Chemistry 1990.

"for his development of the theory and methodology of organic synthesis"



Elias James Corey (1928 - ) was awarded the Nobel Prize for his contributions to the synthesis of organic molecules. Here's the Press Release describing his achievements.

Prize for masterly development of organic synthesis

The development of the art of organic synthesis during little over a hundred years has afforded efficient methods of manufacturing products such as plastics and other artificial fibres, paints and dyes, biocides and pharmaceutical products, all of which have contributed to the high standards of living and health, and the longevity, enjoyed at least in the Western world.

This year's Nobel Prize in Chemistry has been awarded to Professor Elias J. Corey, USA, for his important contributions to synthetic organic chemistry. He has developed theories and methods that have made it possible to produce a large variety of biologically highly active, complicated natural products, thereby making, among other things, certain pharmaceuticals commercially available. Corey's work has also led to new general methods of producing, synthesising, compounds in simpler ways.

The background to Elias J. Corey's successes lies in the fact that he has in a strictly logical way developed the principles of what is termed retrosynthetic analysis. This involves starting from the planned structure of the molecule one wishes to produce, the target molecule, and analysing what bonds must be broken, thus simplifying the structure step by step. One then finds that certain fragments are already known and their structure and synthesis already described. After working backwards in this way from the complex to the already known, it is possible to start building, synthesising, the molecule. This method has proved very amenable to data processing, which has entailed rapid developments in synthesis planning. Combining this synthesis planning with singular creativity, Corey has developed new methods of synthesis. He has produced some hundred important natural products, for example the active substance in an extract from the ginkgo tree, used in folk medicine in China.

Background information

Organic synthesis, that is, the production of complicated organic compounds using simple and cheap starting material, is one of the prerequisites of our civilisation. It is understandable that contributions in this field have often been rewarded with the Nobel Prize in Chemistry. Thus in 1902, only the second year that Nobel Prizes were awarded, the Chemistry Prize went to Emil Fischer for his work on synthesis within sugar and purine chemistry. In 1905 Adolf von Baeyer received the prize in recognition of contributions to the development of the chemical industry through his work on organic dyestuffs. Otto Wallach received the 1910 Prize for contributions to the development of the chemical industry. The 1912 prize went to Victor Grignard for his development of organic magnesium compounds, also termed Grignard reagents, into important intermediates in organic synthesis. In 1950 Otto Diels and Kurt Alder shared the Nobel Prize for discovering the preparatively very useful diene synthesis. Robert B. Woodward received the 1965 prize for his brilliant contributions to the development of the art of organic synthesis. In 1979 Herbert C. Brown and Georg Wittig were rewarded for developing boron compounds and phosphorus compounds, respectively, into important reagents in organic synthesis.

The synthesis of complicated organic compounds often shows elements of artistic creation, as for example architecture. Many earlier syntheses were performed more or less intuitively, so that their planning was difficult to perceive. Asking a chemist how he came upon precisely the starting materials and reactions that so elegantly led to the desired result would probably be as meaningless as asking Picasso why he painted as he did. The process of synthetic planning has been likened to a game of three-dimensional chess using 40 pieces on each side. But the problem may be even harder than this. Over 35,000 usable methods of synthesis are described in chemical literature, each with its possibilities and its limitations. During the synthesis, moreover, new methods appear which can modify the strategy.

Beginning in the 1960's, Corey coined the term, and developed the concept of, retrosynthetic analysis. Starting from the structure of the molecule he was to produce, the target molecule, he established rules for how it should be dissected into smaller parts, and what strategic bonds should be broken. In this way, less complicated building blocks were obtained, which could later be assembled in the process of synthesis. These building blocks were then analysed in the same way until simple compounds had been reached, whose synthesis was already described in the literature, or which are commercially available. Corey showed that strictly logical retrosynthetic analysis was amenable to computer programming. At present, synthesis planning with the help of computers is developing rapidly.

Through his brilliant analysis of the theory of organic synthesis, Corey has contributed in high degree to his own and other researchers' being able, during the last few decades, to complete total syntheses, hitherto impossible, of complicated, naturally-occurring, biologically active compounds, according to simple logical principles.


Elias J. Corey has himself synthesised about a hundred important natural products, of which only a few will be mentioned here. In 1978 he produced gibberellic acid (1), which belongs to a class of very important plant hormones of complicated structure. Recently, he has also synthesised (+)-ginkgolid (2), which owing to its complicated structure is a formidable challenge to anyone working in synthetic chemistry. (+)-ginkgolid is the active substance in an extract from the ginkgo tree, used as a folk medicine in China. The sales value of this natural product is believed to amount to $500 million annually. It is used in treatment of blood circulation disturbances in the elderly, and in asthma. Corey's most important total syntheses concern the medically very important eicosanoids such as prostaglandins, prostacyclins, thromboxanes and leucotrienes, which occur naturally in extremely small quantities. These frequently very unstable compounds answer for multifarious and vital regulatory functions of significance for reproduction, blood coagulation, normal and pathological processes in the immune system, etc. Their importance is witnessed by the award of the 1982 Nobel Prize in Physiology or Medicine to Sune Bergstrom, Bengt Samuelsson and Sir John Vane for the discovery of prostaglandins and closely related biologically active substances. Corey has with enormous skill carried out structural determination and total syntheses of a large number of compounds of many different types of eicosanoids such as prostaglandins and leucotrienes such as lipoxin A (3). It is thanks to Corey's contributions that many of these important pharmaceuticals are commercially available.

To perform the total syntheses successfully, Corey was also obliged to develop some fifty entirely new or considerably improved synthesis reactions or reagents. It is probable that no other chemist has developed such a comprehensive and varied assortment of methods which, often showing the simplicity of genius, have become commonplace in the synthesising laboratory. His systematic use of different types of organometallic reagent has revolutionised recent techniques of synthesis in many respects. He has also in recent years introduced a number of very effective enzyme-like catalysts. These chiral catalysts give only one mirror isomer of the target product, in certain types of synthetically important reaction. The chiral catalysts are simple and easy to recover, and can in some cases be used in their own production.

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The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

[Photo Credit: NIH.]

A Primer on Skepticism

 
What more could you ask for than A Primer on Skepticism from Mike's Weekly Skeptic Rant? Here are some quotations from that posting to tempt you into reading the whole thing ....

If anyone can show me, and prove to me, that I am wrong in thought or deed, I will gladly change. I seek the truth, which never yet hurt anybody. It is only persistence in self-delusion and ignorance which does harm.
                                                Marcus Aurelius

The invisible and the non-existent look very much alike.
                                                Delos B. McKown

The statistics on sanity are that one out of every four Americans are suffering from some form of mental illness. Think of your three best friends. If they're ok, then it's you.
                                                Rita Mae Brown

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Democracy and Lawyers

 
In Canada we vote by marking a "X" on the ballot and putting it in a box. The person with the most "X's" wins.

If the vote is close, we count the ballots again and declare a winner.

It doesn't work that way in America as we learned in 2000. It took several truckloads of lawyers and many judges to count the ballots in Florida. Ultimately it was the US Supreme Court who decided that George Bush would be President.

Now they're doing it again, only this time it's a Senate race in Minnesota [Funny Business in Minnesota]. The lawyers and the judges will decide who actually won. Meanwhile, politicians in Washington will fight over which candidate they will put into the Senate while the court cases are being decided. Apparently the Senate doesn't have to accept the recount as long as the loser is unhappy.

This must be why they call America "the greatest democracy on Earth." It's because America has so many lawyers.

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Probably?

 
In Britain there are 800 buses with the sign, "There’s probably no God. Now stop worrying and enjoy your life." [Atheists Send a Message, on 800 Buses]

Apparently the British atheists wanted to leave out the word "probably" but that wouldn't conform to British advertising guidelines. I wonder if the guidelines apply across the board?

Are there bus and billboard signs that say, "Jesus probably loves you?"

Has the British anthem been changed to, "God probably saves the Queen?"

And what about the coins? Will they be changed to read, "Queen, probably by the grace of God" (D.P.G.) in order to conform to advertising standards?

The best remark comes from an American tourist who spotted the sign on a bus. America is the bastion of free speech (according to some Americans) but only if it's speech that doesn't offend.

Spotting one of the buses on display at a news conference in Kensington, passers-by were struck by the unusual message.

Not always positively. "I think it’s dreadful," said Sandra Lafaire, 76, a tourist from Los Angeles, who said she believed in God and still enjoyed her life, thank you very much. "Everyone is entitled to their opinion, but I don’t like it in my face."

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Denyse O'Leary and a Lesson on Irony

 
I was going to blog about this last weekend but I put it off until Monday, then I didn't get around to it yesterday. Now Canadian Cynic has used the exact same quotation that I was planning to highlight. His posting is funnier than anything I could have written. Read it at ... If the irony were any thicker ...

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Mendel's Garden #27

 
The 27th edition of Mendel's Garden has just been posted on Another Blasted Weblog [Mendel’s Garden No. 27].

Happy Befana from a freezing Rome. Got myself in a bit of a tizz with all this Blog Carnivalia stuff. I thought I was hosting Mendel’s Garden over at the Agricultural Biodiversity Weblog, but it seems I agreed to do it here instead. Not sure why, especially after my recent idleness. P’raps I’ll cross-post. Anyway, on with the show.

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Hot Talks - Fact or Friction: The Continuous Tension Between Science and Religion

 

University of Toronto
Hart House, The Arbor Room
Wednesday, January 21st, 6:30 PM

Join us for an evening of open discussion on the topic of the tension between science and religion. There will be a reception following the event at 8:30pm. Speakers for the evening include:

Professor Jan Sapp

Professor Sapp is a professor of Biology and History at York University. His research is focused on the fields of cell and molecular biology, microbial phylogeny, symbiosis, genetics, evolution and ecology – all from an historical perspective. His historical research on evolutionary biology aims to enlarge the boundaries of that history from focusing solely on Mendelian genetics and the development of neo-Darwinian evolutionary theory.

Professor Yiftach Fehige

Professor Fehige is an assistant professor at St. Michael’s College and the Department of History and Philosophy of Science. His research focuses on Christianity and science, thought experiments, revelation, and research ethics. Professor Fehige is currently working elaborating a pragmatic account of thought experiments in terms of a naturalistic theory of intuition.

Professor Amanda Peet

Professor Peet is a fellow of Trinity College and teaches both within the college and across other disciplines including the Department of physics. She is a member of the Canadian Association of Physicists, the Canadian Institute for Particle Physics and the American Physical Society. She focuses on understanding the fundamental dynamics of all forces and particles seen so far in Nature, especially gravity.

Professor Michael Bourgeois

Professor Bourgoeis is an associate theology professor at Emanuel college. He focuses on constructive, historical, and contextual theologies — including both formative and alternative theological traditions. His particular interests include the relation of theology to the natural sciences, especially on questions of the origin and destiny of the universe and divine action; and expressions of religious ideas in popular culture.

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Get a Job in Newfoundland

 
Memorial University: Departments of Computer Science and Biology

MEMORIAL UNIVERSITY
Tenure-Track Faculty Position in Bioinformatics

The Departments of Computer Science and Biology at Memorial University have each embarked on multi-year renewal programs. Each department currently has more than 20 tenure-stream faculty members, and supports M.Sc., Ph.D. and collaborative graduate programs. For more details, see http://www.mun.ca/biology/Home/ and http://www.mun.ca/computerscience/. Both departments invite applications for a tenure-track position in Bioinformatics, starting no later than September 1, 2009. This will be a joint appointment between the departments. The appointment will be made at the level of Assistant Professor, with the primary appointment in Computer Science, and equal responsibility in both departments, in accordance with the terms of Memorial’s Collective Agreement.

A Ph.D. in Computer Science, Computational Science, Biology, or related fields is required and postdoctoral or equivalent experience is desirable. Applicants should have experience in Bioinformatics, and be keen to do interdisciplinary work between the departments. Applicants should possess a strong research record with outstanding promise for future research, and be able to demonstrate the potential for excellent undergraduate and graduate teaching in Bioinformatics.

Applicants should submit a Curriculum Vitae, statements of research interests, teaching interests and philosophy, and up to three reprints of publications. The application should be accompanied by names of at least three referees of international standing, who are willing to provide letters of recommendation (include details on affiliations, plus phone numbers and email addresses). All material must be received by January 15, 2009; refer to position VPA-COSC-2007-001 in all correspondence, and submit materials to:

Dr. Wolfgang Banzhaf, Head
Department of Computer Science
Memorial University
St. John’s, NL, Canada, A1B 3X5
Email: chair@cs.mun.ca

Memorial University is the largest university in Atlantic Canada. As the Province’s only university, Memorial plays an integral role in the educational and cultural life of the Province of Newfoundland and Labrador. Offering diverse undergraduate and graduate programs to almost 18,000 students, Memorial provides a distinctive and stimulating environment for learning. St. John’s is a very safe and friendly city with great historic charm, a vibrant cultural life, and easy access to a wide range of outdoor activities.

Memorial University is committed to employment equity and encourages applications from qualified women and men, visible minorities, aboriginal people and persons with disabilities. All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority. Partners of candidates for positions are invited to include their resumes for possible matching with other job opportunities.

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Get Several Jobs in British Columbia

 
University of British Columbia: Departments of Botany and Zoology

Tenure track biology instructor positions
Closing date: January 15, 2009 at 5pm

The Departments of Botany and Zoology at the University of British Columbia (Vancouver, Canada) are seeking candidates to fill at least four tenure-track Instructor positions to teach in the Biology Undergraduate Program. At least two positions will be in cellular and molecular biology, with the remaining positions open to biologists in any area. Candidates must hold a PhD in Biology, have a broadly integrative perspective on the biological sciences, and be committed to the improvement of biology undergraduate teaching. Postdoctoral teaching and/or research experience is preferred.

Successful candidates will demonstrate 1) evidence of outstanding teaching, and 2) the ability to contribute to ongoing curriculum and course redevelopment.

Duties of the positions vary, but may include lecturing in introductory and advanced courses, teaching and administration of a large third-year undergraduate laboratory course in the area of specialty, participation in course and curriculum development, and the training and supervision of graduate student teaching assistants. There are also opportunities to work in collaboration with the Carl Wieman Science Education Initiative (www.cwsei.ubc.ca).

Interested candidates should submit a letter of application, a curriculum vitae, a statement of teaching philosophy, an outline of teaching interests, evidence of teaching effectiveness, and the names and contact information for at least three individuals who would be willing to provide letters of references to jobs@zoology.ubc.ca. Candidates are particularly encouraged to highlight previous experience in fostering the education of students from diverse backgrounds.

Review of applications will begin January 15, 2009 and continue until the positions are filled, with appointments anticipated to begin by July 1, 2009.

The University of British Columbia hires on the basis of merit and is committed to employment equity. All qualified persons are encouraged to apply; however, priority will be given to Canadian citizens and permanent residents of Canada.

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Get a Job in Ontario

 
University of Western Ontario: Department of Biology

The University of Western Ontario
Faculty of Science
Department of Biology
Applications are invited for a 3-year Limited Term position in Biology commencing July 1, 2009. As a minimum, the preferred applicant will have a Ph.D. in Biology or a related field, and appropriate training in University level teaching. The successful applicant will be expected to contribute to the department’s commitment to excellence in teaching and provide evidence of his/her ability to teach at the undergraduate level. The successful candidate will be responsible for participating in the teaching of courses in cell and developmental biology as well as general biology.

Applications, including a curriculum vitae and names and addresses of three referees whom we may contact, should be submitted to:

Dr. M. Brock Fenton, Acting Chair
Department of Biology
The University of Western Ontario
London, Ontario
N6A 5B7

Applications for this position will be accepted until January 31, 2009 or until a suitable candidate is found.

Positions are subject to budget approval. Applicants should have fluent written and oral communication skills in English. All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority. The University of Western Ontario is committed to employment equity and welcomes applications from all qualified women and men, including visible minorities, aboriginal people and persons with disabilities.

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Mendel's Stem Length Gene (Le)

The seven traits that Gregor Mendel worked with were: seed shape (R/r), cotyledon color (I/i), seed and flower color (A/a), pod shape (V/v), pod color (Gp/gp), flower position (Fa/fa), and stem length (Le/le). The last trait is also known as Tall (T) and short (t).

The gene responsible for cotyledon color has been identified. It encodes an enzyme that degrades chlorophyll [Identity of the Product of Mendel's Green Cotyledon Gene (Update)]. The gene giving rise to the wrinkled phenotype (r) encodes the starch branching enzyme [Biochemist Gregor Mendel Studied Starch Synthesis].

The gene responsible for stem length has also been identified and cloned (Lester et al., 1997). It encodes an enzyme called 3β-hydroxylase. This enzyme is responsible for one of the last steps in the synthesis of the gibberallin GA₁. See Monday's Molecule #102 for the structure of a similar gibberellin.

Gibberellins are plant growth hormones and GA₁ is required to stimulate the grown of the stem in pea plants. The wild-type enzyme synthesizes GA₁ from its substrate GA₂₀. The pea gene (Le) is related to a similar gene in other flowering plants. Defects in those genes produce dwarf plants.

Lester et al. (1997) cloned the pea gene and identified a restriction length polymorphism that was associated with a mutant version of the gene (le). In the mutant, a single alanine residue was replaced by a threonine residue and this resulted in a 3β-hydoxylase activity that was 20-fold less than the wild type level. The reduced amount of gibberellin GA₁ could account for the smaller plants.

The restriction length polymorphism was used as a genetic marker in crosses between Le/Le plants and le/le plants. It segregated with the le genotype as expected. This experiment establishes that the gene for 3β-hydoxylase is the Le gene that Mendel studied and the phenotype is due to differing levels of the plant hormone gibberellin GA₁.

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Lester, D.R., Ross, J.J., Davies, P.J., and Reid, J. (1997) Mendel’s Stem Length Gene (Le) Encodes a Gibberellin 3β-Hydroxylase. The Plant Cell 9:1435-1443. [PDF]

Darwin Celebrations at the University of Toronto

 
The University of Toronto is hosting a celebration of Darwin next Novermber [Origin of Species at 150: a celebratory conference].

150 Years after Origin: Biological, Historical, and Philosophical Perspectives

Victoria College, University of Toronto, November 21-24, 2009
Darwin wrote in his autobiography, “In July [1837] I opened my first notebook for facts in relation to the Origin of Species, about which I had long reflected, and never ceased working for the next twenty years.” In 1842, he wrote a “very brief abstract” of his theory (35 pages), which in the summer of 1844 he expanded to 230 pages. Beginning in September 1858, after receiving an essay from Alfred Russell Wallace, “On the Tendency of Varieties to Depart Indefinitely from the Original Type,” which outlined the central mechanism of evolution on which Darwin had been working, he began work on completing the manuscript of The Origin of Species by Means of Natural Selection. John Murray, the publisher, launched the book on November 24, 1859 by releasing 1,250 copies. The impact of The Origin of Species has equalled the impact of Newton’s Philosophiæ Naturalis Principia Mathematica. It is the unifying theoretical framework for all modern biology.

November 24, 2009 marks the 150th anniversary of the publication of The Origin and The Institute for the History and Philosophy of Science and Technology, the Department of Ecology and Evolutionary Biology, and the Department of Philosophy at University of Toronto are mounting a Gala Celebratory Conference. The conference will culminate in a gala dinner on November 24 at which participants will toast the tremendous achievement of Charles Robert Darwin.

Five multi-disciplinary symposia have been organized. For each symposium, the panel consists of a biologist, a historian of biology and a philosopher of biology.

The Institute for the History and Philosophy of Science and Technology is located on the elegant, historic Victoria University campus (one of the University of Toronto’s federated universities) and the conference will be held in that location

The emphasis is on history and philosophy. It would be a perfect opportunity to put Darwin into the context of the modern world. It would be a crying shame if the conference was wasted on promoting natural selection and misrepresenting modern evolutionary theory. Do the conference organizers really mean it when they say that a 150 year old book, Origin of Species, is, "the unifying theoretical framework for all modern biology?

Here's the preliminary program.

Saturday November 21, 2009

6-7 pm: Keynote Address: to be announced

7-9pm: Reception

Sunday November 22, 2009

9-10 am: Keynote Address
Evelyn Fox Keller (Massachusetts Institute of Technology)

10 am-12 pm: Symposium:
Gender, Evolution, and Sexual Selection
Lisa Lloyd (Indiana University)
Marlene Zuk (University of California)
Erika Milam (Clemson University)

12-2 pm: Lunch Break

2-3 pm: Keynote Address
Michael Ruse (Florida State University)

3-4 pm: Contributed Papers Session
to be announced

4-5 pm: Contributed Papers Session
to be announced

5-6 pm: Keynote Address
James Moore (University of Cambridge)

Monday November 23, 2009

9-11 am: Symposium:
Evolution and Development
Manfred Laubichler (Arizona State University)
Jane Maienschein (Arizona State University)
Michael Dietrich (Dartmouth College)

11am-12pm: Contributed Papers Session
to be announced

12-2 pm: Lunch Break

2-4 pm: Symposium:
Species
John Beatty (University of British Columbia)
Kevin de Queiroz (National Museum of Natural History)
Marc Ereshefsky (University of Calgary)

4-5 pm: Contributed Papers Session
to be announced

5-6 pm: Keynote Address
Alison Pearn (Darwin Correspondence Project)

6-7 pm: Special Presentation
A Play: "Re: Design (A Dramatisation of the Correspondence of Charles Darwin and Asa Gray)"

Tuesday November 24, 2009

9-11 am: Symposium:
Taxonomy
Mary Winsor (University of Toronto)
Kevin Padian (Berkeley)
Richard Richards (University of Alabama)

11am-12pm

Contributed Papers Session
to be announced

12-2 pm: Lunch Break

2-4 pm: Symposium:
Ecology
Joan Roughgarden (Stanford University)
Gregg Mitman (University of Wisconsin-Madison)
Gregory Cooper (Washington and Lee University)

4-5 pm: Contributed Papers Session
to be announced

5-6 pm: Keynote Address
Sean Carroll (University of Wisconsin-Madison)

6-7 pm: Break

7-8 pm: Keynote Address
Spencer Barrett (University of Toronto)

8-10:30 pm: Origin at 150 Gala Dinner

Most of the speakers are strangers to me. I have no idea where they might be coming from in terms of their understanding of evolutionary theory.

Of the ones I do know, Sean Carroll is a fan of natural selection and Spencer Barrett is a classic adaptationist. It's worrisome that the organizers invited Michael Ruse to give a keynote address. As I've mentioned before, Ruse does not seem to have a very good handle on modern evolutionary theory. I fear that the conference participants will be subjected to a particular point of view that will not be a fair description of how Darwin contributed to modern biology.

If The Institute for the History and Philosophy of Science thinks Michael Ruse is going to give a good overview of Darwin's contribution then this does not bode well for the conference. They should have learned from his appearance at the Royal Ontario Museum last June [Darwinism at the ROM].

At that symposium Ruse asked, "Is Darwin's Theory Past Its "Sell By" Date." I think Michael Ruse has passed his "best before" date. It's time for him to retire.

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Darwin Week Activity at CFI

 
I attended a lecture by Carl Zimmer last summer at the Chautauqua Institute [Carl Zimmer at Chautauqua]. He posted the text on his blog at: Darwin, Linnaeus, and One Sleepy Guy.

Here's one of the important bits ...

I’d like to thank the Chautauqua Institution for inviting me to speak during this week’s series. I’m particularly grateful that the Chautauqua Institute saw fit to make this week’s theme Darwin *and* Linnaeus. We are now descending into a frenzy of Darwin celebrations, and you’re not going to escape it until the end of 2009. We’ve got his 200th birthday in February, and the 150th anniversary of the publication of the Origin of Species in November. The spotlight is going to be on Darwin, and Darwin alone.

I think this is a mistake. Darwin deserves celebrating, but that doesn’t mean we should fall prey to a cult of personality. Darwin did not invent biology. Darwin did not even find most of the evidence that he used to back up his theory of evolution. And he certainly did not discover all there was to know about evolution. Biologists have discovered many new things about evolution since his time. In some cases, they’ve challenged some of his most important arguments. And that’s fine. That’s the great strength of science.

So today I’m going to take advantage of our dual celebration of Linnaeus and Darwin. I’m going to talk about the process of science, how great thinkers challenge the thinkers of the past, how their own great ideas are altered by future generations. I’m going to talk about why Linnaeus was so important, and how Darwin shattered some of Linnaeus’s most cherished claims. I’m also going to talk about modern biologists have done the same to Darwin.

The best way to convey how drastically biology has changed since Darwin’s day is to focus on one group of living things. It’s a group about which Darwin–and Linnaeus–had little to say. I’m going to talk about microbes.

Carl was pointing out the obvious. Science has not stood still since 1859, the year that Origin of Species was published. As we approach the celebrations in February and November it's important to keep this in mind. That's why I'm giving a talk about the modern view of evolution and how it builds upon, but differs from, the views of Charles Darwin in 1859.

Come listen ...

Darwin Week Activity: Pre and Post Darwinian Science with Larry Moran

Starts: Friday, February 13th at 7:00 pm

Ends: Friday, February 13th at 9:30 pm

Location: Centre for Inquiry Ontario, 216 Beverley St, Toronto ON (1 minute south of College St at St. George St)

What was science like before Darwin, and how did it change after Darwin?

Larry Moran will be discussing our modern scientific world in light of the impact Darwin and his theory of evolution due to natural selection has had on it.

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto.

$5, $3 for students and FREE for Friends of the Centre

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How Does Your Blood Clot?

Some of you have been following the smackdown of Casey Luskin over his attempt to revive the irreducible complexity of the blood clotting cascade. This is a complicated pathway so I wrote a bunch of postings last year to try and explain the pathway at the molecular level.

Theme

Blood Clotting
Here's the complete list in case anyone wants more information in order to follow the discussion.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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George Johnson Revists His Defense of Scienc Journalism

 
John Horgan and George Johnson are at it again. They clarify some important points in a followup to their earlier discussion about science journalism (see Who the Heck Is George Johnson?).


John Horgan asks the key question when he says, "Where do we get informed criticism of science these days?"

George Johnson points out that there's a lot of junk on the internet and this includes most science blogs. He does go out of his way to mention the best science blogs but he seems to be surprised and upset at the amount of junk masquerading as legitimate science.

He's right, of course, but that's not the point. What Johnson still seems to ignore is the criticism of traditional print science journalism. I'm not saying that science blogs are perfect—far from it—what I'm saying is that the hubris of science journalists is unjustified. They're not nearly as good as they think they are. As a matter of fact, in my opinion the quality of science on science blogs is superior to the quality of science described by science journalists in the print media.

As a general rule, science journalists are better writers but they are not necessarily better at describing the correct science. It's the content of articles by science journalists that I'm criticizing, not their literary style. I don't think George Johnson gets this. He seems to put all of his emphasis on the literary aspect of science journalism and not enough on the scientific accuracy part of science journalism. Johnson admires good writing.

John Horgan gets it. His main complaint is that it's the scientists, and not the science journalists who are hyping their discoveries and misrepresenting the importance of their work. Horgan points out that scientists are often too deeply immersed in their work to see the big picture. George Johnson is happy to agree with him. I agree too—it's scientists who are behind bad science.¹

However, both Horgan and Johnson see themselves as writers who are able to rise above this self-interest on the part of scientists and put things in proper context. According to them, the role of a science journalist is to pick out the real breakthroughs and to present an accurate view of the science, unencumbered by the prejudices and biases of those scientists who are down in the trenches.

I agree that this should be the goal of science journalism. What I expect of good science journalism is that it avoid the hype and put the science in context. In that sense, Horgan and Johnson are correct—they have identified an important role for science journalism.

So, how's it working out? Badly, I'm afraid. Most science journalists who write about the things I know are failing miserably at this important task. Their prose may be good but they are completely taken in by the scientists who exploit them. This would be unacceptable if we were talking about political reporting or the writings of an art critic. It's just as unacceptable when we're talking about science reporting. That's the issue.

While scientists are responsible for bad science in the first place, it also seems to be scientists who recognize bad science. I don't see too many examples of science journalists who recognize bad science. As a group they seem to be very gullible.

Here's the excerpt where Horgan and Johnson discuss the future of science journalism. Horgan is pessimistic and Johnson is more of an optimist. The first part of this excerpt is where Johnson defends the effort that science journalists put into their work. Science journalists may work hard but you don't get "A's" just for effort.


It's interesting to hear Johnson defend Scientific American and Discovery as good examples of science journalism. It's more evidence that he doesn't know the difference between good science and bad science.

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1. Listen to the exchange when John Horgan describes evolutionary psychology. Horgan knows that a lot of it is garbage. Johnson doesn't. I think this is part of Johnson's problem. He doesn't seem to have a good feel for the difference between good science and bad science in spite of the fact that he (Johnson) brags about the amount of work that goes into good science journalism and how important it is to have good sources. Johnson seems to think that most articles written by science journalists must be accurate because science journalists are supposed to do their homework. That's a bad assumption.

Monday's Molecule #102

 
Name this molecule. Your task is to identify the molecule and give it a biochemically accurate name (the IUPAC name would be perfect, but it's not required). A Nobel Laureate is associated with this molecule, and similar molecules, because the prize was awarded, in part, for synthesizing them in the laboratory.

The first one to correctly identify the molecule and name the Nobel Laureate wins a free lunch at the Faculty Club. 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: Alex Ling of the University of Toronto, Timothy Evans of the University of Pennsylvania, and John Bothwell of the Marine Biological Association of the UK in Plymouth, UK. John, Dale, and a previous winner (Ms. Sandwalk) have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Alex got the first one.

THEME:

Nobel Laureates
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 names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

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

UPDATE: The molecule is gibberellin A3 (GA3), a plant hormone. The Nobel Laureate is Elias Corey. The winner is, once again, Dima Klenchin of the University of Wisconsin. Congratulations Dima.

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The Open Laboratory 2009

 
The best science postings have been selected for the 3rd edition of The Open Laboratory. See the results: The Open Laboratory 2008 - and the Winners are......

There are 50 articles. This year the number of postings from the SEED consortium is only 20% of the total, indicating that there are a lot of other science blogs out there.

Out of the eclectic mix I picked the few that discussed evolutionary biology or the molecular biological sciences. Here they are.

Important new flu paper in Cell: part I

Detecting natural selection: a pika's tale

Space Invader DNA jumped across mammalian genomes

Finches, bah! What about Darwin's tomatoes?

Biochemistry of Halloween: Installment 1

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What Does Your Genome Sequence Reveal?

 
John Hawks has some interesting comments about your DNA. What does it actually tell you about your risk of dying or inheriting some nasty symptoms? What would a third party do with your genome scan? Will newspapers publish the results of secretly obtained genetic information from politicians and other famous people?

Would that be an invasion of privacy? Of course it would.

Read Privacy, politicians, and genetic testing.

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Top Ten Evolution Articles from New Scientist

 
In my opinion, New Scientist is the best of the current crop of science magazines for the general public, although, in all honesty, the competition is not very challenging.

New Scientist has published Darwin's dangerous idea: Top 10 evolution articles. Most of them are fairly respectable. The main exception is an article on epigenetics [Rewriting Darwin: The new non-genetic inheritance]. That article is an embarrassment.

One of the best articles is Evolution: 24 myths and misconceptions. I've already posted my kudos at: Evolution: 24 myths and misconceptions. One of the nicest things about the series of articles is their description of random genetic drift as an important player in evolution; for example, Evolution myths: Natural selection is the only means of evolution.

Which brings me to the last article in the top ten list: Freedom from selection lets genes get creative. Here's what it says about random genetic drift.

Natural selection, first identified by Charles Darwin in On the Origin of Species, occurs when genetic mutations cause changes in the body and behaviour of an animal that affect its ability to survive and pass on its genes. Some mutations will have positive effects, others may kill an animal outright or somehow affect its offspring's ability to survive and reproduce. Harsh climates, sparse food and relentless predators destroy many individuals, leaving only those that survive best under exactly those pressures. As a result, the more intense the pressure of natural selection, the tighter the fit between a species and its niche.

So, what happens when the pressure is off? You might think there would be little impetus to adapt, so that species would pretty much stay the same. Not so, says Deacon. Animals still change because genes mutate all the time. The constant rewriting of DNA supplies the raw material from which natural selection picks its winners and losers, and when selection is relaxed, the process of weeding out is less ferocious. Instead, a process called genetic drift kicks in as mutations proliferate and animals with a much wider variety of traits are able to survive and reproduce. Some of the classic traits of a species may be lost, while others can arise for no reason other than that it simply doesn't matter if they do.

Close, but it doesn't quite merit a cigar. Drift does not "kick in" when selection pressure is lifted. Drift occurs all the time. It even competes with natural selection.

And while it's partially true that, "the more intense the pressure of natural selection, the tighter the fit between a species and its niche" it's also true that intense "pressure" increases the chance of extinction.

It seems strange that popular journals can publish articles about evolution that disagree with each other and nobody (editors?) seems to notice.

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Happy New Year

 
This is a year to celebrate Charles Darwin and evolution. In order to start off on the right foot here are some simple¹ thoughts from our Intelligent Design Creationist friends over at Uncommon Descent [TEN THOUGHTS DARWINISTS NEED TO PONDER BEFORE BREAKFAST].

As we head into the new year and the impending Darwin bi-centennial on February 12th, we’re sure to be regaled with story after story of the wondrous things that Darwinian evolution hath wrought. A friend e-mailed the following to me, and with his permission, I reproduce it here below the fold. Perhaps pondering some of these questions might bring some balance to what is otherwise sure to be a lopsided Darwin love-fest for the next couple of months. The original of this can be found at the University of California Santa Barbara Veritas Forum website.

1. Evolution by natural selection is more plausible in a theistic world than an atheistic world.
2. Darwin never accounted for the arrival of the fittest. Naturalism’s god-of-chance is always called upon to do the job.
3. Science rules out the possibility that natural processes might prevent major evolutionary change simply by definition because biological stability and conservation would imply that creation events had taken place since the creation of the universe.
4. Creation preceded Evolution anyway.
5. Edward Blyth described the process of natural selection well before Darwin and Wallace. He concluded that it acted as a force of conservation eliminating deterimental variations from populations.
6. Darwin admitted that based upon the data published in his Origin of Species, one could come to “directly opposite” conclusions. For example, natural selection can prevent major evolutionary change from occurring on a gradual step-by-step basis by eliminating useless transitional stages thus explaining the lack of transitional sequences leading to all of the major body plans (phyla) in the fossil record.
7. Natural selection better describes biology’s “ordinary rules of stability” than major evolutionary change.
8. Darwinian theory predicts a pervasive pattern of natural history that is upside-down from the pattern found in the fossil record.
9. Natural history is more compatible with progressive creation than Darwinian evolution.
10. The ultimate origin of Nature itself cannot be natural. Either Nature or a Natural Law Giver has always existed. Nature has not always existed. What do you conclude?

All these questions, and more, will be answered at the Darwin 2009 Festival in Cambridge, July 5-10, 2009. Speakers include Sir David Attenborough, Dr. Matt Ridley, Lord John Krebs, Professor Steve Jones, Dame Gillian Beer, Lord Robert May, Richard Dawkins, Professor Dan Dennett, Ian McEwan and AS Byatt.

Is anyone from North America interested in going?

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1. I use the term very literally.

Another Way of Knowing?

Thanks to one of our favorite IDiots, Michael Egnor, we now have an answer to an important question. The question is whether there are ways of knowing other than science (evidence + rationalism). Egnor's answer is .... wait for it .... subjective experience! [My Challenge to Dr. Novella: The Materialist Color Tutor’s Dilemma].

Imagine a tutor who specializes in teaching children about color. He’s a materialist, named…Steve. He knows all that is known about color. He knows the physics, the optics, the chemistry, the neurobiology, everything. A family retains him to teach their child, a prodigy, all that can be known about color.

Tudor Steve goes to work. He teaches the little genius about quantum mechanics with relevant application of string theory to flesh out the more subtle issues, then goes on to teach the precocious child chemistry, optics, neurobiology, all of the material and physical facts about color. The child excels in color class in school, acing all of the exams on the physics and the chemistry and the neurobiology.

Then, one day, the boy confides in tutor Steve: the child is color-blind. He has learned all of the physical facts about color, but he has no idea what color looks like. He knows that tutor Steve is a materialist, so he assumes that all there is to know about color can be explained from a materialistic standpoint, including what color looks like. That’s why the child’s parents hired Steve the materialistic color tutor.

So the boy asks tutor Steve:

"Please explain to me what color looks like."

Materialist color tutor Steve has a dilemma. Material facts about color can, of course, be taught. But can ‘what it is like to see color,’ the subjective experience of color, be taught? If it can’t, then there is knowledge of color that is not material knowledge. Therefore materialism cannot completely explain the subjective experience (the qualia) of color. Therefore subjective experience is something in addition to matter. And therefore dualism is necessary to explain the mind.

How would materialist tutor Steve explain what color looks like to a person who is color blind?

That's a tough question all right. But it's only one of many difficult questions of this type. Here are some others that Michael Egnor might want to ponder.

• How do you explain intelligence to someone who is stupid?
• How do you explain what it's like to be abducted by UFO's if you've never been kidnapped by aliens?
• How does a bat explain echolocation to a human?
• How do you explain astrology to someone who doesn't know their birthday?
• How do you explain love, or anger, to someone who has never been angry or in love?
• How do you explain homeopathy to someone who has never been cured by drinking water?
• How do you explain Canada to someone who has never been there?
• Where are the weapons of mass destruction?
• Does Michael Egnor exist?

Hands up, all those who think these questions reveal non-scientific ways of knowing about the truth? How many think that human feelings and emotions cannot be explained by science and scientific reasoning? Has Michael Egnor proved that UFOs astrology homeopathy God exists?

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