John Lynch Has an Opinion

 
John Lynch has re-opened a debate about whether Dawkins' opinion on religion is valid [Weinberg on expertise]. The discussion was prompted by PZ's review of Weinberg's review of The God Delusion [I am so happy that Steven Weinberg is on our side].

Here's what John says,

Many of us involved with fighting creationism have argued for years that expertise is important in scientific matters. That's why lawyers like Phil Johnson need to demonstrate their knowledge of evolution before they are taken seriously. Any one can express an opinion, but to be taken seriously on a scientific issue, one must have engaged in serious study of the matter at hand. This, of course, also holds for non-scientific areas of study.

Weinberg is attempting to argue that Dawkins is entitled to voicing his opinion about religious matters, and indeed he is, just as I'm entitled to express my opinion about any matter. Unless Dawkin's has demonstrated his knowledge of the subject at hand, one could argue that his opinion on religion is as valid as Johnson's on evolution or mine on bridge building.

The analogy is interesting but I think the logic is facile. Let me try and show why the argument fails in the case of an atheist arguing against religion.

I am an atheist. I have listened to many of the arguments for the existence of God and I am not convinced by any of them. Like Dawkins, I can give you my explanations for why I reject these arguments. They appear very rational to me and I have several decades of experience defending them against all comers. So does Dawkins, he's no spring chicken. (Dawkins is way older than me!)

It seems very disingenuous for religious people to dismiss my atheistic stance on the grounds that I'm not an expert on religion. They rarely criticize believers for being non-experts in religion so, in addition to being disingenuous, it's also hypocritical.

How much religion do I have to study before my rejection of it becomes credible? Is five years in a Buddhist monastery enough to prepare me to reject Buddhism? Is that what the average Christian has done before deciding that Buddhism just isn't for them?

Do I have to become a Jesuit priest before I can reject Roman Catholicism? Is that what John Lynch has done, or is his religious position not valid?

There are even more extreme reductio ad absurdum's. Do we not have a valid opinion about astrology until we've become experts at casting horoscopes? How about my rejection of fascism? I'm not an expert—I haven't read all of the works of the leading fascists—does that mean my opinion isn't valid?

Finally I'd like to ask John what he thinks of the Pope, or Billy Graham, or Ted Haggard, or even Francis Collins. All of them reject atheism. Are they expects on atheism? Is their opinion valid? Do you criticize them for offering just an opinion?

This issue isn't as simple as John makes out. Even if we concede that Dawkins isn't an expert on all religions that's no reason to discredit his defense of atheism. It's not the same as Johnson's ignorance about evolution because evolution isn't about opinions and superstitions. Religion is. It's more like astrology.

The onus is on believers to convince us non-believers to adopt their faith. I'm not convinced, and I think my opinion about the existence of God is just as valid as that of C.S. Lewis, Ted Haggard, or Francis Collins. Instead of whining about whether Dawkins has mastered the subtlety of the Eucharist or the relationship of the Prophet Muhammad to God, why not concentrate on showing where Dawkins went wrong in his rejection of the arguments for the existence of God?

James R. Drummond

 
James R. Drummond is an Emeritus Professor in Residence in the Department of Physics at the University of Toronto [James R. Drummond, Toronto]. He currently holds a Canada Research Chair in Remote Sounding of Atmospheres at Dalhousie University in Nova Scotia [James R. Drummond, Dalhousie]. Prof. Drummond received his B.A.(1972), M.A., and D. Phil.(1977) degrees from Oxford, UK.

Drummond recently attracted attention because of something he said in an article published by the Star Tribune in Minneapolis-St. Paul, Minnesota USA [The secret life of arctic clouds.].

If we compare the debate over the theory of evolution with the debate over the theory of global warming -- global warming's a whole lot more certain at the moment.

That's a remarably stupid thing for a scientist to say and PZ Myers picked up on it right away. So did one of the editors at the Star Tribune who honed right in on Drummond's doubts about evolution [Thanks, Jim Drummond. Thanks a lot].

I contacted Drummond by email to see if he really was an IDiot. Prof. Drummond claims he can't remember exactly what he said because the interview was a long time ago. He says that what he meant was that global warming was just as certain as evolution. When asked if he was a Creationist or a fan of intelligent design, he avoided the question and emphasized the problem of global warming.

The impression I get is that he has some personal doubts about the validity of evolution and that may explain the quoted remark.

I think we've got a live one, folks. I sent him the link to PZ's blog. I can't imagine that he would read that and not take the opportunity to distance himself from those who believe in superstition.

Percy Saltzman Dies

 

Percy Saltzman was one of the first television weatherman personalities. Those of us who are old enough to remember the '50's and '60's will know who he is. He died on Tuesday at the age of 91.

Saltzman had a website and a blog. His last message was posted on Dec. 6, 2006. It was about his visit to a nudist colony [Nudies and Me]. Read it. It's witty and intelligent and a great way to remember a Canadian icon. We'll miss you Percy.

[Hat Tip: Monado]

Gap Penalties

Reed A. Cartwright (De Rerum Natura) has just posted a summary of his recently published paper on the effect of gap costs in sequence alignment [Logarithmic gap costs decrease alignment accuracy].

It sounds esoteric but, in fact, it's a very important problem. Computer driven sequence alignments are behind a great deal of the bioinformatics that's being published today. Surprisingly, no computer program can do as good a job at global sequence alignment as a competent student. This should be cause for concern since it means that all the published work is known to be sub-optimal because the algorithms aren't up to the task. Most workers don't acknowledge this—I suspect they simply don't realize that the alignment programs are inefficient.

Reed looked at a particular problem in sequence alignment. The only difficult part about sequence alignment is placing the gaps that are due to insertions and deletions (indels) arising from the time that two sequences diverged from a common ancestor. During automated sequence alignment the program has to assign a penalty, or cost, for inserting gaps in the alignment. If there was no penalty associated with indels then the program would insert gaps willy-nilly to bring every position into perfect alignment. The idea is to limit the placement of gaps to only those locations where they truly represent an evolutionary event.

The standard penalty is represented by the formula G_k a + bk where G_k is the gap penalty. There are two components to the penalty: "a" is the penalty for creating a gap, and "b" is the penalty for extending it by "k" residues.

Reed tested several other types of gap penalties to see if they did a better job at aligning sequences. You should read his posting to see the surprising result. His paper is available here.

Here's an example of a computer generated multiple sequence alignment from the Pfam database [HSP70 alignments]. The protein is HSP70, the major protein chaperone. If you look at the right-hand side of the first page you can see how the algorithm placed the gaps (represented by dots). Most of you coud do a better job with just a little practice.

Doomsday Clock Advances

 
The Bulletin of the Atomic Scientists has moved the Doomsday Clock two minutes closer to midnight ["Doomsday Clock"].

I think they're right. The world is a much more dangerous place now that the nation with the most weapons of mass destruction is threatening to use them.

Australians Debate "The God Delusion"

 
Listen to four Australians discuss The God Delusion. The show was broadcast last October on Australia's ABC Television.

I found the "debate" unsatisfying and somewhat troubling. Germaine Greer comes across as a bit of a kook and the two agnostics just don't get it. The only person who makes any sense is a Jesuit priest!

[Hat Tip: Richard Dawkins' website]

More Little Mosque on the Prairie

 


See part of an episode of Little Mosque on the Prairie. The rest are here.

[Hat Tip: Alex Palazzo]

What Would You Sequence If the Price Were Only $1000?

 
Nature Genetics has a Question of the Year.

The sequencing of the equivalent of an entire human genome for $1,000 has been announced as a goal for the genetics community, and new technologies suggest that reaching this goal is a matter of when, rather than if. What then? In celebration of its upcoming 15th anniversary, Nature Genetics is asking prominent geneticists to weigh in on this question: what would you do if this sequencing capacity were available immediately?

That's an easy one to answer.

My students are involved in several projects that try to figure out the evolution of our favorite gene family [HSP70]. Many of the projects are limited by the lack of complete information on every member of the gene family in certain key species. (See The Evolution of Gene Families for am explanation of why you need to have sequences of every copy.)

So here's a short list of genome sequences that we desperately need in order to address some important issues:

• any snake; rattlesnake would be good
• any turtle
• any bird other than chicken; ostrich or emu would be good, penguin would be awesome
• lamprey
• octopus
• lobster or crab
• maple tree and dandelion; or any other pair of flowering plants (except rice or Arabidopsis)
• ginkgo
• any bryophyte
• any moss
• horsetail

[Hat Tip: Hsien Hsien Lei]

Nobel Laureates: Furchgott, Ignarro, and Murad

The Nobel Prize in Physiology or Medicine 1998

"for their discoveries concerning nitric oxide as a signalling molecule in the cardiovascular system"


Robert F. Furchgott, Louis J. Ignarro, and Ferid Murad received the Nobel Prize in Physiology or Medicine in 1998 for their discovery that nitric oxide (NO) is a signalling molecule responsible for dilation of blood vessels. (See How Viagra Works.)

Furchgott and Ignarro independently established that nitric oxide was the active stimulatory molecule in vasodilation. Murad recognized that the stimulatory effect of nitroglycerine on cGMP levels was due to the fact that nitroglycerine produced nitric oxide inside the cell. Nitroglycerine had long been used to treat high blood pressure. In fact, Alfred Nobel, the discoverer of nitroglycerine and the founder of the Nobel Prizes, was treated with nitroglycerine for this problem.

How Viagra Works

 
Mondays Molecule was sildenofil (5-[2-ethoxy-5- (4-methylpiperazin-1- ylsulfonyl) phenyl]-1- methyl-3-propyl-1,6-dihydro-7H-pyrazolo [4,3-d] pyrimidin-7-one) better known as its citrate salt, Viagra®.

Viagra® is most often used in the treatment of erectile disfunction. The way it works is to inhibit a specific enzyme called phosphodiesterase-5 located in the smooth muscle of the arteries that supply blood to the penis. In order to understand the significnace of this inhibition, we need a little background.

Nitric oxide (NO) is a chemical produced by special nerve cells called NANC nerve cells. (NANC stands for nonadrenergic-noncholinergic.) Under certain, rather special, conditions the brain sends a signal down the axon of a NANC nerve cell located in the penis. This causes NO to be released into the blood stream in the arteries of the penis.

One of the main roles of NO is to trigger the relaxation of the smooth muscle that lines the arteries. This leads to vasodilation and the lowering of blood pressure. In the penis this causes engorgement as the arteries expand and fill up with blood. The result is an erection that's stimulated by NO.

Nitric oxide acts locally. It diffuses into adjacent cells and binds to an enzyme called guanylyl cyclase. The binding of NO activates the enzyme, stimulating it to produce cyclic guanosine monophosphate or cGMP. The substrate for this reaction is guanosine triphosphate (GTP), a molecule that's similar to ATP except that the base is guanine instead of adenine.

ATP can be also be cyclized to form cAMP—a compound analogous to cGMP. cAMP is a common signal in many hormone-induced signal transduction pathways (and in creating a sense of smell). Like cAMP, cGMP is a signalling molecule. It activates specific enzymes that add phosphate to various proteins causing them to become more, or perhaps less, active. During an erection, the cGMP signal leads to changes in phosphorylation of muscle proteins causing the muscles to relax and the arteries to expand.

As you might expect, cGMP is not infinitely stable; otherwise a man might have an erection forever. cGMP is removed by the action of cGMP phosphodiesterase, which converts it to GMP. The turnover of cGMP in the penis is quite rapid leading to lack of signal unless NO is continually produced by the NANC nerve cells in order to replenish the supply of cGMP by reactivating guanylyl cyclase. This production of NO requires the attention of the brain, which has to keep focused on the task at hand.

The smooth muscle cells in the penis contain a special cGMP phosphodiesterase called phosphodiesterase-5 (PDE5). Sometimes the degradation of cGMP by PDE5 outpaces the production of cGMP by guanylyl cyclase. In such cases, the steady-state levels of cGMP aren't sufficient to signal muscle relaxation and no erection occurs. This is a common cause of erectile disfunction.

Viagra® works by inhibiting PDE5 thus blocking the breakdown of cGMP. This causes levels of cGMP to increase and an erection is prolonged. The structure of the PDE5 enzyme has been solved by Sung et al. (2003) in the presence of bound sildenafil (Viagra®) and two other inhibitors, tadalafil (Cialis®) and vardenafil (Levitra®). The structures are shown as stereo images in the figure below.

The upper image is the PDE5 proetin with overlapping molecules of sildenafil (red) and tadalfil (green) bound to the enzyme. The bottom images shown the structures of the three inhibitors. Viagra® binds to the site where cGMP would normally bind, thus blocking the degradation of cGMP. The structure of Viagra® is similar to cGMP and this exlains why it is such a potent inhibitor.

Sung B-J., Hwang, K.Y., Jeon, Y.H., Lee, J.I., Heo, Y.S., Kim, J.H., Moon, J., Yoon, J.M., Hyun, Y.L., Kim, E., Eum, S.J., Park, S.Y., Lee, J.O., Lee, T.G., Ro, S., and Cho, J.M. (2003) Structure of the catalytic domain of human phosphodiesterase 5 with bound drug molecules. Nature 425:98-102.

The Best Writing on Science Blogs 2006

 
Coturnix (A Blog Around the Clock) has put together an anthology of the best science writing on blogs for 2006. It's being published in a book called "the open laboratory." Read about The Great Unveiling and buy the book. Most of your friends are in it.

None of my contributions made the cut. Maybe next year. I'm still going to buy a copy when I'm in Chapel Hill next weekend.

Ethical Issues in Science

 
One of the things I have to do this week is deal with the teaching of so-called "ethics" in genetics and biochemistry courses. Let me give you two examples in order to focus the debate: genetically modified foods, and a proper diet.

It's almost a requirement these days that introductory genetics courses include a section on genetically modified crops. This invariably leads to tutorials, or labs, or essays, about whether GM-foods are a good thing or not. These discussions are usually lots of fun and the students enjoy this part of the course. Professors are convinced they are teaching ethics and that it's a good thing to show students that ethics is an important part of science.

In introductory biochemistry courses we often have a section on fuel metabolism. That's the part of biochemistry that deals specifically with how your food is converted to energy. It's human biochemistry. In that section of the course the Professor often raises the question of proper diet. Is it okay to eat meat? Are trans fatty acids bad for you? Should you be eating carbohydrates? Our experience is that Professors who teach this section often have very strong opinions and their personal ethical stance is portrayed as scientific fact.

These are two different cases. In the first one, the question is whether the value of debating controversial "ethical" issues outweighs the disadvantages. The biggest downside, in my opinion, is the emphasis on technology as opposed to pure basic science. By giving prominence to "ethical" issues we are emphasizing the consequences of genetic knowledge as it relates to the human condition.

I prefer to spend my time trying to convince students that knowledge for its own sake is valuable. It's hard to do that if the fun part of the course has to do with the application of genetic technology in the creation of genetically modified foods.

The second case involves a different kind of ethics. Here, the students aren't debating whether you should eat trans fatty acids or not. They are being given an ethical perspective disguised as a scientific fact. I don't think this is a good idea. At the very least, the issue should be presented as controversial and students should be encouraged to read the medical literature; which, by the way, has very little to do with the biochemistry being taught in class.

Should students be discussing the benefits of the Atkins diet? Perhaps, but it should be a discussion and not a lecture, right? And does a focus on human eating behavior detract from the importance of basic scientific knowledge? I think it does.

Part of the problem arises from a desire to please the students. How often do we hear the complaint that students aren't interested in biochemistry and genetics? The students are bored by science so we have to add sections on genetically modified foods and genetic screening to our introductory genetics courses. Isn't this strange? Rather than concentrate on making the basic science as interesting and exciting as possible, we cater to the students by giving them the topics they think are interesting. That's no way to educate.

There's another problem; what is ethics? Sometimes it's hard to see the difference between simple controversy and ethics. Sometimes it's hard to define exactly what "ethics" is all about in spite of the fact that "bioethics" is one of the biggest growth industries in science. Here's where a philosopher or two could weigh in.

Plastic Duckies

 
On January 29, 1992 a 40-foot container fell off a ship in the middle of the Pacific Ocean. Inside the container were 29,000 "Floatees," small bathtub toys. There were blue turtles, yellow ducks, red beavers, and green frogs. Over the next few years, these toys washed up on shores all around the Pacific, especially in Indonesia, Australia, and South America [Friendly Floatees].

The story of these Floatees has been told many times. For years beachcombers around the world have been talking about Beachcombing Science from Bath Toys.

Thousands of the Floatees drifted north where they passed through the Bering Straight and became locked in the pack ice north of the Arctic Circle. The prediction was that they would emerge into the Atlantic in 2003 and, sure enough, Floatees started to turn up in New England and Great Britain. More are expected this year [Drake's other armada].

There's a picture of a plastic duckie on the cover of this month's Harpers magazine. The feature story is MOBY-DUCK: Or, the Synthetic Wilderness of Childhood by Donovan Holn. It's a wonderful read. Donaovan Holn has weaved together the story of the Floatees and his personal voyage of discovery. As you follow along you will learn about ocean currents, flotsam and jetsam, beachcombing, childhood, and so much more.

Astrobiology: A Null Set

 
Phil Plait of Bad Astronomy recently lost out to PZ Mierz of Pharyngula in the contest for best blog. His penalty for not getting enough astronomy enthusiasts to cast ballots is to write something about biology.

So naturally he chooses Astrobiology as his example— a discipline without a single living example. Typical astronomer, taking the easy way out.

As I tell my students, biology is much harder than physics and astronomy. Any biologist can handle physics with their eyes closed but physics students (and Professors) are afraid of biology. It's way too messy for them.

The Logic of Irreducible Complexity

 
Ross Thomas (HALFaCANUCK) uses predicate calculus to analyze whether the following argument,

the irreducibly complex nature of the eye proves God's existence

is logically correct. [Irreducible illogicality] The answer will surprise you.

P.S. Don't tell the IDiots about this one!