Mr. Deity

These are hilarious! You've got to see them.
[Hat Tip: Ed Brayton

Mr. Deity Episode 1: Mr. Deity and the Evil

The remaining episodes are below the fold.


Mr. Deity Episode 2: Mr. Deity and the Really Big Favor


Mr. Deity Episode 3: Mr. Deity and The Light


Mr. Deity Episode 4: Mr. Deity and the Messages

American Bloggers Have to Register With the Government or Face Jail

Friday's Urban Legend

From Congress to Send Critics to Jail, Says Richard Viguerie.

The following is a statement by Richard A. Viguerie, Chairman of GrassrootsFreedom.com, regarding legislation currently being considered by Congress to regulate grassroots communications:

"In what sounds like a comedy sketch from Jon Stewart's Daily Show, but isn't, the U. S. Senate would impose criminal penalties, even jail time, on grassroots causes and citizens who criticize Congress."

Does this spell the end of PZ Myers and Ed Brayton?

No, the story is FALSE. Furthermore, there's an evil motive behind the press release. Mike Dunford has the scoop at Someone's Trying to Play Us.

Reciting The Lord's Prayer at City Council Meetings

I recently became aware of the fact that reciting the Lord's Prayer before city council meetiings is still happening in southern Ontario. The latest kerfulffle is in Durham Region, just east of Toronto. Apparently the Regional Council members have been reciting the Lord's Prayer and a group called Secular Ontario wants them to stop.

The practice was declared illegal following an Ontario Court of Appeals ruling in 1999. Illegal or not, it should stop. It's a really dumb idea.

But that's not what the Council Members of Durham Region think, according to an article in today's Toronto Star [Durham praises the Lord]. The Mayor of Oshawa, John Gray says,

God is the Supreme Being. Period. Full stop

The locals came out in force to support the council. Apparently they want to make sure everyone who attends Council meetings gets the message. Durham is a Christian county—nobody else is welcome.

What are they thinking? What possible benefits come from reciting the Lord's Prayer in a public meeting? If you're a Christian who really needs help from God before deciding anything, then surely you can mumble quietly to yourself before taking your seat?

If you're not a Christian council member then being forced to listen to a Christian prayer is at best useless, and at worst damn annoying and insulting. The only benefit is the bigoted message it sends to everyone else in the room. It says "we're a bunch of Christians" nobody else should run for office.

The real shocker came from seeing the two other councils that recite the Lord's Prayer before meetings: Mississauga and Brampton. That's my neck of the woods. I've written to my council member Katie Mahoney.

Francis Collins and the Middle Ground

 
Francis Collins is interviewed in Christianity Today [Creation or Evolution? Yes!: Francis Collins issues a call to stand on the middle ground].

I'm eagerly waiting for all the appeasers to attack Collins for not being an expert on religion. Meanwhile PZ Myers invites us to take a whack at the worst parts of the interview [Collins in Christianity Today]. Here's my contribution ...

One of the main reasons I wrote The Language of God was to try to put forward a comfortable synthesis of what science teaches us about the natural world and what faith teaches us about God. Yet it seems to be a pretty well kept secret these days that the scientific approach and the spiritual approach are compatible.

It used to be a well-kept secret when the believers dominated the discussion. But now the cat's out of the bag. Science and religion are at war and only one of them is going to emerge victorious.

I think we've allowed for too long extreme voices to dominate the stage in a way that has led many people to assume that's all there is.

Repeat after me ..

ATHEISM IS NOT AN EXTREME VOICE

It only seems that way to believers because they can't conceive of anyone not believing in God. But, in fact, almost everyone rejects 99.99% of all Gods. Atheists just go one God further. It's really not that much of a stretch.

The thesis of my book is that there is no need for this battle. In fact, it's a destructive battle. And we as a society would be well served to recover that happy middle ground where people have been for most of human history.

There is no middle ground between belief and non-belief, or between rationalism and superstition. You can't occupy something that doesn't exist.

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.