Lead in Lipstick Will Cause Cancer

 

Friday's Urban Legend: FALSE

There's an email message circulating that warns women against the dangers of lead in lipstick.

It's currently #9 on the 25 Hottest Urban Legends. (Incidently, the Barack Obama myth has moved up to #1; see Baracl Obama Is a Closet Muslim).

The message claims that lead causes cancer. This is not true. The message claims that lipstick contains lead. This is correct but the levels are way below those allowed by health rules in civilized countries [Easily Lead].

[Photo credit: Wikipedia, Creative Commons]

IDiots and the War

 
Yesterday Ed Brayton posted on DaveScot's silly notions about the war in Iraq [DaveScot's Ridiculous Arguments]. Ed goes into much more detail than I did on Wednesday [The IDiots Understand the War in Iraq]. The most interesting thing about Ed's posting is his description of the censorship imposed on the thread over at Uncommon Descent. If you go there you'll notice that the comments are closed. But they weren't closed yesterday. Find out from Ed what Mike Dunford did to force DaveScot to delete all comments.

And you wonder why we call them IDiots?

Toyota RAV4 Jousting

 
This is too cool. Anyone want to try it with me? I'll drive. We can challenge a team of IDiots.

Teaching Ethics in Science: Science v Technology (Part 2)

[Larry Moran: Part 1] [Janet Stemwedel: Part 1, Part 2]

The issue is whether we should be teaching "ethics" in science classes. The particular examples that we've mentioned are debating whether GM food is good or bad and discussing the consequences of the human genome project.

My concern is not so much whether these issues are topical or fun—they certainly are. I'm worried about the fact that they detract from my main purpose, which is to get students to appreciate science for it's own sake and not just because of some application it might have.

The Next Leader of the Free World?

 
The blogosphere is all abuzz with debate over who's going to be the next leader of the free world. I have a question. Who's the current one?


If I had a vote, I'd vote for the guy in the middle. Anyone who has a blog and supports universal health care coverage for all Americans can't be all that bad. Besides, he lives in Chapel Hill and that's a very nice place.

CODEPINK Women for Peace

 
 
Read Dariana's blog if you have two X chromosomes or want to support those who do.


[Hat Tip: Greg Laden]

I'm not a Darwinist, but I Ain't Signing

Bill Dembski continues to demonstrate his ignorance of evolution by ranting against Darwinism. In his latest posting [Dissenting from Darwin] he urges those of us who are skeptical about the exclusivity of Darwinian evolution to sign a petition.

Increasinginly I find that those with doctorates in the natural and engineering sciences are asking, “What can I do to help in the fight against Darwinism?” For some this will involve research bearing directly on Darwinian theory. But there is also another way to help. Many in the media and the public still do not know that there is scientific dissent from Darwinism. They have no idea that MANY scientists are skeptical of neo-Darwinian theory.

So one way you can help is to put your head on the chopping block and voice your skepticism of Darwinism (if you do, trust me, Darwin’s dogmatic defenders will try to chop off your head). This is why Discovery Institute created their statement “A Scientific Dissent from Darwinism.” It states: “We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.”

There's nothing wrong with the statement. I am skeptical of claims that natural selection accounts for all of the complexity of life. There are lots of other things going on during evolution.

But I will not sign this petition because Dembski and the IDiots will deliberately misinterpret my intentions. They have no idea what dissent from classical Darwinism really means. They have no idea that someone like me could (mostly) agree with the statement while, at the same time, referring to all Intelligent Design Creationists as IDiots. I suspect that some of those who signed the petition would feel the same way about Intelligent Design.

The list of dupes and IDiots is [here]. There are 686 names and two of them claim the University of Toronto as their affiliation. They are,

            Stephen J. Cheesman Ph.D. Geophysics
            Alfred G. Ratz Ph.D. Engineering Physics

Neither of them are listed in the phone directory and they have no affiliation with the university according to a search of the website. Chessman was involved in writing some software for an undergraduate lab back in 1992.

Eva Amsen's Cocktail Recipe

 
Eva Amsen is a graduate student in my department and a blogger (easternblot.net). She was at the 2007 North Carolina Science Blogging Conference last weekend and now she's written an article about it at Inkling Magazine [Science Bloggers Avoid the Spinach Dip Brush-Off].

Ageism in Science

 
I'd like to address a thorny issue; namely, discrimination on the basis of age. The focus of this particular posting is the widespread belief that "young" investigators are more valuable to the research community than "old" ones.

By "young" I mean scientists who have graduated with a Ph.D. and completed several years of post-doc. They are either about to be hired as principle investigators for the first time or have already been hired within the past 7 years. Typically, they are under 40 years old and if they have a university position it will be as an Assistant Professor. They do not have tenure.

"Old," or senior, investigators are those over 40. There are two sub-categories: those between the ages of 40 and 55 who are thought to be in their prime and those over 55 who are thought to be well past their prime.

I was prompted to bring up this issue by the recent funding crisis in Canada and especially by some comments made in an open letter from Alan Bernstein, the President of CIHR (but see Old Professors). Alan's opinion, as expressed in the letter, is not that much different from the opinion of most of my colleagues. The difference is that Alan is in a position to act on his view of Canadian scientists. He can redirect funding.

Here's what Alan says about young investigators,

I am very concerned about the impact this situation will have on all members of the research community - new investigators, mid-level established investigators and Canada's most senior researchers. And I am particularly concerned about the impact on new investigators who are at the beginning of their careers. These new investigators represent the future of health research in Canada. Failure to secure grant support for their research in those critical first years can have a lasting detrimental effect on their subsequent careers. Clearly, all of us need to think about how to improve the situation for the very group of investigators who are bringing their energy, superb training and new approaches to health research.

At first glance this seems like a typical harmless motherhood statement that nobody questions. After all, doesn't everyone agree that youth represents the future? Doesn't everyone agree that energy and new approaches come from young investigators and not from old ones? Doesn't everyone agree that failure to get a grant can threaten the careers of young investigators?

Yes and no. There's a lot more going on than what's implied by such facile statements. Let's try and unpack Alan's paragraph and see what we can learn.

Like Alan, I am very concerned about the impact of the funding crisis on all members of the research community. Unlike Alan, I don't reserve any special concerns for young investigators at the expense of older ones. The loss of a grant in the middle of a promising career is just as devastating as the failure to get one in the first place. Perhaps more so, since the mid-career investigator has a lab full of graduate students, post-docs, and research assistants who have to be let go or moved. Given the choice between funding a mid-career investigator with a decent publication track record and a young investigator with no track record, why should we favor the unproven over the proven? Does such a bias make sense?

I question the common belief that young investigators represent the "future" of research. It suggests that a 45-year old doesn't have a future even though they may still have 20-30 years of productive research ahead of them.

Are young investigators more energetic? Perhaps, but I know lots of enthusiastic and energetic investigators who are no longer young. Besides, wisdom and maturity can often beat out energy in a head-to-head competition to do good research.

What about the idea that youth is more innovative? Is there any truth to that myth? Not really. There are lots and lots of senior investigators who are right up there on the cutting edge of science. I daresay there's more innovative work done in the labs of senior investigators than in the labs of young investigators, at least in my field. Part of this is due to the system. You can't take too many risks until you've become established. Part of it is due to experience. Experience is a good teacher—you can see productive new directions once you've mastered the old ones.

None of this means we should abandon young investigators in favor of senior investigators. But, by the same token, we shouldn't sacrifice senior investigators in order to fund younger ones. The excuses used to promote the "youth" strategy need to be questioned to see if they are truly valid. I don't think they are.

In the recent grant competitions, there was a tilt toward funding young investigators at the expense of renewing the grants of senior investigators. That's not right. It's discrimination on the basis of age and it must stop now.

(In the interests of full disclosure, I am not competing for grants from any granting agency. I do not have a direct stake in this issue other than to promote what's good for research and good for my colleagues. If we don't have enough money to support our current crop of researchers then it's stupid to hire more.)

Front Page News: CIHR Funding Crisis

 
Last week the Canadian Institutes of Health Research (CIHR) Funding crisis made the front page of the Globe and Mail (lower left corner)[Cash crunch spurs research warning]. I blogged about this earlier (Massacre in Canada) in order to publicize the effect it was having on my colleagues. We need to do something before we destroy researchers in the most productive part of their careers.

The President of the CIHR is Alan Bernstein. He responded to the crisis by publishing a President's Message to the Research Community - January, 2007. The message does not inspire confidence. The current mess was caused by a downturn in government funding but that downturn might have been foreseen. It could have been managed better.

The crisis is also due, in part, to the diversion of basic research money to new goals; namely, "relevant" research that might lead directly to improvements in health.

Alan has just published a article in an online magazine where he explains his philosophy [Publicly-Funded Research and Innovation: Canada’s Key to the 21st Century]. He says,

The world is in the midst of profound social, scientific, and technological change. How Canada responds to these changes will determine our future quality of life, career opportunities for young Canadians, and whether we will be globally competitive and productive.

Our future success as a nation will depend on our ability to attract and retain top scientific talent (what The Economist magazine recently called “The world’s most sought-after commodity on the planet”), to generate new ideas and transfer them into new products, new policies, and new services.

Real, cutting-edge research is tough to do. But, transforming research into action is even tougher. This process, called knowledge translation or innovation, involves meaningful interaction between researchers and the users of research.

It's the conflict between "knowledge translation" (God, how I hate buzzwords) and pure basic research that's causing angst. I don't see any evidence that the President of CIHR is willing to stand up for curiosity motivated research—the kind done on university campuses across the nation. He talks a lot about competitiveness and new products but not about knowledge and understanding.

This is very disappointing. It suggests that Alan has lost touch with the goals of his former colleagues (he used to be a research scientist at the University of Toronto). If the President of CIHR won't stand up for basic research then we're in big trouble. Maybe it's time to look for a new President who understands that support for basic science is crucial.

Nobel Laureate: Peter D. Mitchell

The Nobel Prize in Chemistry 1978

"for his contribution to the understanding of biological energy transfer through the formulation of the chemiosmotic theory"

Peter D. Mitchell (1920-1992) received the Nobel Prize in 1978 for developing the Chemiosmotic Theory to explain ATP synthesis resulting from membrane-associated electron transport [Ubiquinone and the Proton Pump].

Mitchell is the last of the gentleman scientists. He first proposed the chemiosmotic principle in a 1961 Nature article while he was at the University of Edinburgh. Shortly after that, ill health forced him to move to Cornwall where he renovated an old manor house and converted it into a research laboratory. From then on, he and his research colleague, Jennifer Moyle, continued to work on the chemiosmotic theory while being funded by his private research foundation. [Peter Mitchell: Wikipedia]

The Chemiosmotic Theory was controversial in 1978 and it still has not been fully integrated into some biochemistry textbooks in spite of the fact that it is now proven. The main reason for the resistance is that it overthrows much of traditional biochemistry and introduces a new way of thinking. It is a good example of a "paradigm shift" in biology.

Because he was such a private, and eccentric, scientist there are very few photos of Peter Mitchell or his research laboratory at Glynn House . The best description of him is in his biography Wandering in the Gardens of the Mind: Peter Mitchell and the Making of Glynn by John Prebble, and Bruce Weber. A Nature review by E.C. Slater [Metabolic Gardening] gives some of the flavor and mentions some of the controversy.

Many scientists believe that the Chemiosmotic Theory was the second greatest contribution to biology in the 20th century (after the discovery of the structure of DNA). The case is strong, I think they're right.

The IDiots Understand the War in Iraq

 
DaveScot didn't like the short speech by Senator Jim Webb. Apparently Webb just doesn't get it about Iraq. According to DaveScot, there's a really good reason for being in Iraq [[Off Topic] Senator Jim Webb: Clueless.

Did you know that the real reason is to train the marines?

Here’s the deal Jim. In order to have an effective force in fighting guerilla and urban wars in Arab countries we need actual combat veterans seasoned in that type of warfare leading the unseasoned troops. Use your head, Jim. Now we have an effective force led by NCOs who know how to survive urban and guerilla wars in Arab countries. And Bush managed to build that force without losing 58,000 American lives as were sacrificed in Vietnam but rather limited the losses to 3,000. Use your head for something other than a place to put your hat, Jim. We needed a veteran ground combat force for the Middle Eastern theater. Now we have one. Now what happened to Russia in Afghanistan won’t happen to us.

Clueless.

I can't help but notice some glaring deficiencies in current military training. There are no veterans with experience in colder climates like those we find in Canada. There's also a lack of experience in the European theater—almost all the veterans from World War II have retired. And let's not forget China or India. Nobody in the Marines has ever fought in China or India.

Maybe the USA should start a war in one of those theaters in order to get some veterans?

What Is a Species? John Wilkins Knows

 
As part of the ongoing basic concepts posts, John Wilkins has described Species. John is one of the world's leading authorities on this topic so you can be sure to learn something if you jump over to Evolving Thoughts.

For those of you that don't want to learn about all the various definitions of species here's the bottom line from John ....

So, after all that, what is a species? I think, and this is very much my own opinion, that there is no ....

How to Fix NIH and NSF

 
I recently commented on the funding crisis in Canada. Less than 20% of grants will be funded in the latest CIHR competition. Canadian scientists are trying to see what needs to be done to fix the problem.

There's a similar problem in the USA. At the 2007 Science Blogging Conference we received a flyer from Geoff Davis and Peter Fiske asking people to go to their blog and get involved in the discussion about how to fix NIH and NSF. Here's the site: [Zerhouni for a Day: A challenge].

So far the main suggestions under discussion are to limit the size of grants and to cut back on funding interdisciplinary centers. Both suggestions are worth serious consideration.

Ubiquinone and the Proton Pump

Yesterday's molecule was ubiquinone, also known as coenzyme Q or just plain "Q." Ubiquinone is a lipid soluble cofactor that accepts and donates electrons in oxidation-reduction reactions. These are reactions in which electrons are transferred from one molecule (oxidation) and accepted by another (reduction).

Ubiquinone is confined to lipid membranes where it diffuses laterally. It is synthesized in reactions catalyzed by membrane-bound enzymes. Bacteria contain a structurally similar molecule called menaquinone and photosynthetic organisms have plastoquinone.

All of these quinones play a role in pumping proteins across a membrane in order to create a proton gradient that's used to make ATP. If you understand how this works then you can understand how life first arose 3.5 billion years ago.
Quinones can carry up to two electrons per molecule and they are added one-at-a-time in the reaction shown below.

The reason why ubiquinone is so important is because the ring structure stabilizes the negatively charged semiquinone anion allowing for the addition of another electron to create ubiquinol (QH₂). Note that when two electrons are taken up, two protons (H⁺) are added to neutralize the negative charge. In the reverse reaction (ubiquinol to ubiquinone: bottom to top) two protons are released when the electrons are given up.

The key to understanding the importance of ubiquinone is recognizing that protons can be taken up from one side of the membrane during the reduction of ubiquinone and they can be released on the other side of the membrane when ubiquinol is oxidized in the reverse reaction.

The enzymes responsible for this differential uptake and release are part of the membrane-associated electron transport chain found in mitochondria and in the membranes of bacteria. There are several different reactions that take place as shown in the simple schematic diagram below.

The red line traces the path of electrons released from a molecule called NADH. The electrons pass through three different membrane complexes called complex I, complex III, and complex IV. At each step, protons are pumped across the membrane. In complex IV the electrons are passed to oxygen (O₂) to make water. This final step is why you need oxygen to live.

We are mostly interested in the middle complex (complex III) because that's the one found in all species. It also takes part in photosynthesis, which is a similar process for producing a proton gradient.

The protons accumulate in the intermembrane space between the outer and inner membranes of mitochondria and bacteria. The complexes are located in the inner membrane. (The outer membrane isn't shown in the diagram.) Because there's a higher concentration of protons in the intermembrane space compared to inside the cell, there's pressure to return protons down the concentration gradient to restore the balance. This pressure is called the protonmotive force. It's used to drive ATP synthesis by coupling the transport of protons to the phosphorylation of ADP. ATP is the main energy currency in the cell. It can be used to make other molecules or cause muscles to contract etc.

The idea that electron transport is mainly used to create a proton gradient which is then used up in the synthesis of ATP is known as the Chemiosmotic Theory. It was championed in the 1960's by Peter Mitchell (see tomorrow's Nobel Laureate).

The role of quinone in complex III is complicated. Here's a schematic (left) showing the uptake of protons (H⁺) from the cytoplasmic side (bottom) to form QH₂ and their release on the other side when QH₂ is converted back to Q. This complicated set of reactions is known as the Q cycle and it is responsible for the generation of protonmotive force in all species. Since the protonmotive force is what drives ATP synthesis, this makes the Q cycle one of the most important reactions in biochemistry.

The structure of complex III has been solved. In addition to being one of the most important enzymes, it is also one of the most beautiful. You can easily see the two b heme groups that form the catalytic sites for oxidation and reduction of QH₂ and Q. The iron-sulfur center (Fe-S) helps in the transport of electrons to heme c₁ and eventually to cytochrome c.

This is such a fabulous molecule that I put it on the cover of my biochemistry book.

Students often wonder how the earliest forms of life created energy before the invention of photosynthesis. Once you understand the Chemiosmotic Theory, it isn't difficult to see how this worked 3.5 billion years ago. All you need is a source of energetic electrons to drive the reduction of quinone. In the presence of a cytochrome complex, like complex III, you'll get a protonmotive force generated by the Q cycle. This will power ATP synthesis.

Here's a simplified version of how it's done in chemoautotrophic bacteria that can use hydrogen as an energy source. There are many other possible sources of energy, such as H₂S or NH₄⁺. They are obvious candidates for the kinds of energy production that was common when life first began.

Teaching Ethics in Science: Science v Technology

Janet Stemwedel of Adventures in Ethics and Science has posted a response to my questions about teaching "ethics" in science courses. My original posting is [Ethical Issues in Science] and Janet's response is [Teaching about ethics and other sources of controversy in science class].

When we met at the 2007 North Carolina Science Blogging Conference, Janet said she was going to try and kick-start a debate. That's why I took the picture.

There are several different issues, so in order to keep the discussion focused, I'm going to limit myself to only one topic per posting. This one's about the relationship between science and technology and where "ethics" fits in.

Religion Is Losing, According to Ken Ham

 
Okay, so Ken Ham isn't a very reliable source of information. He's about as kooky as you can get when it comes to science and religion. The only things he has going for him is that he's Australian and he's not in jail.

Ken Ham is worried about the evil atheists and the influence they might have on Christian youth. Over at Answers in Genesis he's published a warning against The New Atheists. Can you guess who they might be? I thought so ....

Ham has an interesting take on the issue. He says,

It prompts me to ask: “Why are atheists now getting so much publicity and gaining ground? What’s happened in the culture to allow this?” As we’ve been saying for years, there’s been a change in this culture—at a foundation level. Generations have been indoctrinated by the secular education system and media to build their thinking on human reason, not the Word of God. And at the base of this is the creation/evolution issue.

Evolutionary indoctrination has produced generations (even in the church) who doubt the Bible. Barna Research discovered that of teenagers today who call themselves born-again Christians, only 9% believe there is such a thing as absolute truth. These young people are ripe for “secular evangelists” like Dawkins and Harris.

Who knew? Rationalism is winning over superstition? Is it time to break out the champagne?

But that's not all. There are serious consequences. If the evil atheists win the hearts and minds of our children then dreadful things could happen. But surely this will never happen ... surely rationalism will never win? Ken Ham isn't so sure,

Some people might say to me, “But there’s no way Americans will go for atheism. Most people believe in God, even if they don’t take the Bible seriously as AiG does.” Think back to the 1950s. What if someone back then said to you, “Beware, the homosexual movement is on the march—if we don’t do something, ‘gay’ marriages will be legalized across the country.” Almost all of us at that time would have said that there’s no way Americans would ever accept this. Most people believe that marriage is one man for one woman, so, no, this will never happen in America.But as you know, it has happened—and continues to happen!

Ohmygod. Not only is rationalism making inroads but tolerance as well. Religion is surely doomed. What will Ken Ham do? Stay tuned—I'm sure he has a plan to restore superstition and bigotry.

What Is "Systems Biology?"

It's an interesting question. One of our departments here at the University of Toronto just renamed itself Cell and Systems Biology so you'd think they would know what "systems biology" is, wouldn't you?

Well, they don't. And neither do I. And neither, as it turns out, does Michael White over at Adaptive Complexity. Read his posting: Is Systems Biology Teaching Us Anything New?. Here's a teaser,

What I find most exciting about basic molecular biology today is the prospect of building a quantitative understanding of how a cell works. Many other scientists are excited about this as well, leading to the current popularity of what's being called 'systems biology.' The idea is that maybe we can understand the design principles behind a cellular process - how the behavior of a cell emerges from all of those detailed physical interactions among proteins, nucleic acids and other components of the cell. If that sounds vague to you, well, that's because it is vague. It's a nice sentiment, but I think biologists still have a hard time defining just what it is we want to learn.

More Comet McNaught

 
Phill Plait of Bad Astronomy has another photo of comet McNaught [Incredible Comet McNaught photo] This is one of those (few) times when I wish I lived in the Southern Hemisphere!

Monday's Molecule #10

 
Name this molecule. You must be specific. We need the correct common name.

This is an easy one for everyone who has ever taken biochemistry. This compound is the substrate for one of the most important reactions in living cells—a reaction that powers every living organism. The enzyme that catalyzes this reaction gets my vote for the most important enzyme in the known universe.

We'll discuss what this molecule does after you've been given a chance to identify it.

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

Mendel's Garden #10

 
Mendel's Garden is a blog carnival devoted to genetics. The latest version (#10) has been posted on Neurotopia 2.0 [Mendel's Garden].

There are lots of interesting articles. I like Alex Palazzo'z execellent summary of work that shows how A silent mutation affects pain perception?. An article from Sunil on lactose intolerance reveals some new information about the origin of mutations causing lactose tolerance.

For me, the most exciting news is the inclusion of two articles from Sandwalk. This is the first time any of my postings have been included in a blog carnival. Maybe this blogging thingy isn't so bad after all!

Denny Doherty Dies

 
Dennis Doherty (Denny) of The Mamas & The Papas is dead [Doherty from Mamas and Papas dies].

Denny was born in Halifax, Nova Scotia, Canada on November 29, 1940. He lived in Mississauga, Ontario, Canada, a city just west of Toronto.

Other members of the original group included Cass Elliot, who died in 1974, John Phillips, who died in 2001, and Michelle Phillips.

California dreaming on such a winter's day.

In Defense of Sam Harris

 
Jason Rosenhouse comments on the criticism of Sam Harris and on Josh Rosenau's take on the issue [Rosenau on Harris].

Here's a quote from Jason. I wish I had said this!

I find this all very frustrating. People like Harris point to specific, irrational fact claims made by certain religious traditions, establishes the harm that comes to society when large numbers of people believe those claims, and encourages people to think a bit more critically about religious beliefs. He is so militant about the subject that you know what he does? He writes books about it. He speaks publicly about it. And he tries to persuade people with nothing more formidable than rational argumentation.

For his trouble he is criticized for being extreme and intolerant. He is branded a fundamentalist. He is lectured for taking clearly stated and widely-held religious beliefs seriously, when everyone knows that real religion is all nuance and metaphor and paradoxically inexpressible cravings. He is told to shut up lest some ignoramus on the local school board hear what he is saying. He is told that he is the one sowing social discord, unlike all those religious folks who are perfectly happy to live together in peace and not engage each other on theological matters.

Teaching Science

 


I'm at a session on Teaching Science hosted by Adnaan Wasey of The Online NewsHour(PBS). There's a lot of provocative stuff. I'll have to post more later on 'cause I need to listen and pay attention.

Janet D. Stemwedel

 
I'm sitting in a lecture theater at the 2007 North Carolina Science Blogging Conference. Right now Janet Stemwedel of Adventures in Ethics and Science is talking about how to be a blogging scientist. The title of her session is "Adventures in Science Blogging: Conversations we need to have and how blogging can help us have them."



Good communication skills are essential but there are many traditional ways of communicating. So, why blog? Because blog conversations happen on a short timescale so there's instant feedback and debate. And the record of this conversation is permanent.

Blogs give us the opportunity to respond quickly to recently published papers and newspaper articles.

How Do We Engage the Public on Science?

 
Here's Hunt Willard talking right now at the 2007 North Carolina Science Blogging Conference. He's telling us what obstacles we face when trying to explain science topics to the general public.

Liveblogging from the 2007 North Carolina Science Blogging Conference

 

Bora Zivkovic is welcoming us to the conference and he's about to introduce Hunt Willard, who will talk about presenting genome information to the public. Hunt is an old friend from back when he was a Professor at the University of Toronto.

Liveblogging is a lot of fun but it does raise a troubling question. What is blogging when it isn't "liveblogging"?

Comet McNaught

 
 
Bad Astronomy Blog has been blogging about comet McNaught for the past week. If you haven't seen any of the photos check out this one on National Geographic News [Photo in the News: Superbright Comet Sweeps Across Southern Skies].

This is a once-in-a-lifetime event. Unfortunately you have to be in Australia or Chile to see it.

UPDATE: Here's a picture of comet McNaught in daylight from Astronomy Picture of the Day!

We Won!

 
Remember the BMJ Online poll on the most important medical advance sinc 1840? [Most Important Medical Advance]. Well, the results are out and we won! That is to say, my choice "sanitation" came out on top with 16% of the votes. Close behind were anaesthesia and antibiotics but they probably got extra votes just because they were at the top of the list on the ballot.

The results are [here]. As you might imagine, the whining from the losers has already begun. See Hsien Hsien Lei posts [We Lost] and [Prof. John Burn Roots for DNA]. Sorry guys, DNA is cool and all that but I'd rather have sewers and clean water.

Dinner in Chapel Hill

 

Here's a list of people I had dinner with last night [Dinner Tonight]. We had a great time and lots of photos were taken. I'll post some of them later.

We spent most of the evening talking to Dave Munger and Greta Munger of Cognitive Daily. BTW, they have a geography quiz posted [Casual Fridays: America versus the world!] that's going to find out whether Americans know more about geography than the rest of the world. Place your bets ....

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.

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!

Alanis Morissette Doesn't Get Irony

 
Guy Kawasaki interviews Jon Winokur [Ten Questions with Jon Winokur: How to Heighten Your Sense of the Absurd]. In response to a question about what he's working on now (Q12) Winokur say he's writing a book called The Big Curmudgeon. Winokur then goes ont to say,

It drives me crazy when people say “ironic” when they mean “coincidental.” The classic example is Morissettian Irony, which I define in the book as “irony based on a misapprehension of irony, i.e., no irony at all.” It’s named for the pop singer Alanis Morissette, whose hit single, “Ironic” mislabels coincidence and inconvenience as irony.

In the song, situations purporting to be ironic are merely sad, random, or annoying (“It's a traffic jam when you're already late/It's a no-smoking sign on your cigarette break”). In other words, “Ironic” is an un-ironic song about irony. Which, of course, is ironic in itself. But wait, there’s more, a “bonus irony” if you will: “Ironic” has been cited as an example of how Americans don’t get irony, despite the fact that Alanis Morissette is Canadian!

I hate it when people don't get irony ... or sarcasm.

[To see the video, go to Alanis Morissette, click on "music" then on "ironic" at the bottom, third from the left.]

[Hat Tip: Jim Lippard]

[Photo Credit: Agência Brasil disponibiliza, gratuitamente, imagens e fotos. Para cumprir a legislação em vigor, solicitamos aos nossos usuários a gentileza de registrar os créditos como no exemplo: nome do fotógrafo—via Wikipedia.]