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!