An Example of Framing by Matt Nisbet

Last summer I blogged about a survey of 149 professional, prominent, evolutionary biologists [Evolutionary Biologists Flunk Religion Poll].

The great majority of the evolutionists polled (78 percent) chose A, billing themselves as pure naturalists. Only two out of 149 described themselves as full theists (F), two as more theist than naturalist (D) and three as theistic naturalists (B). Taken together, the advocacy of any degree of theism is the lowest percentage measured in any poll of biologists' beliefs so far (4.7 percent).

The study was done by Gregory W. Graffin and William B. Provine and you can read the full report in American Scientist [ Evolution, Religion and Free Will]. The study quotes the findings of Larson in 1998 where only 5.5% of biologists in the National Academy of Sciences believe in God.

An earlier study of average scientist by Larson showed that 40% believe in a god and 45% do not [NEW SURVEY: SCIENTISTS "MORE LIKELY THAN EVER" TO REJECT GOD BELIEF]. Couple these results to the fact that somewhere between 30% and 50% of the general population of Western European countries are atheists and agnostics [Atheists and Agnostics] and I think it would be fair to say that the majority of evolutionary biologists do not believe in god. The data supports the statement that, among evolutionary biologists, the consensus is lack of belief in god. This probably applies to all professional scientists.

Now, let's look at how Matt Nisbet spins the story [Francis Collins: The Angry Atheists Do Not Speak for Us]. He opens by quoting an interview with Francis Collins, a deluded scientist, who, quite predictably, says ...

I also think that those of us who are interested in seeking harmony here have to make it clear that the current crowd of seemingly angry atheists, who are using science as part of their argument that faith is irrelevant, do not speak for us. Richard Dawkins, Sam Harris and Christopher Hitchens do not necessarily represent the consensus of science; 40 percent of scientists are believers in a personal God. A lot more are rather uncomfortable about the topic but certainly would not align themselves with a strong atheistic perspective.

Collins is talking about the "angry atheists" when he claims that they don't represent the consensus. Then he spins the argument to make it look like most scientists are believers, or at least have some doubts. Of course, when Collins says they "do not speak for us" he doesn't mean members of the National Academy of Scientists or prominent evolutionary biologists. No, he's referring to the broader survey that included many other categories of scientist. Among that group, there are still more non-believers (45%) than believers (40%).

Matt Nisbet then says ...

As Collins accurately notes, the argument by Dawkins, PZ Myers, and other atheist hardliners that science undermines the validity of religion, even respect for religion, is at odds with the consensus view in the scientific community.

For example, as the recent National Academies report on evolution concludes: "The evidence for evolution can be fully compatible with religious faith. Science and religion are different ways of understanding the world. Needlessly placing them in opposition reduces the potential of each to contribute to a better future."

I don't think Nisbet is representing the consensus view in the scientific community—at least not in the scientific community of professional evolutionary biologists. In that community the overwhelming majority are non-believers in god(s). This is how framing works, is it different from lying?

Furthermore, Nisbet is picking up on a paragraph in Science, Evolution and Creationism, a recent publication of the National Academy of Sciences. That paragraph is, itself, a "frame" and a misrepresentation of the consensus view among scientists as many of us have pointed out [How the National Academy of Sciences Framed their Book on Evolution]. The polls clearly show that the vast majority of members of the National Academy of Sciences are atheists. Thus, Nisbet is putting his own spin frame on the topic and quoting more inaccurate spin framing to support his position. I guess this is how framing is supposed to work.

I don't want any part of it. It's way too close to "lying." Matt Nisbet goes on to beat up on his regular victims by saying ...

Dawkins and Myers are entitled to their opinion and as a fellow atheist I strongly support their right to voice criticism of religion. Yet at some point they need to consider the unintended consequences of their preferred brand of atheist punditry, and to recognize the pragmatism of the consensus message from the National Academies and other leading science organizations.

In their campaign, Dawkins and Myers may honestly believe that they are speaking truth to religion and that by adding their voice to the argument culture, they can raise awareness among the non-religious while potentially shifting society towards greater secularization. However, in coming decades, if the goal is to defend the teaching of evolution in schools and to maintain public trust in science and scientists, their message likely serves as a liability towards that end.

Matt, you are completely wrong about this. The "consensus message" of the National Academies and other leading science organizations is flat-out wrong. Most scientists do not believe in God and among prominent evolutionary biologists Francis Collins is part of a 5.5% minority. You may have convinced the authors of Science, Evolution and Creationism to mislead the public about the beliefs of scientists but you'll never convince the scientists themselves to go along with it.

If the goal is to maintain "public trust in science and scientists" then speaking the truth is always better than framing.

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I Prefer People Who Sign their Names to Comments and Blogs

 
Given a choice between anonymous bloggers (and commenters) and those who sign their real names, I prefer to deal with those who use their real names. In part, this is because I admire their willingness to stand behind what they say regardless of the possible consequences. I do understand that it's easy for a tenured Professor to say this but I've never hidden behind anonymity even when I was an undergraduate, a graduate student, a postdoc, or an untenured Professor.

Greg Laden discusses anonymous bloggers in Some of my best friends are pseudonymous bloggers. I pretty much agree with his position. His posting is well worth reading.

I also agree with his stance on arguing from authority. In the real world, it makes a difference if someone is someone is putting forth an argument based on years of experience in the field or not. Nobody has time to evaluate all of the facts on every issue. We have to learn who we can trust and who we can't. The connection between this and anonymous blogging is obvious.

Please do not interpret this as a blanket recommendation to trust everyone in a position of authority. Similarly, I'm well aware of the fact that non-experts often make insightful contributions to a debate. The issue is much more complex than that. We don't need to list all the exceptions to the general principle that wisdom and experience usually count for something.

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[Cartoon Credits: (top)Anonymity and Sovreignty (bottom) Cerebral Kitchen Productions]

Evolutionary Teapot

 
There's an exhibit of china and pottery inside the Legion of Honor museum in San Francisco. One of the items that caught the attention of Leslie is a funny looking teapot.

The teapot itself isn't that unusual but there's an inscription on the bottom that refers to evolution. Apparently, there was a bit of hysteria and over-reaction to Darwin's ideas in the 1880's and this teapot pokes fun at that era.

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Legion of Honor: San Francisco

 
Last Sunday we visited the Legion of Honor art museum in San Francisco. We went specifically to see the Annie Leibovitz: A Photographer’s Life, 1990–2005 exhibit but there were lots of other wonderful sights to see. The building is a 3/4 scale copy of the Palais de la Légion d’Honneur in Paris.

There are two works of art in the main courtyard. The most impressive is a casting of Rodin's Thinker, which I interpret to be an icon for rationalism and a warning to creationists. The second is clearly an impressionist view of the Flying Spaghetti Monster

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Evolution: 24 myths and misconceptions

 

If you think you understand it, you don't know nearly enough about it.

New Scientist has just published an excellent series of articles on evolution [Evolution: 24 myths and misconceptions]. These are some of the best explanations of evolution that I've ever seen in a popular magazine. Thus, it's all the more tragic that they spoil it all by putting a false picture of evolution (right) on the website.

Shared misconceptions:

Everything is an adaptation produced by natural selection

We tend to assume that all characteristics of plants and animals are adaptations that have arisen through natural selection. Many are neither adaptations nor the result of selection at all.

Natural selection is the only means of evolution

Much change is due to random genetic drift rather than positive selection. It could be called the survival of the luckiest.

Natural selection leads to ever-greater complexity

In fact, natural selection often leads to ever greater simplicity. And, in many cases, complexity may initially arise when selection is weak or absent.

Evolution produces creatures perfectly adapted to their environment

You don't have to be perfectly adapted to survive, you just have to be as well adapted as your competitors. The apparent perfection of plants and animals may be more a reflection of our poor imaginations than of reality.

Evolution always promotes the survival of species

The phrase "survival of fittest" is widely misunderstood (see 'Survival of the fittest' justifies everyone for themselves). Many wrongly assume it means that evolution always increases the chances of a species surviving.

Evolution sometimes results in individuals or populations becoming less fit and may occasionally even lead to extinction.

It doesn't matter if people do not understand evolution

At an individual level, it might not matter much. However, any modern society which bases major decisions on superstition rather than reality is heading for disaster

"Survival of the fittest" justifies "everyone for themselves"

The "fittest" can be the most loving and selfless, not the most aggressive and violent. In any case, what happens in nature does not justify people behaving in the same way

Evolution is limitlessly creative

It might seem like there is no end to nature's inventiveness but there are some features that could probably never evolve, at least on Earth.

Evolution cannot explain traits such as homosexuality

There are numerous evolutionary mechanisms that might explain homosexual behaviour, which is common in many species of animals.

Creationism provides a coherent alternative to evolution

The only thing that creationists agree on is that they don't like evolution. Even Genesis gives two contradictory accounts of creation.

Creationist myths:

Evolution must be wrong because the Bible is inerrant

This argument is undermined by the hundreds of errors and inaccuracies and contradictions found in Bible. It is anything but "inerrant".

Accepting evolution undermines morality

Actually people in more secular countries appear to behave more morally. And even if this claim was true, that would not alter the facts or justify their suppression.

Evolutionary theory leads to racism and genocide

Darwin's ideas have been invoked as justification for all sorts of policies, including some very unpleasant ones. But evolutionary theory is a descriptive science. It cannot tell us what is right and wrong.

Religion and evolution are incompatible

There are various ways in which the known facts about evolution can be reconciled with theistic religions. Some of these ways might be illogical and irrational, but they are no more illogical and irrational than other aspects of religions.

Half a wing is no use to anyone

Just as objects designed for one purpose can be used for another, so genes, structures and behaviours that evolve for one purpose become adapted to do another.

Evolutionary science is not predictive

It might not be possible to predict exactly what life will look like in a billion years but what counts are the predictions that can be made.

Evolution cannot be disproved so is not science

There are all sorts of findings and experiments that could have falsified evolution. In the century-and-a-half since Darwin published his theory, not one has.

Evolution is just so unlikely to produce complex life forms

By weeding out harmful mutations and assembling beneficial ones, natural selection acts like an "improbability drive" that can, given enough time, produce results that appear utterly impossible at first glance.

Evolution is an entirely random process

No and yes. Natural selection is a rigorous testing process that filters out what works from what doesn’t, driving organisms to evolve in particular directions. However, chance events play a big role too.

Mutations can only destroy information, not create it

Biologists are uncovering thousands of examples of how mutations lead to new traits and even new species. This claim not only flies in the face of the evidence, it is also a logical impossibility.

Darwin is the ultimate authority on evolution

Modern evolutionary theory is built on some - but not all - of Darwin's ideas, but has gone far beyond them.

The bacterial flagellum is irreducibly complex

Actually, flagella vary widely from one species to another, and some of the components can perform useful functions by themselves. They are anything but irreducibly complex.

Yet more creationist misconceptions

Evolution is just a theory: Yes it is, like Einstein's theory of special relativity. By theory, scientists mean an explanation backed by evidence. What creationists mean is that evolution is just a hypothesis, unsupported by evidence - which it is not. Evolution is a fact as well a theory.

Evolution violates the second law of thermodynamics

The second law of thermodynamics states that entropy, a measure of randomness, cannot decrease in a closed system. Our planet is not a closed system.

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Tangled Bank #103

 
The latest issue of Tangled Bank is #103. It's hosted at rENNISance woman on the Nature network [The 103rd edition of the Tangled Bank].

Hello from Vancouver! I blog about current genetics, genomics, virology and evolution research. I'll also include posts about grant writing and any other ideas that take my fancy. Don't be shy - leave a comment and start a conversation!

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If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

We Beat the Scientologists!

 
The good news is that atheists are no longer in last place! The bad news is that we have a long way to go to catch up with the Methodists.

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[Hat Tip: Framing Science]

Gene Genie #29

 
The 29th edition of Gene Genie has been posted at My Biotech Life [Gene Genie: the better late than never personal genomics special edition].

It’s a couple of days off schedule but Gene Genie has arrived. I’d like to thank Berci for the opportunity once again. That said, here goes the juicy genetic content.

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

Here are all the previous editions .....

1. Scienceroll
2. Sciencesque
3. Genetics and Health
4. Sandwalk
5. Neurophilosophy
6. Scienceroll
7. Gene Sherpa
8. Eye on DNA
9. DNA Direct Talk
10. Genomicron
11. Med Journal Watch
12. My Biotech Life
13. The Genetic Genealogist
14. MicrobiologyBytes
15. Cancer Genetics
16. Neurophilosophy
17. The Gene Sherpa
18. Eye on DNA
19. Scienceroll
20. Bitesize Bio
21. BabyLab
22. Sandwalk
23. Scienceroll
24. biomarker-driven mental health 2.0
25. The Gene Sherpa
26. Sciencebase
27. DNA Direct Talk
28. Greg Laden’s Blog
29. My Biotech Life

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EXPELLED: The Movie

 
This is a slick trailer for the movie Expelled: No Intelligence Allowed (irony alert!). Unfortunately, the contents of the movie won't measure up to the pre-release hype. Check out EXPELLED EXPOSED for a detailed rebuttal of the claims made in the movie.

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A Slight Error

 

John Wilkins posted a brief note about a German school kid who "corrected" NASA's calculation of the probability of an asteroid hitting the Earth.

You need to read the comments to fully appreciate the irony of the title Oops, a slight error never killed anyone. (Sorry, John, I couldn't resist.)

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[Photo Credit: AAPPL]

What's Wrong with this Tree?

 
Ryan Gregory has published a wonderful article in Evolution: Education & Outreach (Gregory, 2008). The article is about understanding evolutionary trees—a subject we all need to pay attention to because there are so many conceptual pits into which we might tumble. You can read the complete article by clicking on the link below or you can read a short answer to the question on his blog Genomicron [Phylogenetic fallacies: "branching from a main line"].

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Gregory, T.R. (2008) Understanding evolutionary trees. Evolution: Education and Outreach 1: 121-137. [doi:10.1007/s12052-008-0035-x] [PDF]

Scandal at Tim Hortons

 
Every year at this time Tim Hortons runs a promotion called "Roll-up-the-rim." The idea is that you roll up the rim of the paper cup to reveal a prize. There are even special tools to make rolling up the rim easier [Roll Up the Rim]. (As you can see in the photos, you usually get to lose in two different languages.)

This year I only won a single free coffee whereas in previous years I won several cups and several free donuts. (In 1993 I won a stereo system.) I attributed this to bad luck.

Maybe not, according the Globe and Mail. There are lots of customers who think their wins are below the levels of previous years [Coffee junkies say it's a lean 'Roll Up the Rim' season]. Tim Hortons says your chances of winning should be one in nine. According to the article in the Globe and Mail, even Stuart McLean was disappointed that his crew didn't win more often.

For five of the eight weeks that Tim Hortons ran the promotion, CBC host Stuart McLean and his 12-member tour bus drove from Fort St. John, B.C., to Fargo, N.D., perhaps braking for more Hortons outlets than any other vehicle on the road during that period.

“We had logged about 8,000 kilometres on the Vinyl Cafe tour bus,” Mr. McLean, who doesn't drink coffee, later reflected on his show. “[We] made some new friends and rolled up enough rims to make you wonder if anyone ever wins anything.”

This is getting serious. Tim Hortons should not be making Stuart McLean upset [The Vinyl Cafe]. Before you know it, there will be a story about Dave and Morely at Tim Hortons and it won't be pretty watching two Canadian icons duke it out.

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[Hat Tip: Jane]

Oops! Somebody didn't get the message.

 
A group of scientists have published a series of articles about errors and inconsistencies in Al Gore's An Inconvenient Truth [Scientists debate the accuracy of Al Gore's documentary 'An Inconvenient Truth'].

There is no question that Al Gore’s 2006 documentary An Inconvenient Truth is a powerful example of how scientific knowledge can be communicated to a lay audience. What is up for debate is whether it accurately presents the scientific argument that global warming is caused by human activities. Climate change experts express their opinions on the scientific validity of the film’s claims in articles just published online in Springer’s journal, GeoJournal.

I guess they didn't get the message from Mooney and Nisbet. You see, when you develop a spin on climate change every scientist is supposed to stick to the script. You can't have freelancers running off and criticizing the frame.

This is exactly the problem with the concept of framing. Nisbet and Mooney just don't get it. There will always be scientists who disagree with the message being framed and it just not possible to shut them up. That's the exact opposite of what science is all about.

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Back in Canada

 
Vancouver Airport

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Happy 70th Bruce!

 
Last night was the gala 70th birthday party for Bruce Alberts at the Metropolitan Club in San Francisco. Here's Bruce with his first three graduate students; Glenn Herrick (right), Keith Yamamoto (left), and me (looking up).

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Egnor Writes Me a Letter

 
read it at: A Letter To Dr. Larry Moran.

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What's Wrong with Modern Science?

 
Yesterday and today I'm hanging out with some people who care abut science education. We've had some wonderful conversations. I'm pleased to lean that there are some very smart people who think there's something seriously wrong with the way modern science is progressing. I was delighted to learn that there are a growing number of scientists who think the peer review system is broken. A lot of junk is being published.

Speaking of junk, there's an essay in this week's Nature that qualifies in more ways than one [Rise of the Digital Machine]. Mark Pagel is a biologist at Reading University (UK). He's one of those people who just can't accept the fact that humans don't have several times more genes than an insect or a nematode.
THEME

Genomes & Junk DNA

Humans are almost unimaginably complex, with trillions of cells organized into hundreds of different tissues. But we have scarcely more genes than a fruitfly or a worm, and only about four or five times as many as brewers' yeast or some bacteria. Surprising then that the human genome is 250 times larger than the yeast's. It comprises about 99% 'junk DNA' — genetic code that is not used to make the protein building blocks of life.

You know what's coming next, don't you? We're going to hear about one of the seven silly excuses for why we don't really have junk DNA (see The Deflated Ego Problem). Here's how Martin Pagel sets up his choice of excuse.

Junk DNA gives every appearance of fulfilling the metaphor of the selfish gene. It accumulates in organisms' genomes simply because it is good at accumulating; it can even be harmful. Why we put up with it has long been a mystery.

Increasingly, it seems that the genes that do code for proteins may recruit some or all of this junk DNA to regulate when, where and how much they are expressed. Because nearly every cell in the body carries a complete copy of the genome, something has to tell the genes that make eyes not to switch on in the back of the head, or genes for teeth to stay silent in our toes. Something has to instruct genes to team up to produce complex structures such as hearts and kidneys, or the chemical networks that create our metabolism and physiology.

Astute readers will see where this is going—he's going to use the "regulatory DNA" excuse. All this will accomplish is to demonstrate; (a) Martin Pagel's inability to reason like a scientist by considering evidence that has been accumulated over four decades, and (b) Nature's inability to recognize good science from bad science.

Genes, in effect, use regulation to promote their interests within the bodily phenotype: it is how they vary their exposure to the outside world. Regulation is how we can have over 98.5% similarity to chimpanzees in the sequences of our coding genes, yet differ so utterly from them.

Indeed, the huge quantity of junk DNA in the genomes of most complex organisms may act as a vast digital regulatory mechanism. Until recently many common machines, such as aeroplanes, clocks, and even computers were analogue devices, regulated by levers, springs, heat or pressure. Aeroplanes were flown with a stick, springs drove clocks. Digital regulation — instructions encoded in strings of binary numbers arbitrarily long, and hence precise — enabled complexity to increase. Stealth fighters and space shuttles are so complex that they can be flown only by digital computers, not (analogue) human pilots.

Similarly, the emergence of digital regulation derived from unused stretches of junk DNA may have precipitated the transition from single cells to complex multicellular organisms. Long runs of the four chemical bases that make up DNA can easily act like binary strings. How these stretches bind to a gene can regulate exquisitely the degree and timing of that gene's expression. Tellingly, bacteria and some other single-celled organisms have negligible amounts of junk DNA. They rely far more on analogue systems of gene regulation that are protein-based and less precise.

This is, of course, complete nonsense. We know for a fact that large amounts of the human genome are really junk. We know for a fact that you can have complex regulation by using only a small percentage of the genome (1000 bp per gene, or less than 1% of the genome, per gene is more than sufficent [Junk in Your Genome: Protein-Encoding Genes]. We know for a fact that some single-celled species (amoeba) have huge amounts of junk DNA and some some complex multicellular species have genomes that are much smaller than mammalian genomes (Drosohila melanogaster.

All these facts can be found in basic introductory textbooks. In addition, there is an abundant scientific literature on junk DNA, explaining why defective transposons (for example) really are junk. Why can't scientists like Mark Pagel, and the Nature reviewers, learn about junk DNA beore spouting off? What's wrong with science today?

Science is a process and that process involves collecting evidence and making hypotheses that explain the data. In this case the author has ignored the data showing that much of our genome is junk. He has ignored the evidence that the regulation of gene expression can be easily accomplished without invoking huge amounts of (non-conserved) DNA. He has constructed an hypothesis to explain something that doesn't need explaining; namely, why humans have the same number of genes as other mammals. He has failed to read the literature and failed to consider alternative explanations.

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Charlie Rose Science Series: The Imperative of Science

 
In case some of you didn't see the Charlie Rose show on science last week, here it is. The panelists are: Paul Nurse, Lisa Randall, Harold Varmus, Shirley Ann Jackson, and Bruce Alberts. I had a chance to congratulate both Bruce Alberts and Harold Varmus today for their excellent comments. Harold Varmus says he's been on the show several times but I don't see the show very often. Could someone please let me know the next time Charlie Rose covers a science topic?



These guys make a lot of sense. They point out that science education is a mess and that includes science education in the colleges and universities. I particularly like this comment by Harold Varmus.

I do think there's a problem in making science appear frightening and linked to a laboratory activity. As comments you've already heard suggest, science really is a process. A process by which you have ideas, you test them out, you look at evidence, you measure things, and you draw conclusions. And that's a process that applies to almost any phase of life.

Science is a process. It's a way of knowing. That's what we should be teaching.

Too many people think that science is all about doing laboratory exercises but that's actually a very poor way of teaching what science is all about. Just about anyone can be trained in the methodology of a given discipline—like biochemistry—but it takes a lot more work to teach students how to think like a scientist.

My department is currently considering a proposal to dumb down our introductory courses and reduce the numbers of lecture hours in our 3rd year courses. This would be accompanied by an expansion in the number of hours spent doing laboratory exercises. The idea is to prepare students for a career in research as though the way to become a good researcher is to learn how to pipette and not how to acquire fundamental knowledge and learn how to use it to think like a scientist.

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Molecular Biology of the Cell

 
I'm attending the 70th birthday party for Bruce Alberts in San Francisco. Here's a picture of the authors of Molecular Biology of the Cell. From left to right; Bruce Alberts, Alexander (Sandy) Johnson, Martin Raff, Keith Roberts, and Peter Walter. Julian Lewis couldn't be here.

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Pacific

 
Surf.


Surfing at Santa Cruz.



Monterey Bay.

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The Napa Valley

 
Yesterday was my very first trip to the Napa Valley. It was well worth the visit as we had a pleasant day visiting wine country. Our light lunch (above) at Domaine Chandon was a highlight.

The only bad thing about the Napa Valley is getting there (and back). It's only an hour drive from San Francisco but the roads are busy and the route is complicated—at least for tourists like us. On this occasion, however, the trip was a little more exciting because when crossing the Golden Gate bridge we encountered the protesters who were there for the Olympic torch run.

As it turns out, there were more police than protestors but the "free Tibet" and "free Burma" banners elicited a (very) few honks from passing motorists. Leslie was driving so we were one of the cars making noises. You know you're a product of the 60's when most of the protesters are the same age as you are and know how to flash a peace sign!

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Happy Birthday Genomicron

 
It's been one year since Ryan Gregory stated his blog Genomicron [One year of Genomicron. If you don't read his blog regularly, here's a chance to correct that error. Genomicron is one of the best science blogs and Ryan Gregory is one of the experts you can trust.

It's interesting to read Ryan's description of how his blog evolved from being strictly science" to one where his opinion on other things (e.g. science journalism) became increasingly important. That's a good thing, it's what bloggers bring to the table.

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Stupid Press Release

 
I was going to blog about this stupid press release from the Public Library of Science (PLoS) but RPM at evolgen beat me to it [Press Releases are Written by Stupid People].

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Does Acupuncture Work?

 
Orac is the nom-de-plume of a doctor who debunks the claims of non-evidence-based medicine (also known as "woo") on Respectful Insolence. His latest is a posting on the value of acupuncture based on recent scientific studies [Sham acupuncture is better than "true" acupuncture!]. Here's how Orac begins ...

Believe it or not, there was a time when I didn't consider acupuncture to be a form of woo.

I know, I know, it's hard to believe, given the sorts of posts I've done recently on acupuncture, but it's true. Certainly, I didn't believe the whole rigamarole about needles somehow "restoring the flow of qi" or anything like that, but I did wonder if maybe there was some physiologic mechanism at work behind acupuncture that produced real benefits in terms of pain relief above that of placebo. Sure, I may have dismissed homeopathy as the pure magical thinking that it was, but acupuncture I wasn't so sure about.

Obviously, that's changed.

The reason my opinion has changed and now I place acupuncture firmly in the "woo" category is that I've actually been reading the scientific literature on acupuncture over the last year or so....

None of us have time to investigate every form of superstition and irrational thinking. Sometimes we have to rely on trusted experts to do the required homework. Orac is one of those.

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Test Your Evolutionary Knowledge

 
Test Your Evolutionary Knowledge at Bayblab. The blog is run by a bunch of anonymous bloggers but it's pretty good anyway!

BTW, if you cheat, I will be forced to call you mean names.

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Nobel Laureate: Roderick MacKinnon

 

The Nobel Prize in Chemistry 2003.

"for structural and mechanistic studies of ion channels"

Roderick MacKinnon (1956 - ) was awarded the 2003 Nobel Prize in Chemistry for his work on the the structure and mechanism of action of the potassium (K⁺) channel. MacKinnon shared the prize with Peter Agre who discovered water channels.

The presentation speech was delivered by Professor Gunnar von Heijne of the Royal Swedish Academy of Sciences.THEME:Nobel Laureates

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen,

In the days of Alfred Nobel, the learned academies used to entertain and educate the public by holding open demonstrations explaining the latest scientific advances. This tradition has been largely – and perhaps unfortunately – forgotten. So let us try to revive the public demonstration of science, if only for a brief moment.

The demonstration I have in mind is a simple one, and only requires that you do something that is in any case particularly fitting for a Nobel Prize ceremony: to think. But only for exactly 5 seconds!

So, please start thinking, for 5 seconds ... Thank you!

Let us now reflect briefly on what has just happened, in each and every one of us. First, a sudden increase in the activity of the brain when you started to wonder what this is all about – should I really think at this point in the ceremony? – then, cascades of nerve signals when you were actually thinking, and finally a return to the normal resting state. And all this thinking ultimately relied on one of the simplest chemical compounds you can imagine: ordinary salt – sodium, potassium and chloride ions – streaming back and forth across the walls of your nerve cells, thereby generating the signals that activated your mind. And not even very much salt – a rough estimate is that the total amount of salt spent during these five seconds in each one of us was no more than a few grains. Only a fistful of salt to set a whole Concert Hall thinking!

And while all this brain activity was occupying our minds, our kidneys worked on quietly, as they always do, reabsorbing water from the urine to the blood. But in this case, the volumes of water transported are too big, even during five seconds, to be suitable for a demonstration from the podium.

This year's Nobel Prize in Chemistry is all about salt water, and the biochemical mechanisms that control where, when, and how often ions and water are let into or out of the cells in our body. Mechanisms that the two Laureates – Peter Agre and Roderick MacKinnon – have elucidated down to the atomic level.

Agre's was a "serendipity discovery": while working on a completely different problem, he stumbled across a protein in red blood cells that he could soon show was the water channel researchers had been looking for in vain for well over a century. His unexpected discovery opened a whole new field of study.

MacKinnon, on the other hand, decided at an early stage that he should try to do what was then thought impossible: to determine the three-dimensional structure of ion channels at atomic resolution. He bet his career on this vision – and succeeded to an extent that probably surprised even himself.

There is a lesson here, I believe: There is no one way to do science, and our support system must be sufficiently well funded and versatile to prepare the ground for both unexpected serendipity and focused, often risky, attacks on central scientific problems.

Peter Agre and Roderick MacKinnon stand for decisive contributions to the biochemistry of cell membranes, but their discoveries also have an almost tangible aesthetic component. Their work has uncovered an amazing "economy of design" in the atomic structures of the water and ion channels that is breathtaking in its simplicity and perfection. Indeed, after seeing these molecular machines, you find yourself thinking, "Of course, this is how it must be, this is how it must work!" What more could we ask of science?

Professor Agre, Professor MacKinnon, your fundamental discoveries concerning water and ion channels are singular achievements that have made it possible for us to see these exquisitely designed molecular machines in action at the atomic level. The biochemical basis for the transport of water – the most abundant and primordial substance of life – and ions – these tiny, mundane and yet absolutely essential constituents of the living world – can now be understood in unparalleled detail. On behalf of the Royal Swedish Academy of Sciences, I wish to convey to you our warmest congratulations, and I now ask you to step forward to receive the Nobel Prize in Chemistry from the hands of His Majesty the King.

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Nuclear War Is Bad for You

 
A couple of scientists at the University of Colorado have modeled what might happen if there was a nuclear war between India and Pakistan [Regional nuclear conflict would create near-global ozone hole, says CU-Boulder study].

A limited nuclear weapons exchange between Pakistan and India using their current arsenals could create a near-global ozone hole, triggering human health problems and wreaking environmental havoc for at least a decade, according to a study led by the University of Colorado at Boulder.

The computer-modeling study showed a nuclear war between the two countries involving 50 Hiroshima-sized nuclear devices on each side would cause massive urban fires and loft as much as 5 million metric tons of soot about 50 miles into the stratosphere, said CU-Boulder Research Associate Michael Mills, chief study author. The soot would absorb enough solar radiation to heat surrounding gases, setting in motion a series of chemical reactions that would break down the stratospheric ozone layer protecting Earth from harmful ultraviolet radiation, said Mills.

Wow! That sounds really bad. By the way, they forgot to mention one other nasty little detail—about 100 million people will die in the blasts and of radiation poisoning in the aftermath of the attacks.

Sort of make an ozone hole seem insignificant, doesn't it?

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The Bombardier Beetle

 
According to a report in ScienceDaily, there has been progress in understanding how the Bombardier beetle can eject such a powerful spray [The Bombardier Beetle, Power Venom, And Spray Technologies].

The bombardier beetle, found mainly in Africa and Asia, is remarkable in that it can fire a powerful jet of hot, toxic fluid to fight off predators such as birds and frogs. While the chemical reaction that makes the venom has been understood for some time, the actual power behind the venomous squirt, which can travel as far as 20cm, has been cause for speculation.

Quantities of hydroquinone and hydrogen peroxide gases build up in the beetle’s abdomen but, when necessary for defence, get mixed together in a connected ‘combustion chamber’ to produce toxic benzoquinone. This hot fluid is then fired off at force in the face of enemy predators.

Note, there isn't a problem understanding the chemical reaction and how the beetles control it. That's been well understood for several decades. You can watch a young Richard Dawkins debunking the standard creationst claims in a video posted on Genomicron [Bombardier beetles].

Ryan Gregory has followed this up with a more detailed posting that describes the evolution of bombardier beetles [Reducibly complex bombardier beetles]. Ryan was motivated to research this topic because one of the leaders of the University of Guelph creationist groups tried to use the bombardier beetle as evidence that evolution is impossible. I guess he didn't realize that this example has been refuted a long time ago.

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[Photo Credit: Institute of Physics]

Two Non-Scientists Talking about Science

 
Listen to Dr. R.C. Sproul interview Ben Stein. There are lots of very funny bits but let me pick out just one example. Here's what Ben Stein says about scientists ... (around 15 minutes)

People go into academic life in large measure because they're frightened people. They want a kind of sanctuary and uh ... so when they're attacked, or questioned even, they react very, very strongly. They're scared people, and they're really scared of Intelligent Design [Creationism] because if Intelligent Design [Creationism] is true, and if, in fact, Darwinism is ... only goes so far and only covers a small amount of the territory, all kinds of threat to their power and status arise.

Hmmmm ... I wonder why we call them IDiots?

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[Hat Tip: Evolution News & Views]

Have Your Cake and Eat It Too.

 
Matt Nisbet has tried to defend his attacks on PZ Myers and Richard Dawkins with a posting that promotes Paul Kurtz as a "reasonable" atheist [Paul Kurtz: The Local Leader Who Happens to Be an Atheist].

He followed it up with a posting on his comment policy where he notes that he has been forced to delete some of the comments from people who defend PZ Myers and Richard Dawkins [A Note On Comment Policy]. In that comment thread, Matt Nisbet defends his position on framing ...

I've been very active in communicating why my research is worth the money and I have done it very effectively.

-->I've done close to three dozen presentations over the past year and talked face-to-face with several thousand scientists, policymakers, other academics, students, and lay citizens.

-->I regularly post here on the relevance of framing to a range of topics. The top tabs of the blog explain in depth the nature and application of research to science communication.

-->I've done about 40 media interviews on issues related to science communication and/or framing.

-->I followed the Science article with an article at the WPost, a longer cover feature at The Scientist, both articles I link to as PDF copies free for reading. I have also done extended interviews on the topic at the Point of Inquiry podcast.

-->I advise and consult with a range of nonprofits, organizations, and government agencies.

-->I engage almost every serious minded blog post and comment with a respectful, and usually detailed reply.

Here's the problem. Matt Nisbet is promoting the concept of framing science. This is his field and he has every right to do that. I don't buy it and neither do many other scientists who think that framing is too close to "spin."

But that's not all that Matt Nisbet wants to do. Not only does he want scientists to adopt framing as a means to communicate science but he also wants to dictate the frame! In other words, he sets himself up as not only an expert in communication but also an expert in what should be communicated in the rationalism vs superstition debate. He can't tell the difference between the concept of framing, which many scientists reject, and his personal opinion, which is that vocal atheists are hurting the cause of atheism.

Matt want to have his cake and eat it too. He will get neither.

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[Photo Credit: Worst Birthday Cake .. Ever!]

Monday's Molecule #67

 
This is a very important protein. Most living organisms on this planet could not survive if this protein didn't do its job.

Your task for today is to identify the protein (1) and the species from which this particular protein was isolated (2). You also have to describe the function of this protein (3).

In addition you have to identify the Nobel Laureate who was awarded a Nobel Prize for—among other things—working out the structure of this protein. Note that the protein is a tetramer (quaternary structure) showing a nice example of a helix bundle.

The first person to correctly identify the protein, species, and function, and name the Nobel Laureate. wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this week's reward.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly answers the questions and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

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

UPDATE: We have a winner! Matthew Sekedat of Rockefeller University knew that this molecule was the potassium pump from the bacterium Streptomyces lividans. The protein is responsible for pumping potassium ions across the cell membrane. The Nobel Laureate is Roderick whose lab solved the structure of the protein.

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TV Ontario's Best Lecturer

 
I've been critical of the contest for best lecturer because it focuses on style and not on substance [TV Ontario's Best Lecturers]. A few months ago I posted the names and areas of expertise of the three judges. Here's who they picked.


You can see the winning lecture at Ontario's Best Lecturer 2008!. A lot of it discusses naturalism and supernaturalism. Listen for yourself and see if you agree with the judges selection.

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Framing Atheism

 
Here's a video that presents statistics about atheism. Some of it makes me uncomfortable because the numbers can be very misleading. Is this an example of framing according to the ideas of Nisbet and Mooney? If so, to my mind it illustrates all of the bad things about framing that turn scientist off.

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[Hat Tip: Friendly Atheist]

Free Cheesecake!

 
Canadian Cynic just recorded one million page views! Congratulations to whoever you are and to your equally mysterious co-bloggers. The blog is promising free cheesecake for everyone [ Cheesecake for everyone] but the catch is you have to find them first.

BTW, take a look at the statistics posted on the Canadian Cynic website. The average length of each visit is almost 6 minutes!!! This is a long time for most blogs. (It's about 1.5 minutes on Sandwalk and 26 seconds on Pharyngula.)

I wonder if the average visitor to Canadian Cynic is temporarily stunned by the language? Or perhaps by the stupidity of the blogging Tories?

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One Protein - Two Folds

Michael Clarkson at Discount Thoughts posted a discussion of a paper published by Tuinistra et al. (2008) [Two folds for lymphotactin]. The interesting thing about this paper is that it describes a protein (the chemokine lymphotactin) that can adopt two very different folds under physiological conditions.

This is an exception to the general principle that a protein will adopt a single thermodynamically stable three-dimensional structure. Here's how Micheal Clarkson describes it ... (Please read his article.)
THEME:

More posts on
Protein Structure

This is an interesting and important finding because it is (so far) the only example of a protein adopting two completely different stable folds with no hydrogen bonds in common at equilibrium. Trivially, natively disordered proteins adopt multiple conformations under physiological solution conditions, and many proteins alter their conformations in response to ligand binding while keeping most of their hydrogen bond network intact. In this case, however, an existing network of stabilizing bonds is completely disrupted in order to form a new fold with a totally different function. I've already discussed some of the implications of this with respect to protein folding, and in regards to the recent transitive homology studies out of the Cordes group. Lymphotactin offers lessons and ideas for protein folding and evolution that must be taken into account. In particular, the fact that point mutations can significantly stabilize one or the other of these structures implies that there may be previously unsuspected shortcuts through structural space between folded states that avoid unproductive or energetically unfavorable molten globules.

In addition, these results signify that the Anfinsen paradigm that dominates our understanding of protein structure ought not be taken for granted.¹ In many cases it is true that a peptide sequence uniquely determines a single structure under all physiological conditions. Of course we have known for some time that certain peptide sequences do not produce ordered structural ensembles at all. What the lymphotactin example makes crystal clear is that a given sequence can yield an ensemble with multiple energetic minima that reflect related but topologically distinct structures. Tuinstra et al. suspect that this phenomenon has not been noted previously because structures of this kind would not be amenable to crystallization, or would only crystallize in one (of many) structures. If this is so, then as more and more proteins are studied using solution techniques under physiological conditions we may find multiple structural minima in a variety of proteins. Such discoveries may significantly enhance our understanding of the protein regulation, function, and evolution.

Why is this important? Because this example demonstrates that getting from one type of fold to another type of fold isn't as big a problem as most people think.

The key phrase in Michael Clarkson's explanation is, "In particular, the fact that point mutations can significantly stabilize one or the other of these structures implies that there may be previously unsuspected shortcuts through structural space between folded states that avoid unproductive or energetically unfavorable molten globules." As we will see, the Intelligent Design Creationists argue that it is impossible to evolve from one type of protein to another, therefore God must have done it.

Incidentally, it's worth noting that some proteins adopt different conformations when they bind to other molecules (the target they bind to is called a "ligand" and it could be DNA, another protein, or a small molecule like ATP). Michael Clarkson mentions this—he appears to be a pretty knowledgeable guy—but I just want to repeat it so that everyone understands. The idea that parts of a protein (motifs, domain) can change folds under certain conditions isn't new.

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1. I would prefer to say that, like all general concepts in biology, there are exception to the Anfinsen paradigm. I don't believe there are any fundamental concepts that don't have exceptions. That's the nature of biology, and evolution.

Tuinstra, R.L., Peterson, F.C., Kutlesa, S., Elgin, E.S., Kron, M.A., and Volkman, B.F. (2008) Interconversion between two unrelated protein folds in the lymphotactin native state. Proc. Nat. Acad. Sci. (USA) 105:5057-5062. [doi: 10.1073/pnas.0709518105]

Levinthal's Paradox

Back in 1969, Cyrus Levinthal was thinking about protein folding (Levinthal, 1969). He wondered how long it would take for a protein to fold correctly if it had to sample all possible conformations in three-dimensional space.

THEME:

More posts on
Protein Structure
Imagine that there was only a single bond between each amino acid in a protein of 101 amino acid residues. Imagine that there were only three possible configurations around each of those bonds. This means that the protein could adopt 3¹⁰⁰, or 5 × 10⁴⁷ different conformations.

If the protein is able to sample 10¹³ different bond configurations per second then it would take 10²⁷ years to sample all possible conformations of the protein (Zwanzig et al. 1992). This is quite a long time. Far longer, in fact, than the age of the universe.

Small proteins usually fold spontaneously within seconds and even the largest proteins fold within minutes. The difference between the theoretical calculation and the observed result is known as Levinthal's Paradox.

It isn't really a paradox. Levinthal knew full well that proteins did not fold by sampling all possible conformations. He knew that protein folding involved local cooperative interactions such as formation of α helices and that the formation of such secondary structure elements proceeded in parallel and not sequentially as his thought experiment proposed.

We now know that protein folding is largely driven by hydrophobic collapse as the regions of secondary structure come together to exclude water. This process is a global process involving simultaneous rearrangements of hundreds of bonds at the same time. That's why proteins fold so rapidly. Cyrus Levinthal knew this.

The point of Levinthal's paradox is to demonstrate that when a mathematical calculation shows that some routine process is impossible, then it's the calculation that's wrong, or the assumptions behind the calculation. This point is lost on most Intelligent Design Creationists. They are tremendously fond of complex calculations proving that some biological process is impossible. To them, this is not proof that their calculations are flawed—it's proof that a miracle occurred.

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Levinthal, C. (1969) How to Fold Graciously. Mossbauer Spectroscopy in Biological Systems: Proceedings of a meeting held at Allerton House, Monticello, Illinois. J.T.P. DeBrunner and E. Munck eds., University of Illinois Press Pages 22-24 [complete text]

Zwanzig, R., Szabo, A. and Bagchi, B. (1992) Levinthal's paradox. PNAS 89:20-22. [PNAS]

Michael Egnor Gets It Right

 
Michael Egnor has posted a number of quotations from me about how I would deal with people who don't understand the basic principles of science [Dr. Larry Moran and Censorship of Intelligent Design].

He get it mostly right. If they are undergraduates who don't understand that evolution is a scientific fact, the Earth is 4.5 billion years old, and humans share a common ancestor with chimpanzees, then they flunk the course. If they are graduate students in a science department, then they don't get a Ph.D. If they are untenured faculty members in a science department, then they don't get tenure.

Readers might be amused at Michael Egnor's comments regarding Kirk Durston. It's further proof that IDiots are irony deficient. (Note that Kirk has not accepted my invitation to give a seminar here in the Biochemistry Department. I guess his "courage" has limits.)

Why should Mr. Durston’s willingness to present his scientific evidence for intelligent design to other scientists require courage? Isn't the presentation of evidence a routine part of science? Why should presenting evidence for intelligent design put Mr. Durston’s "scientific reputation on the line"?

Are you listening Kirk? Michael Egnor M.D. wonders why you don't come here and defend your evidence that protein folding demonstrates the existence of God.

I gave you two dates last November: you can give a seminar on Tuesday April 22nd or Tuesday April 29th.

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Mike Huckabee Promotes "Expelled"

 
Were you wondering what Mike Huckabee was up to these days? No? Okay, then you probably won't be interested in this video ....


Why is there such a strong correlation between being stupid and believing in the Bible? How can a man like Mike Huckabee be seriously considered as a candidate for "leader of the free world?"

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[Hat Tip: friend fruit]

Buy This Book!!!

 
Carl Zimmer is among the very best—possibly the best—of the modern science writers. His new book Microcosm: E. coli and the New Science of Life is going to be on sale May 6, 2008. Buy it, now. I just did.

Here's a synopsis from Publishers Weekly.

When most readers hear the words E. coli, they think tainted hamburger or toxic spinach. Noted science writer Zimmer says there are in fact many different strains of E. coli, some coexisting quite happily with us in our digestive tracts. These rod-shaped bacteria were among the first organisms to have their genome mapped, and today they are the toolbox of the genetic engineering industry and even of high school scientists. Zimmer (Evolution: The Triumph of an Idea) explains that by scrutinizing the bacteria's genome, scientists have discovered that genes can jump from one species to another and how virus DNA has become tightly intertwined with the genes of living creatures all the way up the tree of life to humans. Studying starving E. coli has taught us about how our own cells age. Advocates of intelligent design often produce the E. coli flagellum as Exhibit A, but the author shows how new research has shed light on the possible evolutionary arc of the flagellum. Zimmer devotes a chapter to the ethical debates surrounding genetic engineering. Written in elegant, even poetic prose, Zimmer's well-crafted exploration should be required reading for all well-educated readers. (May 6)

Copyright © Reed Business Information, a division of Reed Elsevier Inc. All rights reserved.

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Having a Wife Creates More Housework for Men

 
A newly released study looks at the amount of house work done by men and women in different living situations. Like most of these surveys, the data is based on interviews and on diaries kept by men and women. The most remarkable results are reported in a press release from the University of Michigan [Exactly how much housework does a husband create?].

Here's how they describe the data collection process.

For the study, researchers analyzed data from time diaries, considered the most accurate way to assess how people spend their time. They supplemented the analysis with data from questionnaires asking both men and women to recall how much time they spent on basic housework in an average week, including time spent cooking, cleaning and doing other basic work around the house. Excluded from these "core" housework hours were tasks like gardening, home repairs, or washing the car.

Assuming that this is a reliable way of accessing workload, the study published a chart showing the amount of housework done by maried and single men and women.


The 2005 results show that when women get married they end up doing 7 hours more housework per week but when men get married they end up doing 8 hours more housework per week. The take-home message is clear. Women are a lot more costly than men. Women do more to mess up a house than men do.

Pay attention, men. It may not be worth the effort to get married.

The title of the press release is interesting: Exactly how much housework does a husband create?. Here are the opening paragraphs.

ANN ARBOR, Mich.---Having a husband creates an extra seven hours a week of housework for women, according to a University of Michigan study of a nationally representative sample of U.S. families.

For men, the picture is very different: A wife saves men from about an hour of housework a week.

The findings are part of a detailed study of housework trends, based on 2005 time-diary data from the federally-funded Panel Study of Income Dynamics, conducted since 1968 at the U-M Institute for Social Research (ISR).

Is it just me or does there seem to be a disconnect between the statements in the press release and the chart that's published on the same page?

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