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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