Don't Mess with Rob Day

 
Rob Day, better known as Canadian Cynic, finally got tired of the malicious defamations posted by Patrick “Patsy” Ross on his blog The Nexus of Assholery. The result was an $85,000 judgment in Rob's favour—$10,000 in legal costs and $75,000 in punitive damages [Another Mudfish Beached]. Let's hope Patsy pays up before the police have to come knocking on his door.
This is one way to deal with bloggers and trolls who step over the line. Another way is to press criminal charges against those who post serious threats. I think the second way is better, if it's an option, and I'm looking forward to the time when some of the mentally deranged trolls are locked away in an institution without a computer. There are a few such trolls who may soon be getting a visit from the cops.

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Was Darwin Wrong?

 
I understand, and agree with, the basic sentiment behind this poster but I wish they'd chosen better examples. Charles Darwin was wrong about lots of things.¹

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1. But he's still the best scientist who ever lived.

Christopher Hitchens vs. Tony Blair

 
I couldn't get tickets to see the actual debate at Massey Hall in Toronto so I'm doing the next best thing by going to the beer party live streaming of the debate at CFI tomorrow night.

All the cool people will be there (wearing WiFi radiation protection).

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Starts: Friday, November 26th 2010 at 7:00 pm
Ends: Friday, November 26th 2010 at 9:00 pm
Location: Centre for Inquiry, 216 Beverley Street (just south of College and St. George)

Since the debate between well-known atheist and author Christopher Hitchens and former British Prime Minister Tony Blair sold out we will be screening the live video stream of the event at CFI Ontario.

In a world of globalization and rapid social change does religion provide the common values and ethical foundations that diverse societies need to thrive in the 21st century? Or, do deeply held religious beliefs promote intolerance, exacerbate ethnic divisions, and impede social progress in developing and developed nations alike? To encourage a far-ranging discussion on one of human kind's most vexing questions, the 6th semi-annual Munk Debate will tackle the resolution: be it resolved, religion is a force for good in the world.

$5, $4 for students and FREE for CFI Members.

Attendees are invited to stay after the debate to enjoy some food and drinks while they discuss who they thought won the debate!

$3 Beer!

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How to Protect Yourself from WiFi Radiation

A study by some Dutch scientists claims to have shown that WiFi kills trees [Study Says Wi-Fi Makes Trees Sick]. Combine that with the widespread myth evidence that WiFi radiation is harming school children [Sometimes School Trustees Make You Proud] and all of a sudden we've got a serious problem. University campuses are awash with WiFi radiation coming from sites in every building. If you are one of those people who think you're being harmed, I've come up with a simple solution—a tinfoil¹ hat to protect your brain. I have carefully researched the shape of this hat in order to maximize the desired effect. Wear it when you are at your desk studying, when you are in class, and when you're taking a break. Get all your friends to wear one too. Not only will this tinfoil hat protect you, it will also serve as a reminder to others that you are an intelligent person who cares about the environment. Here's a special note to parents of school age children who are worried about WiFi radiation in the public schools. It's easy to make a protective hat. Just roll up some poster board in the shape of a cone and cover it with tinfoil. Make sure your children keep the hat on while they are in school. Your children will rapidly gain the admiration and respect of the other students for being so scientifically literate.

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1. It's actually aluminum foil but who's counting? The photos were taken by Alex Palazzo who wishes to remain anonymous.

Rock Stars of Science

 
This poster is from Rock Stars of Science. There are six people in the photo: one of them is a rock star (I'm told) and five of them are famous scientists (I'm told).

Is this a good way to promote science? Martin Robbins doesn't think so: 'Rockstars of Science' should be 'Scientists of Rock'.

I could be wrong. Maybe this is a good way of reaching out to people. Maybe GQ's readers are getting out their dictionaries and picking through those descriptions, stopping occasionally to stare at the blurry, bearded interloper in the background of Bob's photograph. And maybe those readers are now more inspired by science as a result. If so, I'd like to see some evidence of it - maybe a poll of readers?

But I still can't help but feel that if you have to resort to rockstars make science cool, you're really not very good at communicating science. Because science is way cooler than rock stars.

You won't be surprised to learn that Chris Mooney likes this campaign and ERV doesn't. Jerry Coyne doesn't like it either. Does anyone notice a pattern here? ... The one person who isn't a scientist is the one who thinks he knows how to promote science.

So, who's behind this promotion? It's a company called GEOFFREY BEENE that I've never heard of. But don't take that lack of knowledge seriously because I'm a scientist and I'm definitely not cool.

Here's a video put out by the company. Is this mostly about science or is it mostly about the company exploiting their support for medical technology?

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Don't Mess with Skepchick!

 
Skepchick asked you to boycott movie theaters that were showing the anti-vaccine video promoted by Age of Autism [Let’s all go to the movies and save ourselves some lives]. Many of us posted complaints on the AMC website.

Yesterday Age of Autism and SafeMinds released the following statement as reported in the latest posting on Skepchick [Good guys win!]. Congratulations Skepchick!

SafeMinds was notified late yesterday afternoon that AMC Theaters has decided to block the SafeMinds Public Service Announcement (PSA) on influenza vaccines with mercury. The PSA alerts parents and pregnant women of the presence of mercury in most influenza vaccines and the ample availability of mercury-free alternatives. The CDC has declined to give a preference for the mercury-free versions, so it is important that the public is aware of its options. AMC’s advertising representative had reviewed and approved the PSA to run in AMC cinemas over the Thanksgiving weekend. A small group of vocal vaccine proponents dismissive of mercury concerns learned of the PSA and bombarded the AMC website, leading to the company’s decision to prevent its release. SafeMinds thanks its supporters who viewed the PSA and contributed to its efforts to educate the public to avoid unnecessary mercury exposure. Mercury in all forms is dangerous, especially to the developing fetus and infants, as referenced on the PSA website www.safemindsflu.org. SafeMinds will continue its mission to educate the public on this important healthcare topic.

BTW, the ad was NOT a public service announcement by any stretch of the imagination.

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Nobel Laureates Become Pseudoscientists

 
There are several well-known examples of Nobel Laureates in science who later become enamored with quackery. Orac mentions a few on his blog in The Nobel disease strikes again.

Can you guess who holds the record for the swiftest turn around from getting the Nobel Prize to endorsing quackery? (Hint: mentor of Richard Dawkins).

Of course this record only applies to scientists who became quacks after getting the Nobel Prize. That lets Kary Mullis off the hook.

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Age of Autism Opposes Flu Shots

 
Age of Autism is sponsoring this video to be shown in movie theaters this weekend. Skepchick is on the case: Let’s all go to the movies and save ourselves some lives.

(Flu shots are perfectly safe, but I don't need to tell YOU that, do I?)

Here's a list of theaters that will be showing the video. Boycott them if you live near by.

* Empire 25 in New York City
* Long Beach 26 in Long Beach, California
* River East 21 in Chicago, IL
* Boston Common 19 in Boston
* Phipps Plaza 14 in Atlanta
* Tyson’s Corner 16 in McLean, VA
* Northpark Center 15 in Dallas, TX
* Rosedale 14 in Saint Paul, MN
* Pavillions 15 in Denver, CO

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Skepticism and Atheism—Is there a Difference?

 
PZ Myers reports from Skepticon III in Missouri that some people are upset because there's too much atheism at a skeptical meeting. This leads naturally to a discussion about the difference between being a skeptic and being an atheist. Can you be a theist and still be genuinely skeptical?

Jim Lippard has an interesting point of view on this question. You should read his blog posting [What to think vs. how to think] and join the discussion on The Lippard Blog.

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Can Undergraduates Select Courses?

 
Greg Petsko has written a marvelous criticism of the decision by a university President to eliminate departments of French, Italian, Classics, Russian and Theater Arts. It's part of his regular column in Genome Biology. Read it at: An open letter to George M Philip, President of the State University of New York At Albany.

Several bloggers have discussed the letter.¹ Petsko is defending a traditional liberal education that includes literature and language and I agree with the gist of what he is saying. However, I wish we could have more of a conversation about "liberal science" instead of always referring to "liberal arts." It's not enough to insist that every student be exposed to philosophy and literature—they must also be exposed to science or you can't say that they are getting a truly liberal education. And I'm not just talking about a token science course for humanities students called "Astronomy for Dummies."

But let's leave that conversation for another time. I want to discuss another issue. Here's what Petsko said,

Let's examine these and your other reasons in detail, because I think if one does, it becomes clear that the facts on which they are based have some important aspects that are not covered in your statement. First, the matter of enrollment. I'm sure that relatively few students take classes in these subjects nowadays, just as you say. There wouldn't have been many in my day, either, if universities hadn't required students to take a distribution of courses in many different parts of the academy: humanities, social sciences, the fine arts, the physical and natural sciences, and to attain minimal proficiency in at least one foreign language. You see, the reason that humanities classes have low enrollment is not because students these days are clamoring for more relevant courses; it's because administrators like you, and spineless faculty, have stopped setting distribution requirements and started allowing students to choose their own academic programs - something I feel is a complete abrogation of the duty of university faculty as teachers and mentors. You could fix the enrollment problem tomorrow by instituting a mandatory core curriculum that included a wide range of courses.

Young people haven't, for the most part, yet attained the wisdom to have that kind of freedom without making poor decisions. In fact, without wisdom, it's hard for most people.

My university is run by spineless faculty who think that we should structure the university according to what the students want to take. We are evolving into a university that promotes a wide range of options and degrees that have no major focus of study. This is all in the names of "breadth," "diversity," and "interdisciplinary." It's the smörgåsbord approach to education.

The problem with Petsko's analysis is that the very faculty he assumes to possess the "wisdom" to set curricula are the ones promoting student choice and abrogating responsibility—at least at the University of Toronto.

So, here's the question: Should universities be mandating required courses in order to assure a minimal standard of liberal education or should we be allowing students to choose whatever courses they are interested in taking?²

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1. John Pierot [Knowing Ways] thinks that humanities represent a different way of knowing. Jerry Coyne also has a humanities background [Keeping the humanities alive].

2. Knowing full well that some students will often choose courses on the basis to expected grades rather than interest.

Extraordinary Claims

 
Today marks the official launch of the Extraordinary Claims campaign by the Centre for Inquiry, Canada. A lot of the work behind this campaign was done by members of the Committee for the Advancement of Scientific Skepticism (CASS). While I'm listed as a member of that committee I haven't been very active for the past six months while I've been working on my book. The credit goes to Michael Kruse and Iain Martel and all the other members who worked so hard.

If you're a CFI member, support CFI by attending the Official Launch Part this evening at the Centre for Inquiry, 216 Beverley Street, Toronto (just south of the St. George campus of the University of Toronto).¹ If you're not a member then go anyway and join up!

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1. I wish I could be there but a prior commitment got in the way.

Darwinism and Junk DNA

 
Robert Crowther has posted a criticism of Francis Collins on Evolution News & Views (sic): Francis Collins, Evolution and "Darwin of the Gaps".

Much of Collins’s case for Darwinian evolution is based on so-called “junk DNA.” This is the part of the genome that does not appear to code for the production of proteins. In mammals, the vast majority of DNA has been dismissed as “junk.”

Junk DNA, according to Darwinists like Collins, gives evidence of common descent—the idea that all life, including human life, branches off from a common evolutionary tree. As life evolved, according to this view, garbled, useless genetic information accumulated and has remained fixed—like dirt swept under a carpet—even as mammals, for example, diversified from a common ancestor.

But the argument from junk DNA—also called “ancient repetitive elements” (AREs)— depends on the premise that no function will ever be discovered for AREs. Collins’s faith in Darwinian theory would be severely hamstrung if the premise were shown to be wrong. It is a faith based on gaps in scientific knowledge. Hence, “Darwin of the gaps.”

I don't want to defend Francis Collins. I want to emphasize something else; namely that the concept of junk DNA is about as far removed from "Darwinism" as you can possibly be and still be an evolutionary biologist. If it has any meaning at all, "Darwinism" has to be a synonym for the belief in natural selection as the most potent mechanism of evolution. Junk DNA is completely non-Darwinian and there's no way you could describe it as compatible with "Darwinian theory."

Why do creationists have so much trouble understanding this? It's not that hard.

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What Is Darwinism?

Allen MacNeill at The evolution list asks What is "Darwinism" and am I a "Darwinist"?.

Read his posting to see what real modern scientists actually think about evolution and Darwinism. For more information you can read my own thoughts on the matter at: What Is Evolution, The Modern Synthesis of Genetics and Evolution, and Why I'm Not a Darwinist.

Now, here comes the fun part. Over on Uncommon Descent Barry Arrington asked the Intelligent Design Creationists to define "Darwinism". The contrast between what they're saying in the comments and what the modern textbooks say about evolution is truly astonishing.

And amusing.

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Bad Faith Awards

 
From the New Humanist

After a nomination period that saw you put forward those you feel have made the most egregious contributions to irrationalism and superstition during the course of this year, we've whittled them down to a shortlist of eight. Now all that's left for you to do is vote for the person you think should take the Bad Faith crown from last year's winner, Pope Benedict XVI.

Here's the list. I'm not going to tell you who I voted for.

Lauren Booth
Prince Charles
Baroness Warsi
Sheikh Maulana Abu Sayeed
Ann Widdecombe
Hojatoleslam Kazem Sedighi
Cardinal Walter Kasper
Pastor Terry Jones

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Human Mutation Rates

Calculating the rate of evolution in terms of nucleotide substitutions seems to give a value so high that many of the mutations must be neutral ones.

Motoo Kimura (1968)We know a great deal about the error rate of DNA replication. The replisome makes a mistake about once in every 100 million bases incorporated. This is an error rate of 10^-8. The repair mechanism fixes 99% of these errors for an overall mutation rate of 10^-10. Given the size of the human genome and the number of replications between zygote and germ cells, this translates to approximately 130 mutations per individual per generation [Mutation Rates].

Recently there have been two attempts to verify this calculation. In one, the Y chromosomes of two men separated by 13 generations in a paternal lineage from a common male ancestor were sequenced. The differences correspond to a mutation rate of 0.75 × 10^-10 per generation, or almost the same as theory predicts [Human Y Chromosome Mutation Rates]. This is based on the fact that if most mutations are nearly neutral (they are) then the rate of fixation by random genetic drift should be the same as the mutation rate [Random Genetic Drift and Population Size].

The other study, by Roach et al. (2010), compared the genome sequences of two offspring and their parents. By adding up all the differences in the offspring they arrived at an estimate of 70 mutations in the offspring instead of the expected 130 [Direct Measurement of Human Mutation Rate]. This is half the expected value but the study is fraught with potential artifacts and it's best not to make a big deal of this discrepancy.

John Hawks was worried about this last March [A low human mutation rate may throw everything out of whack ] and he's still worried about it today [What is the human mutation rate?].

What John is really interested in isn't the mutation rate per se since we have pretty good handle on that number. What interests him is Calibrating the Molecular Clock and that's not the same thing. What it boils down to is the number of years per generation—or the number of fixed mutations per million years.

John thinks that if the actual mutation rate is only half of the value we though it was then the dating of many evolutionary events will need to be recalculated. For example, the human-chimp divergence would have to be re-set to eight or nine million years ago. But that's not strictly correct. We don't calibrate the molecular clock by taking the known mutation rate and multiplying by the number of generations then throw in a known value for the number of years per generation.¹

None of those values are known for even the most recent events in the primate lineages. What we usually do is work from a fixed point in the fossil record, count the number of differences between species, and estimate a mutation rate per million years. That value is then used to calibrate other divergences.

Sometimes these rates of change can be related to the mutation rate by estimating the generation times and they often seem reasonable when we come up with generation times of,say, 25 years. Even if the known mutation rate were half of the current consensus value, the most reasonable adjustment would not to be recalibrate the time of divergence but to reconsider our assumption abut generation time. Maybe there were twice as many generations per million years.

But this is actually a non-problem right now since the Roach et al. (2010) estimate is not very reliable. I don't think John Hawks should be worried.

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1. Plus estimates of the effective population size, N_e.

Roach, J.C., Gustavo Glusman, G., Smit, A.F.A., Huff, C.D., Hubley, R., Shannon, P.T., Rowen, L., Pant, K.P., Goodman, N., Bamshad, M., Shendure, J., Drmanac, R., Jorde, L.B., Hood, L., and Galas, D.J. (2010) Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing. Science (Published Online March 10, 2010) [doi: 10.1126/science.1186802]