This Is too Weird

Check out the meowbified version of Sandwalk at http://cat.sandwalk.blogspot.com.meowbify.com/.

The evil deed was performed at Meowbify. Try it on Pharyngula.

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[Hat Tip: PZ Myers]

We Called Out IDiot Jonathan Wells, and He Folded

Carl Zimmer had the audacity to post something about the fusion of two ancestral chromosomes in primitive apes. The data is unequivocal. It shows why humans have one less chromosome than modern chimps [The Mystery of the Missing Chromosome (With A Special Guest Appearance from Facebook Creationists)].

Observations like this lend strong support to the idea that humans and chimps share a common ancestor. This doesn't sit well with the IDiots because they are in the midst of hyping their latest book, Science & Human Origins where they try to counter the overwhelming evidence that humans evolved.

So, what did they do? David Klinghoffer challenged Carl Zimmer to pop on over to Evolution News & Views (sic) and debate one of the authors. Carl refused, as would any sane person since that creationist blog is edited by IDiots and no comments are allowed. It would be embarrassing to have one's name on an article at Evolution News & Views [The Mystery of the Missing Chromosomes, Continued: An Update From Your Preening Blogger].

Here's what Carl said,

I thought the question I asked was pretty simple. I wasn’t asking to hold a Lincoln-Douglas debate. I just asked what the evidence was for one of the claims made by the creationists.

Now it seems that in order to get that answer, I can either buy a book–which apparently is based on no peer-reviewed research of the authors, but just cherry-picked quotes from a ten-year old paper–or I can donate my time to write several thousands words for free for a creationist web site.

Making this offer even richer is Klinghoffer’s ground rules about focusing “strictly on the ideas, not on the personalities.” Klinghoffer himself has used Evolution News & Views to call people pathetic, a worthless bully, cowards, illiterate, and “a tyranny of the unemployed” (referring to Wikipedia editors). In one piece he wrote for Evolution New and Views, Klinhoffer mocked a post by a science blogger as “preening and self-congratulatory.”

That blogger happened to be me.

I will answer Mr. Klinghoffer publicly: no thanks. I never asked for a debate, and your arbitrary decrees, such as a mysterious thousand-word cutoff (my blog post on the chromosomes alone clocked in at over 2,000 words) make it even less appealing. I am particularly opposed to web sites that do not allow readers to comment. That’s how I ended up on Facebook in the first place–because the Discovery Institute’s web sites do not permit commenting. You, on the other hand, are more than welcome to leave a comment on my blog. My comment policy is very lax: I only throw out commenters who curse uncontrollably, hawk their own wares, or can’t stay on topic after repeated warnings. We have a thriving, fascinating discussion here, one from which I regularly learn new things from my readers. You might too.

David Klinghoffer, being David Klinghoffer, responded with a blog posting on Evolution News & Views: We Called Out Darwinist Critic Carl Zimmer, and He Folded.

"Reasoning with a Lynch Mob"

This reminded me of an incident that took place last November. You might remember that I spent a great deal of time and effort reviewing Jonathan Wells' book, The Myth of Junk DNA (see The Myth of Junk DNA by Jonathan Wells). I invited Wells to discuss and debate the issue of junk DNA and my extensive criticism of his book.

Wells declined [Jonathan Wells Sends His Regrets]. Here's what he said ...

Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.

Sort of makes you wonder, doesn't it? Do you think the IDiots really are interested in debating science or is it only on their own terms, on their own blog, with no comments, and moderated by their own kind?

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Better Biochemistry: Good Enough Enzymes

Some enzymes catalyze reactions at extremely fast rates that are only limited by the rate of diffusion of substrate molecules into the active site of the enzyme (diffusion-controlled rate). Some of these enzymes are covered in all the standard biochemistry textbooks; examples are canbonic anhydrase (CAN), triose phosphate ismerase (TIM), and superoxide dismutase (SOD). Superoxide dismutase (right) actually catalyzes reactions at a rate that's faster than the diffusion-controlled limit [Superoxide Dismutase Is a Really Fast Enzyme].

These enzymes are often referred to as "perfect" enzymes but that's a very misleading term because it implies that all other enzyme are less than perfect.

Most enzyme don't need to act any faster than they do. They are quite happy catalyzing reactions at rates that are far below their theoretical optimum [Better Biochemistry: The Perfect Enzyme]. As long as it's good enough there's no selective pressure to get better.

Do Bacteria Have Sex?

There are three different ways for bacterial to exchange information: conjugation, transduction, and transformation. Do any of these count as sex?

It depends on your definition. Rosie Redfield and I had a discussion about this when we were together in Ottawa. I think some species of bacteria do engage in sex because all three mechanisms can result in gene exchange between different individual bacteria. I think that transformation and conjugation may have arisen, in part, as a way of repairing damaged DNA and escaping the effects of Muller's Rachet.

Rosie thinks that sex, by definition, means mixis—the shuffling of alleles due to sex as in eukaryotes. Here's how she explains it in a recent post on her blog [Claims that Bacteria Do Have Sex].

This work addresses a very important question with big/deep/fundamental importance to the colossal problem of the origin of meiotic sex in eukaryotes. The question is 'Do bacteria have any processes that evolved because of selection for recombination of chromosomal alleles?' We think this selection is the reason for the success of meiotic sexual reproduction in eukaryotes, but compelling evidence for this has been elusive. Bacteria have four well-studied processes that do generate homologous recombination; three that transfer DNA between cells and one that carries out homologous recombination. But almost every aspect of these processes has been shown to cause recombination as an unselected side effect of processes selected for other functions.

I don't think sex evolved in eukaryotes in order to promote mixis so this argument doesn't resonate with me.

Read Rosie's post if only to discover why she thinks transformation evolved. She's thinking of applying for a grant to study this problem so I'm sure she would appreciate your feedback.

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[Image Credit: Rosie Redfield]

Where Are the Best University Teachers?

Much to my embarrassment, the University of Toronto is promoting online courses, or MOOCs [Online courses for anyone, anywhere]. These courses seem to be for information only—you can't get a university credit for them.

I'm not opposed to offering free "courses" for people who don't have easy access to a university campus. In fact, I think it's a good thing. But let's make sure we distinguish between public lectures and serious education. In my opinion, if the quality of an online course is equal to the quality of a course given on campus then all that says is that the campus-based course is lousy. We should not refer to these online examples as "university courses." They should be labelled as "public lectures."

I'll have more to say about this later but today I want to return to an issue I raised before. Is it true that the "best" universities also do the best teaching? I have suggested that the answer to this question is probabyy "no" [On the Quality of Online Courses] [Is Canada Lagging Behind in Online Education?].

University Tuitions in Canada and the United States

The University of Toronto is the largest university in North America (70,000 students) and one of the top 20 universities in the world¹ [The World University Rankings 2011-2012]. It ranks near the top among the group of very large public universities [World University Rankings].

The University of Toronto is a public university. A large percentage of its operating budget comes directly from the provincial government. In that sense, it is comparable to many of the large state schools in the United States. When we're judging ourselves,² we use a list of nine American state schools of comparable size and quality.

Tuition costs have been in the news in Canada recently since there have been vocal student protests in Quebec over government plans to raise tuition costs in Quebec schools. The combination of tuition and fees will increase from $2,890 per year to $4,700 per year over a five year phase-in period.

What is the average cost of tuition plus fees at the University of Toronto and how does this compare with similar American schools? President David Naylor gives us the answer on his website where he discusses the problem of student debt in Canada and the United States [Student Debt Redux].

If you're an American, consider sending your children to a Canadian university. You'll save a lot of money and there's an added bonus—we get to show them what a real "socialist" country looks like.

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Note: One of the signs in the protest says, "Marx is dead, God is dead, and I don't feel so good."

1. There are many problems with these ranking but the bottom line is that the University of Toronto is a pretty good university as judged by outsiders.

2. Which we do obsessively every few months.

Stress and Telomere Length—Do You Believe this Study?

Healthy skepticism is an important part of science. One of the biggest differences between scientists and intelligent design creationists, for example, is that the creationists are rarely skeptical of anything they read in the scientific literature. If it appears to support their agenda, then it goes right onto the blogs without any discussion of whether it might be true or not.

Scientists, on the other hand, are often very skeptical of work that appears in the scientific literature. They treat most papers as tentative results that need to be confirmed. The most obvious flawed papers will be refuted by further work, as in the recent arsenic in DNA paper or earlier work on cold fusion. Usually, flawed papers will just be ignored and they will die a quiet death.

Questions for Genetics Students

Rosie Redfield has published a (deliberately) provocative article on teaching genetics in the 21st century (Redfield, 2012). I disagree strongly with her premises and her conclusions but the issues are complex—too complex for a single posting.

Let's start by looking at one aspect of her proposal.

Rosie thinks that a 21st century course on genetics should focus on information that students can use later on. Here's how she would begin her new course ...

Box 4 gives a suggested syllabus for a 21st century genetics course. It begins with a human focus, introducing personal genomics and our natural genetic variation. Students then learn about the underlying molecular explanations—how differences in DNA sequences arise and evolve, and how they cause differences in phenotype—followed by how genetic differences are inherited and recombined.

Evolution Is Purposeless and Unguided—Deal with It!

Many prominent scientists get it right when they say that evolution is purposeless and unguided. The same is true for plate tectonics, supernovas, radioactive decay, and the weather.

If you have a problem with this, read Jerry Coyne at What’s the problem with unguided evolution? and take it up with him. I'm tired of trying to convince theists and accommodationists of something that's as plain as the nose on your face.

Not to beat a dead horse (I think it’s still alive), but I vehemently oppose those evolutionists and accommodationists who won’t affirm that evolution is unguided and purposeless (in the sense of not being directed by a higher intelligence or teleological force). For to the best of our knowledge evolution, like all natural processes, is purposeless and unguided. After all, scientists have no problem saying that the melting of glaciers, the movement of tectonic plates, or the decay of atoms are processes that are unguided and purposeless.

Some beating of dead horses may be ethical, when here and there they display unexpected twitches that look like life.

Emile Zucherkandl and Linus Pauling (1965)

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Eschaton 2012

Most of you missed the exciting Evolution Ottawa 2012 meeting earlier this month but, cheer up, you have another chance to visit Ottawa form Novermber 30 to December 2, 2012.

The meeting is called Eschaton 2012 where "eschaton" refers to the end of the world. That's because, as you all know by now, the world is going to end on December 21, 2012. The Mayans said so and so do a lot of modern kooks.

Here's an outline of the meeting.

The conference opens with a Friday night plenary session on the historical relationship between humans and our apocalypses. Saturday morning and afternoon, we have parallel tracks: 1) Talks and panels on skepticism/science/science communication (including a live recording of Ottawa Skeptics' podcast, The Reality Check) and 2) "The Immaculate Convention" - talks and panels on religion from an academic and sociological perspective. Saturday evening there will be a reception with food and drink in the early evening at the Canadian Museum of Nature (around the corner from the hotel), after which there will be a talk by PZ Myers, followed by a meet-and-greet social, with snacks, cash bar, and access to some of the galleries and exhibits. On Sunday the parallel tracks include panels and workshops on ethics, gender identity, parenting, and other exciting topics to be announced.

Here's the latest list of speakers. (I changed the order somewhat from the one on the website.)

• Larry Moran
• P.Z. Myers
• Ophelia Benson
• Chris DiCarlo
• Ian Cromwell
• Natalie Reed
• Udo Schuklenk
• Eugenie Scott
• Jim Linville
• Sara Mayhew
• Jeff Shallit
• Eric MacDonald
• Ania Bula
• Heina Dadabhoy
• The Reality Check
• Annie Urban
• Allan Daoust
• Crystal Beauvais Daoust
• Anila Asghar
• Steve Tomlins

I'm planning to talk about the accommodationist wars and why science and religion are incompatible. Hopefully, Genie Scott will represent the accommodationist position as promoted by NCSE.

Chris DiCarlo and I are teaching a course at the University of Toronto next Fall on scientific controversies and misconceptions (including evolution vs creationism). Maybe we can have a workshop on Sunday to discuss science literacy?

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Vote for Jesus for President (of the United States)

PZ Myers approves of this plan to cast a vote for Jesus [An excellent suggestion for the Bible-believing Christians].

Isn't there a problem? Who's going to produce a valid birth certificate?

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Monday's Molecule #177

This is a very important molecule. It's found in (almost?) all living species where it serves a very important function. What is the common name of this molecule and what role does it play in metabolism?

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is S adenosylmethionine (SAM). It is the major methyl donor in biochemical reactions. Today's winners are Sean Ridout and William Grecia.


Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia

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Atheist Retention Rates

We live in an era where almost 50% of the citizens in some Western European countries don't believe in God and a solid majority of those in Japan and Vietnam are nonbelievers [Top 50 Countries With Highest Proportion of Atheists / Agnostics].

According to some polls, about 30% of Canadians don't believe in God [Religion in Canada] and in the USA the number of nonbelievers is about 12% of the population {Atheists in America].

A recent survey by The PEW Forum on Religion & Public Life looked at the religious belief of Americans as adults and how they were raised as children. There were 1387 people who self-identified as atheists but only 131 of these were raised as atheists. Thus, 90% of the atheists were raised in a religious household but later on abandoned their belief in God(s).

That's pretty remarkable in a society that's as religious are the USA. It's not surprising that there are so many first generation atheists because a generation ago the number of atheists in the USA was less than 1% of the population.

On the other hand, there were 432 respondents who said they were raised as atheists. Only 131 of these respondents are still atheists so that means that the retention rate for atheism is only 30% and that makes it the worst "religion" at retaining childhood beliefs. The figure and the data are from Mark M. Gray who blogs at Nineteen Sixty-four. He writes ...

What these findings reflect is that in the U.S. Atheists are for the most part "made" as adults after being raised in another faith. It appears to be much more challenging to raise one's child as an Atheist and have them maintain this identity in their life. Of those raised as Atheists, 30% are now affiliated with a Protestant denomination, 10% are Catholic, 2% are Jewish, 1% are Mormon, and 1% are Pagan.

This is perceived as good news by the IDiots who were happy to pass along the information on Uncommon Descent: Why do atheists have such a low retention rate?.

Some of us are tempted to wonder whether they just grow tired of the society of Darwin’s tenure bores and the atheist troll in the mailroom. Or of the uproar around the Skepchick. Re that latter individual, at some point, surely a normal dude must wonder, what is in this for me, long term?

He might be better off with a cute, decent girl who offers free coffee and cake in the parish hall, not sexy pics. But to meet her, he has to sober up, shave, shower, and go to church … so …

So, … maybe it’s just the facts of life that catch up with some of them?

I think there's a better explanation. As we all know, many evangelicals are proud of advertising that they were raised as atheists but were "born again" as teenagers or adults. Perhaps they "misremember" certain aspects of their religious upbringing and "forget" that their parents believed in God? If a few hundred of them declared, incorrectly, that they were raised as atheists then the real retention rate would be much higher.

In any case, religion is in trouble everywhere, including the United States. In many countries, there are millions of second and third generation atheists who will never believe in imaginary supernatural beings. Those who are making a big deal of this apparent retention rate among Americans are a lot like the passengers who concentrated on rearranging the deck chairs while the Titanic was sinking.

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Jeffrey Shallit on the Sandwalk

Jeffry Shallit of Recursivity is in London, England where he recently took a train from Victoria Station to Bromley South, then a bus to Downe, and a rather dangerous walk up a narrow hedge-lined road to Down House [Larry Moran Would Approve ].

He joins a distinguished list of people whose visit to the Sandwalk has been recorded here.

Larry Moran
PZ Myers
John Wilkins
Ryan Gregory
The God Delusion
Cody
John Hawks
Michael Barton
Seanna Watson
Steve Watson
Michael Richards
Jeffrey Shallit
Chris DiCarlo
Bill Farrell and Louis C
Cody

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Trinity, July 16, 1945

The first atomic bomb was detonated on this day in 1945 [Trinity]. The second detonation of an atomic bomb took place over Hiroshima, Japan, on August 6, 1945.

So far, Hiroshima and Nagasaki are the only examples of a nuclear device being used in war. We've managed to avoid dropping atomic bombs on each other for 67 years. If you think about it, that's a pretty remarkable achievement.

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