There are two recent events indicating that change is afoot in America. First, there's the recent poll suggesting that a majority of Americans (54%) could now vote for an atheist candidate who was running for President [Niose: Atheists making political inroads].
Then there's another poll showing that 19% of Americans are now nonreligious ("nones") [“Nones” climb to 19%]. The "nones" are not necessarily atheists or agnostics but it's safe to say that many of them are.
Why are these results significant? They're significant because back in 1958 only 18% of American said they could vote for an atheist and that number didn't change much until the 21st century. Also, the "nones" made up only 6% of the populations in 1990 rising to 15% in 2008.
So, what has happened in the past decade to turn people away from religion and make atheism more respectable?
I can think of two possibilities ...
- The accommodationist approach that has been dominant for several decades has finally started to bear fruit.
- The rise of "militant atheists" in the past decade has forced large numbers of Americans into realizing that atheism and non-belief are respectable options.
Which explanation do you think is likely?
[Hat Tip: RichardDawkins.net]
It's the dog days (dies caniculares) of summer and Sirius is hard at work.
I'm going to let you off easy today. Identify the four molecules whose structures are shown on the right and name the two enzymes that catalyze the reactions. For extra accolades, tell us why those two enzymes are important in evolution and why the blogosphere is currently talking about these kinds of enzymes.
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.
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
I hate it when this happens. I read a book review in yesterday's New York Times Sunday Book Review. If the review is accurate, the book is one of those books that I would probably hurl into the fireplace ... if I had a fireplace.
In order to be fair I have to buy the book (it's not available in Canada) but meanwhile I need to vent about it's probable content.
The book is The New Religious Intolerance by Martha C. Nussbaum and the review is by Damon Linker [Church, Temple, Mosque].
Here's the opening paragraphs of the review...
Mitt Romney’s stump speech during the Republican primaries was filled with appeals to his party’s conservative base, but none consistently inspired more heartfelt cheers than his promise to “stop the days of apologizing for success at home and never again apologize for America abroad.” The statement speaks to the widely held suspicion on the right that liberals in general, and Barack Obama in particular, prefer other forms of democracy (especially those that prevail in Europe) to the American way of life.
Martha C. Nussbaum’s new book could serve as Exhibit A in liberalism’s defense against this charge. The author of 17 previous books on a wide range of topics — from classical Greek philosophy and tragic drama to modern law, literature and ethics — Nussbaum is one of America’s leading liberal thinkers. In “The New Religious Intolerance,” she turns her attention to the rise of antireligious — and specifically anti-Muslim — zealotry since the terrorist attacks of Sept. 11, 2001. Though she writes in her opening chapter that intolerance disfigures “all Western societies,” it quickly becomes clear that there have been far fewer incidents of bigotry in the United States than in Europe — because of America’s vastly superior approach to guaranteeing the rights of religious minorities. When it comes to freedom to worship, at least, Nussbaum is an unabashed proponent of American exceptionalism.
The essence of her thesis is that: (1) several European countries have laws prohibiting Muslim women from wearing the burqa in public, (2) The Swiss government bans the building of minarets outside mosques, and (3) The Norwegian mass murderer, Anders Behring Breivik, didn't like Muslims. The United States hasn't done any of these things. That's because Americans are much more tolerant of other religious beliefs than Europeans.
There are important ways in which the United States protects religious minorities ...
The core of the book explores three preconditions of securing religious liberty for minorities — and in all of them the United States does a much better job than Europe. First, a nation must commit itself to protecting the greatest possible freedom of conscience that is compatible with public order and safety — a principle that the United States codifies in the First Amendment’s disestablishment of religion and guarantee of religious free exercise....
The second precondition of religious liberty is an impartial and consistent civic culture. On this measure, Europe fares especially badly, as Nussbaum demonstrates by methodically exposing the double standards and bias at play in the arguments for banning the burqa.
Finally, there is the need for “sympathetic imagination” on the part of citizens. Here the United States has long taken the lead, cultivating respect for religious differences since the 17th century, when Roger Williams founded Rhode Island, the “first colony (anywhere in the world, it seems) in which genuine religious liberty obtained for all.” Nussbaum is particularly impressed with Williams’s respectful treatment of the Narragansett Indians, whose language and culture he struggled to understand at a time when most of the colonists thought of them as beasts or devils.
Wow! It's news to me that the United States is a paragon of religious tolerance but perhaps that's just my anti-American bias. (For the record, Roger Williams was English, not American, and most of the other colonies were somewhat less tolerant.1)
I tend to think of the USA as a place where religious groups want to restrict women's freedom of choice, infringe on the rights of gays and lesbians, oppose non-Christians (and suspected non-Christians) who run for office, rail against euthanasia, and ban the teaching of evolution.
I was under the impression that there are many states where being an non-fundamentalist Christian would be very uncomfortable. Many of these same states insist that the United States is a Christian nation and there are dozens of political leaders who imply that non-Christians are not real Americans. A majority of citizens see nothing wrong with posting the ten commandments in courtrooms, schools, and legislatures. They don't see anything wrong with reciting the Lord's prayer in schools or putting "In God We Trust" on their money (beginning in 1957).
I seem to recall a recent incident where five representatives of the United States House of Representatives expressed points of view that could be interpreted as possibly anti-Muslim [Michele Bachmann finds plenty of friends back home].
These all seem like pretty intolerant viewpoints to me. Am I wrong?
Apparently, Martha C. Nussbaum is a smart woman. Apparently that's why she says,
As Nussbaum notes, the American and European developments differ in important ways. Above all, she writes, nothing in the United States “even remotely approaches the nationwide and regional bans on Islamic dress in Europe, or the nationwide Swiss minaret referendum” — let alone an anti-Islamic massacre.
I guess I'll have to read the book to see if this is what she really thinks. I hate it when that happens.
1. New Amsterdam, the Dutch colony, was noted for religious tolerance. The French colonies in Canada (somewhat tolerant) were on very good terms with many native tribes. The Narragansett Indians were eventually converted to Christianity but not until many of them had been killed or shipped off to slavery in the Caribbean.
I've been following the latest kerfluffle on the fusion of two chromosome into one during human evolution. I understand the superficial dispute involving Carl Zimmer. He had the audacity to ask for evidence to back up a claim being made by the IDiots on their Facebook page and they responded by going nuclear [The Mystery of the Missing Chromosomes, Continued: An Update From Your Preening Blogger].
Typical.
Let's step back a bit and ask why the IDiots are so upset. Carl Zimmer posted a really nice summary of the evidence that two smallish chimp chromosomes fused to produce human chromosome 2 [The Mystery of the Missing Chromosome]. That evidence is based on an analysis of the chimp, human, and gorilla genomes and it allows scientists to reconstruct the events that led up to the fusion. All of the DNA sequence around the fusion point are consistent with what we might expect, especially the presence of defective telomeres (sequences at the ends of chromosomes).
Why are the IDiots so bothered by this evidence? It's not as if it's new—the essential evidence has been around for decades. There must be something else going on that causes the IDiots to circle the wagons at this time.
It think it's all about their latest book Science & Human Origins by Ann Gauger, Douglas Axe, and Casey Luskin.1 The book is published by the Discovery Institute Press. In that book, two of the authors (Gauger and Luskin), apparently argue that science cannot rule out a recent origin of humans descended from Adam and Eve. The chromosome fusion data threatens that bizarre claim and perhaps that's why they are reacting so strongly.
I think I understand this. The IDiots have made bold claims about some of their recent books (e.g. Signature in the Cell: DNA and the Evidence for Intelligent Design , The Myth of Junk DNA) but those books have been met by yawning indifference from the general public and devastating criticism from real scientists. Two of the authors on this latest book (Gauger and Axe) have substantial scientific credentials so the Discovery Institute must have expected that the book would stand up to criticism by other scientists.
Instead, a "mere" graduate student (Paul McBride) has dimantled the book chapter by chapter [Science & Human Origins: Review] and a "mere" science writer, Carl Zimmer, has challenged the integrity of two "scientists" (and a lawyer). No wonder they're upset. All of their wonderful books are scientific embarrassments.
On what grounds do the IDiots want to deny the chromosomal evidence that humans and chimps share a common ancestor? Carl Zimmer supplies a partial answer when he quotes one of the chief IDiot defenders, David Klinhoffer, who says ...
The evidence from chromosomal fusion, for one, is strikingly ambiguous. In the Darwinian presentation, the fact that humans possess 23 chromosome pairs and great apes 24 clearly points to an event in which human chromosome 2 formed from a fusion, leaving in its wake the telltale sign of telomeric DNA — normally appearing as a protective cap at the end of the chromosome — in the middle where it doesn’t belong. Ergo, common descent.
But Casey [Luskin, of the Discovery Institute and co-author of the book] explains, there’s a lot wrong with this inference. Even if there was such an event and humans once had 24 chromosome pairs, it doesn’t at all follow that this happened in some prehuman past. Nothing stands in the way of picturing a human population bottleneck accomplishing the spread of a fused chromosome 2 from part of an early human community to all of it.
But the idea of such an event having occurred at all is itself far from sure. The telomeric DNA parked in the middle of chromosome 2 is not a unique phenomenon. Other mammals have it too, across their own genomes. Even if it were unique, there’s much less of it than you would expect from the amalgamation of two telomeres. Finally, it appears in a “degenerate,” “highly diverged” form that should not be the case if the joining happened in the recent past, circa 6 million years ago, as the Darwinian interpretation holds.
That's it? The fusion event could have happened relatively recently in human evolution so it's no big deal? And if you don't buy that, then maybe it didn't happen at all because the junction sequence isn't exactly what a typical IDiot might expect if evolution were true?
(Carl asked for the evidence that that the junction sequence isn't what one might expect and that's what caused the latest problem.)
That's why you see people like Cornelius Hunter desperately looking for another way out [Carl Zimmer Doubles Down on Chromosome Two Lies and Misdemeanors] and why the people at Uncommon Descent have picked up on a non-scientific way to defend Intelligent Design Creationism [Why no one can confute Darwinism and, consequently, no one should believe it].
My question for Intelligent Design Creationists is, "why all the fuss?" What is there about the figure at the top of the page that really upsets you? Aren't most of you supporters of common descent in some form or another? Are all of you really going to defend the idea that humans have no evolutionary history with the other apes?
1. I haven't read the book. It's on order but it still hasn't been released in Canada (see Amazon.ca).
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?
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.
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.
[Image Credit: Rosie Redfield]
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?].
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. 
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.
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.
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.
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)
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.)
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?
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?
