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?
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
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.
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
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.
Lots of people don't understand what we mean by a secular society. If you're one of them, watch this video by QualiaSoup. He uses a very good example—the saying of prayers at city council meetings.
Most of you have been to business and/or organization meetings of various sorts. You don't normally start those meetings with a Christian prayer in spite of the fact that you might be making some very big decisions. At the recent evolution conference in Ottawa, for example, there were five society meetings of boards of directors and (I'm told) not one of them began with a prayer!
People believe in many different gods. Evey person on the planet thinks that the vast majority are false gods that do not exist. Some of us think that applies to all gods. You have no right to promote the existence of some gods over others at public meetings in a secular society, especially a multicultural society like those that exist in most modern, industrialized nations.
Whether or not you believe in god(s), the only reasonable approach in a modern society is the secular one where religions is a private matter, not a public one.
A link to this video was sent to Katie Mahoney, city councillor for Ward 8 (my ward) in Mississauga, Ontario, Canada.
Hat Tip: Friendly Atheist
It was only a few months ago that lawyer Casey Luskin presented us with The Top Three Flaws in Evolutionary Theory. Now he's back with the top ten problems with Darwinian evolution. Here they are, read 'em and weep.
- Lack of a viable mechanism for producing high levels of complex and specified information.
- The failure of the fossil record to provide support for Darwinian evolution.
- The failure of molecular biology to provide evidence for a grand "tree of life."
- Natural selection is an extremely inefficient method of spreading traits in populations unless a trait has an extremely high selection coefficient.
- The problem that convergent evolution appears rampant -- at both the genetic and morphological levels, even though under Darwinian theory this is highly unlikely.
- The failure of chemistry to explain the origin of the genetic code.
- The failure of developmental biology to explain why vertebrate embryos diverge from the beginning of development.
- The failure of neo-Darwinian evolution to explain the biogeographical distribution of many species.
- A long history of inaccurate predictions inspired by neo-Darwinism regarding vestigial organs or so-called "junk" DNA.
- Humans show many behavioral and cognitive traits and abilities that offer no apparent survival advantage (e.g. music, art, religion, ability to ponder the nature of the universe).
I started to work on the top 1000 problems with Intelligent Design Creationism but then I realized that it was a waste of time. There are only two essential problems with Intelligent Design Creationism: (1) There's no evidence for supernatural design in nature, and (2) There's no evidence for a supernatural designer.
Many proteins bind to double-stranded DNA and most of them bind specifically to a particular target site. The lac repressor, for example, binds to a specific DNA site that blocks transcription of the genes required for lactose uptake and utilization. The lac repressor protein is a dimer of two identical subunits and each one binds a short segment with the core sequence ATTGT.1
If you look closely at the structure shown above, you can see how parts of the protein lie in the grove of double-stranded DNA where they can detect the sequence by "reading" the chemical groups on the edges of the base pairs. It's important to realize that DNA binding proteins interact with the DNA double helix and not with unwound DNA where the individual bases are exposed.
How does a DNA binding protein like lac repressor find its specific site in the genome? The most obvious explanation is that the protein binds non-specifically to any piece of DNA and checks to see if it's a specific binding site. If it is, the protein binds very tightly and doesn't fall off. If it isn't, the interaction is much weaker and the protein falls off quickly so it can check out another potential site.
The Faculty of Medicine at my university runs a Youth Summer Program (Medicine) for high school students. There are four one-week modules: Human Physiology, Molecular Biology & Genetics, Pharmacology & Toxicology, and Microbiology. The final module is two weeks of working in a research lab.
One of the modules that takes place in my building is the analysis of forensic evidence at a mock crime scene [The Science Behind CSI]. Here's the description from the website.
From stem cell research to criminal convictions, the science of molecular biology and genetics is at the centre of many of today’s most contentious issues. In this module, students learn about DNA fingerprinting, forensic investigations, and genetic transformation through a variety of hands-on laboratory activities and lectures from world-class speakers. Highlighting the program is the mock crime scene investigation where students collect and analyze crime scene evidence. After students have collected the appropriate evidence, they move into the laboratory to perform their analysis and, assuming they have collected the correct pieces of evidence, solve the case.
I can understand why students might find this appealing but there's a problem. One of my goals is to teach students, including high school students, about the wonder and excitement of science as a method of knowing. I would like students to appreciate the knowledge for it's own sake. I would like them to be excited when they learn how life operates at the molecular level (i.e molecular biology & genetics).
One of the major impediments to this goal is the widespread belief that science is just a tool and the main objective is not knowledge for its own sake but applications of science. According to this view, you only learn about molecular biology and genetics because it will somehow cure cancer, detect genetic diseases, and solve crimes.
I think it's wrong to reinforce this belief when we have a chance to educate a select group of high school students. I would much prefer to teach them about molecular evolution, how genes are expressed, and how we solve the structure of proteins.
This isn't going to happen in a program with such a heavy emphasis on medicine and medical applications but, in the long run, science will lose out when these bright students enter medical schools or forensic programs instead of pure science programs.
What's the appropriate balance between catching and holding the attention of students by having them solve a "crime" and trying to teach them the value of scientific discovery for its own sake?
Ms. Sandwalk sent me the link to this video. She knows that I love this sort of thing. It makes me happy.
Basic, fundamental research in Canada is in big trouble. The current government, led by Stephen Harper's Conservatives, have cut back on the funding of basic research while promoting applied research of various sorts. The consequences in academic departments have been nothing short of disastrous. In university biochemistry and molecular biology departments, for example, there are hundreds of mid-career scientists who have lost their grants and many of them will never get back funding for their basic science projects. This means that research technicians are being fired, graduate students and postdocs can't complete their projects, and PI's find themselves unable to do what they've been hired to do, with 15-20 years before retirement age.
The recent protest on Parliament Hill [Protest on Parliament Hill] highlighted some of these problems with science funding in Canada. That prompted a response from Gary Goodyear, Minister of State for Science and Technology (see below). Recall that Gary Goodyear is a chiropractor and a creationist [Gary Goodyear "Clarifies" His Stance on Evolution].
Here's the Harper Government's1 response to criticism that it has neglected basic research in favor of applied research.
The Harper government has made historic investments in science, technology and research to create jobs, grow our economy and improve the quality of life for Canadians.
Support for science and technology has been a fundamental priority of our government since 2006. This year, through Economic Action Plan 2012, we enhanced federal government support for leading-edge research.
As a world leader in post-secondary research with a highly skilled workforce, Canada has strong fundamentals for innovation. While several countries around the world are reducing funding in science and research, our government continues to invest in research, development and technology. In fact, Canadian higher-education research and development expenditures are higher than any other G7 country, as a percentage of GDP.
While the government is returning to a balanced budget, science, technology and innovation remain a strong priority with an added $1.1-billion investment over five years. University presidents, academic leaders and industry leaders have praised our government's leadership in recognizing the important role that research and innovation play in our economic prosperity.
Economic Action Plan 2012 funding allocated to science, technology and innovation includes:
- $12 million per year to make the Business-Led Networks of Centres of Excellence program permanent.
- $6.5 million over three years for a research project at McMaster University to evaluate team-based approaches to health care delivery.
- $17 million over two years to further advance the development of alternatives to existing isotope production technologies.
- $105 million over two years to support forestry innovation.
- $37 million annually starting in 2012-13 to the granting councils to enhance their support for industry-academic research partnerships.
- $60 million for Genome Canada to launch a new applied research competition in the area of human health and to sustain the Science and Technology Innovation Centres until 2014-15.
- $10 million over two years to the Canadian Institute for Advanced Research to link Canadians to global research networks.
- $500 million over five years, starting in 2014-15, to the Canada Foundation for Innovation to support advanced research infrastructure.
- $40 million over two years to support CANARIE's operation of Canada's ultra-high-speed research network.
Our government is investing in science and research that is leading to breakthroughs that are strengthening our economy and the quality of life of all Canadians. Our investments are enabling Canadian scientists in universities, colleges, businesses and other organizations to help secure Canada's prosperity today and into the future.
Does that sound like a government that understands the importance of basic research and knows the difference between research and "innovation"? He forgot to mention that these "increases" in spending are not on top of existing funding but often instead of support for fundamental research. That's why scientists all over the country are losing their grants unless they can find a way to make them sound applied or translational.
UPDATE: See how Denyse O'Leary manages to turn this into whining about Darwinists at Scientists, including evolutionary biologists, carry coffin through streets in Canada, to protest cuts to funding?.
1. Before Stephen Harper took over, it was common to refer to the "Government of Canada" in press releases. Now, it's always the "Harper Government."
Blogs have been around for more than a decade but it's still not clear what purpose they serve (if any). We still don't know how to distinguish a science blog from other types of blogs—perhaps it's foolish to try.
Bora Zivkovic of A blog Around the Clock has written a short history of science blogging [Science Blogs – definition, and a history]. It's well worth reading since Bora has been active for a long time and he's very well connected to the science blogging community.
Here's how he describes the category that applies to Sandwalk.
The earliest science bloggers were those who started out doing something else online – updating their websites frequently, or participating in Usenet groups – then moving their stuff to blogging software once it became available in the late 1990s and early 2000s.
As much of the early online activity focused on countering anti-science claims, e.g., the groups battling against Creationism on Usenet, it is not surprising that many of the early science bloggers came out of this fora and were hardly distinguishable in form, topics and style from political bloggers. They brought a degree of Usenet style into their blogs as well: combative and critical of various anti-science forces in the society.
In my case the usenet groups were talk.origins and sci.bio.evolution. Both of those groups are hosted on a server in my office; talk.origins is still very active but sci.bio.evolution isn't.
PZ Myers is the most famous talk.origins veteran. He's the one who convinced me to start a blog back in 2006 when I realized that blogs had many advantages over usenet, especially images. I don't know how many other talk.origins veterans have a blog. Can you help me out? Here's a partial list. (Some of these blogs are not science blogs.)
PZ Myers: Pharyngula
John Wilkins: Evolving Thoughts
Jeffrey Shallit: Recursivity
Jim Lippard: The Lippard Blog
various people: Panda's Thumb
John (catshark) Pieret: Thoughts in a Haystack
Troy Britain: Playing Chess with Pigeons
I know there are many more but I just can't remember them right now.
The other thing that Bora points out is that many science bloggers were connected to each other in different ways. Often we had met in person—this is certainly true of the talk.origins veterans. The early blogs were characterized by in jokes and incestuous cross links.
This has now disappeared as a whole new generation of science bloggers have entered the blogosphere, although there's still a certain amount of personal contact (see Evolution and Poutine and Beaver Tails.) I don't know if this is important or not. Blogger cliques can be a good thing and a bad thing.
Prime Minister Stephen Harper is destroying basic research in Canadian universities. His government is also shutting down government research facilities and muzzling government scientists. The current Canadian government is famous for ignoring science and evidence on many issues.
Several student organizations and scientists decided to take advantage of Evolution Ottawa 2012 to organize a protest based on the theme "No science, no evidence, no truth, no democracy." The protest took the form of a funeral for the death of evidence.
We gathered at the Conference Centre and marched across Confederation Square, up Wellington Street, and onto Parliament Hill.
Ryan Gregory and I had a good view from the steps of Parliament Hill.
There were about a dozen speakers who addressed the crowd. They included the President of the Canadian Society for Ecology and Evolution, Jeffrey Hutchings (left), Maude Barlow (centre), and Liberal MP Ted Hsu (right). (Ted Hsu has a Ph.D. in physics form Princeton University and he worked at Atomic Energy of Canada's Chalk River Laboratories (AECL) before becoming a member of parliament.
The crowd of 1100 was well-behaved. The police were bored. Everyone had a good time. I've never been to a protest that emphasized good science and support for evidence-based policy. That's the message that all the speakers supported.
Ryan Gregory has more pictures, and a video [Pro-science rally on Parliament Hill].
Ford Denison was there ... check out the photo at: Thousands protest suppression of science in Canada -- the "Death of Evidence" rally.
Rosie Redfield gave a talk on Sunday night. She described the work she did on the so-called "arsenic-incorporating" strain of bacteria that was made famous in a NASA press release and a subsequent Science paper last year [Arsenic and Bacteria] [Arsenic-associated bacteria (NASA's claims)] ["This Paper Should Not Have Been Published"].
You might recall that Rosie was among the first scientists to point out the flaws in the original paper and this led to a delay in its publication. When it finally was published there were several critical comments—including one from Rosie—that appeared in the same issue.
Rosie obtained the GFAJ-1 strain and tested its growth characteristics. She determined that it absoltutely required phosphate for growth and growth stopped when the phosphate in the medium was depleted. The strain did tolerate high levels of arsenic in but there was no evidence that it could replace phosphorus.
Rosie purified DNA from cells grown in the presence of arsenic and sent it to her collaborators. There was no arsenic in the DNA. (Carl Zimmer takes you through a blow-by-blow summary of Rosie's talk at Live-blogging Arsenic Life].)
The work was submitted to Science and the paper was accepted for publication It was due to be published on July 26th which meant that, under the conditions imposed by Science, Rosie wasn't allowed to talk about her work until then. Rosie informed Science that she intended to violate the embargo and describe her results at this meeting. Science responded by moving the publication date forward and posting the paper on their website at 8pm Sunday night [Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells]. Carl Zimmer was watching the website as Rosie spoke and at one point in her talk she turned to Carl to ask if the paper was up—it was.
The audience recognized that this was a major victory for open science. As the moderator put it at the end of her talk, you can mess with NASA, you can mess with Science, but don't mess with Rosie Redfield!
There are two papers being published in Science. The other one [GFAJ-1 Is an Arsenate-Resistant, Phosphate-Dependent Organism] says essentially the same thing as Rosie's paper.
The bottom line here is that the original paper by Wolfe-Simon et al. (2011) was deeply flawed and should never have been published by Science. More importantly, the latest results show that Felisa Wolfe-Simon was dead wrong when she claimed at the NASA press conference that GFAJ-1 incorporated arsenic into its DNA. You can watch her say this in the video I posted at: The Arsenic Affair: No Arsenic in DNA!.
You may be wondering how NASA and the authors of the original paper are handling this issue. In spite of the fact that they held a public press release and in spite of the fact that Felisa Wolfe-Simon was interviewed multiple time in the press and even gave a TED talk, they maintain that the only proper forum to discuss criticism of their paper is in the peer-reviewed literature! (I hate hypocrites.)
When Wolfe-Simon heard that Rosie's paper was in press she said [Arsenic-based life finding fails follow-up] ...
Wolfe-Simon, who says she can’t comment in detail until Redfield’s results appear in a peer-reviewed journal, wrote in an email that her original paper never actually claimed that arsenate was being incorporated in GFAJ-1’s DNA, but that others had jumped to that conclusion. “As far as we know, all the data in our paper still stand,” she wrote. “Yet, it may take some time to accurately establish where the [arsenic] ends up.”
She's right about the fact that the original paper never actually said that arsenic replaced phosphorus in DNA but it did strongly imply that this was the logical conclusion. However, in her press conference, Wolfe-Simon explicitly talked about arsenic replacing phosphorus in DNA and nobody who listened to that talk could have come away with any other impression. You didn't have to "jump to that conclusion" after hearing the presss conference.
So what are they saying today? Read Rosie's blog at: NASA's cowardly responses to their #arseniclife FAIL. And here's what Wolfe-Simon is saying, quoted at: New Studies Say No, Life Can't Live on Arsenic Alone.
These Science authors have made it clear that they are convinced they have tightly shut the door on arsenic incorporation into biomolecules. Yet, low amounts of arsenic incorporation may be challenging to find and unstable once cells are opened," she writes, "so may merit comprehensive and systematic efforts with other assays and conditions.
I don't think it's reasonable to expect Wolfe-Simon to apologize but I do think the scientific community should continue to apply pressure on NASA.
Here's a very good account of what happened and why NASA should be ashamed: Scientist in a Strange Land. It also expresses some sympathy for Felisa Wolfe-Simon.
Photo courtesy of Seanna Watson.
Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D. and Oremland, R.S. (2011) A bacterium that can grow by using arsenic instead of phosphorus. Science. 332:1163-1166. Published online 2 December 2010; published in Science magazine Jun 3, 2011 [doi: 10.1126/science.1197258]
Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D. and Oremland, R.S. (2011) Response to comments on "A bacterium that can grow by using arsenic instead of phosphorus". Science. 332:1149. [doi: 10.1126/science.1202098]
Tonight a bunch of us went for dinner at a pub in the Byward Market area of Ottawa just a short walk from the conference centre. Afterward we ate Beaver Tails.
There were fifteen of us. Four of Ryan Gregory's graduate students, three people I met at the evolution education session, Bjørn Østman, Ford Denison (This Week in Evolution), Carl Zimmer, Steve Watson, Seanna Watson, Ryan Gregory, and Joe Felsenstein.
Everyone liked Beaver Tails. I had chocolate and banana.
We talked about evolution, blogging, science writing, and Rosie Redfield ('cause she wasn't there!).
I'm at Evolution Ottawa 2012 and this afternoon I went to a session on New phylogenetic methods for quantitative trait variation.
I attended two talks.
Introduction and asymptotic behavior of trait evolution models under drift and stabilizing selection by Cecile Ane.
Placing fossils on molecular phylogenise with Brownian motion or Ornstein-Uhlenbeck models of continuous trait evolution by Joe Felsenstein.
It was interesting to be exposed to this kind of theoretical population genetics but I really didn't understand a single thing.
There were more than 200 people in the audience listening with rapt attention. They're a lot smarter than me. It was embarrassing.
There's one thing Joe said that I understood, and it was very impressive. He referred to a paper "published by me." Nowadays, almost everyone would say, incorrectly, "published by myself."
That's a photo of one of the speakers. Can you guess which one?
I attended a workshop on Communicating Science to Society at Evolution Ottawa 2012. The workshop was hosted by two science writers, Peter Calamai and Richard Webster and there were about one hundred people at the session.
The goal was ...
Whether you need to learn the basics or fine tune the dark art of science communication, this half day workshop is for you. Come for insider advice from a group of North America’s top science communicators. The session will open with evolutionary ecologist Tom Sherratt talking about his experience with the media and why he does it. The panellists will introduce an area of journalism and discuss their experiences with interviewing researchers. Then the panel discussion will expand on some of the challenges scientists face and the practical communication solutions. Finally a break-out session will allow for an interactive round table letting participants choose a topic of particular interest (how to give an interview, how to pitch a science book to a publisher, 101 for scientists using social media). The workshop will conclude with a networking session between fellow science communicators and the panellists. By the end, delegates can expect to have built a strategy as to how to effectively approach and handle different media opportunities (such as TV, radio, print & social media) and also leave with a handout of useful tips.
The panelists were ....
- Carl Zimmer (NYT columnist & author of A Planet of Viruses and many other best sellers)
- Penny Park ( Producer of CBC’s Quirks & Quarks and Discovery Channel’s The Daily Planet. Now Executive Director of the Science Media Centre of Canada)
- Elizabeth Howell Ottawa Business Journal, freelance science journalist and social media expert
- Tim Lougheed Freelance science journalist
I've been to half a dozen of these meetings at various conferences. The main theme is always the same. It consists of a bunch of science journalists telling scientists how we should help them (the journalists) make a living at science writing. We are told repeatedly that they have deadlines and editors and that they have to write about science in a way that appeals to the general public. We are told that if we want our research to be publicized then it has to to be cool and sexy and if it isn't then the science writers will help us "frame" it in a way that appeals to the public.
At this meeting, the emphasis was all about deadlines and writing about the latest papers from your labs. The science writers thought that we all wanted to get our latest hot results on the front pages of the newspapers. That's just not true. It's not what science is all about and it's not what we need in order to increase public awareness of science. (To his credit, Carl Zimmer seems to understand this better than other science journalists.)
What we need is not more splash about the latest Nature paper on the evolution of mimicry in insects. What we need is more articles on what evolution is and why it's so important. If science writers were really in the business of communicating science to the public then that's what they would be writing about. That, and topics like; what is DNA, how do genes work, what's in your genome, what causes speciation, why bacteria are important etc. etc.
The public needs to know the basics and they need to appreciate excitement of understanding what life is all about. They need Biology 101, not some senior level course that focuses on the latest research. That kind of science writing doesn't have to be done in a hurry before the embargo expires and it would be a much more useful way of communicating science to society.
Just once, I'd like to attend a meeting like this where the science journalists admit that they have been remarkably unsuccessful at educating the general public about science. Instead of telling us how to fit into the current failed system, I'd like them to ask us how they can change the way they write about science in order to advance science literacy.
I don't think that's ever going to happen. As a general rule, science writers seem to think that they are the experts on communicating science to the general public and all they need to do is teach us scientists how to work the system and tell people what they want to hear. It never occurs to them that the system is broken and that's why we have a scientifically illiterate society.
A bunch of us are attending Evolution Ottawa 2012. We set off to find the best poutine in the region and ended up at Jean Burger in Wakefield Quebec—about 30 minutes north of Ottawa.
Here's the group enjoying "French cuisine." From top left to right there's Bjørn Østman, Seanna Watson, Steve Watson, Ryan Gregory, Rosie Redfield, and Jerry Coyne.
Jerry really liked the poutine. Rosie ... not so much ... although she did say it wasn't as bad as she expected. For the record, it was the best poutine I've ever had so the trip was worth it.
Afterwards we drove into Wakefield and visited the bakery for dessert. I've been going to this bakery for 50 years—my favorite ski hill is nearby.
We talked about a lot of things, especially science, skepticism, and blogging.
