Skepticism and Atheism—Is there a Difference?

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

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

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Can Undergraduates Select Courses?

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

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

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

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

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

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

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

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

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

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

Extraordinary Claims

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

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

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

Darwinism and Junk DNA

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

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

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

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

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

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

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What Is Darwinism?

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

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

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

And amusing.

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Bad Faith Awards

 
From the New Humanist

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

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

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

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Human Mutation Rates

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

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

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

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

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

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

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

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

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

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

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

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

Happy Blogiversary Sandwalk!

 
Today is the 4th anniversary of Sandwalk. My first posting. Welcome to my Sandwalk, went up at 9:07 pm on Nov. 4, 2006. I didn't think I was going public when I created that posting but it contained a link to Pharyngula and PZ noticed. He mentioned it on his blog and that was the end of my attempt to experiment in private. Things have never been the same since then.

That first posting was followed by 3506 others and 28,465 comments from readers—most of whom disagreed with me!

Sandwalk pages have been viewed 3,255,306 times. There are about 3,500 visits per day from Monday to Friday and 2,500 on Saturdays and Sundays.

None of my top five most popular postings are science postings. That's kinda sad.

1. Dear Royal Ontario Museum ...


2. A Challenge to Theists and their Accommodationist Supporters


3. Who's the Grownup in the Science vs Religion Debate?


4. Arguing Against God


5. Sophisticated Religion

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Illinois Federation of Teachers: Resolution #11

The Illinois Federation of Teachers has passed Resolution #11: KEEP SUPERNATURALISM OUT OF THE SCIENCE CURRICULUM. It represents a certain point of view that I don't agree with so I'll make a few comments in order to provoke discussion.

WHEREAS, science is a systematic method for investigating natural phenomena through experimentation, observation and measurement leading to falsifiable explanations that are open to continuous testing; and ...

I think of science as a way of knowing ... everything. It is not limited to "natural phenomena" in the sense that's normally attributed to that phrase. The scientific way of knowing applies rational thinking, evidence, and skepticism to any problem we encounter and this includes history and English literature. Thus, by my definition, "experimentation" isn't a requirement and "measurement" is far too restrictive. I also don't accept "falsifiability" as an important criterion for science.

What the Illinois Federation of Teachers should have said was "There are many different definitions of science. We adopt the following definition, recognizing that many scientists and philosophers disagree."

Right from the start, the teachers have created a situation where they can keep religion out of the science class but not out of art, history, and geography classes.

WHEREAS, science proceeds on the basis of methodological naturalism and assumes observed phenomena of the universe are real, nature is consistent and understandable, and nature is explainable in terms of laws and theories; and ...

The teachers should have said the following, "Whereas many philosophers and scientists restrict science to the practice of methodological naturalism while others disagree, we adopt the methodological naturalism position for the purposes of this resolution."

Then they should have gone on to say, "We believe that nature can eventually be fully explained by laws and theories because so far there's no evidence to suggest otherwise."

WHEREAS, a scientific theory is consistent with evidence from multiple and independent sources of evidence, explains many different facts and allows predictions of subsequent discoveries; and

WHEREAS, the theory of evolution satisfies these criteria fully, is the foundation of biological science, is supported by a coherent body of integrated evidence from other disciplines in science and is consistent with theories from other scientific disciplines including anthropology, geology, physics, astronomy and chemistry; and ...

Evolution is much more than a theory [Evolution Is a Fact, Evolution Is a Fact and a Theory]. Most of what's taught in public school is not evolutionary theory but evolution fact and the history of life. It's a fact that humans and chimpanzees share a recent common ancestor, for example. It's a fact that natural selection leads to antibiotic resistance in bacteria.

We should not be referring to these fact as "the theory of evolution."

WHEREAS, there have been attempts in some states to include supernaturalism in the science curriculum as an alternative to scientific explanations of nature, particularly as an alternative to evolutionary theory; and

WHEREAS, arguments that invoke supernaturalism are grounded in religious or philosophical considerations outside the realm of science; and ...

I do not agree that supernaturalism is outside the realm of science. Supernatural explanations have been investigated by scientists and have been shown to be false or unnecessary. They are excluded from the classroom because they are bad science, not because they are "not science."

Statements like this imply that supernaturalism is a separate way of knowing. A supernatural explanation may even be correct but you can't teach it in science class because we say so. This is a very puzzling situation. What if there really is a God and He guides evolution? How would we be justified in keeping that from our children?

We need to teach critical thinking and this means addressing all claims—including the supernatural—to see if they are right or wrong.

WHEREAS, attempts to subvert the validity or teaching of evolutionary theory are also attacks on all scientific inquiry and, therefore, also attacks on the validity of using reason and experimentation to understand the universe; and ...

This is correct. Attacks on evolution are attacks on science. That's why we need to teach children why those attacks are unjustified and wrong. Ignoring them or banning them from the classroom won't demonstrate why they subvert the validity of science.

WHEREAS, legislation that conflates supernaturalism, or limits, or prohibits the teaching of any scientific theory negatively impacts our ability to make informed decisions; and

WHEREAS, it is the responsibility of the Illinois Federation of Teachers to preserve the integrity of science in the classroom; therefore be it

resolved, that the Illinois Federation of Teachers affirm, through a positional statement on its website, the validity of science as a methodology for understanding the nature of the universe, and affirm the validity and foundational importance of organic evolution to science as a whole and biology, specifically; and be it further

RESOLVED, that the IFT affirm, through a positional statement on its website, that supernaturalism is not a scientific endeavor and, therefore, is inappropriate for inclusion in the science curriculum; and be it further

RESOLVED, that this resolution does not make it the official position of the IFT that there is no God and should not be interpreted as a statement either for or against religion or belief in God; and be it further

RESOLVED, that the IFT call upon its members to assist those engaged in overseeing science education policy to understand the nature of science, the content of contemporary evolutionary theory and the inappropriateness of including non-science subjects (e.g., intelligent design and creationism) in our science curriculum; and be it further

RESOLVED, that the IFT communicate to the local, regional and national public media, to educational authorities and to appropriate legislators its opposition to the inclusion of non-science approaches and subjects (e.g., creationism and intelligent design) into the science education curricula of our public school system; and be it finally

RESOLVED, that the IFT members also promote these concerns and help resolve these issues in their home communities among educators, parents, school boards and students in appropriate public forums.

I hope that Illinois teachers are going to make a strong effort to teach evolution and critical thinking in their classrooms in spite of any opposition they may encounter from local schools boards and parents.

This is one of 27 resolutions that they passed.

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[Hat Tip: Panda's Thumb]

Atheist Don't Have No Songs

 

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[Hat Tip: Canadian Atheist]

Guns and the Moral Law

 
From MSNBC and Associated Press: Police: Teen shot dead after Halloween prank.

ATLANTA — Authorities say a driver enraged after his Mercedes was splattered with eggs on Halloween fatally shot a 17-year-old in the neck and leg as the teen tried to run away.

Atlanta police spokeswoman Kim Jones says the driver confronted the teen and fired 10 shots at him around 8 p.m. Sunday. The Fulton County Medical Examiner's office says the teen, Tivarus King, died as he was being taken to Grady Memorial Hospital.

Just keep repeating to yourself, "Guns aren't the problem, criminals are the problem."

The real problem is that if you give a gun to a Mercedes owner in Atlanta he can soon become a criminal. (Ten Shots!)

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[Hat Tip: Greg Laden]

Carnival of Evolution #29

 
The latest Carnival of Evolution is up on Byte Size Biology [Carnival of Evolution #29].

Check it out ... there's lots of good stuff from all the best biology bloggers.

Sandwalk readers might be interested in the post by Hannah Waters. She not only defends the "Three Domain Hypothesis" but goes one step further by merging eukaryotes and archaebacteria into a single domain making the "Two Domain Hypothesis"!

Of course we all know that she's wrong but her posting is still worth reading.

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Penn Jillette Defines Respect

 
Here's an excerpt from an article in Saturday's Toronto Star [Penn Jillette and the gospel of disbelief ]. I agree with Penn Jillette about the meaning of "respect." This point about respect and confrontation comes up in a discussion on John Wilkins' blog [Tone Wars]. Penn may be impressed by how many people get it but I'm more impressed by how many people don't.

If you know Penn & Teller — the famed magicians, humourists and debunkers, stars of the cable series Bullshit! — you know, broadly speaking, what to expect from their long-running show in Las Vegas and their appearance Wednesday at Massey Hall. If not, you might be surprised by Penn Jillette: first of all by how positively evangelical a man can be about atheism, and secondly by how happy he is to clash with genuinely who fervently disagree.

“We get a lot of people coming up to us after shows and saying ‘I’m a Christian but I really enjoy your passion,’ ” Jillette, 55, says on the phone from Sin City, where Penn & Teller’s show has been running at the Rio Hotel for nine years.

“There’s a big difference between tolerance and respect. Tolerance is you saying something crazy and me smiling and saying ‘that’s nice.’ Respect is when you say something crazy and I say ‘you’re out of your f---ing mind.’ Direct confrontation, direct conversation is real respect. And it’s amazing how many people get that.”

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[Hat Tip: Canadian Atheist]

Saturday Morning Cartoons

 
This one is from Pharyngula. PZ Myers thinks this guy is nuts. I think he's just trying to be funny.

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God Plays Bridge

 
The creationists tell us that anything in biology with a probability of 10^-39 or less is impossible [see God Designed My Great-Grandparents].

That's a very tiny number. Let's see just what kind of probabilities we're dealing with.

Imagine four people sitting down to play a hand of bridge. They shuffle the deck and deal out 13 cards to each player. The probability that the particular hand would be dealt is very low because the total number of possible hands is 51!/13! = 53,644,737,765,488,792,839,237,440,000. Let's round this off to a probability of 0.2 × 10^-28.

Assuming that there have been at least 100,000,000 bridge players and that they've played at least 2000 hands of bridge, that represents a total of 5 × 10¹⁰ separate hands of bridge. The probability that all of these particular hands would have been dealt in a particular time and place is 10^-39. That's equivalent to the total number of bacteria and it's the kind of probability that makes creationists think of God.

I wonder if God plays bridge? If he does, I wonder if he ever loses since he can control the deal?¹

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1. Sounds like a good plot for a Mr. Deity video.