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Tuesday, December 14, 2010

Iconic Delusions

I don't have much time for blogging these days 'cause I'm in the middle of writing a textbook—trying to be as accurate as possible.

Watch Paul Nelson making comments about the authors of biology textbooks. He sounds very sincere. I think he actually believes that biology textbook authors are deliberately lying. Poor deluded Paul Nelson. That's why we call them IDiots.

Friday, December 10, 2010

A Test for True Christians

Denyse O'Leary doesn't think Theodosius Dobzhansky was a true Christian. She's angry at all those so-called "Christians" who accept evolution because, in her mind, science and Christianity are incompatible [If you are a Darwinist, can you be a Christian if people just say so ... ?].

What do you do about all those fake Christians who believe in theistic evolution? You develop a litmus test, of course.
... if you ask me whether someone is a Christian, I say, "Let him recite the Apostle's Creed and affirm that he believes it and renounces contrary doctrines."
Sounds like a plan. I'll quote the English Language Liturgical Consultation (ELLC) version of the Apostle's Creed and we can discuss whether believing it is compatible with science as a way of knowing. Doesn't look like it to me. Denyse is right!
I believe in God, the Father almighty,
   creator of heaven and earth.
I believe in Jesus Christ, God's only Son, our Lord,
   who was conceived by the Holy Spirit,
   born of the Virgin Mary,
   suffered under Pontius Pilate,
   was crucified, died, and was buried;
   he descended into hell.
   On the third day he rose again;
   he ascended into heaven,
   he is seated at the right hand of the Father,
   and he will come to judge the living and the dead.
I believe in the Holy Spirit,
   the holy catholic Church,
   the communion of saints,
   the forgiveness of sins,
   the resurrection of the body,
   and the life everlasting. Amen.

Thursday, December 09, 2010

Sign a Petition on CIHR Funding

Are you a Canadian researcher who cares about the dismal CIHR funding situation?

Sign the petition at: The CIHR Individual Grants Program. It may not do much good but at least you'll have 700+ friends (latest count).

Wednesday, December 08, 2010

The Cause of Speciation

Jerry Coyne is an expert on speciation. That's why it's always informative to read his latest thoughts on the problem. In spite of what many people might believe, the main cause of reproductive isolation—the actual speciation event according to the biological species concept—is due to accident, not adaptation. It's just one more example of the importance of random genetic drift in evolution.

Here's how Coyne puts it in his latest posting [“Reinforcement” and the origin of species].
Genetic barriers aren’t thought to arise for the purpose of keeping species distinct. Rather, they are usually thought to be evolutionary accidents: geographically isolated populations diverge genetically under natural selection or other evolutionary forces like genetic drift, and that divergence leads to the evolution of genetic barriers (mate discrimination, the sterility of hybrids, ecological differences, etc.) as byproducts of evolutionary change. For example, populations could adapt to different environments (one dry, one wet, for example), leading to them becoming genetically different. When these populations meet each other again, this genetic divergence could result in hybrids that don’t develop properly because the parental genomes are sufficiently diverged that they can’t cooperate in building a single individual.
I wish more people would assimilate this message. It seems to be the overwhelming consensus among the experts in speciation but the average scientist still has an adaptationist view of speciation (and of evolution in general).

Speaking of adaptationists, Coyne also likes the idea that some examples of reproductive isolation can be reinforced by natural selection. You can read about those cases on his blog.

Let Oprah know that Kim Tinkham died of cancer

Kim Tinkham died of cancer today. Orac wants you to Let Oprah know that Kim Tinkham died of cancer. I've already sent my message to Oprah. Why don't you send one?

Watch the video. Oprah sends very mixed messages. On the one hand she advises following the advice of doctors but at the same time she supports The Secret.

DNA, Phosphorus, and Arsenic

Most of you know that DNA strands have a sugar-phosphate background. The bases in each strand are covalently linked to each other by phosphodiester linkages between the 5′ and 3′ carbon atoms of the deoxyribose sugar.

Recently there has been a claim by NASA-funded scientists that a certain bacterium can replace those phosphates with arsenic. Close examination of the Science paper has revealed that, at most, a few percent of the phosphorus atoms are replaced and even that amount is challenged. It has become abundantly clear from reading the paper that the bacteria absolutely required phosphorus and sufficient quantities were present in the media as contaminants.

I've already linked to Rosie Redfield's critiques of the paper and the press conference. Now I want to add Carl Zimmer's take on the whole affair—the title tells all: "This Paper Should Not Have Been Published".

Carl raises an issue that has cropped up in many of the comments sections of various blogs. Is criticizing a scientific paper appropriate outside of the peer-reviewed scientific literature? Is it ethical to cast doubt on the integrity of scientists when questioning the quality of their science?

Felisa Wolfe-Simon1 is the lead author of the study and she was the main spokesperson in the video below. Carl Zimmer asked her if she wanted to respond to the criticism of her paper and here's what she said, according to the Slate article,
"Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated," wrote Felisa Wolfe-Simon of the NASA Astrobiology Institute. "The items you are presenting do not represent the proper way to engage in a scientific discourse and we will not respond in this manner."
Carl asked some other scientists about this and the best quote comes from Jonathan Eisen,
But Jonathan Eisen of UC-Davis doesn't let the scientists off so easily. "If they say they will not address the responses except in journals, that is absurd," he said. "They carried out science by press release and press conference. Whether they were right or not in their claims, they are now hypocritical if they say that the only response should be in the scientific literature."
My own impression of this fiasco is that the scientific authors of the paper can be accused of bad science and the lead author, Felisa Wolfe-Simon, is guilty of grossly misrepresenting her work at the press conference. There really can't be any excuse for that behavior if you want to call yourself a scientist. Those who think this is impolite and unethical are dead wrong. It's an absolute requirement of good science that we point out to the general public when scientists are behaving badly, otherwise we lose all credibility.

As you watch this video keep in mind that the bacteria absolutely require phosphate in the media in order to grow and that only a few phosphorus atoms, at most, are replaced by arsenic in DNA. If you think that's what Felisa Wolfe-Simon is telling you then you need to work hard on your listening comprehension skills.

1. The name of the bacterial strain is GFAJ-1. Rumor has it that this stands for "Get Felissa a Job." I wonder how that's working out? Do you think the job offers are pouring in?

John Lennon (1940 - 1980)

John Lennon died on Dec. 8, 1980 when he was shot four times in the back by Mark David Chapman. His ashes were scattered by Yoko Ono in Central Park in New York at the site of the Strawberry Fields Memorial.

That was thirty years ago today. A whole new generation has grown up since then and I fear we are in great danger of forgetting what Lennon and The Beatles did to help change our culture for the better.

Monday, December 06, 2010

The Value of Blogs

Many people have questioned the significance of blogs and bloggers. Some think that science blogs have no useful purpose and that they are undermining the peer review process of publication in scientific journals. Science journalists resent the fact that amateur writers can throw up something on a blog and claim that it's contributing to science education.

Over the years I've come to appreciate that science blogs do at least one thing that's new—they provide instant commentary on science news and that helps to serve as authoritative fact-checking. Science blogs monitor science journalism in the same way that political blogs monitor FOX news and the New York Times.

This role has been illustrated in spades over the past few days as we monitor the response to the NASA hype over bacteria that grow in the presence of arsenic. The weaknesses of the Science paper are now well-known thanks to many science bloggers. In the past, this kind of analysis would have had to wait for the publication of an appropriate critique in a scientific journal and that was very unlikely to happen for a number of very good reasons. Thus, in the past shoddy, over-hyped work got a free pass and science journalists who fell for the hype never even realized that they had been duped.

Read David Dobbs on Wired for a thoughtful analysis of the episode and the lesson we need to learn [Is That Arsenic-Loving Bug — Formerly an Alien — a Dog?]. It's interesting that even Nature News got sucked into promoting the hype. This shows that even journalists at the premier science journals are not very skeptical.

Sunday, December 05, 2010

Arsenic and Bacteria

The blogosphere is not happy with the recent announcement by NASA of bacteria that are able to "thrive and reproduce using the toxic chemical arsenic." [NASA-Funded Research Discovers Life Built With Toxic Chemical]
This finding of an alternative biochemistry makeup will alter biology textbooks and expand the scope of the search for life beyond Earth. The research is published in this week's edition of Science Express.
I read the paper (Wolfe-Simon et al., 2010) and I can assure you that nothing in that paper is going into my biochemistry textbook. I predict that a year from now we'll have forgotten about this discovery. I'm not even sure it's going to be confirmed but, if it is, the result is pretty trivial.

For a start, even the title of the paper is misleading. The title says "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus" but all of the data show that there was phosphorus in the media and that the bacteria used it for growth and reproduction. This selected strain of bacteria incorporated more arsenic than non-selected species but it by no means did it replace all phosphate with arsenic. Only a few percent (at most) of the phosphorus atoms in DNA, for example, were replaced by arsenic.

The purpose of this posting it to alert you to a fantastic article by microbiologist Rosie Redfield at the University of British Columbia. I strongly urge that everyone read her take-down of the science paper [Arsenic-associated bacteria (NASA's claims)]. The problem is not just that a bad paper was published in Science—it's that the paper was so heavily promoted in the media. We've got to do better when it comes to educating the general public about science.

Wolfe-Simon, F., Blum, J.S., 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. (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science Published Online 2 December 2010 [DOI: 10.1126/science.1197258]

Saturday, December 04, 2010

Carnival of Evolution #30


The 30th version of Carnival of Evolution has been posted on The Scientific Life (Bob O'Hara).

The Death of the Sniper Scientist


I've just discovered a new blog called Canadian Girl Postdoc in America. Check it out.

You can start by recommending your favorite science book [The One] but be sure to read the wonderful series on Slow Science: The Death of the Sniper Scientist.

The author is interested in evolution and population genetics and she has been blogging for three years! I think she likes plants.

Wednesday, December 01, 2010

Students vs Icons of Evolution

I teach in a second year course on "Scientific Misconceptions and Controversies." In my part of the course we discuss creationism and evolution. The object is to learn to think rationally about the controversy.

Students have to read Icons of Evolution and write an essay analyzing the arguments in one of the chapters (their choice). They have no problem recognizing the flaws in the logic and the outright mistruths in that book. For typical university students with a rudimentary understanding of evolution it's like shooting fish in a barrel.

The Discovery Institute sees it differently but they must live on another planet.

Here's how David Klinghoffer describes Jonathan Wells in a recent posting on Evolution News & Views [Celebrating Ten Years of Icons of Evolution].
A Berkeley PhD in molecular and cell biology, Wells is among the most lucid and accessible scientist-writers devoted to the modern project of critiquing Darwin. When I say the book is sweetly reasoned, I don't only mean that it's well reasoned but that there's an appealing geniality, a sweetness, to the man's writing that stands out in contrast to the donkey-like braying of a Darwinian biologist Jerry Coyne, the sinister coilings of a Richard Dawkins, the ugly "humor" of a P.Z. Myers. Yes, you can get a sense of a person's character, and perhaps too his credibility, from the words he uses.
And here's an example of "sweet geniality" from page 234 of Icons.
What about scientists who knowingly make false utterances or misleading omissions but believe the overall effect is not misleading because they are teaching "a deeper truth"? Does the commitment to a supposed deeper truth excuse conscious misrepresentations? Such an excuse probably wouldn't help a stock promoter. Under federal law, a stock promoter is not justified in mistating the facts just because he or she deeply believes that a company is destined to prosper. The stock promoter commits fraud by misrepresenting the truth, regardless of his or her underlying beliefs. Shouldn't scientists be held to the same standard?

Fraud is a dirty word, and it should not be used lightly. In the cases described in this book, dogmatic promoters of Darwinism did not see themselves as deceivers. Yet they seriously distorted the evidence—often knowingly. If this is fraud when a stock promoter does it, what is it when a scientist does it?


If dogmatic promoters of Darwinian evolution were merely distorting the truth, that would be bad enough. But they haven't stopped there. They now dominate the biological sciences in the English-speaking world, and they use their position of dominance to censor dissenting viewpoints.

Sunday, November 28, 2010

The Hitchens-Blair Debate: It's Was a Tie!


I thought Hitchens did a much better job that Tony Blair but it's hard to be unbiased. Here are the results of the poll before and after the debate.

On the question "Is Religion a Force for Good?"

Before the debate ...

Yes (Blair): 22%
No (Hitchens): 57%
Undecided: 21%

After the debate

Yes (Blair): 32%
No (Hitchens): 68%

Both speakers increased their numbers by about 10%. In simplistic terms, the undecided members of the audience split 50:50 on the question.

That's a tie by my calculation. The blogosphere is reporting this as a huge victory for Hitchens but it didn't seem that way in Massey Hall in Toronto. Just because Hitchens started out with 57% of the votes doesn't mean he won the debate. (Although I think he did.)

Don't Mess with Rob Day

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

Friday, November 26, 2010

Was Darwin Wrong?

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

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

Thursday, November 25, 2010

Christopher Hitchens vs. Tony Blair

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

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

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

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

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

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

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

$3 Beer!

How to Protect Yourself from WiFi Radiation

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

Rock Stars of Science

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

Is this a good way to promote science? Martin Robbins doesn't think so: 'Rockstars of Science' should be 'Scientists of Rock'.
I could be wrong. Maybe this is a good way of reaching out to people. Maybe GQ's readers are getting out their dictionaries and picking through those descriptions, stopping occasionally to stare at the blurry, bearded interloper in the background of Bob's photograph. And maybe those readers are now more inspired by science as a result. If so, I'd like to see some evidence of it - maybe a poll of readers?

But I still can't help but feel that if you have to resort to rockstars make science cool, you're really not very good at communicating science. Because science is way cooler than rock stars.
You won't be surprised to learn that Chris Mooney likes this campaign and ERV doesn't. Jerry Coyne doesn't like it either. Does anyone notice a pattern here? ... The one person who isn't a scientist is the one who thinks he knows how to promote science.

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

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

Don't Mess with Skepchick!

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

Yesterday Age of Autism and SafeMinds released the following statement as reported in the latest posting on Skepchick [Good guys win!]. Congratulations Skepchick!
SafeMinds was notified late yesterday afternoon that AMC Theaters has decided to block the SafeMinds Public Service Announcement (PSA) on influenza vaccines with mercury. The PSA alerts parents and pregnant women of the presence of mercury in most influenza vaccines and the ample availability of mercury-free alternatives. The CDC has declined to give a preference for the mercury-free versions, so it is important that the public is aware of its options. AMC’s advertising representative had reviewed and approved the PSA to run in AMC cinemas over the Thanksgiving weekend. A small group of vocal vaccine proponents dismissive of mercury concerns learned of the PSA and bombarded the AMC website, leading to the company’s decision to prevent its release. SafeMinds thanks its supporters who viewed the PSA and contributed to its efforts to educate the public to avoid unnecessary mercury exposure. Mercury in all forms is dangerous, especially to the developing fetus and infants, as referenced on the PSA website SafeMinds will continue its mission to educate the public on this important healthcare topic.
BTW, the ad was NOT a public service announcement by any stretch of the imagination.

Tuesday, November 23, 2010

Nobel Laureates Become Pseudoscientists

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

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

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

Sunday, November 21, 2010

Age of Autism Opposes Flu Shots

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

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

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

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

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.

Saturday, November 20, 2010

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

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.

Friday, November 19, 2010

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!

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

Friday, November 12, 2010

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.

Thursday, November 11, 2010

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.

Thursday, November 04, 2010

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

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.

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

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

Tuesday, November 02, 2010

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.

[Hat Tip: Panda's Thumb]

Atheist Don't Have No Songs


[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!)

[Hat Tip: Greg Laden]

Monday, November 01, 2010

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.

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.”

[Hat Tip: Canadian Atheist]

Thursday, October 28, 2010

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

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

God Designed My Great-Grandparents

On the thread Impossible Molecular Machines we are being treated to a lesson in probabilities from several creationists. Here's an example of a comment from Livingstone Morford.
By Darwinism I mean the notion that everything we observe in the biological world are purely the result of stochastic processes, and I am critical of that notion.

On a different topic, I might add that intelligent design proponents need only demonstrate that the odds of a particular biochemical system evolving are 10^-40 or less in order for intelligent design to be a more adequate explanation for the origin of such a biochemical system. This is because there have been no more than 10^39 bacterial cells in the history of life on earth.
Speaking of stochastic processes, the average number of sperm contributed by a man in a mating process is 100,000,000 (108). That means that every single human is the product of a single sperm cell uniting with a single egg cell and the probability that one particular sperm was successful is 10-8.

This probability of existence applies to each of my great-grandparents.

Johann Betker was born in 1859 in Volhynia in the western part of Ukraine. The probability that he was produced from a particular sperm cell is 10-8. His future wife, Amalie Schmuland, was born in 1868, also in Volynia. This was also an improbable event from the point of view of sperm selection. The probability that BOTH of my grandparents were born is (at least): 10-8 × 10-8 = 10-16.

The same probabilities apply to Thomas Keys Foster born 1852 in country Tyrone, Ireland and his wife Eliza Ann Job born 1852 in country Tyrone. Their two births were very lucky with a total probability of only 10-16. Now, if you combine all four of these great-grandparents you end up with a probability of 10-32. Add in the other four great-grandparents and you end up with the total probability that all eight of these individuals would be born = 10-64. (The real probabilities are much, much lower when you take the eggs into account.)

Since this total probability is a lot less than the total number of bacteria that have ever existed, it follows that God must have intervened somewhere. Two of my great-grandparents must have been designed by God. I wonder which two it was? My bet is that it wasn't any of the four mentioned above because they were all born outside of Canada. It was probably the two grand-parents who were born in Canada 'cause God likes Canadians.

Tuesday, October 26, 2010

Michael Egnor Answers the Questions

I treid to answer Michael Egnor's questions as best I could [A Quiz for Atheists from a Creationist]. Now Egnor has answered his own questions at: What I Really Believe.1

Some Sandwalk readers will be delighted to discover that Egnor refers to Aristotle in support of his beliefs, proving that Aristotle is good for something!

Most Sandwalk readers will be interested in this ...
That's what I believe. Note that these beliefs are entirely compatible with modern science; in fact, classical philosophy and classical theism is the source for modern science, which only originated in civilizations that embraced this classical view of the world. Some enlightenment philosophers moved away from some aspects of classical philosophy (e.g. final causes), but classical philosopohy and classical theism remain the foundation of Western Civilization and of modern science.
Many of you are modern scientists. How many think that classical theism is important in your work? How about classical philosophy?

Really? No one thinks that? Where do the IDiots come up with these ideas?

More and more scientists, philosophers, and theists are recognizing that science and theism are incompatible. That sort of makes it hard to claim that classical theism remains the foundation of modern science, doesn't it?

1. Comments aren't allowed on Evolution News & Views so you can leave comments for Michael here.

Jesus and Mo Read Sandwalk

Jesus and Mo

HuffPost Heatlh?

I don't read the Huffington Post but Orac over at Respectful Insolence does. He notes that it is about to start a new section called HuffPost Health. Here's how it's going to work.
HuffPost Health will be a clear and balanced resource to provide a comprehensive view of the state of health and health news in a given day. It will provide a forum for intelligent discourse and divergent but respectful points of view. HuffPost Health will empower you with state of the art information you can use to make informed and intelligent decisions that affect your life in meaningful ways.

In this spirit, HuffPost Health's articles and videos will include the best of evidence-based allopathic Western medicine (including drugs and surgery), lifestyle and functional medicine (including nutrition, fitness, stress management, supplements, and love and support), mind/body medicine (including mental and emotional health), women's and men's health issues, and integrative medicine (including complementary and alternative medicine).
I bet you can hardly wait! Neither can Orac 'cause "there'll be a lot of new blogging material." More importantly, Orac notes that HuffPost Health might soon become a handy source of all quackery: HuffPost Health: A soon-to-be one-stop shop for quackery. We're going to need something like this once the Oprah Show and Larry King Live go off the air.

Taste Receptors on Your Lung Cells

The cells of your lungs express the same bitter taste receptor that is presence in the cells of your tongue (Deshpande et al., 2010). What's the reason for having these receptors in your lungs.

PZ Myers explains the concept of evolution by accident: Lungs with taste, or lungs with a fortuitous receptor?.

This is a very important concept and I'm delighted that PZ is promoting it. Adaptationists will not be happy. For more on this idea see: Evolution by Accident.

For more information about taste receptors see: Theme: A Sense of Smell/

Deshpande, D.A., Wang, W.C.H., McIlmoyle, E.L., Robinett, K.S., Schillinger, R.M., An, S,S,, Sham, J.S.K., Liggett, S.B. (2010) Bitter taste receptors on airway smooth muscle bronchodilate by localized calcium signaling and reverse obstruction. Nature Medicine. Published online October 24, 2010. [PubMed] [doi:10.1038/nm.2237]

Friday, October 22, 2010

"Impossible" Molecular Machines

Someone named vjtorley just posted a list of things that would falsify his faith in Intelligent Design Creationism [The 10^(-120) challenge, or: The fairies at the bottom of the garden].

Normally this wouldn't be very interesting because the IDiots almost always set up impossible criteria reflecting their fundamental misunderstanding of evolution. This posting is no exception but I was intrigued by one of the items on the list.
2. An empirical or mathematical demonstration that the probability of the emergence of any of the irreducibly complex structures listed on this page, as a result of non-foresighted processes (“random mutations plus natural selection”) is greater than 10^(-120).
The link under "this page" is to an article by Casey Luskin from last June [Molecular Machines in the Cell]. He lists a whole bunch of molecular machines and claims that these structures pose a real problem for science.

Here's the list. Judge for yourselves whether they make you believe in God.
Molecular machines are highly complex and in many cases we are just beginning to understand their inner workings. As a result, while we know that many complex molecular machines exist, to date only a few have been studied sufficiently by biologists so that they have directly tested for irreducible complexity through genetic knockout experiments or mutational sensitivity tests. What follows is a non-exhaustive list briefly describing 40 molecular machines identified in the scientific literature. The first section will cover molecular machines that scientists have argued show irreducible complexity. The second section will discuss molecular machines that may be irreducibly complex, but have not been studied in enough detail yet by biochemists to make a conclusive argument.

I Molecular Machines that Scientists Have Argued Show Irreducible Complexity

1. Bacterial Flagellum
2. Eukaryotic Cilium
3. Aminoacyl-tRNA Synthetases (aaRS)
4. Blood clotting cascade
5. Ribosome
6. Antibodies and the Adaptive Immune System

II. Additional Molecular Machines

7. Spliceosome
8. F0F1 ATP Synthase
9. Bacteriorhdopsin
10. Myosin
11. Kinesin Motor
12. Tim/Tom Systems
13. Calcium Pump
14. Cytochrome C Oxidase
15. Proteosome
16. Cohesin
17. Condensin
18. ClpX
19. Immunological Synapse
20. Glideosome
21. Kex2
22. Hsp70
23. Hsp60
24. Protein Kinase C
25. SecYEG PreProtein Translocation Channel
26. Hemoglobin
27. T4 DNA Packaging Motor
28. Smc5/Smc6
29. Cytplasmic Dynein
30. Mitotic Spindle Machine
31. DNA Polymerase
32. RNA Polymerase
33. Kinetochore
34. MRX Complex
35. Apoptosome / Caspase
36. Type III Secretory System
37. Type II Secretion Apparatus
38. Helicase/Topoisomerase Machine
39. RNA degradasome
40. Photosynthetic system

BioLogos vs Discovery Institute—CANCELLED

With breathless anticipation I awaited the showdown between BioLogos and the Discovery Institute at the upcoming conference in Texas this weekend. Here's the teaser from the Disco website [Showdown in Austin].
Next week the Vibrant Dance of Faith and Science becomes the God and evolution showdown in Austin, as the question of whether faith in God can co-exist with Darwinian evolution will be discussed and debated with people of faith on all different points of the spectrum. CSC Director Stephen Meyer will be presenting, as will CSC fellows Bill Dembski, Doug Axe, Richard Sternberg, Paul Nelson, Jack Collins, Walter Bradley, Bruce Gordon, and Ray Bohlin.
Imagine, all those people of faith from the Discovery Institute arguing that God and evolution are incompatible. And all those theistic evolutionists from BioLogos arguing that science and religion are perfectly compatible. The mind boggles.

Unfortunately, the great debate has been cancelled at the last minute. I guess Francis Collins was too busy to attend. Maybe they should have invited me to take on the Intelligent Design Creationists and the other creationists who call themselves Theistic Evolutionists?1

1. They would need reinforcements in order to make it a fair fight.

Leibnizian Cosmological Arguments

An atheist reader send me this argument for the existence of God: Leibnizian Cosmological Arguments. It's from Alexander R. Pruss of Baylor University in Texas, USA.

Here's the guts of the argument ...
The basic Leibnizian argument has the following steps:
(1) Every contingent fact has an explanation.
(2) There is a contingent fact that includes all other contingent facts.
(3) Therefore, there is an explanation of this fact.
(4) This explanation must involve a necessary being.
(5) This necessary being is God.
My first reaction whenever I see arguments like this is to look for evidence that supports the claim.1 I'm not very interested in arguments that hinge on the definition of words and on things that may or may not be real. What is the actual evidence that this God really exists?

What is a "contingent fact" and why should I believe that every one of them has an explanation? The article by Alexander R. Pruss tries to convince me that this belief is related to something called the Principle of Sufficient Reason (PSR) and that it is self-evident. If it's not self-evident to me, then the author tries to show that my worldview is inconsistent—in fact, I can't even believe in evolution unless I accept the Principle of Sufficient Reason and hence, that every contingent fact has an explanation! Who knew?

To me, this just seems like silly sophistry.

Similarly, I don't see any reason to believe that there is a contingent fact (whatever that is) that contains all other contingent facts. What's the point?

Even if I'm willing to consider steps 1,2, and 3 why should I conclude that something called a "necessary being" is part of the explanation?

The god of the cosmological argument is an imaginary god who exists only in the minds of philosophers. There is no connection between that imaginary "necessary being" and a god who actually does anything. If someone wants to believe in the cosmological "necessary being" then that's fine with me as long as they don't try to attribute anything else to that "necessary being" other than satisfying some unprovable premises about contingent facts.

I don't see any reason why I should believe in this "necessary being." More importantly, I don't see how I could possibly distinguish between people who believe in the cosmological "necessary being" and those who don't, if that's the only difference between them. But let's not kid ourselves. There aren't any living theists who just stop when they get to point #5.

The cosmological arguments are just rhetorical devices for satisfying theists who have acquired a belief in God for entirely different reasons. Nobody, including theists, arrives at a belief in a Christian god—or any other personal god—via the cosmological argument. To a non believer, the entire argument looks silly no matter how much you dress it up in philosophical finery. This is not proof of the existence of god so much as post hoc rationalization for believers.

Here's an example of the kind of reasoning you see in this "sophisticated" essay. Remember that Pruss is trying to convince us that you must accept the Principle of Sufficient Reason and that principle leads automatically to the conclusion that "Every contingent fact has an explanation."
It is morally acceptable to redirect a speeding trolley from a track on which there are five people onto a track with only one person. On the other hand, it is not right to shoot one innocent person to save five. What is the morally relevant difference between the two cases? If we denied the PSR, then we could simply say: “Who cares? Both of these moral facts are just brute facts, with no explanation.” Why, indeed, suppose that there should be some explanation of the difference in moral evaluation if we accept the denial of the PSR, and hence accept that there can be facts with no explanation at all?

Almost all moral theorists accept the supervenience of the moral on the non-moral. But without the PSR, would we really have reason to accept that? We could simply suppose brute contingent facts. In this world, torture is wrong. In that world, exactly alike in every other respect, torture is a duty. Why? No reason, just contingent brute fact.

The denial of the PSR, thus, would bring much philosophical argumentation to a standstill.

An interesting thing about this argument is that it yields a PSR not just for contingent truths but also for necessary ones.
Quite frankly, I have no idea what he's talking about and nothing said here prompts me to try harder to understand the point. He lost me in the second sentence because I think it IS right to shoot one person to save five, if that's the only choice.

I've also seen many institutions and societies that condone torture. There was at least one American President who liked the idea and in the not-too-distant past torture was good sport in the Roman Catholic Church. What has this got to do with the Principle of Sufficient Reason?

Notice that up until now I haven't even mentioned the most obvious problem with the cosmological argument; namely, that it doesn't explain anything. If there's really a problem identifying the explanation of everything then what explains god? I know that theists everywhere have elaborate excuses to explain why god falls outside of the original premises of the cosmological argument but isn't it interesting that they never explicitly include them in the argument?

Take the five steps above. There should be another statement along the lines of "(4b) This necessary being does not require an explanation because it isn't a contingent fact. This doesn't violate the Principle of Sufficient Reason because I say so."

Man, those Courtier's of the Emperor sure are clever!

1. Actually that's not quite true. My real first reaction is more like, "Holy shit! Are there really people who believe this nonsense!