I try really hard not to ban anyone from commenting on Sandwalk but there are some things I will not tolerate.
Someone named David Roemer recently tested the limits of my patience, and failed. He is now banned.
Here's what happened. I received an email message from David Roemer about a comment of his that did not appear on Sandwalk. I don't know why it didn't appear. I don't remember seeing it.
Shortly after receiving the email message I received a copy of a message David Roemer sent to the chair of my department. Here's the beginning ...
Dear Dr. XXX,
Prof. Moran, I believe, didn't approve of the following comment I made on his Sandwalk blog. He has every right to do so, but he has a moral duty not to coverup the misinformation contained in the AJP article I mention in my censored comment:
Natural selection only explains the adaptation of species to the environment. Not enough is known about the innovations natural selection acts upon to understand how mammals evolved from bacteria in only 3.5 billion years (common descent). The only theory that attempts to explain common descent is ID, but there is no evidence for ID.
IDiots try to make their theory look better by comparing it with natural selection. Atheists go along with this scam because they don’t want to admit that ID is a better theory than natural selection in some sense.
A corollary of the limitations of natural selection is that the second law of thermodynamics doesn’t apply to evolution, just as it doesn’t apply to the evolution of stars. Nevertheless, there is scientific literature about whether evolution violates the second law. Authors on the “does not” side argue that heat energy from the sun accounts for the increase in order (decrease in entropy). Heat, of course, tends to increase disorder.
This nonsense reached an extreme level in an article published by the American Journal of Physics (Entropy and evolution, Nov. 2008). This article actually calculates the entropy of the biosphere using the Boltzmann constant and an estimate of the thermodynamic probability of life. I’m trying to get the AJP to retract this absurd article.
I'm copying David Novak because he is on the Institute Board of First Things, which is refusing to publish my attached essay explaining why the AJP article is absurd. Both Novak and Moran are helping the AJP lie about evolution and thermodynamics.
My chair will be amused by this sort of thing. There's nothing he could do about it even if he wanted to.
This is one of the criteria for banning. Anyone who tries to get someone fired or reprimanded by going over their head to their employer will be banned. Anyone who harasses the family and friends of someone they disagree with will be banned. There are no exceptions.
I've also banned John Kwok for doing the same thing in an attempt to silence Jim Shapiro.
John starts his defense by explaining the correct use of "begging the question." I agree with him 100%. I hate it when people misuse this phrase by thinking it means "prompts me to ask the question."
He then goes on to give an example ... [Begging questions about philosophy, science and everything else]
But we expect better of the educated and cosmopolitan. It comes, therefore, as a continuing pain to me that scientists will often offer this piece of question beggary:
- Science finds out things
- Philosophy does not find out things the scientific way
- Therefore philosophy is a waste of time and effort
The begged premise here is that only knowing things the scientific way is knowledge, or if the philosopher in question doesn’t say that knowledge is what philosophy offers, that only knowing things the scientific way is worthwhile. Some may even hint that only science delivers beauty, too.
It pains me to read this because I expect so much better of an educated and cosmopolitan Australian.
I'm not aware of any scientist who argues like this.
There was a time, not so long ago, when science and philosophy coexisted in (relative) peace and harmony. This began to change when science came under increasing attack from religion and from others who simply denied the knowledge that had been produced by the scientific way of thinking. (The latter group included advocates of parapsychology. The modern versions include those who deny climate change and those who think vaccinations cause autism. These groups are not necessarily religious.)
The rise of anti-scientism provoked a response from scientists, just as you might expect. Scientists began to speak out against the irrational claims of these science deniers. The counter-attack necessarily covered many people with strong religious beliefs. Gradually, many scientists came to the realization that the main problem was not the specifics of evolution or whether ESP could be tested. The real battleground was a war between rationalism and superstition. This led to a number of scientists coming out in support of atheism and focusing their attention on the flaws in religious thinking (i.e. superstition).
Now, you would think that philosophy would be a natural ally in this fight since the most important feature of philosophy is its ability to distinguish logical arguments from ones that are illogical. In other words, philosophy should be on the side of rationalism and not on the side of superstition.
I been watching proceedings at the Republican National Convention in Florida. If you think it's annoying for most liberal Americans, imagine what it's like for us furriners!
Coincidentally, we watched the last episode of The Newsroom a few days ago then decided to re-watch all ten episodes. It's one of the best shows on television. Makes me sad that The West Wing was cancelled. It's not a show that Republicans will enjoy.
Here's the clip from the first episode that sets the tone for a new kind of TV news show. The hero, Will McAvoy, is a cable news anchor who wants to tell it like it is instead of chasing ratings. The excerpt is from a town hall meeting at Northwestern University. A student has just asked why America is the greatest country in the world. (The student shows up again in Episode #10 when she wants to become a "greater fool.")
The short video by Bill Nye ("The Science Guy") attracted a lot of attention [Bill Nye: Creationism Is Not Appropriate For Children ].
Not to be outdone, Ken Ham and the Creation Museum have taped a response ...
We are [responding to Nye] today with a video rebuttal featuring our “science guys” — Dr. David Menton and Dr. Georgia Purdom of our AiG and Creation Museum staff. These two PhD scientists were asked to reply to Mr. Nye, whose academic credentials do not come close to Drs. Menton and Purdom.
I present this for your amusement. I feel a bit sorry for Georgia Purdom since there's a high probability that some of her grandchildren are going to reject creationism. I wonder how she'll deal with that?
Tim Radford reviews The Selfish Gene by Richard Dawkins [The Selfish Gene by Richard Dawkins – book review]. The review is a bit late—the book was published in 1976—but I suppose the old adage of "better late than never" applies.
Actually it's not as bizarre as you might think. Lot's of people don't understand the ideas that Dawkins was pushing. He was mostly pointing out that evolution is a phenomenon that takes places at the level of genes and populations. Dawkins tweets that Rafford "gets it" in his review.
Lovely retrospective review of The Selfish Gene by Tim Radford, the Guardian's distinguished science writer. He gets it.
Jerry Coyne and I have been thinking along the same lines. We've been reading a lot of books by philosophers and reading their articles and blogs. We're exploring the idea that philosophy and science are different ways of knowing, as the philosophers want us to believe. We've taken to heart the criticism from our philosopher friends that scientists have to understand more about philosophy.
Jerry and I (and many others) have reached the tentative conclusion that much of what passes for modern philosophy is a house of cards. It doesn't tell us anything. It doesn't produce knowledge, or truth.
A few years ago my university (University of Toronto) decided to take a look at student evaluations. A committee was formed and this was its terms of reference.
In recognition of the need to periodically revisit practices related to the evaluation of teaching, the Course Evaluation Working Group was formed in the Fall 2009 (Appendix B) and was asked to:
- Review current course evaluation practices across the University of Toronto and at peer institutions;
- Review current research on course evaluation policies and practices;
- If necessary, make recommendations to improve existing policies and practices.
This sounds like a good idea. As you know, I am very skeptical about student evaluations [On the Significance of Student Evaluations]. It's abut time that universities took a long hard look at the process with a view to abolishing student evaluations or drastically revising them and reviewing their importance in promotion and tenure decisions. It's even more important to revise the policy on using student evaluations to judge the effectiveness of part-time lecturers and teaching assistants. At the very least, their role in determining teaching awards should be critically examined.
If I were in charge of this project I would pick a committee composed almost entirely of the following groups:
- front-line lecturers in introductory classes, including tenured faculty, untenured faculty, full-time lecturers, and part-time lecturers
- teaching assistants (graduate students)
- undergraduates
There would have to be substantial representation from undergraduates since they feel strongly about the issue and any drastic changes would require their consent and cooperation.
I would avoid having any administrators on the committee since the purpose of the committee was to evaluate existing university policy. In general, administrators are reluctant to make radical changes and they have trouble thinking outside the box. Furthermore, most of them don't have time to think seriously about the issue.
Administrators think differently than I do. Here's how they constructed the committee (see Course Evaluation Working Group.
- Edith Hillan (Vice-Provost, Faculty and Academic Life; Co-Chair)
- Jill Matus (Vice-Provost, Students; Co-Chair)
- Grant Allen (Vice-Dean, Undergraduate, Faculty of Applied Science and Engineering)
- Gage Averill (Dean and Vice-Principal, Academic, UTM)
- Cleo Boyd (Director, Robert Gilliespie Academic Skills Centre, UTM)
- Corey Goldman (Associate Chair [Undergraduate], Department of Ecology & Evolutionary Biology, Faculty of Arts & Science)
- Pam Gravestock (Associate Director, Centre for Teaching Support & Innovation)
- Emily Greenleaf (Faculty Liaison & Research Associate, Centre for Teaching Support & Innovation)
- Jodi Herold-McIlroy (Wilson Centre, Faculty of Medicine)
- Glen Jones (Associate Dean, Academic, OISE) Helen Lasthiotakis (Director of Academic Programs and Policy)
- Marden Paul (Director, Planning, Governance & Assessment)
- Cheryl Regehr (Vice-Provost, Academic Programs)
- Carol Rolheiser (Director, Centre for Teaching Support & Innovation)
- Jay Rosenfield (Vice-Dean, Undergraduate Medical Education, Faculty of Medicine)
- John Scherk (Vice-Dean, UTSC)
- Elizabeth Smyth (Vice-Dean, Programs, School of Graduate Studies)
- Suzanne Stevenson (Vice-Dean, Teaching & Learning, Faculty of Arts & Science)
No students. No teaching assistants. No part-time lecturers. Very few people who are currently teaching large undergraduate courses. Almost every person has an administrative positions of some sort—most of the positions take up a considerable portion of their time and some of them are full-time jobs.
That's what thinking like an administrator looks like.
I don't think my university is unusual. We have thousands of very smart students and teachers but all the important committees seem to be composed of people with heavy administrative responsibilities. Does anyone understand the logic here?
Maybe it's just my imagination, but I think I detect a change on Evolution News & View and on Uncommon Descent. For years these blogs have been attacking evolution without paying the least attention to what their opponents are saying. Lately, however, there seem to be some authors who are actually listening to their opponents and trying to address the main criticisms of the IDiot position.
Sometimes you even see articles that are close to being scientifically correct and I've even seen articles that recognize the existence of modern evolutionary theory (i.e. not Darwinism).
The good articles are still quite rare but I'm encouraged by the fact that they are listening.
The latest contribution is by Stephen A. Batzer, a contributor to Evolution News & Views since May 10, 2012. Batzer has a Ph.D. in Mechanical Engineering (see The Salem Conjecture). He's responding to an earlier post of mine where I attempted to explain to Casey Luskin why he was wrong about evolutionary theory [Is "Unguided" Part of Modern Evolutionary Theory?]. Recall that Luskin was saying that the "unguided" nature of evolution was a core part of the theory of Darwinian evolution.
The Flying Spaghetti Monster is all-powerful and all-knowing and she loves meatballs. She is also very sneaky and doesn't want to leave any evidence of her existence. That's why she's very careful to only steal meatballs that won't be missed. (How often do you count the meatballs in your spaghetti?).
As far as I know this is a perfectly valid philosophical argument. If you accept the premises then it's quite possible that meatballs are disappearing from kitchens and restaurants without us ever being aware of the problem.
I'm not a philosopher but I strongly suspect that there aren't any papers on the possible existence of the Flying Spaghetti Monster in the philosophical literature. I doubt that there are any Ph.D. theses on the topic.
Last week's molecule was a small protein machine that pumps protons across a membrane (ubiquinol:cytochrome c oxidoreductase) [Monday's Molecule #182]. The winner was Stephen Spiro. I think he's a student at the University of Toronto (UT) but it's a campus I haven't heard of in a place called "Dallas."
This week's molecule is a lot less complicated although it's rather strange looking. This molecule has a very specific use. Name the molecule—the common name will do—and describe its use.
Post your answers 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.
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. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.
Comments are invisible for 24 hours. Comments are now open.
UPDATE: The molecule is raltitrexed, also known as Tomudex. It's an inhibitor of the enzyme thymidylate synthase, the enzyme responsible for converting dUMP to dTMP. The drug is effective as an anti-cancer agent since it prevents cell division by blocking DNA synthesis. The winner is Raul A. Félix de Sousa (again).
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
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa
Aug. 7: Raul A. Félix de Sousa
Aug. 13: Matt McFarlane
Aug. 20: Stephen Spiro
Aug. 27: Raul A. Félix de Sousa
Lots of people are having their genomes sequenced or otherwise analyzed for specific alleles. Those people should get all the information that comes out of the analyses although, hopefully, it will be scientifically correct information and any medical relevance will be explained by experts.1
There's another group of people who submit their genomes for research purposes only and they usually sign consent forms indicating that their name will not be associated with the results. Under those circumstances, the researchers should never have access to the individual's name or any circumstances that are not relevant to the study.
Apparently that simple ethical rule is not always standard practice. Gina Kolatea writes about some ethical issues in the New York Times: Genes Now Tell Doctors Secrets They Can’t Utter.
Here's an example from her article ...
One of the first cases came a decade ago, just as the new age of genetics was beginning. A young woman with a strong family history of breast and ovarian cancer enrolled in a study trying to find cancer genes that, when mutated, greatly increase the risk of breast cancer. But the woman, terrified by her family history, also intended to have her breasts removed prophylactically.
Her consent form said she would not be contacted by the researchers. Consent forms are typically written this way because the purpose of such studies is not to provide medical care but to gain new insights. The researchers are not the patients’ doctors.
But in this case, the researchers happened to know about the woman’s plan, and they also knew that their study indicated that she did not have her family’s breast cancer gene. They were horrified.
This is a rather simple case of the researchers violating a standard protocol. They should not have known the identity of the patient and they should not have known what she intended to do.
Most of the "ethical problems" in the article are of this type. They involve researchers who are supposed to be concentrating on research and not on the treatment of individual patients. Those researchers have no idea whether the patients already know which alleles they carry or whether they are already undergoing medical treatment. That's just as it should be. If a DNA donor doesn't want to be contacted then it's ethically wrong for the researchers to violate that contract no matter how justified they think they are being. Furthermore, it should be impossible for them to find out the name and address of the donor so the issue should never come up.
John Hawks thinks this is an interesting ethical problem and he wants his students to discuss it in his classes [Grasping the genomic palantir].
That case is ethically straightforward compared to others, because the researchers could make a difference to an immediate medical decision. On the other hand, how many risk-free research participants went ahead with prophylactic mastectomies because researchers didn't know about their plans?
I think the article will be a good one for prompting student discussions in my courses, and I'll likely assign it widely. But I think the central ethical problem discussed in the article is temporary.
What will students learn from discussing issues like these? What controls are in place to make sure that students are informed about all the ethical issues? Will they be told that standard scientific protocols were violated once the researchers knew what the patient intended to do?
1. "Experts" do NOT include employees of any for-profit company that took money for sequencing the genome.
Jeff Mahr is trying to teach his students how to think critically so he asked them a question about a graph. Check it out to see if you would pass his course: Clearly Critical Thinking?.
